bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complementary description of three species of the subgenus Anthoseius De Leon (Acari: Phytoseiidae) from India
Authors: Jose Anna , Döker Ismail , Gowda Channegowda Chinnamade , Hiremath Renuka 
Published: February 2024

Taxonomy of the subgenus Anthoseius De Leon (Acari: Phytoseiidae) has become challenging and often causing confusions among taxonomists. We here provide complementary descriptions of three species, T. (A.) bengalensis Karmakar et al., T. (A.) bulbosis Karmakar et al., and T. (A.) serrulatus Ehara, based on the specimens collected from Karnataka, India. During the identification of our specimens, we observed several important morphological differences between the new specimens and the original descriptions of the first two species. The morphological differences include number of dorsal solenostomes (absence or presence of gd5), position of preanal pores, chelicera dentition including position of teeth, shape of calyx of spermatheca, and leg chaetotaxy including number of setae on genu II, number of macrosetae and shape of ventral setae. Since these characters are crucial for phytoseiid taxonomy, we decided to examine the type specimens of these two species. Our examination on their holotypes confirmed that the morphological characters mentioned above are different than those reported in their original descriptions, but identical to the complementary descriptions provided here. In addition, T. (A.) serrulatus has not been recognized by several acarologists and repeatedly described under different names. We proposed five new and three suspected synonymies for this species. Lastly, we also provided the first description of males of T. (A.) bengalensis.
Staphylococcus aureus
AbcA transporter enhances persister formation under β-lactam exposure
Authors: Truong-Bolduc Q. C. , Wang Y. , Ferrer-Espada R. , Reedy J. L. , Martens A. T. , Goulev Y. , Paulsson J. , Vyas J. M. , Hooper D. C. 
Published: February 2024

ABSTRACT

We evaluated the role of
Staphylococcus aureus
AbcA transporter in bacterial persistence and survival following exposure to the bactericidal agents nafcillin and oxacillin at both the population and single-cell levels. We show that AbcA overexpression resulted in resistance to nafcillin but not oxacillin. Using distinct fluorescent reporters of cell viability and AbcA expression, we found that over 6–14 hours of persistence formation, the proportion of AbcA reporter-expressing cells assessed by confocal microscopy increased sixfold as cell viability reporters decreased. Similarly, single-cell analysis in a high-throughput microfluidic system found a strong correspondence between antibiotic exposure and AbcA reporter expression. Persister cells grown in the absence of antibiotics showed neither an increase in nafcillin MIC nor in
abcA
transcript levels, indicating that survival was not associated with stable mutational resistance or
abcA
overexpression. Furthermore, persister cell levels on exposure to 1×MIC and 25×MIC of nafcillin decreased in an
abcA
knockout mutant. Survivors of nafcillin and oxacillin treatment overexpressed transporter AbcA, contributing to an enrichment of the number of persisters during treatment with pump-substrate nafcillin but not with pump-non-substrate oxacillin, indicating that efflux pump expression can contribute selectively to the survival of a persister population.
Diversity profiling of microbiomes associated with selected alpine plants and lichens from Mt. Suisho, Japan
Authors: Nakai Ryosuke , Munekawa Shouno , Murai Yoshinori , Ohmura Yoshihito , Tani Kenichiro 
Published: February 2024

ABSTRACT

We report 16S rRNA gene amplicon data for the microbiomes in selected alpine plants (genera
Artemisia
,
Parnassia
, and
Phyllodoce
) and lichens (genera
Cladonia
and a mixture of
Miriquidica
and
Rhizocarpon
) from Mt. Suisho, Japan. Most of these samples were dominated by
Pseudomonadota
, while some contained the rarely cultivated phylum
Vulcanimicrobiota
(
Candidatus
Eremiobacterota/WPS-2).
Genome-scale metabolic modeling of the human milk oligosaccharide utilization by
Bifidobacterium longum
subsp.
infantis
Authors: Román Loreto , Melis-Arcos Felipe , Pröschle Tomás , Saa Pedro A. , Garrido Daniel 
Published: February 2024

ABSTRACT

Bifidobacterium longum
subsp.
infantis
is a representative and dominant species in the infant gut and is considered a beneficial microbe. This organism displays multiple adaptations to thrive in the infant gut, regarded as a model for human milk oligosaccharides (HMOs) utilization. These carbohydrates are abundant in breast milk and include different molecules based on lactose. They contain fucose, sialic acid, and N-acetylglucosamine.
Bifidobacterium
metabolism is complex, and a systems view of relevant metabolic pathways and exchange metabolites during HMO consumption is missing. To address this limitation, a refined genome-scale network reconstruction of this bacterium is presented using a previous reconstruction of
B. infantis
ATCC 15967 as a template. The latter was expanded based on an extensive revision of genome annotations, current literature, and transcriptomic data integration. The metabolic reconstruction (
i
LR578) accounted for 578 genes, 1,047 reactions, and 924 metabolites. Starting from this reconstruction, we built context-specific genome-scale metabolic models using RNA-seq data from cultures growing in lactose and three HMOs. The models revealed notable differences in HMO metabolism depending on the functional characteristics of the substrates. Particularly, fucosyl-lactose showed a divergent metabolism due to a fucose moiety. High yields of lactate and acetate were predicted under growth rate maximization in all conditions, whereas formate, ethanol, and 1,2-propanediol were substantially lower. Similar results were also obtained under near-optimal growth on each substrate when varying the empirically observed acetate-to-lactate production ratio. Model predictions displayed reasonable agreement between central carbon metabolism fluxes and expression data across all conditions. Flux coupling analysis revealed additional connections between succinate exchange and arginine and sulfate metabolism and a strong coupling between central carbon reactions and adenine metabolism. More importantly, specific networks of coupled reactions under each carbon source were derived and analyzed. Overall, the presented network reconstruction constitutes a valuable platform for probing the metabolism of this prominent infant gut bifidobacteria.

IMPORTANCE

This work presents a detailed reconstruction of the metabolism of
Bifidobacterium longum
subsp.
infantis
, a prominent member of the infant gut microbiome, providing a systems view of its metabolism of human milk oligosaccharides.
Development of a rapid detection method for the macrolide resistance gene in
Mycobacterium avium
using the amplification refractory mutation system–loop-mediated isothermal amplification method
Authors: Inagaki Takayuki , Asahi Shoki , Ogawa Kenji , Nakagawa Taku , Ohkura Teruko , Osada Yukari , Nikai Toshiaki , Yamada Kiyofumi , Yagi Tetsuya , Uchiya Kei-ichi 
Published: February 2024

ABSTRACT

Macrolide antibiotics such as clarithromycin (CLR) and azithromycin are the key drugs used in multidrug therapy for
Mycobacterium avium
complex (MAC) diseases. For these antibacterial drugs, drug susceptibility has been correlated with clinical response in MAC diseases. We have previously demonstrated the correlation between drug susceptibility and mutations in the 23S rRNA gene, which confers resistance to macrolides. Herein, we developed a rapid detection method using the amplification refractory mutation system (ARMS)–loop-mediated isothermal amplification (LAMP) technique to identify mutations in the 23S rRNA gene of
M. avium
. We examined the applicability of the ARMS–LAMP method to genomic DNA extracted from six genotypes of
M. avium
clinical isolates. The
M. avium
isolates were classified into 21 CLR-resistant and 9 CLR-susceptible strains based on the results of drug susceptibility tests; the 23S rRNA genes of these strains were sequenced and analyzed using the ARMS–LAMP method. Sequence analysis revealed that the 9 CLR-sensitive strains were wild-type strains, whereas the 21 CLR-resistant strains comprised 20 mutant-type strains and one wild-type strain. Using ARMS–LAMP, no amplification from genomic DNAs of the 10 wild-type strains was observed using the mutant-type mismatch primer sets (MTPSs); however, amplification from the 20 mutant-type strain DNAs was observed using the MTPSs. The rapid detection method developed by us integrates ARMS–LAMP with a real-time turbidimeter, which can help determine drug resistance in a few hours. In conclusion, ARMS–LAMP might be a new clinically beneficial technology for rapid detection of mutations.

IMPORTANCE

Multidrug therapy for pulmonary
Mycobacterium avium
complex disease is centered on the macrolide antibiotics clarithromycin and azithromycin, and resistance to macrolides is an important prognosticator for clinical aggravation. Therefore, it is important to develop a quick and easy method for detecting resistance to macrolides. Drug resistance is known to be correlated with mutations in macrolide resistance genes. We developed a rapid detection method using amplification refractory mutation system (ARMS)–loop-mediated isothermal amplification (LAMP) to identify a mutation in the 23S rRNA gene, which is a macrolide resistance gene. Furthermore, we examined the applicability of this method using
M. avium
clinical isolates. The rapid method developed by us for detection of the macrolide resistance gene by integrating ARMS–LAMP and a real-time turbidimeter can help in detection of drug resistance within a few hours. Since this method does not require expensive equipment or special techniques and shows high analytical speed, it would be very useful in clinical practice.
SARS-CoV-2 infection in brown-headed spider monkeys (
Ateles fusciceps
) at a wildlife rescue center on the coast of Ecuador—South America
Authors: Carvajal Mateo , Saenz Carolina , Fuentes Nathalia , Guevara Rommel , Muñoz Erika , Prado-Vivar Belen , Diaz Eduardo , Alfonso-Cortes Felipe , Coloma Josefina , Grunauer Michelle , Rojas-Silva Patricio , Cardenas Paul A. , Barragan Veronica 
Published: February 2024

ABSTRACT

Human populations can be affected in unpredictable ways by the emergence and spread of zoonotic diseases. The COVID-19 (coronavirus disease of 2019) pandemic was a reminder of how devastating these events can be if left unchecked. However, once they have spread globally, the impact of these diseases when entering non-exposed wildlife populations is unknown. The current study reports the infection of brown-headed spider monkeys (
Ateles fusciceps
) at a wildlife rescue center in Ecuador. Four monkeys were hospitalized, and all tested positive for SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) by RT-qPCR (Quantitative Reverse Transcription PCR). Fecal samples (
n
= 12) from monkeys at the rescue center also tested positive; three zookeepers responsible for feeding and deworming the monkeys also tested positive, suggesting human-animal transmission. Whole genome sequencing identified most samples’ omicron clade 22B BA.5 lineage. These findings highlight the threat posed by an emerging zoonotic disease in wildlife species and the importance of preventing spillover and spillback events during epidemic or pandemic events.

IMPORTANCE
Although COVID-19 (coronavirus disease of 2019) has been primarily contained in humans through widespread vaccination, the impact and incidence of SARS-CoV-2 (Severe acute respiratory syndrome coronavirus) and its transmission and epidemiology in wildlife may need to be addressed. In some natural environments, the proximity of animals to humans is difficult to control, creating perfect scenarios where susceptible wildlife can acquire the virus from humans. In these places, it is essential to understand how transmission can occur and to develop protocols to prevent infection. This study reports the infection of brown-headed spider monkeys with SARS-CoV-2, a red-listed monkey species, at a wildlife recovery center in Ecuador. This study reports the infection of brown-headed spider monkeys with SARS-CoV-2, indicating the potential for transmission between humans and wildlife primates and the importance of preventing such events in the future.
Paleozoic evolution of the Yukon-Tanana terrane of the North American Cordillera, NW British Columbia
Authors: Soucy La Roche R. , Zagorevski A. , Joyce N.L. , Crowley J.L. 
Published: February 2024

Abstract
The origins and primary relationships between tectono-stratigraphic units are fundamental to the terrane concept in accretionary orogens, but they are challenging to assess in metamorphic terranes. In NW British Columbia, three tectonically bounded metamorphic suites of the Yukon-Tanana terrane formed in distinct tectonic settings, based on high-spatial-resolution geochronology and immobile trace-element geochemistry. The Florence Range suite comprises late Neoproterozoic or younger to pre–latest Devonian metasedimentary rocks derived from continental crust, 360 ± 4 Ma calc-alkaline intermediate orthogneiss, and 357 ± 4 Ma amphibolite with oceanic-island basalt composition, consistent with rifting of a continental margin. The detrital signature is dominated by late Mesoproterozoic zircon, which indicates different sources than other parts of the Yukon-Tanana terrane. The Boundary Ranges suite comprises pre–Late Devonian metasedimentary rocks derived in part from a mafic source, amphibolite derived from subduction-zone metasomatized mantle, and 369 ± 4 Ma to 367 ± 7 Ma calc-alkaline felsic to intermediate orthogneiss. The Whitewater suite comprises meta-chert, graphite-rich metapelite, and amphibolite with back-arc basin basalt composition consistent with an anoxic basin near a volcanic source. Our data indicate that the Florence Range and Boundary Ranges suites were separate until at least the Early Mississippian and may have formed a composite terrane since the Permian, whereas the relationship with the Whitewater suite is uncertain. We compare the Paleozoic evolution of the Yukon-Tanana terrane in NW British Columbia with several modern analogues in the west and southwest Pacific Ocean.
Extended CPAP or low-flow nasal cannula for intermittent hypoxaemia in preterm infants: a 24-hour randomised clinical trial
Authors: Yazdi Siamak , Carlo Waldemar A , Nakhmani Arie , Boateng Ernestina O , Aban Immaculada , Ambalavanan Namasivayam , Travers Colm P 
Published: February 2024

ObjectiveOptimal timing of continuous positive airway pressure (CPAP) cessation in preterm infants remains undetermined. We hypothesised that CPAP extension compared with weaning to low-flow nasal cannula (NC) reduces intermittent hypoxaemia (IH) and respiratory instability in preterm infants meeting criteria to discontinue CPAP.DesignSingle-centre randomised clinical trial.SettingLevel 4 neonatal intensive care unit.Patients36 infants <34 weeks’ gestation receiving CPAP≤5 cmH2O and fraction of inspired oxygen (FiO2) ≤0.30 and meeting respiratory stability criteria.InterventionsExtended CPAP was compared with weaning to low-flow NC (0.5 L/kg/min with a limit of 1.0 L/min) for 24 hours.OutcomesThe primary outcome was IH (number of episodes with SpO2<85% lasting ≥10 s). Secondary outcomes included: coefficient of variability of SpO2, proportion of time in various SpO2ranges, episodes (≥10 s) with SpO2<80%, median cerebral and renal oxygenation, median effective FiO2, median transcutaneous carbon dioxide and bradycardia (<100/min for≥10 s).ResultsThe median (IQR) episodes of IH per 24-hour period was 20 (6–48) in the CPAP group and 76 (18–101) in the NC group (p=0.03). Infants continued on CPAP had less bradycardia, time with SpO2<91% and <85%, and lower FiO2(all p<0.05). There were no statistically significant differences in IH<80%, median transcutaneous carbon dioxide or median cerebral or renal oxygenation.ConclusionIn preterm infants meeting respiratory stability criteria for CPAP cessation, extended CPAP decreased IH, bradycardia and other hypoxaemia measures compared with weaning to low-flow NC during the 24-hour intervention.Trial registration numberNCT04792099.
Why a good law is not always good enough: a global review of restrictions to supportive laws for sexual and reproductive health and rights
Authors: Ferguson Laura , Anderson Michelle Elizabeth , Liang Mengjia , Filmer-Wilson Emilie 
Published: February 2024

Laws and regulations provide the framework for implementing sexual and reproductive health and rights (SRHR)-related policies, programmes and services. They can promote the fulfilment of health and human rights; however, they may also limit the achievement of these goals. This study uses data collected under Sustainable Development Goal Indicator 5.6.2 to analyse SRHR-related laws and restrictions from 153 countries. Looking beyond the existence of supportive laws to assess the constellation of legal restrictions and contradictions such as criminalisation and plural legal systems provides a more nuanced understanding of factors involved in achieving full and equal access to SRHR.The interaction between restrictions and contradictions within the law disproportionately impacts some populations’ health access and outcomes. Restrictions based on third-party authorisations and age are the most common restriction types, disproportionately impacting young women. Contraception, emergency contraception and abortion face the greatest number of restrictions, indicating a significant layering of barriers to family planning services. Further, plural legal systems commonly contradict guarantees of contraceptive services and emergency contraception. Our analyses suggest that one of the populations most affected by restrictions to SRH services as they appear in legal and regulatory frameworks is adolescent girls and young women in sub-Saharan Africa seeking abortion or contraceptive services.Study findings provide a critical starting point for advocacy to address legal barriers to SRH services and evidence for future policy and programming. For individual countries, this study can serve as a model for analysis of their own legal and regulatory frameworks to identify priority areas for reform efforts.
Preoperative surgeon evaluation of corneal endothelial status: the Viability Control of Human Endothelial Cells before Keratoplasty (V-CHECK) study protocol
Authors: Airaldi Matteo , Zheng Yalin , Aiello Francesco , Bachmann Björn , Baydoun Lamis , Ní Dhubhghaill Sorcha , Dickman Mor M , Kaye Stephen B , Fontana Luigi , Gadhvi Kunal A , Moramarco Antonello , Rodriguez Calvo de Mora Marina , Rocha de Lossada Carlos , Scorcia Vincenzo , Viola Pietro , Calza Stefano , Levis Hannah J , Parekh Mohit , Ruzza Alessandro , Ferrari Stefano , Ponzin Diego , Semeraro Francesco , Romano Vito 
Published: February 2024

IntroductionThe success of keratoplasty strongly depends on the health status of the transplanted endothelial cells. Donor corneal tissues are routinely screened for endothelial damage before shipment; however, surgical teams have currently no means of assessing the overall viability of corneal endothelium immediately prior to transplantation. The aim of this study is to validate a preoperative method of evaluating the endothelial health of donor corneal tissues, to assess the proportion of tissues deemed suitable for transplantation by the surgeons and to prospectively record the clinical outcomes of a cohort of patients undergoing keratoplasty in relation to preoperatively defined endothelial viability.Methods and analysisIn this multicentre cohort study, consecutive patients undergoing keratoplasty (perforating keratoplasty, Descemet stripping automated endothelial keratoplasty (DSAEK), ultra-thin DSAEK (UT-DSAEK) or Descemet membrane endothelial keratoplasty) will be enrolled and followed-up for 1 year. Before transplantation, the endothelial viability of the donor corneal tissue will be evaluated preoperatively through trypan blue staining and custom image analysis to estimate the overall percentage of trypan blue-positive areas (TBPAs), a proxy of endothelial damage. Functional and structural outcomes at the end of the follow-up will be correlated with preoperatively assessed TBPA values.Ethics and disseminationThe protocol will be reviewed by the ethical committees of participating centres, with the sponsor centre issuing the final definitive approval. The results will be disseminated on ClinicalTrials.gov, at national and international conferences, by partner patient groups and in open access, peer-reviewed journals.Trial registration numberNCT05847387.
Initiating medical abortion in an emergency department in the United States
Authors: Preiksaitis Carl , Saxena Monica , Henkel Andrea 
Published: February 2024

ObjectivesThe primary objective of this study was to assess the feasibility of initiating medical abortions in a large, academic emergency department (ED) in the United States.MethodsA retrospective case series analysis was conducted to evaluate a protocol for initiating medical abortion in the ED implemented from January 2020 to October 2023 at an academic, tertiary care hospital in California, USA. Participants included ED patients diagnosed with pregnancies in the first trimester that were undesired and who opted for medical abortion. The medical abortion protocol was collaboratively designed by a multidisciplinary team and follow-up was conducted by our institution’s gynaecology department. Data were sourced from a data repository of electronic health records and subjected to descriptive statistical analysis.ResultsA total of 27 eligible patients initiated medical abortions in the ED during the study period. The cohort was diverse in terms of racial and ethnic backgrounds and almost evenly split between private and public insurance. No patients had significant complications identified in the medical record. Two patients required uterine aspiration by the gynaecology team; one patient in clinic and one during a return visit to the ED.ConclusionsData from this case series suggest that initiating medical abortion in the ED is feasible. The ED may be considered as an additional access point for abortion care services, especially in areas where other care options are not readily available. Educational, legal and regulatory frameworks that allow emergency physicians to take a greater role in providing this care should be considered.