bluuebunny/crossref_metadata_2025_split huggingface dataset:
Flower colour contrast, ‘spectral purity’ and a red herring
Authors: van der Kooi C. J. , Spaethe J. 
Published: January 2025

AbstractNature offers a bewildering diversity of flower colours. Understanding the ecology and evolution of this fantastic floral diversity requires knowledge about the visual systems of their natural observers, such as insect pollinators. The key question is how flower colour and pattern can be measured and represented to characterise the signals that are relevant to pollinators. A common way to interpret flower colours is using animal vision models that incorporate the spectral sensitivity of a focal observer (e.g. bees). These vision models provide a measure of colour contrast, which represents the perceived chromatic difference between two objects, such as a yellow flower against green leaves. Colour contrast is a behaviourally and physiologically validated proxy for relative conspicuousness of a stimulus. A growing number of studies attempt to interpret flower colouration through parameters that are grafted on to principles of human colour perception. A perpetuating measure to describe floral colours is via saturation, which is a metric in human perception describing a certain aspect of colourfulness and is, in pollination literature, often referred to as ‘spectral purity’. We caution against the concept, calculation and biological interpretation of ‘spectral purity’ and similar measures that rest on an anthropocentric view, because it does not represent the diversity and complexity of animal visual systems that are the natural observers of flowers. We here discuss the strengths and weaknesses of common ways to interpret flower colouration and provide concrete suggestions for future colourful research.
Antibiotic Resistance in Vibrio parahaemolyticus: Mechanisms, Dissemination, and Global Public Health Challenges—A Comprehensive Review
Authors: Li Yingpeng , Lin Gongshi , Pengsakul Theerakamol , Yan Qingpi , Huang Lixing 
Published: January 2025

ABSTRACTVibrio parahaemolyticus, a ubiquitous pathogen in marine and estuarine environments, is a foodborne microorganism whose infections have become a global public health challenge. In recent years, the overuse and misuse of antibiotics have led to the emergence of increasing numbers of antibiotic‐resistant strains of V. parahaemolyticus worldwide. These strains harbor resistance genes that mediate various resistance mechanisms, presenting a significant challenge to antibiotic therapy. Furthermore, horizontal gene transfer (HGT) of resistance genes and the accelerating impacts of global climate change have facilitated the formation and spread of resistance, contributing to the proliferation of resistant strains and exacerbating the public health threat. This review aims to provide a comprehensive overview of the resistance genes and mechanisms in V. parahaemolyticus, the effects of climate change on its resistance, and strategies to curb the transmission of resistant strains. Additionally, we conducted a statistical analysis of resistance data from 6727 V. parahaemolyticus isolates obtained from 27 countries across Asia, Africa, the Americas, and Europe, through the literature review, to better understand the distribution and trends of resistance in this pathogen. We hope that this study will serve as an important reference for controlling the spread of antibiotic resistance in V. parahaemolyticus and addressing this critical public health issue.
Identification of Novel MICB Alleles in Haematopoietic Stem Cell Donors of Indian Origin
Authors: Agarwal Disha , Sharma Gaurav , Khadwal Alka , Malhotra Pankaj 
Published: January 2025

ABSTRACTNovel MICB alleles MICB*004:01:31, MICB*004:01:32, MICB*004:01:33 and MICB*005:02:59, were identified using next generation sequencing.
Modal better: A corpus‐based investigation in World Englishes
Authors: Basile Carmelo Alessandro 
Published: January 2025

AbstractWhile previous studies have investigated the productivity of the better construction (in the forms had better, ’d better and better) in British and US English (USE), to present knowledge, no large‐scale comparisons on the use of this construction in other English dialects have been carried out. The present paper aims to address the existing research gap by exploring the synchronic use and grammaticalization rate of better in 20 world Englishes. The analysis of corpus data reveals that better is more grammaticalized in USE than in British English, and even more in Singapore English (SgE) data, where the construction seems to be more grammaticalized than in any other dialect. The hypothesis of a functional need in SgE for deontic better is tested. It is shown why SgE ‘needs’ alternative deontic constructions in a modal system where (semi‐)modals of necessity have been shown to express higher rates of ‘dynamic’ modality than in other dialects. The substrate reinforcement from a parallel construction in Mandarin is presented as a potential driving factor justifying the selection of better as a deontic marker in this particular variety.
Investigation of the Dynamic Response of Soil/Steel Composite Structures of Vacuum Explosion Containment Vessels
Authors: Zhou Dezheng , Li Xiaojie , Wang Xiaohong , Liu Zhenfeng , Yan Honghao 
Published: January 2025

Abstract
Vacuum explosive welding technology has better performance, lower production cost, more environmentally friendly and other advantages. In order to meet the industrial demand for production in the area of metal composite plate, it is urgent to develop a super-large vacuum explosion containment vessel which can be used for explosive welding. Since soil is generally regarded as an effective energy-absorbing material, covering a certain thickness of soil above the steel plate can tremendously dissipate the energy of shock waves. Therefore, the dynamic response of the soil/steel composite structure on the explosion containment vessel under different explosive quantities and vacuum degrees was analyzed by experiments and numerical simulations. The dynamic strain curve collected by the experiment consists of an abruptly rising phase and a gradually decreasing vibration recovery phase. Comparing the peak strains, it was found that near-vacuum environment can significantly weaken the dynamic strain of soil/steel composite structures. Comparing the variation of the vibration amplitude of the composite structure with the cycles, it was found that reducing the amount of explosive and the vacuum degree inside the explosion containment vessel can effectively weaken the peak strain of the cover, and can also reduce the vibration amplitude of the composite structure. The dynamic response of soil/steel composite structure can be analyzed in four phases: Abrupt Increasing, Followed Impulse, Inertia Hysteresis, Static Pressure Stabilization.
Evolution of Thermoelastic Stresses in a Finite-Width Slab or Thick Cylinder With a Growing or Receding Boundary
Authors: Kumar Pavan , Segall Albert E. , Drapaca Corina 
Published: January 2025

Abstract
Semi-analytical thermoelastic stress solutions for a single phase, homogeneous, and finite-width slab or thick cylinder with a constant-velocity growing or receding boundary under Unit-Loading were derived. Initially, a semi-analytical solution for the heat equation for a slab with a growing or receding boundary was derived in the Laplace domain and a series representation then used to approximate the inverse Laplace transform in the time domain. Conformal mapping was then used to transform the slab solution to an annulus. The resulting semi-analytical solutions were used with the compatibility equations to determine the resulting transient thermoelastic stresses. All solutions allow for convection on the fixed boundary that is the opposite side for a plate and outer radius for the cylinder. Once derived, the semi-analytical stress predictions were compared to finite-element simulations with excellent agreement. Given the changing thickness, both the thermal and stress-states cannot reach true steady-state equilibrium, especially for faster growth or recession rates. Indeed, the temperature states and resulting stresses become somewhat linear with respect to time, reflecting the constant velocity of growth or recession. In practice, the resulting solutions can be used to determine transient stresses during machining, wear, erosion, corrosion, and/or additive manufacturing, especially for lower temperature solid-state methods such as cold-spray.
A novel polysaccharide in the envelope of
S. aureus
influences the septal secretion of preproteins with a YSIRK/GXXS motif
Authors: Ibrahim Amany M. , Missiakas Dominique 
Published: January 2025

ABSTRACT

Bacteria transport proteins across the plasma membrane to assemble their envelope, acquire nutrients, and establish appropriate interactions with their environment. The majority of these proteins are synthesized as precursors with a cleavable N-terminal signal sequence for recognition by the Sec machinery. In
Staphylococcus aureus
, a small subset of secreted precursors carries a YSIRK/GXXS motif. This motif provides a pre-translocation function by promoting the targeting of precursors to septal membranes, but the
trans-
acting factors that regulate such spatial distribution are not known. Here, we used immunofluorescence-microscopy to compare the spatial trafficking of Staphylococcal protein A (SpA), an abundant YSIRK/GXXS bearing precursor, between mutants of an arranged transposon library. This genetic search identified a cluster of five genes predicted to encode enzymes responsible for the synthesis of a novel surface polymer referred to as Staphylococcal surface carbohydrate, Ssc. Mutants in the
ssc
gene cluster no longer restrict the secretion of SpA into the cross-walls of
S. aureus. ssc
mutants replicate like wild-type bacteria unless grown in phosphate-limited conditions, and do not contribute to virulence when examined in a mouse model of bloodstream infection. Together, our observations suggest that
S. aureus
may encode a minor, phosphate-free carbohydrate, and propose a possible assembly pathway for this polymer.

IMPORTANCE

Gram-positive bacteria assemble peptidoglycan-linked polymers known as wall teichoic acids (WTA). Both
Staphylococcus aureus
and
Bacillus subtilis
elaborate WTAs made of poly-glycerol or poly-ribitol phosphates. WTAs contribute to cell shape maintenance, cation homeostasis, and resistance to antimicrobial compounds. Yet,
B. subtilis
replaces its phosphate-rich polymer with minor teichuronic acids whose functions remain elusive.
S. aureus
also encodes a minor wall polymer that may be required for growth under phosphate-limited condition. Here, we find that this polymer could help define the composition of the septal compartment, the site of cell division also used to recruit preproteins with a YSIRK/GXXS motif. Thus, the envelope of
S. aureus
may be more complex than previously thought with minor wall polymers contributing some discrete functions.
mSphere of Influence: The challenge of screening for essential protein kinases in
Trypanosoma cruzi
Authors: Chiurillo Miguel A. 
Published: January 2025

ABSTRACT

Miguel Chiurillo works in the field of protein kinases, studying their role in cell signaling and cell cycle progression in
Trypanosoma cruzi
. In this mSphere of Influence article, he reflects on how the research articles “Systematic functional analysis of
Leishmania
protein kinases identifies regulators of differentiation or survival” by Baker et al. and “Screening the
Toxoplasma
kinome with high throughput tagging identifies a regulator of invasion and egress” by Smith et al. made an impact on his understanding of the complexity of the
Trypanosoma cruzi
kinome and the challenges to unravel it.
The circulating plasma microRNA signature in human visceral leishmaniasis
Authors: Roy Ritirupa , Hudachek Cinthia L. , Bhushan Chauhan Shashi , Kumar Shashi , Kumar Awnish , Zhanbolat Bayan , Rai Madhukar , Kumar Rajiv , Sundar Shyam , Wilson Mary E. 
Published: January 2025

ABSTRACT

Visceral leishmaniasis (VL) is a vector-borne disease caused by the obligate intracellular protozoan
Leishmania donovani
in India. VL can be complicated by post-kala-azar dermal leishmaniasis (PKDL), a macular or nodular rash that develops in 10%–20% of patients after treatment of VL in India. Patients with PKDL are infectious to sand flies, promoting further transmission of the parasite. MicroRNAs (miRNAs) are 18–25 nt, non-coding RNAs that simultaneously regulate the expression of several or many target transcripts. This study was based on the hypothesis that the host response to
L. donovani
is modified by distinct sets of miRNAs in VL or PKDL and that these might differ from healthy controls. We investigated this hypothesis using a NanoString panel to profile the miRNAs expressed in the plasma of patients with VL or PKDL diagnosed at a hospital in Bihar, India. We compared these to plasma microRNAs of healthy control individuals from the same endemic villages. miRNAs
hsa-miR-223-3p, hsa-miR-191-5p, hsa-miR-23a-3p,
and
hsa-1285-5p
were significantly higher in the plasma samples from patients with VL compared to either PKDL or endemic controls. Prediction programs highlighted potential mRNA targeted by these miRNAs, among which we verified the down-modulation of several transcripts belonging to the NFκB and NLRP3 inflammasome pathways in circulating leukocytes of VL patients. By contrast, miRNA patterns in subjects with PKDL were similar to control subjects, possibly suggesting that the pathogenic immune response during PKDL is primarily localized in the skin.

IMPORTANCE

Infection of humans with the protozoan
Leishmania donovani
can be asymptomatic or it can cause fatal visceral leishmaniasis (VL), sometimes followed by the cutaneous complication PKDL. Parasites are spread through sand fly bites in endemic regions, and parasites in post-kala-azar dermal leishmaniasis (PKDL) skin lesions are a source of prolonged parasite transmission to sand flies, compromising disease eradication efforts. Since microRNAs can simultaneously modify the expression of multiple genes, we examined microRNAs in the blood that might be partial determinants of pathogenic responses leading to VL or PKDL. Our studies revealed several miRNAs expressed that are elevated in the plasma of patients with VL, which suppress some of the inflammatory responses that promote parasite killing. However, miRNA profiles were very similar between PKDL patients and controls, raising the possibility that major factors that lead to prolonged retention of parasites in the skin during PKDL are not systemic but are localized in the skin.
Ribosome profiling reveals differences in global translational vs transcriptional gene expression changes during early
Candida albicans
biofilm formation
Authors: Mundodi Vasanthakrishna , Choudhary Saket , Smith Andrew D. , Kadosh David 
Published: January 2025

ABSTRACT

Candida albicans,
a major human fungal pathogen, can form biofilms on a variety of inert and biological surfaces.
C. albicans
biofilms allow for immune evasion, are highly resistant to antifungal therapies, and represent a significant complication for a wide variety of immunocompromised patients in clinical settings. While transcriptional regulators and global transcriptional profiles of
C. albicans
biofilm formation have been well-characterized, much less is known about translational regulation of this important
C. albicans
virulence property. Here, using ribosome profiling, we define the first global translational profile of genes that are expressed during early biofilm development in a human fungal pathogen,
C. albicans
. We show that
C. albicans
biofilm formation involves altered translational regulation of genes and gene classes associated with protein synthesis, pathogenesis, transport, plasma membrane, polarized growth, cell cycle, secretion, and signal transduction. Interestingly, while similar, but not identical, classes of genes showed transcriptional alterations during early
C. albicans
biofilm development, we observed very little overlap between specific genes that are upregulated or downregulated at the translational vs transcriptional levels. Our results suggest that distinct translational mechanisms play an important role in regulating early biofilm development of a major human fungal pathogen. These mechanisms, in turn, could serve as potential targets for novel antifungal strategies.

IMPORTANCE

The major human fungal pathogen
Candida albicans
is known to form biofilms or complex aggregated microbial communities encased in an extracellular matrix. These biofilms allow
C. albicans
to escape detection by the immune system as well as resist a variety of antifungal drugs. In this study, we define the first global profile of genes that show altered translation during
C. albicans
biofilm formation. These genes are involved in a variety of key cellular processes, including polarized growth, pathogenesis, transport, protein synthesis, cell cycle, plasma membrane, signal transduction, and secretion. Interestingly, while similar classes of genes are induced at both the transcriptional and translational levels during early
C. albicans
biofilm formation, we observed very little overlap among specific genes with altered transcription and translation. Our results suggest that
C. albicans
biofilm formation is controlled by distinct translational mechanisms, which could potentially be targeted by novel antifungal drugs.
Optimal processing of tongue swab samples for
Mycobacterium tuberculosis
detection by the Xpert MTB/RIF Ultra assay
Authors: Chilambi Gayatri Shankar , Reiss Robert , Daivaa Naranjargal , Banada Padmapriya , De Vos Margaretha , Penn-Nicholson Adam , Alland David 
Published: January 2025

ABSTRACT

Tongue swabs represent a potential alternative to sputum as a sample type for detecting pulmonary tuberculosis (TB) with molecular diagnostic tests. The methods used to process tongue swabs for testing in the World Health Organization-recommended Xpert MTB/RIF Ultra (Xpert Ultra) assay vary greatly. Here, we aimed to identify the optimal tongue swab processing for Xpert Ultra testing. We compared four methods for treating dry tongue swabs with the Xpert Sample Reagent (SR) mixed with various concentrations of Tris–EDTA–Tween to treatment with SR alone or to a commonly used heat inactivation protocol. In each condition, swabs obtained from volunteers without TB were placed into test buffer spiked with known amounts of
Mycobacterium tuberculosis
(
Mtb
) H37Rv-mc
2
6230. Swabs processed with 1:1 diluted SR buffer had the lowest
Mtb
limit of detection (LOD) at 22.7 CFU/700 µL (95% confidence interval (CI) 14.2–31.2), followed by 2:1 diluted SR buffer at 30.3 CFU/700 µL (95% CI 19.9–40.7), neat SR at 30.9 CFU/700 µL (95% CI 21.5–40.3), and SR prefilled in the Xpert Ultra at 57.1 CFU/700 µL (95% CI 42.4–71.7). Swabs processed using the heat-based protocol had the highest LOD (77.6 CFU/700 µL; 95% CI 51.2–104.0). Similar findings were observed for the LOD of RIF susceptibility. The 2:1 diluted SR buffer condition produced similar LODs when swabs were tested in the presence of sputum matrix or phosphate buffer saline. Further studies are needed to assess the performance of this processing protocol in a clinical setting.

IMPORTANCE

Xpert MTB/RIF Ultra (Xpert Ultra) is approved by the World Health Organization for the diagnosis of tuberculosis (TB). This test is typically performed using sputum specimens obtained from people with presumptive TB. In order to inactivate
Mycobacterium tuberculosis
(
Mtb
) and aid liquefaction, sputum must be mixed with Xpert SR prior to transfer into the Xpert Ultra. However, some people under evaluation for TB are unable to produce sputum. Alternative sample types for TB diagnosis would, therefore, be of value. Oral swabs, including tongue swabs, have shown promise, but there are technical challenges associated with sample processing. In this study, several new tongue swab processing conditions were evaluated by utilizing SR, either neat or diluted in buffer. The ability of Xpert Ultra to detect TB was improved under these conditions compared with the previously published heat-processing method; processing steps were simplified; and technical challenges were overcome.
Gold in Pyrite: a Thermodynamic Model of Co-crystallization in Chloride Fluids
Authors: Prokofiev V. Yu. , Akinfiev N. N. , Bortnikov N. S. 
Published: January 2025

Abstract
A thermodynamic description of gold-bearing pyrite as a substitution solid solution is proposed depending on external conditions and gold content in the fluid. The model is based on experimental data of the synthetic pyrite grown in hydrothermal chloride solutions in the presence of metallic gold. The proposed model makes it possible to estimate the upper limit of gold content in pyrite. The thermodynamic model of gold-bearing pyrite was verified by modeling the process of formation of mineral associations of gold ores of the Darasun and Talatui deposits by chloride aqueous fluids in an integrated fluid-magmatic system of the Darasun ore field. Previously it was revealed that the average gold content in pyrite from the Darasun and Talatui deposits, intergrown with native gold, does not exceed 1 ppm, while synthetic pyrite grown in equilibrium with metallic gold under similar conditions contains 10–150 ppm of gold. This contradiction does not allow explaining the formation of gold ores of the Darasun ore field by its direct crystallization from hydrothermal fluid. A possible explanation is the presence of an additional stage of ore transformation, in which recrystallization of sulfides occurred with gold undersaturated solutions. It was shown that a decrease in gold concentration in the mineral-forming fluid below the saturation limit should lead to a synchronous decrease in the gold concentration in the resulting pyrite. The calculated values of gold concentration in model pyrite make it possible to estimate gold concentrations in mineral-forming chloride fluids at different stages of the formation of the Darasun ore field deposits at a known temperature. It has been shown that natural gold-bearing pyrite from various gold deposits was formed mainly from chloride fluids undersaturated to gold.