bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metagenomic assembled genomes indicated the potential application of hypersaline microbiome for plant growth promotion and stress alleviation in salinized soils
Authors: Dindhoria Kiran , Kumar Raghawendra , Bhargava Bhavya , Kumar Rakshak 
Published: February 2024

ABSTRACT

Climate change is causing unpredictable seasonal variations globally. Due to the continuously increasing earth’s surface temperature, the rate of water evaporation is enhanced, conceiving a problem of soil salinization, especially in arid and semi-arid regions. The accumulation of salt degrades soil quality, impairs plant growth, and reduces agricultural yields. Salt-tolerant, plant-growth-promoting microorganisms may offer a solution, enhancing crop productivity and soil fertility in salinized areas. In the current study, genome-resolved metagenomic analysis has been performed to investigate the salt-tolerating and plant growth-promoting potential of two hypersaline ecosystems, Sambhar Lake and Drang Mine. The samples were co-assembled independently by Megahit, MetaSpades, and IDBA-UD tools. A total of 67 metagenomic assembled genomes (MAGs) were reconstructed following the binning process, including 15 from Megahit, 26 from MetaSpades, and 26 from IDBA_UD assembly tools. As compared to other assemblers, the MAGs obtained by MetaSpades were of superior quality, with a completeness range of 12.95%–96.56% and a contamination range of 0%–8.65%. The medium and high-quality MAGs from MetaSpades, upon functional annotation, revealed properties such as salt tolerance (91.3%), heavy metal tolerance (95.6%), exopolysaccharide (95.6%), and antioxidant (60.86%) biosynthesis. Several plant growth-promoting attributes, including phosphate solubilization and indole-3-acetic acid (IAA) production, were consistently identified across all obtained MAGs. Conversely, characteristics such as iron acquisition and potassium solubilization were observed in a substantial majority, specifically 91.3%, of the MAGs. The present study indicates that hypersaline microflora can be used as bio-fertilizing agents for agricultural practices in salinized areas by alleviating prevalent stresses.

IMPORTANCE
The strategic implementation of metagenomic assembled genomes (MAGs) in exploring the properties and harnessing microorganisms from ecosystems like hypersaline niches has transformative potential in agriculture. This approach promises to redefine our comprehension of microbial diversity and its ecosystem roles. Recovery and decoding of MAGs unlock genetic resources, enabling the development of new solutions for agricultural challenges. Enhanced understanding of these microbial communities can lead to more efficient nutrient cycling, pest control, and soil health maintenance. Consequently, traditional agricultural practices can be improved, resulting in increased yields, reduced environmental impacts, and heightened sustainability. MAGs offer a promising avenue for sustainable agriculture, bridging the gap between cutting-edge genomics and practical field applications.
Investigating inhibitors of 1-deoxy-
d
-xylulose 5-phosphate synthase in a mouse model of UTI
Authors: Chen Eric C. , Shapiro Rachel L. , Pal Arindom , Bartee David , DeLong Kevin , Carter Davell M. , Serrano-Diaz Erika , Rais Rana , Ensign Laura M. , Freel Meyers Caren L. 
Published: February 2024

ABSTRACT

The rising rate of antimicrobial resistance continues to threaten global public health. Further hastening antimicrobial resistance is the lack of new antibiotics against new targets. The bacterial enzyme, 1-deoxy-
d
-xylulose 5-phosphate synthase (DXPS), is thought to play important roles in central metabolism, including processes required for pathogen adaptation to fluctuating host environments. Thus, impairing DXPS function represents a possible new antibacterial strategy. We previously investigated a DXPS-dependent metabolic adaptation as a potential target in uropathogenic
Escherichia coli
(UPEC) associated with urinary tract infection (UTI), using the DXPS-selective inhibitor butyl acetylphosphonate (BAP). However, investigations of DXPS inhibitors
in vivo
have not been conducted. The goal of the present study is to advance DXPS inhibitors as
in vivo
probes and assess the potential of inhibiting DXPS as a strategy to prevent UTI
in vivo
. We show that BAP was well-tolerated at high doses in mice and displayed a favorable pharmacokinetic profile for studies in a mouse model of UTI. Further, an alkyl acetylphosphonate prodrug (homopropargyl acetylphosphonate, pro-hpAP) was significantly more potent against UPEC in urine culture and exhibited good exposure in the urinary tract after systemic dosing. Prophylactic treatment with either BAP or pro-hpAP led to a partial protective effect against UTI, with the prodrug displaying improved efficacy compared to BAP. Overall, our results highlight the potential for DXPS inhibitors as
in vivo
probes and establish preliminary evidence that inhibiting DXPS impairs UPEC colonization in a mouse model of UTI.

IMPORTANCE

New antibiotics against new targets are needed to prevent an antimicrobial resistance crisis. Unfortunately, antibiotic discovery has slowed, and many newly FDA-approved antibiotics do not inhibit new targets. Alkyl acetylphosphonates (alkyl APs), which inhibit the enzyme 1-deoxy-
d
-xylulose 5-phosphate synthase (DXPS), represent a new possible class of compounds as there are no FDA-approved DXPS inhibitors. To our knowledge, this is the first study demonstrating the
in vivo
safety, pharmacokinetics, and efficacy of alkyl APs in a urinary tract infection mouse model.
The Linearly Polarized Light Effect on Maize Development
Authors: Kulchin Yu. N. , Kozhanov S. O. , Kholin A. S. , Subbotin E. P. , Kovalevsky K. V. , Subbotina N. I. , Gomolsky A. S. 
Published: February 2024

Abstract
The main purpose of the work was to study the linearly polarized light impact on the maize plants development. The other purpose was to confirm the model proposed earlier. The methods used in this work include the development of LED light sources, the polarization parameter (degree of polarization) assessment and statistical analysis. Maize (Zea mays L.) plants, Hansatech FMS 1+ pulsed fluorimeter and software TXP Series Instrumentation were used. Plants were grown under white light (WW) with intensity of 200 µmol m–2 s–1. The morphometric parameters measured on the 21st day demonstrated that maize plants of different varieties grown under linearly polarized light developed better than under non-polarized light conditions. In addition, the fact was confirmed by chlorophyll fluorescence measurements. The mechanism has been proposed to explain significant polarized radiation impact on maize, according to which this impact depends on the shape and arrangement of the leaf epidermal cells. The monocotyledonous maize plants have leaves with an ordered arrangement of epidermal cells in comparison with dicotyledonous plants, which cells placed in chaotic order and have no certain shape. Thus, the maize cells layer can transform linearly polarized radiation into elliptically polarized radiation, thus latter should be more efficiently absorbed by the chiral chromophores of photosensitive structures in underlying photosynthetic cells.
Economic impact on local businesses of road safety improvements in Seattle: implications for Vision Zero projects
Authors: Osterhage Daniel R , Acolin Jessica , Fishman Paul A , Dannenberg Andrew L 
Published: February 2024

BackgroundLocal transportation agencies implementing Vision Zero road safety improvement projects often face opposition from business owners concerned about the potential negative impact on their sales. Few studies have documented the economic impact of these projects.MethodsWe examined baseline and up to 3 years of postimprovement taxable sales data for retail, food and service-based businesses adjacent to seven road safety projects begun between 2006 and 2014 in Seattle. We used hierarchical linear models to test whether the change in annual taxable sales differed between the 7 intervention sites and 18 nearby matched comparison sites that had no road safety improvements within the study time frame.ResultsAverage annual taxable sales at baseline were comparable at the 7 intervention sites (US$44.7 million) and the 18 comparison sites (US$56.8 million). Regression analysis suggests that each additional year following baseline was associated with US$1.20 million more in taxable sales among intervention sites and US$1.14 million more among comparison sites. This difference is not statistically significant (p=0.64). Sensitivity analyses including a random slope, using a generalised linear model and an analysis of variance did not change conclusions.DiscussionResults suggest that road safety improvement projects such as those in Vision Zero plans are not associated with adverse economic impacts on adjacent businesses. The absence of negative economic impacts associated with pedestrian and bicycle road safety projects should reassure local business owners and may encourage them to work with transportation agencies to implement Vision Zero road safety projects designed to eliminate traffic-related injuries.
The difficulty with measuring the largest melanoma tumour diameter in sentinel lymph nodes
Authors: Laeijendecker Annelien E , El Sharouni Mary-Ann , Stathonikos Nikolaos , Spoto Clothaire P E , van de Wiel Bart A , Eijken Erik J E , Mulder Marijne , Mooyaart Antien L , Szumera-Cieckiewicz Anna , Mihic-Probst Daniela , Massi Daniela , Cook Martin , Koljenovic Senada , Alos Llucia , van Diest Paul J , van Akkooi Alexander C J , Blokx Willeke 
Published: February 2024

ABSTRACTIdentification of sentinel node (SN) metastases can set the adjuvant systemic therapy indication for stage III melanoma patients. For stage IIIA patients, a 1.0 mm threshold for the largest SN tumour diameter is used. Therefore, uniform reproducible measurement of its size is crucial. At present, the number of deposits or their microanatomical sites are not part of the inclusion criteria for adjuvant treatment. The goal of the current study was to show examples of the difficulty of measuring SN melanoma tumour diameter and teach how it should be measured. Histopathological slides of SN-positive melanoma patients were retrieved using the Dutch Pathology Registry (PALGA). Fourteen samples with the largest SN metastasis around 1.0 mm were uploaded via tele-pathology and digitally measured by 12 pathologists to reflect current practice of measurements in challenging cases. Recommendations as educational examples were provided. Microanatomical location of melanoma metastases was 1 subcapsular, 2 parenchymal and 11 combined. The smallest and largest difference in measurements were 0.24 mm and 4.81 mm, respectively. 11/14 cases (78.6%) showed no agreement regarding the 1.0 mm cut-off. The median discrepancy for cases ≤5 deposits was 0.5 mm (range 0.24–0.60, n=3) and 2.51 mm (range 0.71–4.81, n=11) for cases with ≥6 deposits. Disconcordance in measuring SN tumour burden is correlated with the number of deposits. Awareness of this discordance in challenging cases, for example, cases with multiple small deposits, is important for clinical management. Illustrating cases to reduce differences in size measurement are provided.
Notification of hand eczema as an occupational disease among Danish hairdressers: a national survey on patients’ perception
Authors: Kursawe Larsen Christoffer , Havmose Martin S , Johansen Jeanne Duus 
Published: February 2024

ObjectivesSelf-reported hand eczema was previously found under-reported as an occupational disease to the authorities among Danish hairdressers graduating from 1985 to 2007. This study investigates whether self-reported hand eczema among Danish hairdressers graduating from 2008 to 2018 is under-reported as an occupational disease to the authorities.MethodsA cross-sectional study on all Danish hairdressers graduating from 2008 to 2018 was conducted. The participants were identified using information from the Danish Hairdressers’ and Beauticians’ Union. In May 2020, a self-administered survey on hand eczema was sent to all hairdressers.ResultsA response rate of 30.7% (1485/4830) was obtained. The lifetime prevalence of self-reported hand eczema was 40.1%, and 84.1% of hairdressers with hand eczema believed it to be occupational of whom 27.0% answered it was reported as an occupational disease to the authorities. Of hairdressers believing their hand eczema was occupational, consulting a doctor and answering it was reported as an occupational disease, 94.4% had consulted a dermatologist. The main reason for not reporting was ‘I would probably not gain anything from it anyway’ (40.0%).ConclusionsBased on hairdressers’ perception, occupational hand eczema still seems to be an under-reported disease which may lead to underestimation of the problem and impair prevention, diagnosis and treatment.
Mucus clears from the trachea in a helix: a new twist to understanding airway diseases
Authors: Abelson David , Di Michiel James , Frater Clayton , Pearson Mark , Russo Robert , Wechselberger Martin , Cottee Alice , Morgan Lucy 
Published: February 2024

BackgroundMucociliary clearance (MCC) is critical to lung health and is impaired in many diseases. The path of MCC may have an important impact on clearance but has never been rigorously studied. The objective of this study is to assess the three-dimensional path of human tracheal MCC in disease and health.MethodsTracheal MCC was imaged in 12 ex-smokers, 3 non-smokers (1 opportunistically imaged during acute influenza and repeated after recovery) and 5 individuals with primary ciliary dyskinesia (PCD). Radiolabelled macroaggregated albumin droplets were injected into the trachea via the cricothyroid membrane. Droplet movement was tracked via scintigraphy, the path of movement mapped and helical and axial models of tracheal MCC were compared.Measurements and main resultsIn 5/5 participants with PCD and 1 healthy participant with acute influenza, radiolabelled albumin coated the trachea and did not move. In all others (15/15), mucus coalesced into globules. Globule movement was negligible in 3 ex-smokers, but in all others (12/15) ascended the trachea in a helical path. Median cephalad tracheal MCC was 2.7 mm/min ex-smokers vs 8.4 mm/min non-smokers (p=0.02) and correlated strongly to helical angle (r=0.92 (p=0.00002); median 18oex-smokers, 47onon-smokers (p=0.036)), but not to actual speed on helical path (r=0.26 (p=0.46); median 13.6 mm/min ex-smokers vs 13.9 mm/min non-smokers (p=1.0)).ConclusionFor the first time, we show that human tracheal MCC is helical, and impairment in ex-smokers is often caused by flattened helical transit, not slower movement. Our methodology provides a simple method to map tracheal MCC and speed in vivo.
Cardioprotective effects of losartan and diminazene against the ischemia/reperfusion injury in hyperthyroidism rats
Authors: Pashaei Mosayeb , Hesari Mahvash , Shackebaei Dareuosh , Godini Aliashraf 
Published: February 2024

Hyperthyroidism is a condition where the thyroid gland produces high levels of thyroid hormone. Heart diseases are one of the main complications of hyperthyroidism. Several studies have shown that losartan (LOS) and diminazene aceturate (DIZE) possess cardioprotection effects against cardiac hypertrophy, ischemic heart disease, and heart failure. The research aimed to investigate the cardioprotection of LOS, DIZE, and their combination in the case of levothyroxine (LT4)-induced cardiomyopathy in rats. Hyperthyroidism was induced by LT4 in drinking water (12 mg/L) for 28 days. LOS (10 mg/kg, orally) and/or DIZE (15 mg/kg, subcutaneously) were administrated in rats with hyperthyroidism for 28 days. Decreased serum creatine kinase myoglobin and lactate dehydrogenase levels and cardiac hypertrophy by DIZE and combination therapy in hyperthyroidism rats have been reported. Cardiac hemodynamic findings showed that DIZE and its combination with LOS decreased the LT4-mediated left ventricular developed pressure (LVDP), rate pressure product (RPP), and RPP recovery percentage. Elevated cardiac oxidative stress and inflammation were confirmed by decreasing cardiac superoxide dismutase (SOD) activity and increasing the total oxidative stress and tumor necrosis factor-alpha (TNF-α) levels. SOD activity and TNF-α level were reversed by LOS and DIZE administration, respectively. Generally, DIZE and combination therapy with LOS improved cardiac dysfunction caused by hyperthyroidism in rats, whereas LOS alone has not been able to effectively respond to this dysfunction.
The October 2023 Issue
Authors: Uhlig Steve 
Published: February 2024

This October 2023 issue contains three editorial notes.
The observing reader of CCR will have noticed that there is no July 2023 issue. There are three main factors at play here. Given the timing of our SIGCOMM conferences, summer is a low period for submissions to CCR. Then, as CCR is selective and its scope limited to timely works relevant to our community, few technical papers make it above our bar. Finally, I have witnessed a healthy shift away from technical papers towards more thought-provoking editorials over the last few years. We have enough conference and journals for technical papers to find an appropriate venue. On the other hand, our conferences and journals, due to their selective nature and the overly critical nature of the reviewing process, do not lend themselves to welcome thought-provoking and contentious contributions. Let CCR be their home.
The Long Term Results of Hyaluronic Acid/Dextranomer Injection Laryngoplasty in Unilateral Vocal Fold Paralysis
Authors: Alaskarov Elvin , Batıoğlu-Karaaltın Ayşegül , Erdur Zülküf Burak , Gülmez Züleyha Dilek , İnan Hakkı Caner , Öztürk Özcan 
Published: February 2024

Objective: This study was conducted to present the long-term functional outcomes of injection laryngoplasty (IL) with hyaluronic acid/dextranomer (HA/D) in unilateral vocal fold paralysis (UVFP). Methods: A total of 40 patients who underwent HA/D injection for UVFP were enrolled. The acoustic analysis of the voice was evaluated with jitter percentage, shimmer percentage, maximum phonation time, harmonics-to-noise ratio, and fundamental frequency. The psychosocial effect of the voice was determined using the Voice Handicap Index-10. Fiberoptic endoscopic evaluation of swallowing was performed and 2 scales were used for quantification: a modified penetration-aspiration scale and a dysphagia score. All measurements were performed at preoperative day and postoperative months 1, 6, and 24. Results: A statistically significant improvement was observed for all of the evaluated parameters except the maximum phonation time for postoperative months 1, 6, and 24 ( P < .05). In the evaluation of the maximum phonation time, although there was a significant improvement for the postoperative months 1 and 6, no significant difference was observed between the postoperative 24th month and the preoperative value. Conclusions: HA/D injection laryngoplasty is an effective method both in the short- and long-term to improve voice and swallowing functions in patients with UVFP.
Applying models of care for total hip and knee arthroplasty: External validation of a published predictive model to identify extended stay risk prior to lower-limb arthroplasty
Authors: Harrison-Brown Meredith , Scholes Corey , Ebrahimi Milad , Bell Christopher , Kirwan Garry 
Published: February 2024

Objective This study aimed to externally validate a reported model for identifying patients requiring extended stay following lower limb arthroplasty in a new setting. Design External validation of a previously reported prognostic model, using retrospective data. Setting Medium-sized hospital orthopaedic department, Australia. Participants Electronic medical records were accessed for data collection between Sep-2019 and Feb-2020 and retrospective data extracted from 200 randomly selected total hip or knee arthroplasty patients. Intervention Participants received total hip or knee replacement between 2-Feb-16 and 4-Apr-19. This study was a non-interventional retrospective study. Main measures Model validation was assessed with discrimination, calibration on both original and adjusted forms of the candidate model. Decision curve analysis was conducted on the outputs of the adjusted model to determine net benefit at a predetermined decision threshold (0.5). Results The original model performed poorly, grossly overestimating length of stay with mean calibration of −3.6 (95% confidence interval −3.9 to −3.2) and calibration slope of 0.52. Performance improved following adjustment of the model intercept and model coefficients (mean calibration 0.48, 95% confidence interval 0.16 to 0.80 and slope of 1.0), but remained poorly calibrated at low and medium risk threshold and net benefit was modest (three additional patients per hundred identified as at-risk) at the a-priori risk threshold. Conclusions External validation demonstrated poor performance when applied to a new patient population and would provide limited benefit for our institution. Implementation of predictive models for arthroplasty should include practical assessment of discrimination, calibration and net benefit at a clinically acceptable threshold.
Revitalizing oncology medications access in Saudi Arabia: Current challenges and recommendations by the Saudi Oncology Pharmacy Assembly
Authors: Alkhudair Nora , Howaidi Jude , Alnuhait Mohammed , Alshamrani Majed , Khan Mansour , Alharbi Atika , Alnajjar Fouad , Bajnaid Eshtyag , Almodaheem Hajer , Alhowimel Mansour , Alzahrani Ali , Khardaly Amr , Alnahedh Mohammed , Elsoudi Hamdi , Alabdulkareem Hana , Alrashidan Ahmed , Alzahrani Musa , Alrajhi Abdullah 
Published: February 2024

Background Cancer care is posing immense challenges to healthcare systems globally. Advances in screening, monitoring, and treating cancer improved patient outcomes and survival rates yet amplified the disease burden. Multiple barriers might impede early access to innovative therapies. We thoroughly examined the current challenges in oncology medication access in Saudi Arabia and provided consensus recommendations to revitalize the process. Methods A focus group discussion was conducted. Expert healthcare providers (pharmacists and physicians) were invited to participate based on prespecified criteria. The research team conducted a qualitative analysis of the discussion to identify themes and formulate recommendations. Results Fourteen experts were equally distributed into two groups, limiting the number in each group to 7. Pharmacists were 12 (∼86%), and physicians were 2 (∼14%). Ten were practicing in governmental hospitals, four representing different sectors; regulatory bodies, including Ministry of Health, National Unified Procurement Company, and Saudi Food and Drug Authority. Five themes were identified: national cancer burden, local data availability, pharmacoeconomic evaluation, patients reported outcomes, administration, and procurement. Consensus recommendations were formulated to optimize the formulary management process, enabling informed decision-making and facilitating early medication access for cancer patients. Conclusions The formulary management process can be enhanced by addressing the national cancer burden, promoting local data availability, conducting pharmacoeconomic evaluations, focusing on patient outcomes, and improving administration and procurement procedures. Implementing these recommendations can improve access to oncology medications and improve patient care outcomes in Saudi Arabia.