bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simulating Window Designs in Residential Buildings to Analyze Energy Savings in an Arid Region
Authors: Sexton Charles E. , Tahir Furqan , Al-Ghamdi Sami G. 
Published: September 2024

Abstract
According to the climate change future projections, the Middle East and North Africa regions could experience a temperature increase of 2.5 °C by the end of the century. The climate in the Middle East is characterized by hot-arid regions with high temperatures. Therefore, climate-controlled buildings are essential for modern societies to function in these high temperatures. In Saudi Arabia, the Saudi Electricity Company has stated that the residential sector alone accounts for 50% of the electricity consumption in the Kingdom. A rising global temperature and population growth will heighten the need for building cooling, contributing to increased CO2 emissions. Therefore, this study analyzes and simulates innovative window applications to reduce heat gain in traditional buildings in Jeddah, Saudi Arabia. Utilizing OpenStudio software, a representative building is modeled, and various window types are assessed for energy savings. The study aims to decrease residential energy consumption substantially, inform future building codes, and positively affect the environment, economy, and society.
Selective human milk oligosaccharide utilization by members of the
Bifidobacterium pseudocatenulatum
taxon
Authors: Sanchez-Gallardo Rocio , Bottacini Francesca , O’Neill Ian J. , Esteban-Torres Maria , Moore Rebecca , McAuliffe Fionnuala M. , Cotter Paul D. , van Sinderen Douwe 
Published: September 2024

ABSTRACT

Human milk oligosaccharides (HMOs) are essentially unaffected by the digestive enzymes of the nursling and are known for their ability to enrich certain microbial species in the infant gut microbiota, in particular bifidobacteria. HMO metabolism has been studied in various bifidobacterial species such as
B. breve
,
B. bifidum,
and
B. longum
subsp.
infantis
. In the current study, we describe differential growth abilities elicited by twenty-three newly isolated
Bifidobacterium pseudocatenulatum
strains on particular HMOs, such as 2’-fucosyllactose (2’FL), 3-fucosyllactose (3FL), lacto-N-tetraose (LNT), and lacto-N-neotetraose (LNnT). Through gene-trait matching and comparative genome analysis, we identified genes involved in the degradation of fucosylated HMOs in this strain set, while we employed a transcriptomic approach to facilitate the identification and characterization of genes and associated enzymes involved in LNT metabolism by strain
B. pseudocatenulatum
MM0196. A total of 252 publicly available genomes of the
B. pseudocatenulatum
taxon were screened for homologs of the glycosyl hydrolases (GHs) identified here as being required for selected HMO metabolism. From this analysis, it is clear that all members of this species possess homologs of the genes involved in LNT degradation, while genes required for degradation of fucosylated HMOs are variably present.

IMPORTANCE

Our findings allow a better understanding of the complex interaction between
Bifidobacterium
and its host and provide a roadmap toward future applications of
B. pseudocatenulatum
as a probiotic with a focus on infant health. Furthermore, our investigations have generated information on the role of HMOs in shaping the infant gut microbiota, thus also facilitating applications of HMOs in infant nutrition, with potential extension into the mature or adult gut microbiota. Supplementation of HMOs is known to result in the modulation of bacterial communities toward a higher relative abundance of bifidobacteria, which in turn enforces their ability to modulate particular immune functions and strengthen the intestinal barrier. This work may therefore inspire future studies to improve the formulation of neonatal nutritional products, aimed at facilitating the development of a healthy digestive and immune system and reducing the differences in gut microbiota composition observed between breastfed and formula-fed babies or full-term and preterm infants.
Only time will tell: lipopolysaccharide glycoform and biofilm-formation kinetics in
Salmonella
species and
Escherichia coli
Authors: Laekas-Hameder Magdalena , Daigle France 
Published: September 2024

ABSTRACT

In Gram-negative bacteria, LPS (lipopolysaccharide) has been thoroughly characterized and has been shown to play a major role in pathogenesis and bacterial defense. In
Salmonella
and
Escherichia coli
, LPS also influences biofilm development. However, the overall role of LPS glycoform in biofilm formation has not been conclusively settled, as there is a lack of consensus on the topic. Some studies show that LPS mutants produce less biofilm biomass than the wild-type strains, while others show that they produce more. This review summarizes current knowledge of LPS biosynthesis and explores the impact of defective steps on biofilm-related characteristics, such as motility, adhesion, auto-aggregation, and biomass production in
Salmonella
and
E. coli
. Overall, motility tends to decrease, while adhesion and auto-aggregation phenotypes tend to increase in most LPS-mutant strains. Interestingly, biofilm biomass of various LPS mutants revealed a clear pattern dependent on biofilm maturation time. Incubation times of less than 24 h resulted in a biofilm-defective phenotype compared to the wild-type, while incubation exceeding 24 h led to significantly higher levels of biofilm production. This explains conflicting results found in reports describing the same LPS mutations. It is therefore critical to consider the effect of biofilm maturation time to ascertain the effects of LPS glycoform on biofilm phenotype. Underlying reasons for such changes in biofilm kinetics may include changes in signalling systems affecting biofilm maturation and composition, and dynamic LPS modifications. A better understanding of the role of LPS in the evolution and modification of biofilms is crucial for developing strategies to disperse biofilms.
Deletion of
luxI
increases luminescence of
Vibrio fischeri
Authors: Bellissimo Kathryn A. , Septer Alecia N. , Whistler Cheryl A. , Rodríguez Coralis , Stabb Eric V. 
Published: September 2024

ABSTRACT

Bioluminescence in
Vibrio fischeri
is regulated by a quorum-dependent signaling system composed of LuxI and LuxR. LuxI generates
N-
3-oxohexanoyl homoserine lactone (3OC6-HSL), which triggers LuxR to activate transcription of the
luxICDABEG
operon responsible for bioluminescence. Surprisingly, a ∆
luxI
mutant produced more bioluminescence than the wild type in culture. In contrast, a 4 bp duplication within
luxI
, resulting in a frameshift mutation and null allele, decreased luminescence tenfold. A second signaling system encoded by
ainSR
affects bioluminescence by increasing levels of LuxR, via the transcriptional activator LitR, and the
N-
octanoyl homoserine lactone (C8-HSL) signal produced by AinS is considered only a weak activator of LuxR. However,
ainS
is required for the bright phenotype of the ∆
luxI
mutant in culture. When 3OC6-HSL was provided either in the medium or by expression of
luxI in trans
, all cultures were brighter, but the ∆
luxI
mutant remained significantly brighter than the
luxI
frameshift mutant. Taken together, these data suggest that the enhanced bioluminescence due to the LuxI product 3OC6-HSL counteracts a negative
cis
-acting regulatory element within the
luxI
gene and that when
luxI
is absent the C8-HSL signal is sufficient to induce luminescence.

IMPORTANCE

The regulation of bioluminescence by
Vibrio fischeri
is a textbook example of bacterial quorum-dependent pheromone signaling. The canonical regulatory model is that an autoinducer pheromone produced by LuxI accumulates as cells achieve a high density, and this LuxI-generated signal stimulates LuxR to activate transcription of the lux operon that underlies bioluminescence. The surprising observation that LuxI is dispensable for inducing bioluminescence forces a re-evaluation of the role of
luxI
. More broadly, the results underscore the potential deceptiveness of complex regulatory circuits, particularly those in which bacteria produce multiple related signaling molecules.
Genome sequences of
Enterobacter asburiae mcr-9
harboring and
Enterobacter roggenkampii mcr-10
harboring isolated from a wastewater treatment plant in Japan
Authors: Izawa Hiroki , Eda Ryotaro , Niida Nagi , Nakamura Masaki , Furukawa Takashi , Sei Kazunari , Kubo Makoto , Suzuki Masato , Maehana Shotaro 
Published: September 2024

ABSTRACT

Severe infections caused by multi-drug-resistant Gram-negative rods pose a clinical threat due to their high mortality risk. The global spread of plasmid-mediated colistin-resistance genes has become a serious problem. In this study, we identified
Enterobacter
spp. harboring
mcr-9
and
mcr-10
from a wastewater treatment plant in Japan.
Glycogen synthase activity in
Candida albicans
is partly controlled by the functional ortholog of
Saccharomyces cerevisiae
Gac1p
Authors: Miao Jian , Williams David L. , Kruppa Michael D. , Peters Brian M. 
Published: September 2024

ABSTRACT

To adapt to various host microenvironments, the human fungal pathogen
Candida albicans
possesses the capacity to accumulate and store glycogen as an internal carbohydrate source. In the model yeast
Saccharomyces cerevisiae
,
Sc
Glc7p and
Sc
Gac1p are the serine/threonine type 1 protein phosphatase catalytic and regulatory subunits that control glycogen synthesis by altering the phosphorylation state of the glycogen synthase Gsy2p. Despite recent delineation of the glycogen synthesis pathway in
C. albicans
, the molecular events driving synthase activation are currently undefined. In this study, using a combination of microbiologic and genetic techniques, we determined that the protein encoded by uncharacterized gene
C1_01140C
, and not the currently annotated
C. albicans
Gac1p, is the major regulatory subunit involved in glycogen synthesis. C1_01140Cp contains a conserved GVNK motif observed across multiple starch/glycogen-binding proteins in various species, and alanine substitution of each residue in this motif significantly impaired glycogen accumulation in
C. albicans
. Fluorescent protein tagging and microscopy indicated that C1_01140Cp-GFPy colocalized with
Ca
Glc7p-tdTomato and
Ca
Gsy1p-tdTomato accordingly. Co-immunoprecipitation assays further confirmed that C1_01140Cp associates with
Ca
Glc7p and
Ca
Gsy1p during glycogen synthesis. Lastly,
c1_01140c
Δ/Δ exhibited colonization defects in a murine model of vulvovaginal candidiasis. Collectively, our data indicate that uncharacterized C1_01140Cp is the functional ortholog of the PPP1R subunit
Sc
Gac1p in
C. albicans
.

IMPORTANCE

The capacity to synthesize glycogen offers microbes metabolic flexibility, including the fungal pathogen
Candida albicans
. In
Saccharomyces cerevisiae
, dephosphorylation of glycogen synthase by the
Sc
Glc7p-containing phosphatase is a critical rate-limiting step in glycogen synthesis. Subunits, including
Sc
Gac1p, target
Sc
Glc7p to α-1,4-glucosyl primers for efficient
Sc
Gsy2p synthase activation. However, this process in
C. albicans
had not been delineated. Here, we show that the
C. albicans
genome encodes for two homologous phosphatase-binding subunits, annotated
Ca
Gac1p and uncharacterized C1_01140Cp, both containing a GVNK motif required for polysaccharide affinity. Surprisingly, loss of
Ca
Gac1p only moderately reduced glycogen accumulation, whereas loss of C1_01140Cp ablated it. Fluorescence microscopy and co-immunoprecipitation approaches revealed that C1_01140Cp associates with
Ca
Glc7p and
Ca
Gsy1p during glycogen synthesis. Moreover, C1_01140Cp contributed to fungal fitness at the vaginal mucosa during murine vaginitis. Therefore, this work demonstrates that glycogen synthase regulation is conserved in
C. albicans
and C1_01140Cp is the functional ortholog of
Sc
Gac1p.
Single-colony MALDI mass spectrometry imaging reveals spatial differences in metabolite abundance between natural and cultured
Trichodesmium
morphotypes
Authors: Romanowicz Karl J. , Zhang Futing , Wang Siyuan , Veličković Dušan , Chu Rosalie K. , Shaked Yeala , Boiteau Rene M. 
Published: September 2024

ABSTRACT

Trichodesmium
, a globally significant N
2
-fixing marine cyanobacterium, forms extensive surface blooms in nutrient-poor ocean regions. These blooms consist of a dynamic assemblage of
Trichodesmium
species that form distinct colony morphotypes and are inhabited by diverse microorganisms.
Trichodesmium
colony morphotypes vary in ecological niche, nutrient uptake, and organic molecule release, differentially impacting ocean carbon and nitrogen biogeochemical cycles. Here, we assessed the poorly studied spatial abundance of metabolites within and between three morphologically distinct
Trichodesmium
colonies collected from the Red Sea. We also compared these results with two morphotypes of the cultivable
Trichodesmium
strain IMS101. Using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) coupled with liquid extraction surface analysis (LESA) tandem mass spectrometry (MS
2
), we identified and localized a wide range of small metabolites associated with single-colony
Trichodesmium
morphotypes. Our untargeted MALDI-MSI approach revealed 80 unique features (metabolites) shared between
Trichodesmium
morphotypes. Discrimination analysis showed spatial variations in 57 shared metabolites, accounting for 62% of the observed variation between morphotypes. The greatest variations in metabolite abundance were observed between the cultured morphotypes compared to the natural colony morphotypes, suggesting substantial differences in metabolite production between the cultivable strain IMS101 and the naturally occurring colony morphotypes that the cultivable strain is meant to represent. This study highlights the variations in metabolite abundance between natural and cultured
Trichodesmium
morphotypes and provides valuable insights into metabolites common to morphologically distinct
Trichodesmium
colonies, offering a foundation for future targeted metabolomic investigations.

IMPORTANCE

This work demonstrates that the application of spatial mass spectrometry imaging at single-colony resolution can successfully resolve metabolite differences between natural and cultured
Trichodesmium
morphotypes, shedding light on their distinct biochemical profiles. Understanding the morphological differences between
Trichodesmium
colonies is crucial because they impact nutrient uptake, organic molecule production, and carbon and nitrogen export, and subsequently influence ocean biogeochemical cycles. As such, our study serves as an important initial assessment of metabolite differences between distinct
Trichodesmium
colony types, identifying features that can serve as ideal candidates for future targeted metabolomic studies.
The role of dysbiotic gut mycobiota in modulating risk for abdominal aortic aneurysm
Authors: Yao Guixiang , Zhang Xinjie , Zhang Tongxue , Jin Jiajia , Qin Zihan , Ren Xiaoyu , Wang Xiaowei , Zhang Shucui , Yin Xianlun , Tian Zhenyu , Zhang Yun , Zhang Jingyong , Wang Zhe , Zhang Qunye 
Published: September 2024

ABSTRACT

Abdominal aortic aneurysm (AAA) is a large-vessel disease with high mortality, characterized by complex pathogenic mechanisms. Current therapeutic approaches remain insufficient to halt its progression. Fungi are important members of the gut microbiota. However, their characteristic alterations and roles in AAA remain unclear. This study investigated the role of gut fungal communities in the development of AAA through metagenomic sequencing of fecal samples from 31 healthy individuals and 33 AAA patients. We observed significant dysbiosis in the gut mycobiomes of AAA patients compared to healthy individuals, characterized by an increase in pathogenic fungi like
Candida
species and a decrease in beneficial yeasts such as
Saccharomyces cerevisiae
. The changes in fungal populations correlated strongly with clinical indicators of AAA, highlighting their potential for diagnosing and predicting AAA progression. Furthermore, our animal experiments demonstrated that
Saccharomyces cerevisiae
significantly ameliorated pathological alterations in AAA mice, suggesting a protective role for specific yeast strains against AAA development. These findings underscore the significant impact of gut mycobiomes on AAA and suggest that modulating these fungal communities could offer a novel therapeutic approach. Our research advances the understanding of the influence of gut microbiome on vascular diseases and suggests potential non-surgical approaches for managing AAA. By elucidating the diagnostic and therapeutic potential of gut fungi in AAA, this study provided important clues for future clinical strategies and therapeutic developments in the field of vascular medicine.

IMPORTANCE

Our research highlights the crucial role of gut fungi in abdominal aortic aneurysm (AAA) development. By analyzing fecal samples from AAA patients and healthy controls, we discovered significant dysbiosis in gut fungal communities, characterized by an increase in harmful
Candida
species and a decrease in beneficial yeasts like
Saccharomyces cerevisiae
. This dysbiosis was correlated with the severity of AAA. Importantly, in animal experiments, supplementing with
Saccharomyces cerevisiae
significantly slowed AAA progression. These findings suggest that modulating gut fungi may offer a novel, non-surgical approach to the diagnosis and treatment of AAA, potentially reducing the need for invasive procedures.
Laser-assisted endoscopic transoral surgery in apnoeic phase—management strategy for acquired supracarinal tracheal stenosis
Authors: Sarwar Mavra , Sarwar Zahra , Khan Muhammad Sarwar , Khan Saifullah 
Published: September 2024

Acquired supracarinal tracheal stenosis can be defined as postintubation tracheal stenosis of the lower third of the trachea that cannot be bypassed by standard or adjustable flange tracheostomy tubes. Owing to difficulty of access in the deep trachea, the transoral laser-assisted endoscopic surgical management of such stenoses is a challenge both for the surgeon and the anaesthetist alike. It requires good rapport and efficient cooperation between the teams to ensure appropriate oxygenation and carbon-dioxide washout while providing intermittent apnoeic phases to the surgeon for clear visualisation of the target area and use of Diode laser which is otherwise hazardous in an oxygen/nitrous oxide rich environment.From our tertiary care referral centre with strong work load for such pathologies, we report one such case of acquired tracheal stenosis successfully managed with transoral Diode laser-assisted surgery.
Investigations and referral for suspected gastric cancer by primary care physicians: a cross-sectional study in Southeastern China
Authors: Chen Jiayi , Xu Xiaonan , Liu Yiyang , Cai Carla Zi , Wong Li Ping , Lin Yulan 
Published: September 2024

BackgroundEarly recognition and accurate diagnosis are particularly important in the context of gastric cancer. This study mainly aimed to investigate primary care physicians’ (PCPs’) clinical behaviour and their readiness to consider investigation or referral for symptoms possibly indicative of gastric cancer.DesignCross-sectional study.SettingA self-administered online survey was carried out in five selected cities in the Fujian province of China between February 2022 and May 2022.ParticipantPCPs working in the departments, such as Internal Gastroenterology and Hepatology, General Internal Medicine, Internal Medical Oncology Gastrointestinal Surgery or other clinical departments, have the chance to diagnose or treat patients with suspected gastric cancer.Main outcome measuresPercentage of PCPs identifying gastric cancer patients either by undertaking an endoscopy at the primary hospital or by referring patients to an upper-level hospital.ResultsA total of 1210 complete responses were received. Nearly half of responding PCPs (46.4%) only had less than 5 years of clinical experience, and the majority worked in suburban or rural regions (64.4%). Direct access to blood tests for cancer diagnosis (77.9%), X-ray (77.2%), CT (55.7%), ultrasound (85.3%), upper gastrointestinal endoscopy (54.4%) and colonoscopy (51.9%) was common. Of the respondents, 85.5% reported that they could get specialist advice for a suspected cancer patient within 48 hours in terms of investigations and 84.0% in terms of referral. Patients’ waiting time to either conduct a test or have a result was mostly less than 1 week. In patients indicative of gastric cancer, a total of 1148 (94.8%) physicians were ready to investigate cancer either by sending patients to an endoscopy test (49.7%) or referring them to an upper-level hospital (45.1%).ConclusionsFindings indicate that PCPs in five selected cities of Southeastern China have wide and rapid access to diagnostic tests and specialist advice. Furthermore, PCPs in this region seem to have a high level of readiness to consider investigation or referral for symptoms possibly indicative of gastric cancer.
Incidence and risk factors of common infections among children in Wonago, southern Ethiopia: a prospective cohort study
Authors: Hailu Samrawit , Loha Eskindir , Moen Bente E 
Published: September 2024

ObjectiveThere are limited data in Ethiopia on common childhood illnesses. We aimed to measure the incidence and risk factors of common childhood illnesses in rural parts of southern Ethiopia.DesignA community-based cohort study.Participants and study settingA total of 903 children of 5 years or younger were included between July 2017 and January 2018. We randomly selected households from three administrative units (kebeles) in Wonago district in Ethiopia.OutcomesData on incidence of illnesses were collected by interviewing the mothers of the children every second week, in 6 months. Incidence densities per child-week of observation were calculated, and predictors or recurrent illnesses were evaluated in multilevel Poisson regression models.ResultsOut of 903 children, 882 were included (97.6%). At least one illness was experienced among 87.3% of the children. Overall illness incidence rate was 19.7 episodes per 100 child-weeks, 95% CI 18.4 to 20.7. The incidence rate of fever symptoms was 5.5 episodes per 100 child-weeks; of acute respiratory infections (ARIs) 4.2 episodes per 100 child-weeks; of diarrhoea, 3.4 episodes per 100 child-weeks. In the multilevel analysis, household wealth status, child age, child nutritional status, source of drinking water, place for cooking and number of children below 5 years of age in the household were main risk factors for illnesses.ConclusionsChildren below 5 years of age in Ethiopia often experience fever, ARIs and diarrhoea. The identified risk factors were related to poverty and highlighted the importance of preventive measures to reduce the incidence of these diseases.