bluuebunny/crossref_metadata_2025 huggingface dataset:
A 3‐bp deletion in the SLC45A2 gene is associated with loss of fleece pigmentation in black‐fleeced Suffolk sheep
Authors: Tearle R. G. , Chen T. , Brien F. D.
Published: November 2024

Sheep have naturally pigmented wool which interferes with dyeing. Selection has been carried out over many years to remove pigment, with substantial success, but most wool still contains some pigment. As an alternative to selection, it has been proposed to take a naturally occurring mutation found in black Suffolk sheep, that blocks wool pigmentation, and introgress it into other breeds. However, the nature of the mutation has not been identified, prompting us to characterise it. The Suffolk white‐fleece phenotype is associated with a novel 3‐bp deletion in the gene SLC45A2, which encodes a membrane bound transporter that mediates melanin synthesis. The deletion results in the removal of one amino acid from the protein. The assignment of this deletion as the likely causative mutation is supported by it: being homozygous in the genome of nine animals with a white fleece and not homozygous in the genomes of eight animals with a black fleece; having a high level of conservation of the encoded amino acid sequence in the region surrounding the deleted amino acid across Mammalia; and the same deletion (but in a compound heterozygous state) being found in human SLC45A2 in a person with albinism.
Using real‐time Delphi methods to develop a consensus‐based framework to improve nursing assessment in residential aged care
Authors: Fry Margaret , Curtis Kate , Considine Julie , Viengkham Catherine , Watson Karen , Dunsmore Moira , Shaban Ramon Z.
Published: November 2024

Objectives

Evidence‐based tools are needed to support aged care nurses in recognising and responding to changes in residents' conditions and clinical deterioration. Systematised emergency nursing frameworks such as HIRAID® (History including Infection risk, Red flags, Assessment, Interventions, Diagnostics, reassessment and communication) assist nurses in accurately assessing and documenting a patient's condition and identifying and prioritising care needs. This study aimed to adapt the HIRAID® emergency nursing framework for use in the residential aged care setting.

Methods

A real‐time Delphi method was employed to contextually adapt the HIRAID® framework. Twelve expert health‐care clinical leaders with understanding of patient assessment and residential aged care management were recruited through purposive sampling. Panel consensus was established a priori at 80%. A secondary measure of panel stability was used to understand panel consensus.

Results

Consensus was reached after two survey rounds. In Round 1, 105 (88%) of 119 items were accepted after reaching consensus. In Round 2, all remaining 29 items reached consensus, whereby 20 were accepted and nine rejected. Key modifications were identified for ‘History’, which needed to consider more comprehensive and adaptive techniques, and ‘Interventions’ and ‘Diagnostics’, where differences arose in the scope of practice of aged care nurses compared to their acute care counterparts.

Conclusion

The study demonstrated how a small expert multidisciplinary health‐care panel can be stable and reach consensus to adapt and contextualise an emergency care framework to the aged care setting. These findings will form the content to scaffold educational resources to support learning and practice change.
Contributions of self‐efficacy, L2 grit and digital literacy to informal digital learning of English: A structural equation modelling approach
Authors: Barkati Maryam , Kiyanfar Zhila , Azari Noughabi Mostafa , Ershadi Fatemeh
Published: November 2024

Despite the proliferation of studies on computer‐assisted language learning, scant research attention has been paid to informal digital learning of English (IDLE) and its antecedents. Therefore, the current study aimed to investigate whether Iranian EFL learners' L2 grit, digital literacy and self‐efficacy contributed to their IDLE. A total of 313 EFL learners (96 males, 217 females), selected through snowball sampling, completed an electronic survey. Structural equation modelling (SEM) was employed to analyse the relationships between the main variables. The results of SEM analysis revealed that EFL learners' digital literacy, L2 grit and self‐efficacy significantly influenced their engagement with IDLE activities. In addition, the findings revealed that digital literacy was the strongest predictor of EFL learners' IDLE. These findings highlight the significance of digital literacy skills coupled with positive personality‐based and cognitive variables in forming learners' tendency to learning English in informal digital settings. The study implied that positive characteristics could enhance cognitive and psychological resources, leading to positive outcomes (ie, IDLE). Finally, implications were offered.

Practitioner notes

What is already known about this topic

Gritty language learners with high self‐efficacy are more likely to master language skills inside and outside the classroom.

Digital literacy can increase learners' tendency to learn English through digital platforms.

What this paper adds

Digitally literate EFL learners with high levels of grit and self‐efficacy practise IDLE activities.

Digital literacy plays a more important role in IDLE compared to personality‐related and cognitive factors.

Implications for practice

EFL teachers are recommended to model using digital platforms for language learning in out‐of‐class digital settings.

EFL teachers can increase EFL learners' grit and self‐efficacy through interventions to enhance their engagement in IDLE‐embedded activities.
Prolonged ischaemia during partial nephrectomy: impact of warm vs cold
Authors: Kazama Akira , Munoz‐Lopez Carlos , Lewis Kieran , Attawettayanon Worapat , Rathi Nityam , Maina Eran , Campbell Rebecca A. , Wood Andrew , Lone Zaeem , Bartholomew Angelica , Kaouk Jihad , Haber Georges‐Pascal , Haywood Samuel , Almassi Nima , Weight Christopher , Li Jianbo , Campbell Steven C.
Published: November 2024

Objective

To evaluate the impact of prolonged ischaemia during partial nephrectomy (PN), which remains understudied despite its potential clinical relevance.

Patients and Methods

Of 1371 patients managed with on‐clamp PN (2011–2014), 759 (55%) had imaging and assessment of serum creatinine levels before and after PN within the appropriate timeframes necessary for inclusion. This timeframe was chosen to allow for a robust analysis of both warm and cold ischaemia. Recovery from ischaemia (Recischaemia) was defined as ipsilateral glomerular filtration rate (GFR) preserved, normalized by percentage of parenchymal volume preserved (PPVP), and would be 100% if all nephrons recovered completely from ischaemia. Pearson correlation and multivariable linear regression models were used to assess associations between Recischaemia and ischaemia type and duration.

Results

Of 759 patients, 525 (69%) were managed with warm ischaemia. The median warm/cold ischaemia times were 22 and 30 min, respectively. Overall, the median percent ipsilateral GFR preserved, PPVP and Recischaemia were 79%, 83% and 96%, respectively. Segmented regression analysis demonstrated substantially greater decline in Recischaemia, beginning at approximately 30 min for warm ischaemia, which was not observed for hypothermia. Prolonged ischaemia (defined as >30 min) occurred in 197 patients (26%; 88 warm/109 cold). For limited ischaemia (≤30 min), hypothermia was often used for tumours with increased tumour size and complexity (P < 0.01), while for prolonged ischaemia, the warm/cold subgroups had similar patient and tumour characteristics. For limited ischaemia and prolonged hypothermia, median Recischaemia remained >95%, independent of ischaemia time. Differences in Recischaemia between the warm and cold cohorts became significant only after 30 min (P < 0.05). On multivariable analysis, prolonged warm ischaemia was associated with reduced Recischaemia (P = 0.02), which fell 3.9% for every additional 10 min beyond 30 min.

Conclusions

Our data suggest that Recischaemia begins to decline significantly after 30 min during PN, although hypothermia was protective. Avoidance of prolonged warm ischaemia should be prioritized in patients with solitary kidneys and/or significant pre‐existing chronic kidney disease.
What Makes Non‐Directed Living Kidney Donors Tick? Actionable Items to Increase Non‐Directed Live Organ Donation
Authors: Wang Amy S. , McCune Kasi , Wiener Ilona , Runge Brian , Pasantes Daniela , Johnson Eric , Ratner Lloyd E.
Published: November 2024

Background

Non‐directed donors (NDDs), individuals who donate their organs with no intended recipient, in the United States increased 90‐fold from 1999 to 2019. There is a paucity of studies investigating the motivations of NDDs. The objective of our study is to identify actionable items to increase NDDs.

Methods

A survey of kidney NDDs at CUIMC from 2009 to 2021 was conducted. The survey was conducted via Qualtrics.

Results

Seventy individuals met the study criteria. Forty‐seven (67.1%) individuals completed the survey. A total of 98% of respondents reported participating in other altruistic activities prior to donation. A total of 70% donors identified as religious, and 57% reported religion/spirituality positively affected the decision to donate. The three most common factors that got respondents interested in NDD included: (1) hearing about an individual in need of a transplant, (2) knowing someone who had donated an organ, and (3) as a next step in altruistic behavior. A total of 85% said that donating a kidney met or exceeded expectations. A total of 44% and 31% of NDDs were interested in being either liver or uterus NDDs, respectively.

Conclusions

We identified six potential action items: (1) Identify pools of receptive individuals who participated in other altruistic behaviors and/or identify as religious. (2) Outreach to individuals who came forward as directed donors, but whose intended recipient was successfully transplanted with a kidney from another donor. (3) Promote stories of those who need organ transplants or whose lives have been changed by transplantation. (4) Promote NDDs as resources for potential NDDs. (5) Educate interested kidney NDDs about liver and uterus transplant programs. (6) Decrease financial barriers to donation.
‘No TV programme is made about boring magistrates’ cases’: Revisiting the ‘ideology of triviality’ in magistrates’ justice
Authors: Kirby Amy
Published: November 2024

Magistrates’ courts in England and Wales deal with around 95% of cases from start to completion, with many cases heard by lay magistrates. Despite this reliance on both the lower courts and decision making by lay adjudicators, it has been repeatedly argued that magistrates’ justice receives little attention. McBarnet (1981) argues that this is due to an ‘ideology of triviality’ in which the work of the magistrates’ courts is constructed as ‘trivial’, when in fact the cases heard are serious in nature and consequence. This article draws upon the framing of the ‘ideology of triviality’ to present findings from a qualitative study which examined contemporary workings of magistrates’ justice through court observations and interviews with lay court users. The findings suggest that the fallacy of ‘triviality’ continues to pervade magistrates’ justice. This has consequences for both those with personal experience of the magistrates’ courts and wider society.
Analysis of the Heat Transfer Properties of a Dispersion System With Rice Grain Particles
Authors: Nagahama Tamaki , Watanabe Yoshiyuki
Published: November 2024

We investigated steady heat transfer in rice grains at various temperatures to evaluate the heat transfer properties of food solid–liquid dispersions and their particle size dependence. The two dispersion systems, comprising homogeneously dispersed and heterogeneously precipitated solutions with various volumetric solid–liquid fractions and diameters of rice grain particles, were prepared using media with different specific gravities. The thermal conductivity of both dispersion solutions depended on the solid–liquid fraction and particle diameter, and the effective interfacial area between the dispersion phase and the medium was suggested to contribute to thermal conductivity. That is, reducing the effective interfacial area was indicated to make heat transfer in the dispersion solution more efficient. In addition, the thermal conductivity of the dispersion phase was estimated using a model equation, and it was suggested that the thermal conductivity at the temperature above the gelatinization temperature might reflect the effect of water sorption by rice grains and gelatinization. The experimental and analytical methods used in this study could potentially provide useful information for simulations of thermal manipulation in the manufacturing and processing not only of rice grains but also other granular foods, especially food materials containing a large quantity of starch, such as beans.
Innovation in delirium care: A standardized intervention to reverse inattention using touch and movement
Authors: Bisson Dana E. , Clancy Burgess Shannon C. , Gamache Michelle E. , Dunn Maureen P. , Valeras Aimee B. , Lindpaintner Lyn S.
Published: November 2024

Delirium is a complex neurocognitive disorder characterized by an acute disturbance in attention, awareness, and perception. It is a dangerous syndrome that is independently associated with higher rates of morbidity and mortality, inpatient complications, and is a predictor of long‐term cognitive dysfunction. Although delirium can occur in persons of all ages, the prevalence among and impact on older adults is particularly significant. Current gold standard approaches for delirium include treating medical precipitants and physiological perturbations and optimizing the environment using multicomponent nonpharmacological interventions. Although these approaches are proven effective in preventing delirium, evidence has not shown them to significantly improve delirium once it occurs. The need for a safe, effective, and specific treatment for the phenotype of delirium itself is an urgent priority worldwide. The intervention described in this article, Attention and Awareness Through Movement technique followed by Movement To Capacity (AATM/MTC), targets cortical dysfunction through sustained sequential touch, cranial nerve stimulation, and muscular movement. It raises the tantalizing possibility that a specific method to reduce inattention and normalize arousal levels may not only be feasible but also safe and inexpensive. For these reasons, preliminary observations are described in the hope of stimulating interest in further exploration of this novel approach to delirium therapy.
Personal Communication in an Automated World: Evidence from Loan Repayments
Authors: LAUDENBACH CHRISTINE , SIEGEL STEPHAN
Published: November 2024

We examine the effect of personal, two‐way communication on the payment behavior of delinquent borrowers. Borrowers who speak with a randomly assigned bank agent are significantly more likely to successfully resolve the delinquency relative to borrowers who do not speak with a bank agent. Call characteristics related to the human touch of the call, such as the likeability of the agent's voice, significantly affect payment behavior. Borrowers who speak with a bank agent are also significantly less likely to become delinquent again. Our findings highlight the value of a human element in interactions between financial institutions and their customers.
LsKN1 and LsOFP6 synergistically regulate the bolting time by modulating the gibberellin pathway in lettuce
Authors: Qi Yetong , Shao Wei , Chen Haoyu , Ahmed Temoor , Zhao Xinhui , Wang Yong , Zhu Lei , Sun Shouru , Kuang Hanhui , An Guanghui
Published: November 2024

Bolting time is an important agronomic trait in lettuce (Lactuca sativa) production. Premature bolting significantly reduces crop quality and marketability. Here, we report map‐based cloning and characterization of a LsKN1 gene that controls bolting in lettuce.

A segregating population was developed by crossing a crisphead‐type cultivar with a stem‐type cultivar to genetically map and clone the LsKN1 gene. In the late‐bolting parent (crisphead), the LsKN1 was activated by a CACTA‐like transposon which was inserted into the first exon of LsKN1. Complementation test, overexpression, and CRISPR/cas9 knockout showed that the activated LsKN1 allele (LsKN1TP) delays bolting in lettuce.

ChIP‐seq and phytohormone analysis demonstrated that LsKN1 regulates gibberellin (GA) biosynthesis and response. LsKN1TP binds to the promoter of the LsGA20ox1 and LsRGA1, and down‐ and upregulates their expression, respectively. Furthermore, LsRGA1 interacts with LsKN1TP to enhance the repression of GA biosynthesis. LsOFP6 acts as a safeguard, interacting with LsKN1TP to prevent excessive inhibition of GA biosynthesis and response during the vegetative‐to‐reproductive phase transition.

The LsKN1‐LsOFP6 module orchestrates the GA pathway to regulate bolting time in lettuce, which provides insight into the bolting development in lettuce and offers valuable genetic resources for breeding lettuce varieties resistant to premature bolting.
The dynamics of constituency representation on immigration policy in the U.S. house
Authors: Cayton Adam , Siemers Lena
Published: November 2024

We examine how legislative representation and issue activism change as parties polarize on an issue by examining immigration politics in the U.S. House. Using an original data set of the policy positions in immigration bills from 1983 to 2014, an original coding of email newsletters from 2010 to 2020, and existing speech data, we show that increased partisan disagreement on immigration and the sorting of immigrants into the Democratic Party changed the way lawmakers represent their districts on that issue. Larger foreign‐born populations consistently have representatives who take pro‐immigration positions, but the effect has changed from a direct effect to one mediated by partisanship. Issue attention also became asymmetrical, with Democratic lawmakers who represent more immigrants being more active on immigration policy, but no such relationship for Republicans. This suggests that for Democrats, immigration is a distributive issue driven by geographically concentrated “policy demanders” but for Republicans, it is a partisan issue that is less connected to geography. These findings have implications for who and where new policy proposals come from.
Being good and doing good in behavioral policymaking
Authors: Mills Stuart
Published: November 2024

Libertarian paternalism (LP) draws on behavioral economics to advocate for noncoercive, nonfiscal policy interventions to improve individual well‐being. However, growing criticism is encouraging behavioral policymaking—long dominated by LP approaches—to consider more structural and fiscally impactful interventions as valid responses to behavioral findings. Keynesian social philosophy allows behavioral policymaking to incorporate these new perspectives alongside existing LP approaches.
Changes in tillage characteristics of albic soil with various soil amendment materials
Authors: Chen Aihui , Wang Qiuju , Zhang Haibin , Liang Yucheng , Qi Zhongjun , Zhou Weiyan , Li Jingyang , Tu Huanyu
Published: November 2024

To improve the crop yield of low‐yield Albic soil, the application of amendment materials has become a widely considered method. However, understanding how these materials impact the physical and mechanical properties of the soil for tillage purposes is an important area of research. This study aimed to examine the effects of fertilizers, straw, and biochar on the tillage characteristics of Albic soil. The focus was on analysing changes in soil consistency limits and cultivability in both the humic (Ap) layer and the Albic (Aw) layer, while also exploring the underlying mechanisms. The results showed that the use of amendment materials significantly improved the consistency limits of Albic soil, enhanced its cultivability, and positively affected its tillage characteristics. These improvements were reflected in a decrease in the soil's plasticity index (PI) and an increase in the shrinkage index (FI). Among the three materials tested, biochar had the most notable impact on plasticity, with significant increases in the liquid limit (LL) and plastic limit (PL), while straw primarily influenced the swell‐shrink characteristics, leading to a significant decrease in the shrinkage limit (SL). The Aw layer was more significantly impacted by the amendment materials than the Ap layer. This was largely owing to the strong positive correlation between the Brunauer–Emmett–Teller (BET) surface area, soil maximum hygroscopicity (W), and LL and PL of the Ap layer, as well as their negative relationship with the PI. In contrast, the Aw layer was most influenced by organic matter content (OMC) and soil organic carbon (SOC). It is important to note that the addition of fertilizer or straw at concentrations above 6% by weight could lead to different changes in the tillage characteristics of Albic soil. This study provides valuable insights for agricultural practice, offering guidance on overcoming soil‐related challenges in tillage operations, and it also opens new possibilities for a comprehensive, multi‐faceted approach to soil management.
On quasimap invariants of moduli spaces of Higgs bundles
Authors: Nesterov Denis
Published: November 2024

We compute odd-degree genus 1 quasimap and Gromov–Witten invariants of moduli spaces of Higgs

${\rm{S}}{{\rm{L}}_2}$

-bundles on a curve of genus

$g \geqslant 2$

. We also compute certain invariants for all prime ranks. This proves some parts of the author’s conjectures on quasimap invariants of moduli spaces of Higgs bundles. More generally, our methods provide a computation scheme for genus 1 quasimap and Gromov–Witten invariants in the case when degrees of maps are coprime to the rank. This requires an analysis of the localisation formula for certain Quot schemes parametrising higher-rank quotients on an elliptic curve. Invariants for degrees that are not coprime to the rank exhibit a very different structure for a reason that we explain.
KSB stability is automatic in codimension
$\boldsymbol{\geq 3}$
Authors: Kollár János , Kovács Sándor J.
Published: November 2024

KSB stability holds at codimension

$1$

points trivially, and it is quite well understood at codimension

$2$

points because we have a complete classification of

$2$

-dimensional slc singularities. We show that it is automatic in codimension

$3$

.
Revivable self-assembled supramolecular biomass fibrous framework for efficient microplastic removal
Authors: Wu Yang , Chen Shixiong , Wu Jun , Liu Fangtian , Chen Chaoji , Ding Bin , Zhou Xue , Deng Hongbing
Published: November 2024

Microplastic remediation in aquatic bodies is essential for the entire ecosystem, but is challenging to achieve with a universal and efficient strategy. Here, we developed a sustainable and environmentally adaptable adsorbent through supramolecular self-assembly of chitin and cellulose. This biomass fibrous framework (Ct-Cel) showcases an excellent adsorption performance for polystyrene, polymethyl methacrylate, polypropylene, and polyethylene terephthalate. The affinity for diverse microplastics is attributed to the transformation of multiple intermolecular interactions between different microplastics and Ct-Cel. Meanwhile, the strong resistance of Ct-Cel to multiple pollutants in water enables an enhanced adsorption when coexisting with microorganisms and Pb
2+
. Moreover, Ct-Cel can remove 98.0 to 99.9% of microplastics in four types of real water and maintains a high removal efficiency of up to 95.1 to 98.1% after five adsorption cycles. This work may open up prospects for functional biomass materials for cost-efficient remediation of microplastics in complex aquatic environments.
The redox sensor KEAP1 facilitates adaptation of T cells to chronic antigen stimulation by preventing hyperactivation
Authors: Zhu Ziang , Luo Ying , Lou Guohua , Yihunie Kiddist , Wizzard Safuwra , DeVilbiss Andrew W. , Muh Sarah , Ma Chaoyu , Shinde Sejal S. , Hoar Jonathan , Hu Taidou , Zhang Nu , Biswal Shyam , DeBerardinis Ralph J. , Wu Tuoqi , Yao Chen
Published: November 2024

During persistent antigen stimulation, exhausted CD8
+
T cells are continuously replenished by self-renewing stem-like T cells. However, how CD8
+
T cells adapt to chronic stimulation remains unclear. Here, we show that persistent antigen stimulation primes chromatin for regulation by the redox-sensing KEAP1-NRF2 pathway. Loss of KEAP1 in T cells impaired control of chronic viral infection. T cell–intrinsic KEAP1 suppressed NRF2 to promote expansion and persistence of virus-specific CD8
+
T cells, drive a stem-like T cell response, down-regulate immune checkpoint molecules, and limit T cell receptor (TCR) hyperactivation and apoptosis. NRF2 epigenetically derepressed BACH2 targets and opposed a stem-like program driven by BACH2. In exhausted T cells induced by tonic GD2 chimeric antigen receptor (CAR) signaling, the effects of KEAP1 deficiency were rescued by inhibiting proximal TCR signaling. Enhancing mitochondrial oxidation improved the expansion and survival of KEAP1-deficient CD8
+
GD2 CAR T cells and up-regulated markers associated with stem-like cells. Thus, the KEAP1-NRF2 axis regulates stem-like CD8
+
T cells and long-term T cell immunity during chronic antigen exposure.
Spatiotemporal analysis of lung immune dynamics in lethal
Coccidioides posadasii
infection
Authors: Davalos Oscar A. , Sebastian Aimy , Leon Nicole F. , Rangel Margarita V. , Miranda Nadia , Murugesh Deepa K. , Phillips Ashlee M. , Hoyer Katrina K. , Hum Nicholas R. , Loots Gabriela G. , Weilhammer Dina R.
Published: November 2024

Coccidioidomycosis, or Valley fever, is a lung disease caused by inhalation of
Coccidioides
fungi, prevalent in the Southwestern United States, Mexico, and parts of Central and South America. Annually, the United States reports 10,000–20,000 cases, although those numbers are expected to increase as climate change expands the fungal geographic range. While 60% of infections are asymptomatic, 40% symptomatic infections are often misdiagnosed due to similarities with bronchitis or pneumonia. A small subset of infection progress to severe illness, necessitating a better understanding of immune responses during lethal infection. Using single-cell RNA sequencing and spatial transcriptomics, we characterized lung responses during
Coccidioides
infection. We identified monocyte-derived
Spp1
-expressing macrophages as potential mediators of tissue remodeling and fibrosis, marked by high expression of profibrotic and proinflammatory transcripts. These macrophages showed elevated TGF-β and IL-6 signaling, pathways involved in fibrosis pathogenesis. Additionally, we observed significant neutrophil infiltration and defective lymphocyte responses, indicating severe adaptive immunity dysregulation in lethal, acute infection. These findings enhance our understanding of
Coccidioides
infection and suggest new therapeutic targets.

IMPORTANCE

Coccidioidomycosis, commonly known as Valley fever, is a lung disease caused by the inhalation of
Coccidioides
fungi, which is prevalent in the Southwestern United States, Mexico, and parts of Central and South America. With climate change potentially expanding the geographic range of this fungus, understanding the immune responses during severe infections is crucial. Our study used advanced techniques to analyze lung responses during
Coccidioides
infection, identifying specific immune cells that may contribute to tissue damage and fibrosis. These findings provide new insights into the disease mechanisms and suggest potential targets for therapeutic intervention, which could improve outcomes for patients suffering from severe Valley fever.
Phenotypic and genomic changes in enteric
Klebsiella
populations during long-term ICU patient hospitalization: the role of RamR regulation
Authors: Langlois Benedicte , Guerin Francois , Isnard Christophe , Gakuba Clement , Du Cheyron Damien , Giard Jean-Christophe , Brisse Sylvain , Le Hello Simon , Gravey Francois
Published: November 2024

Acquired antimicrobial resistance and metabolic changes are central for bacterial host adaptation during the long-term hospitalization of patients. We aimed to analyze the genomic and phenotypic evolution of enteric
Klebsiella
populations in long-term intensive care unit (ICU) patients. Weekly rectal swabs were prospectively collected from all patients admitted to the ICU in a teaching hospital from December 2018 to February 2019. The inclusion criterion for patients was hospitalization for more than 15 days in the ICU without any history of hospitalization or antibiotic treatment for the 3 months prior to admission. Among them, enteric
Klebsiella pneumoniae
species complex (KpSC) populations were detected. For each isolate, extensive antimicrobial resistance profiles were determined using the disk diffusion method, and the whole genome was sequenced using an Illumina platform.
In silico
typing methods, such as Multilocus Sequence Typing (MLST), core-genome MLST, SNP typing, resistome characterization and mutation point detection, were applied. During the study period, 471 patients were admitted to ICUs. Among them, 21 patients met the inclusion criteria, and only 5 patients (24%) carried unique and distinct KpSC populations during 2–10 weeks in the gut that as detected at admission and excluding acquisition during the ICU stay. One patient showed a rare ST1563
K. variicola
persistent carriage for 7 consecutive weeks, which displayed important antimicrobial resistance phenotype changes in the 2 last weeks. In-depth
in silico
characterization and RNA sequencing of these strains revealed a mutation within the
ramR
transcriptional regulator resulting in overexpression of the
ramA
regulator and decreased expression of
acrR
, which controls antibiotic efflux. This mutation also impacts tolerance to biliary salts. This study revealed the importance of endogenous colonization of KpSC populations in the gut throughout the patient’s long-term ICU stay and highlighted the role of
ramR
in drug susceptibility.

IMPORTANCE

The
Klebsiella pneumoniae
species complex (KpSC) is one of the major causes of nosocomial infections, especially in intensive care unit (ICUs). These bacteria are frequently highly resistant to antibiotics, leading to an increase in morbidity and mortality. The origins of multidrug-resistant KpSC strains isolated from ICU patients are still unclear, with at least two hypotheses of acquisition paths: (i) endogenous KpSC populations that are or became resistant to antibiotics and/or (ii) hospital acquisition of circulating KpSC clones. Genomic changes observed in this study might reveal mechanisms to better adapt to KpSC in the patient’s gut in the face of heavy ICU medical care pressure.
Quantifying synthetic bacterial community composition with flow cytometry: efficacy in mock communities and challenges in co-cultures
Authors: Mermans Fabian , Chatzigiannidou Ioanna , Teughels Wim , Boon Nico
Published: November 2024

Determination of bacterial community composition in synthetic communities is critical for understanding microbial systems. The community composition is typically determined through bacterial plating or through PCR-based methods, which can be labor-intensive, expensive, or prone to bias. Simultaneously, flow cytometry has been suggested as a cheap and fast alternative. However, since the technique captures the phenotypic state of bacterial cells, accurate determination of community composition could be affected when bacteria are co-cultured. We investigated the performance of flow cytometry for quantifying oral synthetic communities and compared it to the performance of strain specific qPCR and 16S rRNA gene amplicon sequencing. Therefore, axenic cultures, mock communities and co-cultures of oral bacteria were prepared. Random forest classifiers trained on flow cytometry data of axenic cultures were used to determine the composition of the synthetic communities, as well as strain specific qPCR and 16S rRNA gene amplicon sequencing. Flow cytometry was shown to have a lower average root mean squared error and outperformed the PCR-based methods in even mock communities (flow cytometry: 0.11 ± 0.04; qPCR: 0.26 ± 0.09; amplicon sequencing: 0.15 ± 0.01). When bacteria were co-cultured, neither flow cytometry, strain-specific qPCR, nor 16S rRNA gene amplicon sequencing resulted in similar community composition. Performance of flow cytometry was decreased compared with mock communities due to changing phenotypes. Finally, discrepancies between flow cytometry and strain-specific qPCR were found. These findings highlight the challenges ahead for quantifying community composition in co-cultures by flow cytometry.

IMPORTANCE

Quantification of bacterial composition in synthetic communities is crucial for understanding and steering microbial interactions. Traditional approaches like plating, strain-specific qPCR, and amplicon sequencing are often labor-intensive and expensive and limit high-throughput experiments. Recently, flow cytometry has been suggested as a swift and cheap alternative for quantifying communities and has been successfully demonstrated on simple bacterial mock communities. However, since flow cytometry measures the phenotypic state of cells, measurements can be affected by differing phenotypes. Especially, changing phenotypes resulting from co-culturing bacteria can have a profound effect on the applicability of the technique in this context. This research illustrates the feasibility and challenges of flow cytometry for the determination of community structure in synthetic mock communities and co-cultures.
Stenotrophomonas maltophilia
bacteremia in adult patients with hematological diseases: clinical characteristics and risk factors for 28-day mortality
Authors: Guo Wenjing , Lin Qingsong , Li Jia , Feng Xiaomeng , Zhen Sisi , Mi Yingchang , Zheng Yizhou , Zhang Fengkui , Xiao Zhijian , Jiang Erlie , Han Mingzhe , Wang Jianxiang , Feng Sizhou
Published: November 2024

Patients with hematological diseases are at high risk for
Stenotrophomonas maltophilia
(SM) bacteremia. This study retrospectively analyzed the clinical characteristics and risk factors for 28-day mortality among 140 adult hematological patients diagnosed with SM bacteremia from January 2012 to July 2023. he overall 28-day mortality was 31.43% (44/140), with a median age of 44 years. The median hospital stay before SM bacteremia onset was 25 days, and 69.29% of patients had unresolved neutropenia. All patients had received broad-spectrum antibiotics in the past month, and 69.29% developed breakthrough bacteremia during carbapenem therapy. Independent risk factors for mortality included a Sequential Organ Failure Assessment (SOFA) score ≥5, tigecycline exposure, age ≥60, and pulmonary infection. Patients with ≥2 risk factors were stratified into the high-risk group, with a significantly higher 28-day mortality compared with the low-risk group (56.52% vs 7.04%,
P
< 0.001). Treatment with trimethoprim-sulfamethoxazole (TMP/SMX) (
P
= 0.008) or TMP/SMX combined with cefoperazone/sulbactam (CSL) (
P
= 0.005) was associated with survival benefits among high-risk patients. Overall, SM bacteremia usually occurs in hematological patients with prolonged hospitalization, unresolved neutropenia, and extensive use of broad-spectrum antibiotics, especially carbapenems. Patients with high SOFA scores, advanced age, pulmonary infection, or recent tigecycline exposure are at higher risk of mortality. The preferred treatment is TMP/SMX rather than fluoroquinolones, with combination therapy of TMP/SMX and CSL considered a feasible treatment option.

IMPORTANCE

This study, representing the largest cohort of adult hematological patients with SM bacteremia to date, strengthens the validity of existing findings and provides new insights into its clinical management. We identify risk factors for 28-day mortality, revealing that patients with two or more risk factors experience particularly high mortality rates. This highlights the importance of early identification and targeted management of high-risk individuals. Our findings also demonstrate that TMP/SMX is superior to fluoroquinolones and suggest that combining TMP/SMX with CSL may offer additional survival benefits.
Adaptation for
Staphylococcus aureus
to hosts via insertion mutation in the accessory gene regulator
agrC
gene: decreased virulence and enhanced persistence capacity
Authors: Chen Jiawei , Wu Yun , Zhu Ying , Zhang Li , Xu Yingchun , Liu Yali
Published: November 2024

Staphylococcus aureus
is an important human pathogen due to its vast array of virulence factors regulated by multiple regulatory mechanisms, including the accessory gene regulator. In this study, two
S
.
aureus
strains were simultaneously isolated from the blood of a febrile patient, belonging to the same clone, designated as 23H with a complete hemolytic phenotype, and 23B, exhibiting an incomplete hemolytic phenotype. The genomic comparison between strains 23B and 23H revealed that 23B had a single adenine base insertion at position 923 in the
agrC
gene, leading to a functional loss of the encoded AgrC. Experimental findings showed that strain 23B had decreased hemolytic activity, lower cytotoxicity against human alveolar epithelial A549 cells and in the
Galleria mellonella
model, and a reduced ability to survive intracellularly after infecting macrophages, in comparison to 23H. Conversely, 23B exhibited enhanced biofilm formation, greater adherence to A549 cells, and increased persistence in the face of vancomycin and daptomycin treatment. Transcriptomic analysis revealed that 23B upregulated surface protein-encoding genes while simultaneously reducing the expression levels of virulence factors, highlighting the intricate regulatory adjustments facilitating its persistence and reducing pathogenic potential. ATP assay results indicated that 23B maintained elevated ATP levels during the exponential phase yet exhibited reduced levels in the stationary phase when compared with 23H. Our findings suggested that the mutation in the
agrC
gene of
S. aureus
results in diminished virulence but markedly enhances persistence. This mutated strain warrants clinical attention because it may lead to treatment failures and persist in patients.

IMPORTANCE

In clinical antimicrobial therapy, bacterial strains often develop resistance to antimicrobial agents. Additionally, mutations in their gene regulatory networks can increase their persistence, especially in immunocompromised patients. This study identified an insertion mutation in the accessory gene regulator,
agrC
gene, carried by a
Staphylococcus aureus
strain isolated from the blood of a febrile patient, leading to the functional loss of AgrC. Further research revealed that despite the reduced virulence of the mutated strain, it significantly bolstered the capacity to adapt and endure within the host during prolonged infections. This was evidenced by increased adhesion and biofilm formation capabilities, development of antimicrobial tolerance, and decreased ATP levels linked to persistence. Therefore, monitoring these mutations in
S. aureus
is crucial clinically, as they can complicate treatment strategies.
Development of SacB-based counterselection for efficient allelic exchange in
Fusobacterium nucleatum
Authors: Zhou Peng , G C Bibek , Hu Bo , Wu Chenggang
Published: November 2024

Fusobacterium nucleatum
, prevalent in the oral cavity, is significantly linked to overall human health. Our molecular comprehension of its role in oral biofilm formation and its interactions with the host under various pathological circumstances has seen considerable advancements in recent years, primarily due to the development of various genetic tools for DNA manipulation in this bacterium. Of these, counterselection-based unmarked in-frame mutation methods have proved notably effective. Under suitable growth conditions, cells carrying a counterselectable gene die, enabling efficient selection of rare, defined allelic exchange mutants. The
sacB
gene from
Bacillus subtilis
, encoding levansucrase, is a widely used counterselective marker partly due to the easy availability of sucrose. Yet, its potential application in
F. nucleatum
genetic study remains untested. We demonstrated that
F. nucleatum
cells expressing
sacB
in either a shuttle or suicide plasmid exhibit a lethal sensitivity to supplemental sucrose. Utilizing sucrose counterselection, we created an in-frame deletion of the
F. nucleatum tonB
gene, a critical gene for energy-dependent transport processes in Gram-negative bacteria, and a precise knock-in of the luciferase gene immediately following the stop codon of the
hslO
gene, the last gene of a five-gene operon possibly related to the natural competence of
F. nucleatum
. Post-counterselection with 5% sucrose, chromosomal plasmid loss occurred in all colonies, leading to gene alternations in half of the screened isolates. This
sacB
-based counterselection technique provides a reliable method for isolating unmarked gene mutations in wild-type
F. nucleatum
, enriching the toolkit for fusobacterial research.

IMPORTANCE

Investigations into
Fusobacterium nucleatum
’s role in related diseases significantly benefit from the strategies of creating unmarked gene mutations, which hinge on using a counterselective marker. Previously, the
galk
-based allelic exchange method, although effective, faced an inherent limitation—the need for a modified host. This study aims to surmount this limitation by substituting
galK
with
sacB
for gene modification in
F. nucleatum
. Our application of the
sacB
-based methodology successfully yielded a
tonB
in-frame deletion mutant and a luciferase gene knock-in at the precise chromosomal location in the wild-type background. The new method augments the existing toolkit for
F. nucleatum
research and has far-reaching implications due to the easy accessibility to the counterselection compound sucrose. We anticipate its broader adoption in further exploration, thereby reinforcing its critical role in propelling our understanding of
F. nucleatum
.
Gardenoside attenuates
Staphylococcus aureus
-induced mastitis by inhibiting inflammation and ferroptosis through Nrf2/SLC7A11/GPX4 signaling pathway
Authors: Sui Guoqing , Jiang Wei , Guan Lianyue
Published: November 2024

The occurrence of mastitis is mainly due to the infection of mammary tissue by pathogens, which causes the inflammation of mammary tissue. Gardenoside (GAD), an iridoid active ingredient extracted from
Gardenia Jasminoides Ellis
, has been revealed to exhibit anti-inflammatory and anti-oxidative roles. However, the therapeutic effect of GAD on mastitis remains unclear. Our aim was to identify the therapeutic effect of GAD on
Staphylococcus aureus (S. aureus
)-induced mastitis and clarify its mechanism. To carry out this work,
S. aureus
-induced mastitis of mice model was established. Enzyme-Linked Immunosorbent Assay (ELISA) was conducted to detect the production of Interleukin-1β (IL-1β) and tumor necrosis factor-α (TNF-α). The biochemical method was used to detect the antioxidant factors glutathione (GSH), malondialdehyde (MDA), and iron content. Western blot was used to detect the expression of Nrf2/SLC7A11/GPX4 signal-related proteins. The results demonstrated that GAD alleviated Myeloperoxidase (MPO) activity, IL-1β and TNF-α production, and NF-κB activation. MDA and iron contents were also inhibited by GAD. Meanwhile, GSH level and GPX4, SLC7A11, and ferritin expressions were increased by GAD treatment. In addition, the expressions of Nrf2 and HO-1 were upregulated by GAD. In conclusion, GAP may inhibit
S. aureus
-induced mastitis in mice by triggering the Nrf2/SLC7A11/GPX4 signaling pathway and alleviating inflammation and ferroptosis.

IMPORTANCE

Mastitis, as an important disease that endangers the development of the dairy industry, causes huge economic losses to the breeding industry.
Staphylococcus aureus
is one of the important pathogenic bacteria that cause mastitis. Antibiotics are considered to be the first choice in the treatment of the
S. aureus
-induced mastitis. However, the overuse of antibiotics leads to bacterial resistance and antibiotic residues. Therefore, this study explored whether effective extracts of traditional herbs could be used as alternatives to antibiotics.
Alkalothermophilic Iron-Reducing Bacteria of the Goryachinsk Thermal Water Basin
Authors: Zavarzina D. G. , Klyukina A. A. , Merkel A. Y. , Maslova T. A. , Maslov A. A.
Published: November 2024

A study of iron-reducing prokaryotes that use the poorly crystalline mineral ferrihydrite as an electron acceptor revealed their widespread occurrence on the planet. However, the ability of iron reducers to develop under polyextreme conditions (at elevated values of pH and temperature) has not been previously demonstrated. To confirm the existence of alkalothermophilic iron reducers, we studied the water and sediment samples from the Goryachinsk nitrogen-rich thermal water basin. These springs are associated with young tectonic fractures in the Baikal rift zone; their water is characterized by low salinity, alkaline pH (8.8‒9.2) and temperature of 53‒55°C. Enrichment cultures reducing synthesized ferrihydrite were obtained by adding this mineral to the water and sediment samples from the Goryachinsk thermal springs, followed by anaerobic incubation at 50 and 55°C. The 16S rRNA gene profiling of the water and sediment samples and of the primary enrichment cultures revealed high taxonomic diversity, almost exclusively represented by bacterial taxa. Subsequent transfers with ferrihydrite and organic acids or hydrogen as electron donors resulted in stable enrichment cultures of organo- and lithotrophic alkalothermophilic iron reducers. Members of the genus Parvivirga, one of the first cultured representatives of the OPB41 group (now the order Anaerosomatales, phylum Actinomycetota), constituted 30 to 50% of the total abundance.
Retrolental pigment collection as a complication of uneventful Kahook Dual Blade goniotomy treated with yttrium aluminium garnet (YAG) hyaloidotomy
Authors: Sethi Sahebaan , Pandit Rinal
Published: November 2024

This case report presents a rare complication following combined phacoemulsification and excisional goniotomy using the Kahook Dual Blade in a patient with primary angle-closure glaucoma. A male in his 60s developed persistent visual disturbances, including bothersome floaters and halos, postoperatively. These symptoms were attributed to the accumulation of brownish retrolental pigments in the patellar fossa, likely originating from the trabecular meshwork and migrating posteriorly through a pre-existing laser peripheral iridotomy (LPI). The complication persisted despite initial conservative treatment with topical steroids. Ultimately, a neodynamium yttrium aluminium garnet hyaloidotomy was performed, successfully dispersing the pigments and resolving the visual symptoms. This case underscores the importance of recognising and managing this rare but significant complication of excisional goniotomy, and suggests a preventive strategy involving a dispersive viscoelastic barrier over the LPI to reduce the risk of pigment migration.