bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of the molecular FluoroType Mycobacteria VER 1.0 and the Maldi BioTyper Mycobacteria assays for the identification of non-tuberculous mycobacteria
Authors: Guiraud Jennifer , Piau Caroline , Enault Cécilia , Nkpa Charron Emilie , Ducos Danièle , Lafuente Christine , Ménard Armelle , Peuchant Olivia 
Published: December 2024

ABSTRACT

Accurate identification of non-tuberculous mycobacterial (NTM) species is crucial for the diagnosis and appropriate management of NTM infections. This study aimed to evaluate the performance of two assays, FluoroType Mycobacteria VER 1.0 and Maldi BioTyper (MBT) Mycobacteria. The two assays were evaluated using 119 NTM, including 85 slow-growing mycobacteria and 34 rapid-growing mycobacteria, representing a total of 33 species isolated in three French clinical laboratories. We used the GenoType assays as reference method for species identification, followed by 16S rRNA gene sequencing if the GenoType kits returned
Mycobacterium
sp. Compared to the reference method, the FluoroType Mycobacteria assay provided correct species identification in 89.9% of cases (107/119). Among the most frequently encountered species in clinical settings, low concordance was obtained for
Mycobacterium intracellulare
(82.4%, 14/17),
Mycobacterium gordonae
(66.7%, 6/9), and
Mycobacterium xenopi
(75%, 6/8). Misidentification was obtained in two cases (
Mycobacterium smegmatis
instead of
Mycobacterium mageritense
, and
Mycobacterium mucogenicum
instead of
Mycobacterium phocaicum
). Using the MBT Mycobacteria assay, 78.1% (93/119) of NTM isolates were correctly identified at the species level. One
Mycobacterium europaeum
isolate was misidentified as
M. intracellulare
/
Mycobacterium chimaera
. In five cases, the assay provided more accurate NTM identification compared to GenoType assays, in which closely related species are identified as a group. The FluoroType Mycobacteria VER 1.0 and the MBT Mycobacteria assays are useful tools for NTM identification from positive cultures, reducing handling time compared to GenoType assays. Their routine use in laboratories must take into consideration their performance and limitations in clinical settings.
mSphere of Influence: How the single cell contributes to the collective
Authors: Lewin Gina R. 
Published: December 2024

ABSTRACT

Gina Lewin works in the field of microbial ecology, with a focus on the human microbiota. In this mSphere of Influence article, she reflects on how two papers describing bacterial single-cell RNA-seq—“Prokaryotic single-cell RNA sequencing by
in situ
combinatorial indexing” by S. B. Blattman, W. Jiang, P. Oikonomou, and S. Tavazoie (Nat Microbiol 5:1192–1201, 2020,
https://doi.org/10.1038/s41564-020-0729-6
) and “Microbial single-cell RNA sequencing by split-pool barcoding” by A. Kuchina, L. M. Brettner, L. Paleologu, C. M. Roco, et al. (Science 371:eaba5257, 2021,
https://doi.org/10.1126/science.aba5257
)—impacted her work by developing a new approach to study how single cells of bacteria contribute to ecosystem-level processes.
Combined mutations in nonstructural protein 14, envelope, and membrane proteins mitigate the neuropathogenicity of SARS-CoV-2 Omicron BA.1 in K18-hACE2 mice
Authors: Sangare Kotou , Liu Shufeng , Selvaraj Prabhuanand , Stauft Charles B. , Starost Matthew F. , Wang Tony T. 
Published: December 2024

ABSTRACT

We previously reported that mutations outside the spike protein play a role in the attenuation of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron BA.1 variant in human ACE2 transgenic mice (K18-hACE2). Here, we assessed the pathogenicity of SARS-CoV-2 (WA1/2020) containing mutations from the Omicron BA.1 variant in K18-hACE2 mice. At an infection dose of 10
4
plaque-forming units (PFU), WA1 virus carrying Omicron BA.1 Nsp14(I42V), E(T9I), M(D3G/Q19E/A63T), but not Nsp6(Δ105–107, I189V), substitutions showed significant reduction in lethality. Interestingly, reduction of viral load is more pronounced in the brains than in the lungs. Subsequent analyses suggest that BA.1 E(T9I) and M(D3G/Q19E/A63T) substitutions result in less efficient packaging of virus-like particles. Given that Nsp14(I42V), E(T9I), M(Q19E/A63T) are well preserved in subsequent omicron subvariants, including currently circulating variants, our findings highlight the importance of understanding how non-spike mutations affect the pathogenicity of SARS-CoV-2 variants.

IMPORTANCE
Inoculation of transgenic mice expressing human angiotensin-converting enzyme 2 (hACE2) with SARS-CoV-2 often leads to a fatal brain infection. Omicron BA.1 variant, however, was found to be non-lethal in this model. Here, we systematically assessed the effect of individual mutations of Omicron BA.1 on the pathogenicity of the virus in hACE2 transgenic mice and found that combination of 5 mutations of Nsp14, E, and M of BA.1 variant significantly lowered brain viral load and reduced lethality. These results provide new insights into how SARS-CoV-2 Omicron BA.1 is attenuated.
Development and validation of genome-informed and multigene-based qPCR and LAMP assays for accurate detection of
Dickeya solani
: a critical quarantine pathogen threatening the potato industry
Authors: Dobhal Shefali , Santillana Gem , Stulberg Michael J. , Arizala Dario , Alvarez Anne M. , Arif Mohammad 
Published: December 2024

ABSTRACT

Dickeya solani
one of the most aggressive pectinolytic phytopathogens, causes blackleg disease in potatoes, resulting in significant economic losses and adversely impacting one of the world’s most important food crops. The diagnostics methods are critical in monitoring the latent infection for international trade of potato seed tubers and in implementation of control strategies. Our study employed a whole-genome comparative approach, identifying unique target gene loci (LysR and TetR family of transcriptional regulators gene regions) and designing loop-mediated isothermal amplification (LAMP) and a multi-gene-based multiplex TaqMan qPCR assays for specific detection and differentiation of
D. solani
. Both methods underwent meticulous validation with extensive inclusivity and exclusivity panels, exhibiting 100% accuracy and no false positives or negatives. The LAMP method demonstrated the detection limit of 100 fg and 1 CFU per reaction using pure genomic DNA and crude bacterial cell lysate, respectively. The qPCR detection limit was 1 pg, 100 fg and 10 fg with quadplex, triplex, and singleplex, respectively. None of the assays were impacted by any inhibitory or competitive effects after adding host DNA (in qPCR) or crude lysate (in LAMP). The assays proved robust and reproducible in detecting the target pathogen in infected samples, with the LAMP assay being field-deployable due to its simplicity and rapid results acquisition within approximately 9 min. The reproducibility was confirmed by performing the assay in two independent laboratories. These assays offer a robust, rapid, and reliable solution for routine testing, with applications in phytosanitary inspection, disease diagnosis, and epidemiological studies.

IMPORTANCE

Dickeya solani
, one of the most aggressive soft rot causing bacteria and a quarantine pathogen, poses a severe threat to food security by causing substantial economic losses to the potato industry. Accurate and timely detection of this bacterium is vital for monitoring latent infections, particularly for international trade of potato seed tubers, and for implementing effective control strategies. In this research, we have developed LAMP and multi-gene-based multiplex TaqMan qPCR assays for specific detection of
D. solani
. These assays, characterized by their precision, rapidity, and robustness, are crucial for distinguishing
D. solani
from related species. Offering unparalleled sensitivity and specificity, these assays are indispensable for phytosanitary inspection and epidemiological monitoring, providing a powerful tool enabling management of this threatening pathogen.
MANIPULATION CORROSION RESISTANCE AND SUPER-HYDROPHOBICITY OF LASER SURFACE TEXTURED AISI 316 STAINLESS STEEL DECORATED WITH HEXADECYLTRIMETHOXYSILANE (HDTMS)
Authors: LIU LIN , ZHANG LUXIA , LIN NAIMING , YUAN SHUO , YANG YANG , LIU ZHIQI , ZENG QUNFENG , NOURI MEISAM 
Published: December 2024

Super-hydrophobicity inspired by natural water-repellent surfaces has received tremendous attention for surface functionalization of metallic materials in many applications. Problems of corrosion and/or contamination that happens on the surface can be partially solved as the material obtained super-hydrophobicity. Appropriate surface pattern and low surface energy are the two key factors that can realize super-hydrophobicity. In the present paper, laser surface texturing (LST) followed by decoration of Hexadecyltrimethoxysilane (HDTMS) was conducted to manipulate the super-hydrophobicity and corrosion resistance of AISI 316 stainless steel (SS) on the surface. Scanning electron microscopy (SEM) and an ultra-depth field microscope were employed to characterize the surface morphologies of the received samples before and after corrosion tests. Corrosion resistance and super-hydrophobicity for the related samples were investigated using electrochemical tests and water contact angle measurements. It was found that various surface patterns differed with intervals (250, 150, 80, and [Formula: see text]m,) between two micro-dimples have formed on 316 SS sample surfaces after LST treatment. The surface roughness values gradually increased with the decrease of interval. The 316 SS samples obviously reduced surface energy values after HDTMS decoration. In simulated haze solution, electrochemical tests demonstrated that the 316 SS sample treated with [Formula: see text] (HT-316 SS, [Formula: see text]m) exhibited lower corrosion and higher corrosion potential current density than the smooth 316 SS (S-316 SS), [Formula: see text]-316 SS (HS-316 SS), and LST 316 SS (T-316 SS, [Formula: see text]m) samples. As expected, the HT-316 SS ([Formula: see text]m) exhibited the highest water contact angle of 155.85∘ as compared to HS-316 SS and other HT-316 SS samples. Meanwhile, the superhydrophobic surface of HT-316 SS ([Formula: see text]m) exhibits super-oleophilic and self-cleaning properties.
Diagnostic Performance of Dermoscopy and Clinical Visual Diagnosis for Plantar Warts
Authors: León-Herce Diego , García-Oreja Sara , Navarro-Pérez David , Tardáguila-García Aroa , Lázaro-Martínez José Luis , Álvaro-Afonso Francisco Javier 
Published: December 2024

Background: Plantar warts caused by the human papilloma virus (HPV) are one of the most frequent pathologies in podiatry. Diagnosis is usually limited to the clinical presentation of the lesion. Biopsy and polymerase chain reaction (PCR) are expensive and can be difficult to access. However, the dermatoscope is a noninvasive tool that covers the gap between microscopic and macroscopic diagnosis.Objective: This study compares the effectiveness of diagnosis of plantar warts using a dermatoscope versus visual clinical signs.Methods: The study evaluated 25 patients with suspected HPV plantar warts by visual or dermatoscopic signs. Upon clinical suspicion of HPV, a sample was taken for PCR analysis. A dermatoscopic image of the plantar wart was collected, and the characteristic clinical signs were evaluated, including the discontinuity of dermatoglyphs, hemorrhagic dots, reddish linear vessels, verruciform surface and frog‐spawn appearance.Results: All 25 patients showed positive results in molecular testing. Dermatoscopic findings compatible with HPV were obtained for 100% (25/25) of patients, while clinical signs were observed in 84% (21/25). The most common finding was the alteration of dermatoglyphs, which was present in all patients at the dermoscopic level. The sensitivity of the dermatoscope was 100% and identical to that of PCR.Conclusion: The dermatoscope appears to be a useful, noninvasive and rapid tool for clinical use in the diagnosis of plantar warts.
Participación de niñas, niños y adolescentes institucionalizados: perspectivas durante la emergencia sociosanitaria
Authors: Zúñiga Daniela , Mardones Rodolfo , Wentzel Viether Marianne , Sanhueza José 
Published: December 2024

(analytical)This work explores the perspectives of directors, educators, children and adolescents institutionalized under protection measures, regarding the principle of participation and the right to be heard in the context of a health emergency. The study has a qualitative approach, instrumental single case design. 21 focused interviews were carried out in 4 residences in the Los Ríos Region, Chile, and their contents were analyzed. The perspectives about the right to be heard and participation are linked to the organizational characteristics of the residences; highly structuring, precarious and with high responsibility in the care of children and adolescents. Although the rights are known and valued by the actors, the application is difficult since it challenges building a sensitive and flexible relationship with children and adolescents in an adverse residential context.
Keywords: Youth participation; institutionalization; pandemic; child welfare; child rights; governmental policy.
Da aculturação à formação: o papel dos estudos sobre a imigração na obra de Florestan Fernandes
Authors: Fernandes Júnior João Gilberto Belvel 
Published: December 2024

Having received little attention from the interpreters of Florestan Fernandes’ work until recently, the author’s migratory studies, although revisited by specialists in this field, have been the object of implicit or explicit accusations of blame for the poor development of the theme in sociology, and especially at Escola Sociológica Paulista, from the 1940s onwards. This work aims to respond to this “sociology of abandonment” in the interpretation of Fernandes’ work, showing, through a systematic interpretation, that the author’s supposed departure from migratory studies did not happen without the provisions of an accumulative movement, characteristic of the formative model that the author fought for.
A corte sem nobreza: polemistas e anti-intelectualismo na mídia
Authors: Meirelles Allana 
Published: December 2024

This paper intends to present a genesis of the polemicist position in the press, which mobilizes anti-intellectualism as the main strategy, during the period of the New Republic in Brazil. Based on the correlation between social trajectories, modalities of intellectual and journalistic practices, public representations, strategies of the institutions and the configuration of lines of force in the space of production and reproduction of opinions in Brazil from the late 1980s to 2018, we seek to make intelligible the diffusion of anti-intellectual and anti-academic views in the media. The article traces the constitution, sedimentation and proliferation of a position that guarantees its permanence and collective power, but at the same time becomes depersonalized, routinized and loses prestige.
Philanthropy and the neoliberal government of inequalities
Authors: Duvoux Nicolas 
Published: December 2024

The article discusses the tension between philanthropy and the governance of inequalities in the neoliberal era by first showing the tension between the egalitarian imperative of democracy and philanthropy, drawn from private wealth and the social power of its owner. Then it analyses the very conception of wealth that the consideration of philanthropy allows to develop, emphasizing the relationship between well-being on the one hand and social control on the other hand. This conception puts forward the relationship of capture that emerges between philanthropy and public action. The final part of the analysis is dedicated to discussing a case of mutual learning, inviting to a processual analysis of reform.
Experts, neoliberal doxa, and the rollback of high-stakes school rankings in Chile (2006-2024)
Authors: Chouhy Gabriel 
Published: December 2024

O que impulsiona a implementação e a reversão de classificações escolares de alto risco baseadas em testes? Adaptando a teoria dos campos de ação estratégica ao caso chileno e mobilizando o conceito de doxa de Bourdieu, vejo a reforma de mercado na educação como o resultado de relações competitivas, cooperativas e conflitantes entre atores titulares e desafiadores. Enquanto os primeiros dominam o campo e, portanto, exercem poder de definição sobre como o campo deve ser organizado e reformado, os últimos competem por formas alternativas de estruturar o campo. Essa lógica de campo configura uma dinâmica contingente na qual o campo é transformado à medida que quadros desafiadores ganham moeda ideacional. Com base nessa estrutura conceitual, evidencio como ideias concorrentes sobre a educação baseada no mercado moldaram a construção técnica e o uso público de classificações de qualidade escolar. Implicações para uma sociologia da reforma seguem.
Os experts do gosto doméstico entre juízo estético e social: Do dossiê “L’économie de la maison” aos arquivos do Centre de Sociologie Européenne
Authors: Pulici Carolina 
Published: December 2024

Desde a publicação de A Distinção (1979), de Pierre Bourdieu, diversas pesquisas buscam apreender as relações entre as preferências culturais e as lógicas de diferenciação social. Este artigo busca contribuir com esses trabalhos por meio do estudo dos prescritores do gosto doméstico na França dos anos 1980, à luz dos dados morfológicos de seus públicos conservados nos arquivos do Centre de Sociologie Européenne. Como se verá, as revistas dedicadas à casa que, para Bourdieu e sua equipe, constituíam um dos principais vetores de aspirações legítimas em matéria de moradia se estruturavam em oposições que reproduziam, segundo as normas de expressão da imprensa da casa, as desigualdades sociais de seus leitores.
Characterizing the Origins of Primary Aldosteronism
Authors: Brown Jenifer M. , Honzel Brooke , Tsai Laura C. , Milks Julia , Neibuhr Yvonne M. , Newman Andrew J. , Cherney Michael , Stouffer David G. , Auchus Richard J. , Vaidya Anand 
Published: December 2024

BACKGROUND:
Renin-independent aldosterone production in normotensive people increases risk for developing hypertension. In parallel, normotensive adrenal glands frequently harbor aldosterone-producing micronodules with pathogenic somatic mutations known to induce primary aldosteronism (PA). A deeper understanding of these phenomena would inform the origins of PA and its role in hypertension pathogenesis.

METHODS:
Prospectively recruited normotensives underwent detailed characterization of PA features via the following: oral sodium suppression test to evaluate renin-independent aldosterone production, dexamethasone suppression and adrenocorticotropic hormone-stimulation tests to evaluate adrenocorticotropic hormone-mediated aldosterone production, and 24-hour ambulatory blood pressure monitoring. The magnitude of renin-independent aldosterone production was defined via tertiles of 24-hour urinary aldosterone production during the oral sodium suppression test to create unbiased categorizations of the magnitude of PA. Serum aldosterone, serum 18-hybrid steroids, urine tetrahydroaldosterone (biomarkers of aldosterone synthase activity), urinary potassium, and blood pressure (biomarkers of mineralocorticoid receptor activation) were evaluated across tertiles.

RESULTS:

There was a spectrum of autonomous, nonsuppressible, and renin-independent production of aldosterone, 18-hybrid steroids, and 24-hour urinary tetrahydroaldosterone (
P
-trend <0.01). Correspondingly, there was a continuum of adrenocorticotropic hormone-mediated aldosterone production and 18-hybrid steroid production that also paralleled renin-independent aldosterone production. The spectrum of PA pathophysiology was associated with higher ambulatory daytime systolic BP (
P
-trend <0.05), even within the normotensive range, and greater urinary potassium excretion (
P
-trend <0.05), indicating a continuum of mineralocorticoid receptor activation.

CONCLUSIONS:
The pathophysiologic continuum of PA, characterized by renin-independent and adrenocorticotropic hormone-mediated aldosterone production, and enhanced aldosterone synthase and mineralocorticoid receptor activity, is evident in normotensive people. These findings provide mechanistic explanations to implicate PA in the pathogenesis of a substantial proportion of hypertension.
A reassessment of the taxonomic status and distribution of the subspecies of Lyroderma lyra (Chiroptera: Megadermatidae)
Authors: Feng Lei , Győrössy Dorottya , Portela Miguez Roberto , Kokkini Phaedra , Görföl Tamás , Khan Shahneaz Ali , Saikia Uttam , Talmale Shyamkant S. , Yu Wenhua , Liu Shaoying , Jiang Tinglei , Csorba Gábor 
Published: December 2024

Abstract
Lyroderma lyra is one of the six currently recognised species of the family Megadermatidae. Previous studies have suggested subspecific division within L. lyra, wherein the nominate subspecies is predominantly distributed in South Asia, and the other subspecies, L. lyra sinense is occurring in southern China and Southeast Asia. Based on the congruent results of comparative morphology of skulls and bacula, as well as phylogenetic tree reconstructions – the first ones including both subspecies and incorporating the most extensive geographic sampling of “sinense” to date – using COI and cytb sequences, we have elevated the Southeast Asian subspecies to a distinct species status, Lyroderma sinense.
Potential Method for Warning the First Lightning Flash of Isolated Thunderstorm Cells over South China
Authors: Zhao Chuanhong , Zhang Yijun , Zheng Dong , Yao Wen , Du Sai 
Published: December 2024

Abstract
This study improved the first lightning flash (FLF) warning method of isolated thunderstorm cells in the warm season over South China. The S-band polarimetric radar and three independent lightning location systems provided 57 thunderstorm and 39 nonthunderstorm cells. The results indicated the median value of horizontal reflectivity below the melting layer when the cloud detected by the radar first was a good indicator for forecasting the FLF with the longest lead time (threshold value ≤ 15 dBZ in this study). The algorithm produced 0.96–1 probability of detection (POD), 0.32–0.38 false alarm ratio (FAR), 0.63–0.66 critical skill index (CSI), and 12–21-min average lead time. Methods of minimum echo (20 dBZ) top height extending to −10°C and the 35 dBZ at −10°C were more accurately for warning the FLF but with a shorter lead time; the former algorithm resulted in 1 POD, 0.08–0.29 FAR, 0.71–0.92 CSI, and 5–9-min average lead time. The latter algorithm resulted in 1 POD, 0–0.06 FAR, 0.94–1 CSI, and 3–5.5-min average lead time. The fluctuation of lead time depended on the FLF occurrence time. The differential reflectivity ZDR column and the height of graupel were not as effective as the reflectivity information on warning the FLF in this study. The results are expected to improve the FLF forecasting in considering accuracy and lead time within warm-season thunderstorm cells over South China based on the radar.

Significance Statement
It is difficult to forecast the first lightning flash (FLF) occurrence. While many methods are provided based on weather radars, the threshold values for hitting the start of lightning activity are dominated by mixed-phase ice microphysics, especially associated with graupel particles; therefore, to improve the lead time of the FLF nowcasting, usage of knowledge of warm-phase microphysics is possible. Fortunately, the latest discovery indicates the difference is recognizable in warm-phase microphysics during the first radar echo between thunderstorms and nonthunderstorms based on the weather radar. This study utilized the finding to construct a method for the FLF warning. The early lead time and accuracy are considered comprehensively in this method. It is important for the FLF warning.