bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbiota diversity and anti-
Pseudogymnoascus destructans
bacteria isolated from
Myotis pilosus
skin during late hibernation
Authors: Lu Yaping , Ren Huilan , Li Zhongle , Leng Haixia , Li Aoqiang , Dai Wentao , Huang Long , Feng Jiang , Sun Keping 
Published: July 2024

ABSTRACT

Symbiotic microorganisms that reside on the host skin serve as the primary defense against pathogens in vertebrates. Specifically, the skin microbiome of bats may play a crucial role in providing resistance against
Pseudogymnoascus destructans
(
Pd
), the pathogen causing white-nose syndrome. However, the epidermis symbiotic microbiome and its specific role in resisting
Pd
in highly resistant bats in Asia are still not well understood. In this study, we collected and characterized skin microbiota samples of 19
Myotis pilosus
in China and explored the differences between
Pd
-positive and negative individuals. We identified inhibitory effects of these bacteria through cultivation methods. Our results revealed that the Simpson diversity index of the skin microbiota for positive individuals was significantly lower than that of negative individuals, and the relative abundance of
Pseudomonas
was significantly higher in positive bats. Regardless of whether individuals were positive or negative for
Pd
, the relative abundance of potentially antifungal genera in skin microbiota was high. Moreover, we successfully isolated 165 microbes from bat skin and 41 isolates from positive individuals able to inhibit
Pd
growth compared to only 12 isolates from negative individuals. A total of 10 genera of
Pd
-inhibiting bacteria were screened, among which the genera
Algoriella
,
Glutamicibacter
, and
Psychrobacter
were newly discovered as
Pd
-inhibiting genera. These
Pd
-inhibiting bacteria metabolized a variety of volatile compounds, including dimethyl trisulfide, dimethyl disulfide, propylene sulfide, 2-undecanone, and 2-nonanone, which were able to completely inhibit
Pd
growth at low concentrations.

IMPORTANCE

Recently, white-nose syndrome has caused the deaths of millions of hibernating bats, even threatening some with regional extinction. Bats in China with high resistance to
Pseudogymnoascus destructans
can provide a powerful reference for studying the management of white-nose syndrome and understanding the bats against the pathogen’s intrinsic mechanisms. This study sheds light on the crucial role of host symbiotic skin microorganisms in resistance to pathogenic fungi and highlights the potential for harnessing natural defense mechanisms for the prevention and treatment of white-nose syndrome. In addition, this may also provide promising candidates for the development of bioinsecticides and fungicides that offer new avenues for addressing fungal diseases in wildlife and agricultural environments.
mSphere of Influence: Predicting the evolution of pathogen populations
Authors: Mortimer Tatum D. 
Published: July 2024

ABSTRACT

Tatum D. Mortimer works in the field of pathogen population genomics and evolution. In this mSphere of Influence article, she reflects on how “Frequency-dependent selection can forecast evolution in
Streptococcus pneumoniae
” by Azarian et al. and “Contingency, repeatability, and predictability in the evolution of a prokaryotic pangenome” by Beavan et al. made an impact on her by highlighting the ways in which genomic data can be used to predict pathogen evolution.
Learning metabolic dynamics from irregular observations by Bidirectional Time-Series State Transfer Network
Authors: Xu Shaohua , Xu Ting , Yang Yuping , Chen Xin 
Published: July 2024

ABSTRACT

Modeling microbial metabolic dynamics is important for the rational optimization of both biosynthetic systems and industrial processes to facilitate green and efficient biomanufacturing. Classical approaches utilize explicit equation systems to represent metabolic networks, enabling the quantification of pathway fluxes to identify metabolic bottlenecks. However, these white-box models, despite their diverse applications, have limitations in simulating metabolic dynamics and are intrinsically inaccurate for industrial strains that lack information on network structures and kinetic parameters. On the other hand, black-box models do not rely on prior mechanistic knowledge of strains but are built upon observed time-series trajectories of biosynthetic systems in action. In practice, these observations are typically irregular, with discontinuously observed time points across multiple independent batches, each time point potentially containing missing measurements. Learning from such irregular data remains challenging for existing approaches. To address this issue, we present the Bidirectional Time-Series State Transfer Network (BTSTN) for modeling metabolic dynamics directly from irregular observations. Using evaluation data sets derived from both ideal dynamic systems and a real-world fermentation process, we demonstrate that BTSTN accurately reconstructs dynamic behaviors and predicts future trajectories. This approach exhibits enhanced robustness against missing measurements and noise, as compared to the state-of-the-art methods.

IMPORTANCE
Industrial biosynthetic systems often involve strains with unclear genetic backgrounds, posing challenges in modeling their distinct metabolic dynamics. In such scenarios, white-box models, which commonly rely on inferred networks, are thereby of limited applicability and accuracy. In contrast, black-box models, such as statistical models and neural networks, are directly fitted or learned from observed time-series trajectories of biosynthetic systems in action. These methods typically assume regular observations without missing time points or measurements. If the observations are irregular, a pre-processing step becomes necessary to obtain a fully filled data set for subsequent model training, which, at the same time, inevitably introduces errors into the resulting models. BTSTN is a novel approach that natively learns from irregular observations. This distinctive feature makes it a unique addition to the current arsenal of technologies modeling metabolic dynamics.
Salinity reconstruction in Proterozoic depositional systems
Authors: Liu Zhanhong , Algeo Thomas J. , Brocks Jochen J. , van Maldegem Lennart M. , Gilleaudeau Geoffrey J. , Kah Linda C. , Cheng Meng , Yu Wenchao 
Published: July 2024

Abstract
Although elemental proxies (i.e., boron/gallium [B/Ga], strontium/barium [Sr/Ba], and sulfur/total organic carbon [S/TOC]) have been extensively used to evaluate paleo-watermass salinities in Phanerozoic shales and marls, their application to Precambrian-age formations has been limited. Here, we evaluate these proxies for five depositional systems ranging in age from late Paleoproterozoic to late Neoproterozoic. Our analysis shows that the range of B/Ga ratios encountered (~2–9) matches that seen in Phanerozoic deposits and is consistent with a spectrum of salinity conditions ranging from freshwater (B/Ga &lt; 3) to brackish (B/Ga 3–6) to marine (B/Ga 6–12). Furthermore, all B/Ga-based salinity assignments are consistent with existing paleosalinity inferences, including fully marine conditions for the ca. 650 Ma Areyonga-Aralka and ca. 1640 Ma Barney Creek formations in Australia, mixed brackish-marine conditions for the ca. 650 Ma Datangpo Formation in China and the ca. 1100 Ma El Mreiti Group shales in Mauritania, and low-brackish conditions for the ca. 1080 Ma Nonesuch Formation in North America. Our salinity assessment for the Nonesuch Formation is particularly significant in view of extended debate regarding the lacustrine versus marine character of this unit. The influences of diagenesis and clay-mineral assemblages on B/Ga-based salinity interpretations are generally minor to insignificant. The Sr/Ba proxy yielded systematically lower salinity estimates than the B/Ga proxy based on salinity facies thresholds established from modern aqueous systems, a pattern that we interpret to reflect reduced Sr concentrations in Proterozoic seawater. The S content and S/TOC ratios of all units are sufficiently high as to preclude freshwater conditions (incidentally indicating that Proterozoic seawater sulfate concentrations were higher than sometimes inferred). These findings demonstrate that elemental salinity proxies, especially B/Ga, are broadly applicable to shale formations of Proterozoic age, providing an important new tool for paleoenvironmental analysis that has the potential to reshape our understanding of life-environment co-evolution in deep-time systems.
Petrocella pelovolcani sp. nov., an Alkaliphilic Anaerobic Bacterium Isolated from Terrestrial Mud Volcano
Authors: Frolova A. A. , Merkel A. Yu. , Kopitsyn D. S. , Slobodkin A. I. 
Published: July 2024

Abstract
Diversity of extremophilic microorganisms in mud volcanoes is largely unexplored. Here we report the isolation of a novel alkaliphilic, mesophilic, fermentative bacterium (strain FN5sucT) from a terrestrial mud volcano located at the Taman Peninsula, Russia. Cells of strain FN5sucT are gram-stain-positive, non-sporeforming, motile rods. The temperature range for growth is 10–37°C, with an optimum at 30°C. The pH range for growth is 7.5–10.0, with an optimum at pH 9.0. The isolate utilizes various organic polymeric substances, organic acids, carbohydrates, and proteinaceous compounds. The end products of carbohydrates fermentation are acetate, CO2 and trace amounts of H2 and formate. The major cellular fatty acid compounds are C16:0, C16:1 ω7c, and monounsaturated dimethyl acetal C14:1. Phylogenetic analysis reveals that strain FN5sucT is most closely related to Petrocella atlantisensis = DSM 105309T (98.4% 16S rRNA gene identity). The total size of the genome of strain FN5sucT is 3.35 Mb, and a genomic DNA G+C content is 37.0 mol %. The genome contains complete glycolisis/glyconeogenesis pathway. We propose to assign strain FN5sucT to the genus Petrocella, as a new species, Petrocella pelovolcani sp. nov. The type strain is FN5sucT (=DSM 113898T = UQM 41591T).
Patient safety in actioning and communicating blood test results in primary care: a UK wide audit using the Primary care Academic CollaboraTive (PACT)
Authors: Watson Jessica , Duncan Polly , Burrell Alexander , Bennett-Britton Ian , Hodgson Sam , Merriel Samuel W D , Waqar Salman , Razumovskaya-Hough Alexandra , Whiting Penny F 
Published: July 2024

BackgroundErrors associated with failures in filing, actioning and communicating blood test results can lead to delayed and missed diagnoses and patient harm. This study aimed to audit how blood tests in primary care are filed, actioned and communicated in primary care, to identify areas for patient safety improvements.MethodsUK primary care clinicians were recruited through the Primary Care Academic CollaboraTive (PACT). PACT members audited 50 recent sets of blood tests from their practice and retrospectively extracted data on blood test result coding, actioning and communication. PACT members received a practice report, showing their own results, benchmarked against other participating practices.ResultsPACT members from 57 general practices across all four UK nations collected data on 2572 patients who had blood tests in April 2021. In 89.9% (n=2311) they agreed with the initial clinician’s actioning of blood tests; 10.1% disagreed, either partially (7.1%) or fully (3.0%).In 44% of patients (n=1132) an action (eg, ‘make an appointment’) was specified by the filing clinician. This action was carried out in 89.7% (n=1015/1132) of cases; in 6.8% (n=77) the action was not carried out, in 3.5% (n=40) it was unclear. In the 117 cases where the test result had not been actioned 38% (n=45) were felt to be at low risk of harm, 1.7% (n=2) were at high risk of harm, 0.85% (n=1) came to harm.Overall, in 47% (n=1210) of patients there was no evidence in the electronic health records that results had been communicated. Out of 1176 patients with one or more abnormal results there was no evidence of test communication in 30.6% (n=360). There were large variations between practices in rates of actioning and communicating tests.ConclusionThis research demonstrates variation in the way blood test results are actioned and communicated, with important patient safety implications.
ImmunoPET imaging of LAG-3 expression in tumor microenvironment with68Ga-labelled cyclic peptides tracers: from bench to bedside
Authors: Zhou Ming , Chen Bei , Lu Chenxi , Yang Jinhui , Liu Peng , Wang Xiaobo , Hu Shuo 
Published: July 2024

BackgroundLymphocyte activation gene 3 (LAG-3) has been considered as the next generation of immune checkpoint and a promising prognostic biomarker of immunotherapy. As with programmed cell death protein-1/programmed death-ligand 1 and cytotoxic T-lymphocyte antigen-4 inhibitors, positron emission tomography (PET) imaging strategies could benefit the development of clinical decision-making of LAG-3-related therapy. In this study, we developed and validated68Ga-labeled cyclic peptides tracers for PET imaging of LAG-3 expression in bench-to-bedside studies.MethodsA series of LAG-3-targeted cyclic peptides were modified and radiolabeled with68GaCl3and evaluated their affinity and specificity, biodistribution, pharmacokinetics, and radiation dosimetry in vitro and in vivo. Furthermore, hu-PBL-SCID (PBL) mice models were constructed to validate the capacity of [68Ga]Ga-CC09-1 for mapping of LAG-3+lymphocytes infiltrates using longitudinal PET imaging. Lastly, [68Ga]Ga-CC09-1 was translated into the first-in-human studies to assess its safety, biodistribution and potential for imaging of LAG-3 expression.ResultsA series of cyclic peptides targeting LAG-3 were employed as lead compounds to design and develop68Ga-labeled PET tracers. In vitro binding assays showed higher affinity and specificity of [68Ga]Ga-CC09-1 in Chinese hamster ovary-human LAG-3 cells and peripheral blood mononuclear cells. In vivo PET imaging demonstrated better imaging capacity of [68Ga]Ga-CC09-1 with a higher tumor uptake of 1.35±0.33 per cent injected dose per gram and tumor-to-muscle ratio of 17.18±3.20 at 60 min post-injection. Furthermore, [68Ga]Ga-CC09-1 could detect the LAG-3+lymphocyte infiltrates in spleen, lung and salivary gland of PBL mice. In patients with melanoma and non-small cell lung cancer, primary lesions with modest tumor uptake were observed in [68Ga]Ga-CC09-1 PET, as compared with that of [18F]FDG PET. More importantly, [68Ga]Ga-CC09-1 delineated the heterogeneity of LAG-3 expression within large tumors.ConclusionThese findings consolidated that [68Ga]Ga-CC09-1 is a promising PET tracer for quantifying the LAG-3 expression in tumor microenvironment, indicating its potential as a companion diagnostic for patients stratification and therapeutic response monitoring in anti-LAG-3 therapy.
Sensitivity to change of structural outcomes in axial spondyloarthritis after 10 years of follow up. Data from the DESIR cohort
Authors: López-Medina Clementina , Molto Anna , Sepriano Alexandre , Ramiro Sofia , Tournadre Anne , Dougados Maxime 
Published: July 2024

ObjectiveTo evaluate the sensitivity to change in structural imaging outcomes over 10 years of follow-up in patients with axial spondyloarthritis (axSpA).MethodsPatients with axSpA from the Devenir des Spondyloarthropathies Indifferénciées Récentes cohort were included. Radiographs and MRIs of the sacroiliac joints (SIJ) and spine were obtained at baseline and at 1, 2, 5 and 10 years. The yearly rate of change of each structural outcome was analysed using generalised estimating equation models, including all patients with ≥1 score from ≥1 reader from ≥1 reading wave, using the time (years) as an explanatory variable and adjusting for reader and wave. All outcomes were standardised, and the relative standardised rate of change was calculated (ie, the standardised rate of an outcome divided by the rate of a reference outcome).ResultsA total of 659 patients (46% males and mean age 33.6 years) were included. The most sensitive outcome to change in the SIJ (both MRI and radiographs) was the presence of ≥3 fatty lesions at a specific timepoint, with a relative standardised rate of change per year of 5.28 using the modified New York criteria as reference.Similarly, the most sensitive to change (in both MRI and radiographs) outcome in the spine was the modified Stoke Ankylosing Spondylitis Spinal Score (mSASSS; relative standardised yearly change 1.76) using ≥1 syndesmophyte as reference.ConclusionMRI structural outcomes in the SIJ (ie, fatty lesions) are more sensitive to change than radiographic outcomes. Conversely, the mSASSS remains the most sensitive method, even when compared with MRI of the spine.
Reframing social media discourse following the FDA’s menthol ban announcement as industry agenda setting rather than public sentiment
Authors: Silver Nathan A , Kierstead Elexis C , Emery Sherry L , Binns Steven , Guy Mignonne C , Schillo Barbara 
Published: July 2024

BackgroundThe tobacco industry has spent millions of dollars promoting racialised narratives against the US Food and Drug Administration’s recently announced ban on menthol as a characterising cigarette flavour. This research investigates racialised narratives in online discourse following the ban’s announcement.MethodsTweets and users responding to the April 2022 menthol ban announcement were content analysed to examine the influence of tobacco industry affiliates and potentially organic African-American/Black (AA/B) users. Next we investigated the extent to which the menthol ban was discussed on AA/B subreddits and used Latent Dirichlet Allocation topic modelling to provide an overview of the menthol ban discussion on Reddit.ResultsOnly 28 (13.9%) tweets by 22 users claimed that the menthol ban would lead to police violence and/or racial discrimination. Of users who tweeted about over-policing, eight (36.4%) had financial connections to the tobacco industry. There were only three tweets receiving a combined seven retweets from potentially organic AA/B users. On Reddit, only two posts with one comment discussed the menthol ban on subreddits dedicated to AA/B issues and culture. Topic modelling showed that the most common topic related to the menthol ban involved the social and political implications of the ban followed by illicit markets and protecting youth.ConclusionTweets claiming a menthol ban will lead to police violence are indicative of industry agenda-setting. The menthol ban was not a prominent topic of discussion in AA/B subreddits although users discussing news and politics expressed concern for how AA/B people would respond to a ban politically.
Totarol exhibits antibacterial effects through antibiofilm and combined interaction against vancomycin-resistant Enterococcus faecalis
Authors: Hyeon Ga-Eun , Eom Yong-Bin 
Published: July 2024

The rise of vancomycin-resistant enterococci (VRE) due to antibiotic overuse poses a significant threat to long-term care patients and those with impaired immune systems. Therefore, it is imperative to seek alternatives to overcome multidrug resistance. This study aimed to evaluate totarol, a natural compound derived from Podocarpus totara, for its antibacterial activity against vancomycin-resistant Enterococcus faecalis (VREF). Totarol exhibited potent antibacterial activity at a very low concentration of 0.25 µg/mL and demonstrated antibiofilm effects through biofilm inhibitory concentration and biofilm eradication concentration assays. Confocal laser scanning microscopy confirmed that totarol inhibited not only biofilm mass but also bacterial cell viability. The combinatorial use of sublethal concentrations of totarol and vancomycin showed antibacterial activity, as observed in the time-kill assay. Quantitative polymerase chain reaction assays revealed a concentration-dependent downregulation of key virulence genes ( vanA, ace, asa, efaA, and esp) in VREF when exposed to totarol. In summary, totarol emerges as a promising adjuvant with vancomycin for inhibiting VREF, addressing vancomycin resistance and biofilm formation—critical challenges associated with VRE infection. Since this was an in vitro study, the role of totarol in the clinical implications of VREF treatment remains to be demonstrated.
Fully charmed tetraquark states in $$8_{[c\bar{c}]}\otimes 8_{[c\bar{c}]}$$ color structure via QCD sum rules
Authors: Tang Chun-Meng , Duan Chun-Gui , Tang Liang 
Published: July 2024

AbstractStimulated by the recent experimental results on the fully-charm tetraquark states, we systematically calculate the mass spectra of the fully-charm tetraquark states in $$8_{[c\bar{c}]}\otimes 8_{[c\bar{c}]}$$

8

[
c

c

¯

]

⊗

8

[
c

c

¯

]

color configuration via QCD sum rules. By constructing nine $$8_{[c\bar{c}]}\otimes 8_{[c\bar{c}]}$$

8

[
c

c

¯

]

⊗

8

[
c

c

¯

]

type currents with quantum numbers $$J^{PC}=0^{-+},0^{--},1^{-+},1^{+-},1^{--}$$

J

PC

=

0

-
+

,

0

-
-

,

1

-
+

,

1

+
-

,

1

-
-

and $$2^{++}$$

2

+
+

, we perform analytic calculation up to dimension six in the operator product expansion (OPE). We find the fully-charm tetraquark states with $$J^{PC}=1^{+-},2^{++}$$

J

PC

=

1

+
-

,

2

+
+

lie around 6.48 $$\sim $$
∼
6.62 GeV while the fully-charm tetraquark states with $$J^{PC}=0^{-+},0^{--},1^{--},1^{-+}$$

J

PC

=

0

-
+

,

0

-
-

,

1

-
-

,

1

-
+

are about 6.85 $$\sim $$
∼
7.02 GeV. Notably, the mass predictions for the $$c\bar{c}c\bar{c}$$

c

c

¯

c

c

¯

tetraquarks, specifically those with $$J^{PC}=2^{++}$$

J

PC

=

2

+
+

, align with the broad structure identified by LHCb. Moreover, the masses of fully-charm tetraquarks with $$J^{PC}=0^{-+}$$

J

PC

=

0

-
+

and $$1^{-+}$$

1

-
+

are anticipated to match closely with the mass of X(6900), considering the margin of error. Such findings hint at the presence of some $$8_{[c\bar{c}]}\otimes 8_{[c\bar{c}]}$$

8

[
c

c

¯

]

⊗

8

[
c

c

¯

]

components within the di-$$J/\psi $$

J
/
ψ

structures observed by LHCb. The predictions for tetraquark states with $$J^{PC}=0^{--},1^{+-},1^{--}$$

J

PC

=

0

-
-

,

1

+
-

,

1

-
-

may be accessible in the future BelleII, Super-B, PANDA, and LHCb experiments.
Development and Application of Genetic Ancestry Reconstruction Methods to Study Diversity of Patient-Derived Models in the NCI PDXNet Consortium
Authors: Lott Paul C. , Chiu Katherine , Quino Juanita Elizabeth , Vang April Pangia , Lloyd Michael W. , Srivastava Anuj , Chuang Jeffrey H. ,   for the PDXNet Consortium, Carvajal-Carmona Luis G. 
Published: July 2024

Abstract

Precision medicine holds great promise for improving cancer outcomes. Yet, there are large inequities in the demographics of patients from whom genomic data and models, including patient-derived xenografts (PDX), are developed and for whom treatments are optimized. In this study, we developed a genetic ancestry pipeline for the Cancer Genomics Cloud, which we used to assess the diversity of models currently available in the National Cancer Institute–supported PDX Development and Trial Centers Research Network (PDXNet). We showed that there is an under-representation of models derived from patients of non-European ancestry, consistent with other cancer model resources. We discussed these findings in the context of disparities in cancer incidence and outcomes among demographic groups in the US, as well as power analyses for biomarker discovery, to highlight the immediate need for developing models from minority populations to address cancer health equity in precision medicine. Our analyses identified key priority disparity-associated cancer types for which new models should be developed.

Significance:
Understanding whether and how tumor genetic factors drive differences in outcomes among U.S. minority groups is critical to addressing cancer health disparities. Our findings suggest that many additional models will be necessary to understand the genome-driven sources of these disparities.