bluuebunny/crossref_metadata_2025_split huggingface dataset:
PlasGO: enhancing GO-based function prediction for plasmid-encoded proteins based on genetic structure
Authors: Ji Yongxin , Shang Jiayu , Guan Jiaojiao , Zou Wei , Liao Herui , Tang Xubo , Sun Yanni 
Published: December 2024

Abstract

Background
Plasmid, as a mobile genetic element, plays a pivotal role in facilitating the transfer of traits, such as antimicrobial resistance, among the bacterial community. Annotating plasmid-encoded proteins with the widely used Gene Ontology (GO) vocabulary is a fundamental step in various tasks, including plasmid mobility classification. However, GO prediction for plasmid-encoded proteins faces 2 major challenges: the high diversity of functions and the limited availability of high-quality GO annotations.

Results
In this study, we introduce PlasGO, a tool that leverages a hierarchical architecture to predict GO terms for plasmid proteins. PlasGO utilizes a powerful protein language model to learn the local context within protein sentences and a BERT model to capture the global context within plasmid sentences. Additionally, PlasGO allows users to control the precision by incorporating a self-attention confidence weighting mechanism. We rigorously evaluated PlasGO and benchmarked it against 7 state-of-the-art tools in a series of experiments. The experimental results collectively demonstrate that PlasGO has achieved commendable performance. PlasGO significantly expanded the annotations of the plasmid-encoded protein database by assigning high-confidence GO terms to over 95% of previously unannotated proteins, showcasing impressive precision of 0.8229, 0.7941, and 0.8870 for the 3 GO categories, respectively, as measured on the novel protein test set.

Conclusions
PlasGO, a hierarchical tool incorporating protein language models and BERT, significantly expanded plasmid protein annotations by predicting high-confidence GO terms. These annotations have been compiled into a database, which will serve as a valuable contribution to downstream plasmid analysis and research.
A mixed-methods exploration of the food retail environment of a low-income area of Montevideo, Uruguay
Authors: Ares Gastón , Girona Alejandra , Brunet Gerónimo , Alcaire Florencia , Fajardo Gabriela , Paroli Carolina , Amado Marcelo , Santín Viviana , Vidal Leticia 
Published: December 2024

Abstract
Creating supportive food environments has been identified as one of the most effective strategies to promote healthy diets. In this context, the present work aimed to characterize the retail food environment in a low-income area of the city of Montevideo (Uruguay). The study relied on a mixed-methods approach. A survey of food retail outlets was conducted. All the outlets were geocoded, and service areas were created considering a 600 m threshold. Quantitative information was supplemented with qualitative information from semi-structured interviews with residents and grocery store owners. A total of 415 outlets selling a variety of foods were identified. Adequate physical access to the foods recommended by the Uruguayan dietary guidelines was found in most of the residential areas. Small behind-the-counter grocery stores were identified as the key source of healthy foods in the area. However, the accounts of residents highlighted problems related to the price, variety and quality of the foods sold by the local grocery stores. Therefore, strategies to ensure access to healthy food in the study area should go beyond physical access and tackle food affordability, variety and quality. The promotion of short food supply chains in the area should be a key element of the strategies to achieve sustainable urban food systems in Montevideo.
Trade-offs and complementarities between regional, sectoral, and national support policies for firms’ innovation
Authors: Roper Stephen , Vanino Enrico , Hewitt-Dundas Nola 
Published: December 2024

Abstract
Public support for R&D can play a crucial role in addressing systemic failures that hinder the functioning of innovation systems, whether national, sectoral, or region-specific. However, little is known about the trade-offs and complementarities between subnational and national innovation policies. Here, we consider trade-offs and complementarities between national R&D support measures managed by UK Research and Innovation (UKRI), regional support provided by the Northern Ireland government, and sectoral support provided by the UK’s Catapult network. Using a propensity score matching combined with a difference-in-difference event study analysis, we find evidence of dynamic complementarities between subnational and national innovation policies. Both regional and sectoral innovation support measures have positive effects on both employment and turnover growth. However, each subnational policy targets somewhat different groups of firms to national policy measures. Strong static and dynamic complementarities are also evident between sectoral and national support, as firms initially supported by the Catapults are significantly more likely to secure national R&D funding in the future.
A Geometric Approach to Poincaré Inequality and Minkowski Content of Separating Sets
Authors: Caputo Emanuele , Cavallucci Nicola 
Published: December 2024

Abstract
The goal of this paper is to continue the study of the relation between the Poincaré inequality and the lower bounds of Minkowski content of separating sets, initiated in our previous work [5]. A new shorter proof is provided. It is based on the study of the lower bound of a new geometric quantity, called separating ratio. The main result in this work is the quantitative comparison, in the locally quasigeodesic case, of the infima of the separating ratio and the Minkowski content of separating sets. The proof is based on a novel approach: it uses a new function, called the position function, which allows to fibrate a set in boundaries of separating sets. No Poincaré assumption is needed to prove the main result. We also extend the proof to measure graphs, where due to the combinatorial nature of the problem, the approach is more intuitive. In the appendix, we revise some classical characterizations of the $p$-Poincaré inequality, showing that the equivalences remain true if the several conditions hold only for a fixed couple of points.
On Finite Analogues of Euler’s Constant
Authors: Kaneko Masanobu , Matsusaka Toshiki , Seki Shin-ichiro 
Published: December 2024

Abstract
We introduce and study finite analogues of Euler’s constant in the same setting as finite multiple zeta values. We define a couple of candidate values from the perspectives of a “regularized value of $\zeta (1)$” and of Mascheroni’s and Kluyver’s series expressions of Euler’s constant using Gregory coefficients. Moreover, we reveal that the differences between them always lie in the ${\mathbb{Q}}$-vector space spanned by 1 and values of a finite analogue of logarithm at positive integers.
New Lower Bound on Ball Packing Density in High-Dimensional Hyperbolic Spaces
Authors: Gil Fernández Irene , Kim Jaehoon , Liu Hong , Pikhurko Oleg 
Published: December 2024

Abstract
We present a new lower bound on the Bowen–Radin maximal density of radius-$R$ ball packings in the $m$-dimensional hyperbolic space, improving on the basic covering bound by factor $\Omega (m(R+\ln m))$ as $m$ tends to infinity. This is done by applying the recent theorem of Campos, Jenssen, Michelen, and Sahasrabudhe on independent sets in graphs with sparse neighbourhoods.
NaHCO3 modulates the bla operon and β-lactam susceptibility in borderline oxacillin-resistant Staphylococcus aureus (BORSA)
Authors: Ersoy Selvi C , Madrigal Sabrina L , Proctor Richard A , Chambers Henry F , Xiong Yan Q , Bayer Arnold S 
Published: December 2024

Abstract

Background
Methicillin-resistant Staphylococcus aureus (MRSA) are resistant to nearly all β-lactam antibiotics under standard testing conditions. However, a novel phenotype exists wherein certain MRSA strains exhibit β-lactam susceptibility in the presence of bicarbonate (termed ‘NaHCO3-responsive’), an abundant ion in mammalian tissues and blood. This suggests that specific MRSA infections may be treatable by β-lactams. NaHCO3 responsiveness appears due to effects of NaHCO3 on the expression mecA/PBP2a and other accessory genes required for PBP functionality. mecA expression can be co-regulated by the bla operon regulatory genes, blaI and blaR1.

Objectives
To elucidate the influence of NaHCO3 specifically on the bla operon via investigations of the impact of NaHCO3 on β-lactamase hyper-producing, mecA-negative, borderline oxacillin-resistant Staphylococcus aureus (BORSA) strains.

Methods
Evaluate the effect of NaHCO3 on β-lactam susceptibility via minimum inhibitory concentrations (MIC) assay, expression of genes within the bla operon (blaZ, blaI, blaR1) via RT–qPCR, and β-lactamase (BlaZ) activity via nitrocefinase assay in BORSA.

Results
NaHCO3 enhanced susceptibility to β-lactamase-susceptible β-lactams penicillin and ampicillin. NaHCO3 had no impact on susceptibility to the anti-staphylococcal β-lactams oxacillin and cefazolin, or the anti-MRSA antibiotics vancomycin and daptomycin. NaHCO3 repressed expression of all genes within the bla operon and reduced β-lactamase production.

Conclusions
These data demonstrate that NaHCO3 influences expression of genes within the bla operon, translating to reduced β-lactamase production and enhanced β-lactam susceptibility in BORSA strains. Furthermore, this indicates that the classical blaZ regulators, blaI and blaR1, are the likely mediators of NaHCO3-mediated repression of mecA. However, questions still remain regarding the mechanism via which NaHCO3 regulates the bla operon.
Changes in NNRTI use have not altered the ecology of NNRTI resistance over the last 10 years in people with HIV experiencing virological failure on antiretroviral drugs
Authors: Soulie Cathia , Agher Rachid , Fauchois Antoine , Abdi Basma , Wirden Marc , Teyssou Elisa , Sayon Sophie , Katlama Christine , Valantin Marc-Antoine , Tubiana Roland , Schneider Luminita , Faycal Antoine , Palich Romain , Pourcher Valérie , Marcelin Anne-Geneviève , Calvez Vincent 
Published: December 2024

Abstract

Background
We aimed to determine how non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance profiles have changed over the last decade in people living with HIV (PLWHIV) experiencing virological failure on all antiretroviral treatments, including different NNRTIs.

Materials and methods
We analysed the use of the different NNRTIs in PLWHIV treated with antiretroviral drugs at an academic centre and the HIV NNRTI resistance profiles observed in cases of virological failure over the last 10 years (2014–23). We used the latest ANRS-MIE algorithm (v33; https://hivfrenchresistance.org/) to analyse the resistance mutation profiles of the HIV reverse transcriptase sequences.

Results
During this period, the frequency of NNRTI use remained high, fluctuating slightly between 43.5% (n = 1782/4094) and 39.9% (n = 1758/4421). The use of efavirenz (10.8%–1.5%), nevirapine (7.0%–1.2%), and etravirine (11.0%–1.1%) decreased, whereas the use of rilpivirine (14.7%–26.3%) and doravirine (available from 2018, rising to 9.7% in 2023) increased. These trends were statistically significant for etravirine (P = 0.033) and rilpivirine (P &lt; 0.001). Resistance rates for efavirenz, nevirapine and rilpivirine remained above 15% (efavirenz: 17.3%–16.6%, nevirapine: 16.9%–15.4% and rilpivirine: 17.6%–16.1%). This reflects significant cross-resistance between these three NNRTIs. By contrast, resistance rates were lower for etravirine (7.8%–6.0%) and doravirine (4.9%–4.6%), probably due to differences in their resistance profiles and higher genetic barriers to resistance.

Conclusions
The NNRTI class of antiretroviral drugs remains widely used. Changes in the usage of drugs from this class have not altered the ecology of NNRTI resistance in antiretroviral drug-treated PLWHIV with virological failure during the studied period.
Bacillus safensis LS01 provides biological control of potato common scab with potential effects from secondary metabolites
Authors: Wang Lixue , Liu Song , Liu Lihe , Wang Lichun , Pan Yang , Fu Xuepeng 
Published: December 2024

Abstract

Aims
Potato common scab (CS), caused by pathogenic Streptomyces, is a devastating disease affecting potato crops worldwide. Antagonistic microorganisms have been used as biological control agents to inhibit Streptomyces scabies and reduce the use of synthetic pesticides. However, identifying beneficial microorganisms for controlling CS remains undetermined.

Methods and Results
Strain LS01 was isolated from the geocaulosphere soils of healthy potato tubers. In vitro and pot experiments demonstrated that strain LS01 significantly inhibited the mycelial growth and sporulation of S. scabies, thereby reducing the severity of CS. Sequencing of the 16S rRNA of LS01 indicated that the strain belonged to the species Bacillus safensis. Whole-genome sequencing, metabolomic analysis with liquid chromatograph mass spectrometer, and uultra-high performance liquid chromatography with quadrupole time-of-flight mass spectrometry analyses indicated that hygromycin B and plantazolicin may be the active secondary metabolites by which B. safensis LS01 inhibits S. scabies.

Conclusions
Bacillus safensis LS01 is a potential biocontrol agent for CS, with its secondary metabolites exerting effective inhibitory effects.
Insights from the timber rattlesnake (Crotalus horridus) genome for MHC gene architecture and evolution in threatened rattlesnakes
Authors: Roseman Marissa A , Mason Andrew J , Bode Emily R , Bolton Peri E , Nachtigall Pedro G , Peterman William E , Gibbs H Lisle 
Published: December 2024

Abstract
Conservation of threatened species can benefit from an evaluation of genes in the major histocompatibility complex (MHC), whose loci encode proteins that bind pathogens and are often under strong selection to maintain diversity in immune response to diseases. Despite this gene family’s importance to disease resistance, little is known about these genes in reptiles including snakes. To address this issue, we assembled and annotated a highly contiguous genome assembly for the timber rattlesnake (Crotalus horridus), a pit viper which is threatened or endangered in parts of its range, and analyzed this new genome along with three other rattlesnake genomes to characterize snake MHC loci. We identified highly duplicated MHC Class I and Class IIβ genes in all species typified by a genomic architecture of discrete gene clusters localized on chromosome 2. The number of loci varied between species from 14 to 23 for MHC I and from 8 to 32 for MHC IIβ and was greater than previously identified in the few non-genome-based studies of reptile MHC to date. We present evidence of the gene family’s complex evolutionary history, with extensive duplication and loss concurrent with speciation resulting in incomplete lineage sorting. The differences in gene number between species combined with a dynamic evolutionary history suggest that gene family expansion/contraction via rapid duplication/gene loss may represent an important mechanism for generating genetic diversity in rattlesnake MHC. Our work demonstrates the utility of whole-genome sequences for identifying functional genetic variation in the form of MHC genes relevant for conservation genomic studies in threatened snakes.
Cell walls: a comparative view of the composition of cell surfaces of plants, algae, and microorganisms
Authors: Fuertes-Rabanal María , Rebaque Diego , Largo-Gosens Asier , Encina Antonio , Mélida Hugo 
Published: December 2024

Abstract
While evolutionary studies indicate that the most ancient groups of organisms on Earth likely descended from a common wall-less ancestor, contemporary organisms lacking a carbohydrate-rich cell surface are exceedingly rare. By developing a cell wall to cover the plasma membrane, cells were able to withstand higher osmotic pressures, colonize new habitats, and develop complex multicellular structures. Thus, the cells of plants, algae, and microorganisms are covered by a cell wall, which can generally be defined as a highly complex structure whose main framework is usually composed of carbohydrates. Rather than static structures, they are highly dynamic and serve a multitude of functions that modulate vital cellular processes, such as growth and interactions with neighbouring cells or the surrounding environment. Thus, despite its vital importance for many groups of life, it is striking that there are few comprehensive studies comparing the cell wall composition of these groups. Thus, the aim of this review was to compare the cell walls of plants with those of algae and microorganisms, paying particular attention to their polysaccharide components. It should be highlighted that, despite the important differences in composition, we have also found numerous common aspects and functionalities.
A simple HPLC method for the determination of plasma progesterone levels in the third trimester of human pregnancy
Authors: Albayrak Mevlut , Kadioglu Yucel , Demirkaya-Miloglu Fatma , Borekci Bunyamin 
Published: December 2024

Abstract
Progesterone is a steroid hormone primarily associated with pregnancy. A simple, rapid, and reliable high-performance liquid chromatography (HPLC) method has been developed and validated for the quantification of progesterone in human plasma. The method consists of a simple liquid-liquid extraction of progesterone and internal standard (estriol) from human plasma using a mixture of hexane and diethyl ether. The chromatographic determination of progesterone was performed using an acetonitrile-water (70:30, v/v) mobile phase with a C18 reversed-phase column. The method achieved an extraction recovery of greater than 96.4% from spiked plasma samples. Intra- and inter-day precision were generally acceptable, with relative SD% less than ≤6.60% and accuracy (relative error %) better than 3.64%. The developed and validated method was used to successfully quantify progesterone levels in plasma samples collected from women during the third trimester of pregnancy. Furthermore, a statistical comparison was conducted between progesterone concentrations in plasma samples obtained from 2 groups of pregnant women: group 1 (n = 9) at 30-35 weeks and group 2 (n = 9) at 36-41 weeks.
The developed and validated HPLC method described in this study enables the successful determination of progesterone in human plasma, offering advantages such as shorter analysis time, simplicity, cost-effectiveness, and potential routine use during pregnancy.
Diagnostic approach for multiple sclerosis: optimizing algorithms for intrathecal synthesis of immunoglobulins
Authors: Ferriz Jorge , Guallart Cristina , Timoneda Pilar , Fandos Marta , Lopez-Arqueros Javier , Sierra-Rivera Antonio , Garcia-Hita Marta , Marcaida Goitzane , Carcelén-Gadea Maria 
Published: December 2024

Abstract

Background
The kappa-free light chain (κFLC) index has shown its value in detecting the intrathecal synthesis of immunoglobulins. We aimed to evaluate the diagnostic performance of the κFLC index for multiple sclerosis (MS) and compare different algorithms proposed in the literature to optimize its use for our population.

Methods
Based on the results of the oligoclonal bands (OCBs) and κFLC index of 255 patients with suspected MS different optimization strategies were evaluated, for which the optimal κFLC index cut-off thresholds were calculated.

Results
The best diagnostic performance was achieved by using a reflexive algorithm, in which OCBs are only performed according to the κFLC index result. With a single cut-off (κFLC index = 7.9), an accuracy of 92.2% was obtained (sensitivity = 92.4%, specificity = 92%) with an OCB performance rate of 58.1%. When applying 2 cut-offs (κFLC index = 4.2 and 13), the accuracy was the same (92.2%, sensitivity = 89.6%, specificity = 94%), but the OCB performance rate dropped to 29.4%.

Conclusion
The 2-step strategy proposed with κFLC determination followed by OCB analysis in the borderline cases appears to be the most suitable solution, further optimized by adjusting the decision thresholds to 4.2 &lt; κFLC index &lt; 13, resulting in high accuracy and the most saving of OCBs.
A combined therapy of meropenem–ZnO nanoparticles efficiently eliminates carbapenem-resistant Klebsiella pneumoniae biofilms, with reduced nephrotoxicity (in vitro)
Authors: Mohamed Alzhraa Ali , Saed Safaa , El-Sayed Sara Ramadan , Yassin Mohamed Taha , Gad Mohamed , Tartour Eman , Fathey Hoda A , Taha Asmaa S , Mohamed Asmaa H , Al-Otibi Fatimah Olyan , AbdelGawwad Mohamed Ragab , Ahmed Mohamed M Sayed , Almalki Susan Ahmed , Abdel-Haleem Mohamed 
Published: December 2024

Abstract
In response to the World Health Organization’s research agenda of antimicrobial resistance in human health, this study appraised the antibacterial and antibiofilm synergistic activity of meropenem and ZnO nanoparticles (ZnO-NPs) combination against carbapenem-resistant Klebsiella pneumoniae (CRKP). The minimum inhibitory concentration (MIC) of meropenem in combination was found to be ~1/12 of its MIC alone. The results of microtiter dilution assay showed that the combination was more efficient in reducing the biofilm biomass than meropenem alone or ZnO-NPs alone. The scanning-electron-microscopy micrographs elucidated that the combination of meropenem with ZnO-NPs has significantly enhanced its competence in eradicating the preformed biofilms of CRKP strains. In addition, the relative gene expression results showed that the combination compared to the meropenem alone and ZnO-NPs alone eloquently down-regulated the expression of biofilm genes (mrkA, fimA, and ecpA). Besides, the MTT-assay demonstrated that the combination has limited cytotoxicity against Vero-cells (in vitro). Overall, this study represents an efficient safe enhancement of meropenem to tackle the growing health threat of CRKP and carbapenem-resistant Enterobacterals prevalence.
Polarized dust emission in Arp220: magnetic fields in the core of an ultraluminous infrared Galaxy
Authors: Clements D L , Zhang Qizhou , Pattle K , Petitpas G , Ding Y , Cairns J 
Published: December 2024

ABSTRACT
Arp 220 is the prototypical ultraluminous infrared Galaxy (ULIRG), and one of the brightest objects in the extragalactic far-infrared sky. It is the result of a merger between two gas rich spiral galaxies which has triggered starbursting activity in the merger nuclear regions. Observations with the submillimeter array centred at a frequency of 345 GHz and with a synthesized beamsize of $0.77\times 0.45$ arcsec were used to search for polarized dust emission from the nuclear regions of Arp 220. Polarized dust emission was clearly detected at 6 $\sigma$ significance associated with the brighter, western nucleus, with a peak polarization fraction of 2.7$\pm 0.35$ per cent somewhat offset from the western nucleus. A suggestive 2.6 $\sigma$ signal is seen from the fainter eastern nucleus. The dust emission polarization is oriented roughly perpendicular to the molecular disc in the western nucleus suggesting that the magnetic field responsible is orientated broadly in the plane of the disc, but may be being reordered by the interaction between the two nuclei. Unlike more evolved interacting systems, we see no indication that the magnetic field is being reordered by the outflow from the western nucleus. These observations are the first detection of dust polarization, and thus of magnetic fields, in the core of a ULIRG.