bluuebunny/crossref_metadata_2025 huggingface dataset:
Light Element (C, N, O) Quantification by EDXS: Application to Meteorite Water Content and Organic Composition
Authors: Le Guillou Corentin , Zanetta Pierre-Marie , Leroux Hugues , Blanchenet Anne-Marie , Marinova Maya
Published: August 2024

Quantifying light elements such as carbon, nitrogen, and oxygen in a transmission electron microscope (TEM) is a challenging however essential task in biology, materials, or earth and planetary sciences. We have developed an approach that allows precise quantification by energy-dispersive X-ray spectroscopy (EDXS), using sensitive windowless silicon drift detectors and homemade Python routines for hyperspectral data processing. K-factors were determined using wedge-shaped focused ion beam sections. To correct for X-ray absorption within the sample, the sample mass thickness is determined by the—revisited—two-lines method (Morris, 1980). No beam current measurement is required. Applying this method to the K and L lines of iron, we found that the tabulated mass absorption coefficient at the energy of the iron L lines was too low. This is due to X-ray self-absorption at the iron edge. Using reference material, we experimentally determined an absorption coefficient that gave the expected results. We then analyzed the complex phyllosilicate mixture of the Orgueil meteorite. We show that the N/C ratio of organics can be obtained with an accuracy better than 5 at.% and that oxygen can be quantified accurately enough to infer the hydroxyl content of phyllosilicates.
Evaluating cell type deconvolution in FFPE breast tissue: application to benign breast disease
Authors: Liu Yuanhang , Vierkant Robert A , Bhagwate Aditya , Jons William A , Stallings-Mann Melody L , McCauley Bryan M , Carter Jodi M , Stephens Melissa T , Pfrender Michael E , Littlepage Laurie E , Radisky Derek C , Cunningham Julie M , Degnim Amy C , Winham Stacey J , Wang Chen
Published: August 2024

Transcriptome profiling using RNA sequencing (RNA-seq) of bulk formalin-fixed paraffin-embedded (FFPE) tissue blocks is a standard method in biomedical research. However, when used on tissues with diverse cell type compositions, it yields averaged gene expression profiles, complicating biomarker identification due to variations in cell proportions. To address the need for optimized strategies for defining individual cell type compositions from bulk FFPE samples, we constructed single-cell RNA-seq reference data for breast tissue and tested cell type deconvolution methods. Initial simulation experiments showed similar performances across multiple commonly used deconvolution methods. However, the introduction of FFPE artifacts significantly impacted their performances, with a root mean squared error (RMSE) ranging between 0.04 and 0.17. Scaden, a deep learning-based method, consistently outperformed the others, demonstrating robustness against FFPE artifacts. Testing these methods on our 62-sample RNA-seq benign breast disease cohort in which cell type composition was estimated using digital pathology approaches, we found that pre-filtering of the reference data enhanced the accuracy of most methods, realizing up to a 32% reduction in RMSE. To support further research efforts in this domain, we introduce SCdeconR, an R package designed for streamlined cell type deconvolution assessments and downstream analyses.
SGLT2 inhibitors and nephrolithiasis risk: a meta-analysis
Authors: Kanbay Mehmet , Brinza Crischentian , Copur Sidar , Sekreter Ozge , Burlacu Alexandru , Tuttle Katherine R , Rossing Peter , Covic Adrian
Published: August 2024

Background

Sodium–glucose co-transporter 2 (SGLT2) inhibitors are novel anti-diabetic medications with potential beneficial effects on cardiovascular and renal outcomes, metabolic parameters and body weight. In addition to the beneficial effects on renal function, including estimated glomerular filtration rate and reduction in proteinuria, recent studies have investigated the potential role of SGLT2 inhibitor (SGLT2i) therapy on nephrolithiasis development. Nephrolithiasis, a condition affecting almost 10% of the general population at least once during a lifetime, is a common disorder with considerable risk for acute and chronic kidney injury and relatively few effective therapeutic options.

Methods

We performed a literature search through multiple databases, including PubMed, Ovid MEDLINE, Web of Science, Scopus and Cochrane Library. We followed the systematic review and meta-analysis guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses. We included a total of 11 635 698 patients who experienced nephrolithiasis from six clinical trials in this meta-analysis study.

Results

In the pooled analysis, nephrolithiasis occurred in 1.27% of patients in the SGLT2i group (n = 739 197), compared with 1.56% of patients (n = 10 896 501) in the control arm (active control, placebo or no therapy). SGLT-2 inhibitor therapy has been associated with a lower risk for nephrolithiasis compared with placebo {odds ratio [OR] 0.61 [95% confidence interval (CI) 0.53–0.70], P < .00001} or active therapy such as glucagon-like peptide 1 and dipeptidyl peptidase 4 inhibitors [OR 0.66 (95% CI 0.47–0.93), P = .02].

Conclusion

We demonstrated a lower risk of nephrolithiasis with SGLT2i therapy compared with placebo or active control. Potential underlying mechanisms include osmotic diuresis leading to a reduction in the concentration of lithogenic substances, anti-inflammatory and anti-fibrotic effects and an increase in urine pH. There is a clear need for future large-scale randomized clinical trials evaluating such associations for better understanding.
Simulating learning methodology (SLeM): an approach to machine learning automation
Authors: Xu Zongben , Shu Jun , Meng Deyu
Published: August 2024

This paper introduces a ‘simulating learning methodology’ (SLeM) approach for the learning methodology determination in general and for Auto6 ML in particular, and reports the SLeM framework, approaches, algorithms and applications.
Outcomes of Antiviral Retreatment for Immunocompromised Hosts With Prolonged Severe Acute Respiratory Syndrome Coronavirus 2 Polymerase Chain Reaction Positivity: A Multicenter Australian Retrospective Case Series
Authors: Bond K A , Dendle C , Guy S , Slavin M A , Smibert O , Ibrahim N , Kinsella P M , Morrissey C O , Moso M A , Sasadeusz J J
Published: August 2024

Outcomes are presented for a multisite retrospective case series, describing a contemporary cohort of 22 immunocompromised patients with persistent coronavirus disease 2019 (COVID-19) polymerase chain reaction positivity who were retreated with antiviral therapy. For those with data available 14 and 30 days after commencement of antiviral therapy, 41% (9 of 22) and 68% (15 of 22), respectively, cleared COVID-19.
Usefulness of Xpert MTB/RIF and Xpert Ultra to Categorize Risk of Tuberculosis Transmission to Household Contacts
Authors: Mol Alexander , Sánchez-Montalvá Adrián , Espinosa-Pereiro Juan , Aznar Maria Luisa , Salvador Fernando , Bosch-Nicolau Pau , de Souza-Galvão Maria-Luiza , Jiménez María Ángeles , Rodrigo-Pendás José Ángel , Millet Joan-Pau , Saborit Nuria , Broto Claudia , Molina Israel , Tórtola Teresa
Published: August 2024

Background

People with pulmonary tuberculosis (PTB) are contagious, particularly to their household contacts. Their infectivity has been associated with the bacterial load in sputum samples. This study investigated if the bacterial load in sputum samples as quantified by Xpert MTB/RIF and Xpert Ultra is correlated with the extent that latent tuberculosis infection (LTBI) occurred in household contacts of people with PTB.

Methods

A retrospective study was performed including people with PTB presenting at Vall d’Hebron University Hospital, Barcelona, between 2011 and 2021. Their infection ratio, representing the proportion of household members found with LTBI in contact tracing investigation, was compared with the quantitative results of Xpert MTB/RIF and Xpert Ultra using ordinal regression analysis.

Results

A total of 107 people with PTB were included. Among their 398 household contacts, 126 (31.7%) cases of LTBI and 14 cases with active TB disease (3.5%) were reported. Higher bacterial load in Xpert MTB/RIF and Xpert Ultra baseline sputum was significantly associated with increased infection ratios, providing better estimates than conventional acid-fast bacilli (AFB) smear grading.

Conclusions

Xpert MTB/RIF and Xpert Ultra could serve as an alternative to AFB sputum-smear grading in determining contact tracing priorities.
Modulation of cell differentiation and growth underlies the shift from bud protection to light capture in cauline leaves
Authors: Le Gloanec Constance , Gómez-Felipe Andrea , Alimchandani Viraj , Branchini Elvis , Bauer Amélie , Routier-Kierzkowska Anne-Lise , Kierzkowski Daniel
Published: August 2024

Plant organs have evolved into diverse shapes for specialized functions despite emerging as simple protrusions at the shoot apex. Cauline leaves serve as photosynthetic organs and protective structures for emerging floral buds. However, the growth patterns underlying this dual function remain unknown. Here, we investigate the developmental dynamics shaping Arabidopsis (Arabidopsis thaliana) cauline leaves underlying their functional diversification from other laminar organs. We show that cauline leaves display a significant delay in overall elongation compared with rosette leaves. Using live imaging, we reveal that their functional divergence hinges on early modulation of the timing of cell differentiation and cellular growth rates. In contrast to rosette leaves and sepals, cell differentiation is delayed in cauline leaves, fostering extended proliferation, prolonged morphogenetic activity, and growth redistribution within the organ. Notably, cauline leaf growth is transiently suppressed during the early stages, keeping the leaf small and unfolded during the initiation of the first flowers. Our findings highlight the unique developmental timing of cauline leaves, underlying their shift from an early protective role to a later photosynthetic function.
O-Glycosylation of a male seminal fluid protein influences sperm binding and female postmating behavior
Authors: Zhang Liping , Ten Hagen Kelly G
Published: August 2024

Glycoproteins are abundant within the human reproductive system and alterations in glycosylation lead to reproductive disorders, suggesting that glycans play an important role in reproductive function. In this study, we used the Drosophila reproductive system as a model to investigate the biological functions of O-glycosylation. We found that O-glycosylation in the male accessory glands, an organ responsible for secreting seminal fluid proteins, plays important roles in female postmating behavior. The loss of one O-glycosyltransferase, PGANT9, in the male reproductive system resulted in decreased egg production in mated females. We identified one substrate of PGANT9, lectin-46Ca (CG1656), which is known to affect female postmating responses. We further show that the loss of lectin-46Ca O-glycosylation affects its ability to associate with sperm tails, resulting in reduced transfer within the female reproductive system. Our results provide the first example that O-glycosylation of a seminal fluid protein affects its ability to associate with sperm in vivo. These studies may shed light on the biological function of O-glycans in mammalian reproduction.
Bending-driven patterning of solid inclusions in lipid membranes: Colloidal assembly and transitions in elastic 2D fluids
Authors: Xin Weiyue , Santore Maria M
Published: August 2024

Biological or biomimetic membranes are examples within the larger material class of flexible ultrathin lamellae and contoured fluid sheets that require work or energy to impose bending deformations. Bending elasticity also dictates the interactions and assembly of integrated phases or molecular clusters within fluid lamellae, for instance enabling critical cell functions in biomembranes. More broadly, lamella and other thin fluids that integrate dispersed objects, inclusions, and phases behave as contoured 2D colloidal suspensions governed by elastic interactions. To elucidate the breadth of interactions and assembled patterns accessible through elastic interactions, we consider the bending elasticity-driven assembly of 1–10 μm solid plate-shaped Brownian domains (the 2D colloids), integrated into a fluid phospholipid membrane (the 2D fluid). Here, the fluid membranes of giant unilamellar vesicles, 20–50 μm in diameter, each contain 4–100 monodisperse plate-domains at an overall solid area fraction of 17 ± 3%. Three types of reversible plate arrangements are found: persistent vesicle-encompassing quasi-hexagonal lattices, persistent closely associated chains or concentrated lattices, and a dynamic disordered state. The interdomain distances evidence combined attractive and repulsive elastic interactions up to 10 μm, far exceeding the ranges of physio-chemical interactions. Bending contributions are controlled through membrane slack (excess area) producing, for a fixed composition, a sharp cooperative multibody transition in plate arrangement, while domain size and number contribute intricacy.
Long-term surveillance study of rituximab originator treated patients with granulomatosis with polyangiitis (GPA) or microscopic polyangiitis (MPA)
Authors: Uchida Lisa , Jones Rachel B , Smith Rona M , Nodale Marianna , Bond Simon , Loechel Claudia , King Maria , Luqmani Raashid , Gray David , Barrett Joe , Jayne David R W
Published: August 2024

Objectives

Rituximab is used for remission induction and the prevention of relapse in anti-neutrophil cytoplasmic antibody-associated vasculitis (AAV). This study evaluated the incidence of safety events and compared time to first serious adverse event (SAE) between a rituximab cohort and a cohort treated with non-rituximab therapies in a real-life setting.

Methods

Rituximab surveillance study in vasculitis was a retrospective observational study of patients with AAV who received rituximab (MabThera) or other treatments between 2003 and 2017 at a specialist vasculitis clinic. The primary endpoint was time to first SAE.

Results

392 patients were enrolled: 247 in the rituximab and 145 in the control cohorts with a total follow up of 2217 person-years (mean study duration 5.7 years). Mean age was 61 years, 77% had granulomatosis with polyangiitis (GPA). There were differences in baseline characteristics (disease duration and prior immunosuppressive use) between groups. 134/247 patients (54%) in the rituximab and 58/145 (40%) of controls experienced at least one SAE. Time to first SAE was shorter in the rituximab group (hazard ratio (HR) 1.55, 95% CI 1.07–2.26, P = 0.022). Predictors of first SAE were higher vasculitis damage index and the presence of chronic pulmonary or kidney disease. The risk of serious infection was higher in the rituximab group (relative risk (RR) 2.12, 95% CI 1.31–3.43).

Conclusion

Over 40% of patients with AAV experienced at least one SAE. Although shorter time to first SAE and higher risk of infection were observed in the rituximab group, baseline imbalances necessitate a careful interpretation of these results.
Kidney whole-transcriptome profiling in primary antiphospholipid syndrome reveals complement, interferons and NETs-related gene expression
Authors: Tektonidou Maria G , Verrou Kleio-Maria , Gakiopoulou Harikleia , Manoloukos Menelaos , Lembessis Panagiotis , Hatzis Pantelis , Sfikakis Petros P
Published: August 2024

Objective

Pathogenesis of antiphospholipid syndrome (APS) remains poorly elucidated. We aimed to evaluate for the first time kidney transcriptome profiles in primary APS vs systemic lupus erythematosus (SLE) and control subjects.

Methods

We performed RNA sequencing on archival formalin-fixed paraffin-embedded kidney biopsies from APS (n = 4), SLE (n = 5) and control (n = 3) individuals, differential gene expression analysis (DGEA) and enrichment analysis using gene ontology (GO) and CORUM, KEGG and Reactome pathway databases.

Results

Two-dimensional projection showed a distinct gene profile in primary APS vs control kidneys samples, but similar to SLE. DGEA in APS vs controls returned 276 upregulated and 217 downregulated genes, while the comparison between APS and SLE identified 75 upregulated and 111 downregulated genes. In 276 upregulated genes, enriched GO terms were (innate) immune response, inflammatory response, leucocyte and lymphocyte activation, cytokine production and T cell activation. CORUM and KEGG revealed complement-related genes (C3, C4A, C4B). Expression levels showed logFC values of 2.25 (P = 1.58e-05) for C3, 2.17 (P = 2.69e-06) for C4A and 2.135 (P = 3.7e-06) for C4B in APS vs controls, without differences between APS and SLE. Interferon (IFN) alpha/beta signalling was revealed by Reactome. Expression levels of nine IFN-regulated genes found upregulated in APS vs control kidneys (P-values ≤ 0.001 for all). Examining neutrophil-extracellular traps (NETs)-related gene expression, 13 of 15 upregulated NETs-related genes exhibited higher expression in APS vs controls but not vs SLE.

Conclusion

Complement, interferon and NETs-related genes are highly expressed in APS kidney tissues, similarly to SLE, pointing out the role of innate immunity in APS nephropathy pathogenesis and potential treatment targets.
De novo manifestations during adalimumab treatment in Behçet’s syndrome
Authors: Esatoglu Sinem Nihal , Sonmez Ozge , Ucar Didar , Kaymaz Elif , Ozguler Yesim , Ugurlu Serdal , Seyahi Emire , Melikoglu Melike , Fresko Izzet , Hamuryudan Vedat , Uygunoglu Ugur , Kutlubay Zekayi , Hatemi Ali Ibrahim , Celik Aykut Ferhat , Hatemi Gulen
Published: August 2024

Objectives

Treatment response may be variable across organ manifestations of Behçet’s syndrome (BS). We aimed to determine the frequency of de novo manifestations during adalimumab treatment.

Methods

We conducted a chart review of all BS patients who received adalimumab in our centre between 2008 and 2023. Demographic data, reasons for initiating adalimumab, concurrent medications, previous treatments, and outcomes were recorded. We defined de novo manifestations as new BS manifestations that occurred for the first time during treatment with adalimumab. For patients with vascular involvement, a new vascular event at another vessel was also considered as a de novo manifestation.

Results

Among the 335 patients, a de novo manifestation developed in 14 (4%) patients. De novo manifestations were vascular involvement in five patients, arthritis in three, anterior uveitis in two, nervous system involvement in two, gastrointestinal involvement in one, and epididymitis in one patient. The primary reasons for adalimumab treatment were vascular involvement in five patients, uveitis in four, arthritis in three, mucocutaneous involvement in one, and epididymitis in one patient. Upon the development of de novo manifestation, adalimumab was switched to another biologic in four patients, dose was intensified in three, colchicine, conventional immunosuppressives and/or glucocorticoids were added in five, and topical eye drops were added in two patients, leading to remission of de novo manifestations in all patients.

Conclusion

De novo manifestations were infrequent (4%) among BS patients treated with adalimumab. Of these, 57% were major organ involvement, mainly vascular involvement. None of the patients developed posterior uveitis.
Association of rare single-nucleotide variant MUC5B rs35705950 with interstitial lung disease in Japanese rheumatoid arthritis
Authors: Higuchi Takashi , Oka Shomi , Shimada Kota , Tsunoda Shinichiro , Ito Satoshi , Okamoto Akira , Fujimori Misuzu , Nakamura Tadashi , Katayama Masao , Suzuki Michita , Saisho Koichiro , Shinohara Satoshi , Matsui Toshihiro , Migita Kiyoshi , Nagaoka Shouhei , Tohma Shigeto , Furukawa Hiroshi
Published: August 2024

Objectives

RA is sometimes complicated by interstitial lung disease (ILD) with a poor prognosis. A single-nucleotide variant (SNV) in MUC5B was associated with ILD in European RA patients. However, associations of this SNV were not found in Japanese RA patients, because its frequency in Japanese populations is very low. We investigated the associations of candidate SNVs including the MUC5B variant with ILD in Japanese RA.

Methods

Genotyping of MUC5B rs35705950, MUC2 rs7934606, MAD1L1 rs12699415 and PPFIBP2 rs6578890 in Japanese RA patients was conducted for association analyses.

Results

MUC5B rs35705950 was associated with usual interstitial pneumonia (UIP) (P = 0.0039, Pc = 0.0156, odds ratio [OR] 10.66, 95% CI 2.05–55.37) or ILD (P = 0.0071, Pc = 0.0284, OR 7.33, 95% CI 1.52–35.44) in Japanese RA under the allele model. MUC2 rs7934606 was associated with UIP (P = 0.0072, Pc = 0.0288, OR 29.55, 95% CI 1.52–574.57) or ILD (P = 0.0037, Pc = 0.0148, OR 22.95, 95% CI 1.27–416.13) in RA. Haplotype analyses suggested the primary association of MUC5B rs35705950 with UIP in Japanese RA. No significant association of MAD1L1 rs12699415 or PPFIBP2 rs6578890 with UIP, nonspecific interstitial pneumonia, or ILD in RA was observed.

Conclusion

MUC5B rs35705950 is associated with, and might be involved in the pathogenesis of ILD, especially UIP, in Japanese RA.
Stress-induced increase in heart-rate during sleep as an indicator of PTSD risk among combat soldiers
Authors: Simon Lisa , Levi Shlomi , Shapira Shachar , Admon Roee
Published: August 2024

Study Objectives

Discerning the differential contribution of sleep behavior and sleep physiology to the subsequent development of posttraumatic-stress-disorder (PTSD) symptoms following military operational service among combat soldiers.

Methods

Longitudinal design with three measurement time points: during basic training week (T1), during intensive stressed training week (T2), and following military operational service (T3). Participating soldiers were all from the same unit, ensuring equivalent training schedules and stress exposures. During measurement weeks soldiers completed the Depression Anxiety and Stress Scale (DASS) and the PTSD Checklist for DSM-5 (PCL-5). Sleep physiology (sleep heart-rate) and sleep behavior (duration, efficiency) were monitored continuously in natural settings during T1 and T2 weeks using wearable sensors.

Results

Repeated measures ANOVA revealed a progressive increase in PCL-5 scores from T1 and T2 to T3, suggesting an escalation in PTSD symptom severity following operational service. Hierarchical linear regression analysis uncovered a significant relation between the change in DASS stress scores from T1 to T2 and subsequent PCL-5 scores at T3. Incorporating participants’ sleep heart-rate markedly enhanced the predictive accuracy of the model, with increased sleep heart-rate from T1 to T2 emerging as a significant predictor of elevated PTSD symptoms at T3, above and beyond the contribution of DASS stress scores. Sleep behavior did not add to the accuracy of the model.

Conclusion

Findings underscore the critical role of sleep physiology, specifically elevated sleep heart-rate following stressful military training, in indicating subsequent PTSD risk following operational service among combat soldiers. These findings may contribute to PTSD prediction and prevention efforts.
The glucocorticoid receptor elicited proliferative response in human erythropoiesis is BCL11A-dependent
Authors: Mazzarini Maria , Cherone Jennifer , Nguyen Truong , Martelli Fabrizio , Varricchio Lilian , Funnell Alister P W , Papayannopoulou Thalia , Migliaccio Anna Rita
Published: August 2024

Prior evidence indicates that the erythroid cellular response to glucocorticoids (GC) has developmental specificity, namely, that developmentally more advanced cells that are undergoing or have undergone fetal to adult globin switching are more responsive to GC-induced expansion. To investigate the molecular underpinnings of this, we focused on the major developmental globin regulator BCL11A. We compared: (1) levels of expression and nuclear content of BCL11A in adult erythroid cells upon GC stimulation; (2) response to GC of CD34+ cells from patients with BCL11A microdeletions and reduced BCL11A expression, and; (3) response to GC of 2 cellular models (HUDEP-2 and adult CD34+ cells) before and after reduction of BCL11A expression by shRNA. We observed that: (1) GC-expanded erythroid cells from a large cohort of blood donors displayed amplified expression and nuclear accumulation of BCL11A; (2) CD34 + cells from BCL11A microdeletion patients generated fewer erythroid cells when cultured with GC compared to their parents, while the erythroid expansion of the patients was similar to that of their parents in cultures without GC, and; (3) adult CD34+ cells and HUDEP-2 cells with shRNA-depleted expression of BCL11A exhibit reduced expansion in response to GC. In addition, RNA-seq profiling of shRNA-BCL11A CD34+ cells cultured with and without GC was similar (very few differentially expressed genes), while GC-specific responses (differential expression of GILZ and of numerous additional genes) were observed only in control cells with unperturbed BCL11A expression. These data indicate that BCL11A is an important participant in certain aspects of the stress pathway sustained by GC.
Genetic Diversity of Cotton Leafroll Dwarf Virus from the Southwestern United States and Its Implications for the Multi-Introduction Event Hypothesis and Future Evolution
Authors: Ferguson Connor , Ali Akhtar
Published: August 2024

Cotton leafroll dwarf virus (CLRDV) is a viral agent recently identified in the United States in 2017 in Alabama. Since its identification, CLRDV has spread to every cotton-growing state east of New Mexico. Oklahoma, Kansas, and Texas make up the westernmost border of reported CLRDV incidence, making monitoring of these states vital for proper control. Additionally, as the virus evolves, mutations that alter symptomology, such as mutations in the F-box-like motif in ORF0/P0, may occur and need to be monitored thoroughly during the growing seasons. Using high-throughput sequencing and PCR-derived Sanger sequencing, 4 CLRDV genomes and 21 P0 gene isolates were sequenced from Oklahoma, Kansas, and Texas from 2019 to 2021 to determine the genetic diversity among CLRDV isolates. Phylogenetic analyses of the complete genomes revealed seven clades, whereas ORF0 gene analyses resulted in large polytomic clusters. BEAST analyses of the 114 total P0 sequences from GenBank, downloaded before 2024, revealed a lower mean substitution rate than previously reported as well as an earlier root year (1914). In addition, using all available CLRDV genome sequences, 11 likely recombination events were determined. Examination of the P0 amino acid sequences revealed 13 mutations unique to the isolates collected in this study. Based on the phylogenetic and amino acid analyses, the CLRDV isolates from Texas (TX clade) may represent evidence for the multi-introduction event hypothesis into the United States. Additionally, based on our analyses in this study, we propose the Asian CLRDV isolates should be constituted as a potentially separate strain of CLRDV.
Fungicide Sensitivity Survey of Pecan Scab in Texas Pecan Orchards
Authors: Goetze Paul K. , Nesbitt Monte L. , Jo Young-Ki
Published: August 2024

A fungicide sensitivity survey of pecan scab ( Venturia effusa) from eight different locations in seven pecan orchards in Texas was conducted during the summer of 2021. Using a rapid fungicide sensitivity assay based on single discriminatory concentrations, sensitivities to five fungicides (dodine, fentin hydroxide, thiophanate-methyl, propiconazole, and tebuconazole) were evaluated. Pecan orchards with frequent fungicide use tended to have greater levels of reduced sensitivities to demethylation inhibitor (propiconazole and tebuconazole; >40% of conidial germination at 1 µg/ml of active ingredient) and fentin hydroxide fungicides (>64% of conidial germination at 3 µg/ml of active ingredient) compared to those with fewer fungicide applications in the past. All populations tested in this survey exhibited a high level of resistance to the thiophanate-methyl fungicide but no resistance to dodine. Thiophanate-methyl did not inhibit conidial germination for six scab populations, while dodine consistently inhibited conidial germination for scab populations tested at the discriminatory concentration. The cytochrome b gene was sequenced for determining mutations associated with quinone outside inhibitor (QoI) fungicides. The mutation that results in a substitution of glycine 137 to serine (G137S) in the cytochrome b gene and is related to high resistance to QoI was not found in the representative isolates of scab populations tested in this survey. Our findings are the first report of fungicide resistance development in Texas pecan orchards. Information about fungicide sensitivities of scab populations in orchards will help pecan producers to prepare proper fungicide treatment plans.
Grapevine Vein Clearing Virus Is Seedborne but Not Seed Transmitted in Ampelopsis cordata and Chardonel Vines
Authors: Manu Matthew , Petersen Sylvia , Qiu Wenping
Published: August 2024

Grapevine vein clearing virus (GVCV) seriously affects grape production in the Midwest region of the United States. It infects cultivated and native grapevines and wild vines of Ampelopsis cordata and is transmitted by grape aphids in native sites and in vineyards. In this study, we asked if GVCV is transmitted vertically via seeds. To this end, seeds were collected from both healthy and GVCV-infected A. cordata from native sites and Chardonel vines from vineyards. The seeds and seedlings of both Vitaceae genotypes were tested for GVCV by PCR. GVCV was detected in the seeds obtained from GVCV-infected A. cordata and Chardonel but not from the cotyledons and true leaves of their seedlings. Seeds from healthy vines of both Vitaceae genotypes and their seedlings were negative for GVCV by PCR. The results indicate that GVCV is seedborne but not seed transmitted, an important contribution to the knowledge on the ecology of the virus.
Defining the Pathobiomes Associated with Drippy Blight in Colorado and Drippy Nut in California
Authors: Raymond Hope , Sitz Rachael A. , Pearse Ian S. , Caballero Jorge R. Ibarra , Lalande Bradley M. , Stewart Jane E.
Published: August 2024

Drippy blight, an emergent bacterial disease of oaks, was described recently from urban oaks in the Front Range of Colorado, U.S.A. This disease, which causes branch dieback and oozing of bacterial exudates from cankers, is caused by Lonsdalea quercina and primarily affects red oaks, with northern red oak ( Quercus rubra) being the most susceptible. Drippy nut is a similar, less acute condition that exists in California, U.S.A., and affects acorns of interior live oak ( Q. wislizenii) and coastal live oak ( Q. agrifolia). The objective of this study was to compare the microbial communities of drippy blight in Colorado to those of drippy nut in California and to determine whether other pathogenic fungal or bacterial taxa are associated with the diseases. Symptomatic and asymptomatic tissues were sampled in California and Colorado, and metagenomic analyses were performed to describe the fungal and bacterial communities. We found a suite of bacterial species, dominated by taxa within the genus Zymobacter, that were associated with symptomatic tissues for both drippy nut and drippy blight. L. quercina is the main pathogenic associate of both diseases. We found fungal yeasts associated with symptomatic tissues, and although not pathogens, these taxa were present in the pathobiome of drippy nut and drippy blight in California and Colorado. We did, however, identify taxa belonging to Gnomoniopsis, a known pathogen, associated with California symptomatic samples. Our study found an overlapping suite of bacterial associates of drippy blight and drippy nut, though more variation occurred within the fungal genera associated with these oak diseases.

[Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Evidence of Differential Attainment in Canadian Medical School Admissions: A Scoping Review
Authors: Ngo Thuy-Anh , Choi Joshua , McIntosh Alexander , Elma Asiana , Grierson Lawrence
Published: August 2024

Purpose

In Canada, many groups (e.g., Black, Indigenous, rural backgrounds) have historically faced and continue to encounter systemic barriers in accessing the medical profession. These barriers often manifest in performance disparities, known as differential attainment, during medical school admissions. This scoping review summarizes the nature and extent of evidence on the association of differential attainment in medical school admissions selection tools and outcomes with applicant social identity in the Canadian context.

Method

The authors used Arksey and O’Malley’s scoping review framework to summarize research studies published between 2000 and 2022 with empirical evidence of differential attainment in admissions selection tools and outcomes with respect to a range of applicant social identity categories. The authors recorded whether studies adopted a structuralist and/or intersectional perspective.

Results

Ultimately, 15 studies were included in the review. While the evidence on differential attainment associated with social identity in Canadian medical education was heterogeneous, numerous studies highlight differential attainment in the admissions process associated with applicant race and/or ethnicity (6 studies), age (5 studies), gender (4 studies), socioeconomic status (3 studies), geographic location (4 studies), and rural or urban background (5 studies). These attainment differences were reported at 3 phases of the admissions process (invitation to interview, offer of admission, and acceptance of offer) and were driven by several admissions selection tools, including grade point average, Medical College Admission Test score, and interview performance.

Conclusions

The review highlights evidence that suggests systemic, structural inequities in admissions systems manifest as differential attainment in Canadian medical school admissions. Based on this evidence, those who identify as Black or Indigenous and those with low socioeconomic status or rural backgrounds were generally more adversely affected. Admission practices must be studied and improved so medical education systems can better avow equality and human dignity and achieve equity goals.
In-office Maximal Voluntary Ventilation Testing Demonstrates Pulmonary Improvement Following Posterior Spinal Fusion for Adolescent Idiopathic Scoliosis
Authors: Jalloh Hulaimatu , Andras Lindsay M. , Redding Greg , Villamor Gabriela A. , Yang Joshua , Skaggs David L.
Published: August 2024

Objective:

Pulmonary function can be impaired in patients with adolescent idiopathic scoliosis (AIS). Maximal voluntary ventilation (MVV) has been shown to be more strongly correlated with major coronal curve, and a more easily obtained measurement of pulmonary function, than forced vital capacity (FVC). We evaluated changes in pulmonary function using these 2 measures in patients with AIS in relation to changes in major coronal curves over time.

Methods:

Forty-seven patients with AIS with thoracic curves ≥10 degrees performed pulmonary function tests using the Carefusion MicroLoop Spirometer at enrollment and 1 year later. Major coronal curve worsening >5 degrees was considered curve progression.

Results:

At enrollment, 47 patients had a mean major coronal curve of 38 degrees (range: 10 to 76 degrees). One year later, 17 patients had undergone posterior spinal fusion, 9 had curve progression >5 degrees, and 21 had no progression. MVV and major coronal curve were negatively correlated (r = -0.36, P = 0.01) at enrollment. After fusion, the major coronal curve improved by a mean of 41 degrees, and MVV improved by 23% (P < 0.01), but FVC did not improve significantly (6%, P = 0.29). In stable curves, MVV improved 12% (P = 0.01) and FVC improved 9% (P = 0.007). In patients without surgery whose curves progressed an average of 11 degrees, there was no significant change in MVV or FVC (P > 0.44).

Conclusion:

This is the first study using office-based spirometry in an orthopaedic clinic showing improved pulmonary function with posterior spinal fusion and growth in patients with AIS. It is notable that MVV improved after spinal fusion, but FVC did not, as MVV appears to be a more sensitive measurement for the assessment of pulmonary function in these patients.

Level of Evidence:

Level II.
Biomarker-stratified first-line treatment of right-sided metastatic colon cancer with interdisciplinary collaboration in the IVOPAK II trial
Authors: Vitali Francesco , Merkel Susanne , Schubart Christoph , Schmid Axel , Eckstein Markus , Stöhr Robert , Kersting Stephan , Hartmann Arndt , Grützmann Robert , Wein Axel
Published: August 2024

Patients with right-sided metastatic colon carcinoma have a significantly worse prognosis than those with left-sided colorectal cancer (CRC), regardless of treatment. The aim of the prospective IVOPAK II study was to implement an interdisciplinary guideline-conform personalized CRC palliative therapy of metastatic colorectal carcinoma and to improve the overall survival (OS) by multidisciplinary approach via secondary metastatic resection. We present the efficacy data of first-line treatment and the benefit of interdisciplinary collaboration of right-sided metastatic colon carcinoma patients: n = 25. RAS mutation: n = 20 (80%): received systemic first-line treatment: FOLFIRI plus bevacizumab. All-RAS-wildtype: n = 5 (20%): received systemic first-line treatment: FOLFIRI plus cetuximab. Last date evaluation: 31 January 2024. Median age: 59.6 years (range 42–71), men/women: 14/11. Eastern Cooperative Oncology Group (ECOG) index: 0/1/2 : 11/10/4. Evaluable for response: n = 25. Complete response: n = 0, partial response: n = 14 (56%), stable disease: n = 8 (32%), progressive disease: n = 3 (12%), early tumor shrinkage: n = 13 (52%), estimates progression-free survival: 13 months (95% CI 8–17 months), estimated OS: 48 months (95% CI 25–71 months), median follow-up: 26 months (1–61 months), no evidence of disease: n = 4 (16%). A chemotherapy doublette regimen with FOLFIRI plus a biological as first-line treatment shows promising efficacy and secondary metastatic resection after interdisciplinary discussion was associated with a survival benefit in right-sided metastatic colon carcinoma.
Integrated single-cell and bulk RNA sequencing analyses identify an immunotherapy nonresponse-related fibroblast signature in gastric cancer
Authors: Peng Qian , Zhang Peiling , Liu Guolong , Lu Lin
Published: August 2024

Factors that determine nonresponse to immune checkpoint inhibitor (ICI) remain unclear. The protumor activities of cancer-associated fibroblasts (CAFs) suggest that they are potential therapeutic targets for cancer treatment. There is, however, a lack of CAF-related signature in predicting response to immunotherapy in gastric cancer (GC). Single-cell RNA sequencing (scRNA-seq) and RNA sequencing (RNA-seq) data of GC immunotherapy were downloaded from the Gene Expression Omnibus database. Bulk RNA-seq data were obtained from The Cancer Genome Atlas. The R package ‘Seurat’ was used for scRNA-seq data processing. Cellular infiltration, receptor-ligand interactions, and evolutionary trajectory analysis were further explored. Differentially expressed genes affecting overall survival were obtained using the limma package. Weighted Gene Correlation Network Analysis was used to identify key modules of immunotherapy nonresponder. Prognostic model was constructed by univariate Cox and least absolute contraction and selection operator analysis using the intersection of activated fibroblast genes (AFGs) with key module genes. The differences in clinicopathological features, immune microenvironment, immunotherapy prediction, and sensitivity to small molecule agents between the high- and low-risk groups were further investigated. Based on scRNA-seq, we finally identified 20 AFGs associations with the prognosis of GC patients. AFGs' high expression levels were correlated with both poor prognosis and tumor progression. Three genes (FRZB, SPARC, and FKBP10) were identified as immunotherapy nonresponse-related fibroblast genes and used to construct the prognostic signature. This signature is an independent significant risk factor affecting the clinical outcomes of GC patients. Remarkably, there were more CD4 memory T cells, resting mast cells, and M2 macrophages infiltrating in the high-risk group, which was characterized by higher tumor immune exclusion. Moreover, patients with higher risk scores were more prone to not respond to immunotherapy but were more sensitive to various small molecule agents, such as memantine. In conclusion, this study constructed a fibroblast-associated ICI nonresponse gene signature, which could predict the response to immunotherapy. This study potentially revealed a novel way to overcome immune resistance in GC.
Enhanced Negative Pressure Wound Therapy Shortens Hospital Stay for Major Burn Patients: Case Series
Authors: Donoso-Samper Andrea , Camacho-Obando David , Garzón Santiago , Gómez-Ortega Viviana
Published: August 2024

The length of hospital stay (LOS) serves as a key metric for forecasting resource allocation and assessing quality of care in burn treatment. Negative pressure wound therapy with instillation and dwell time (NPWTi-d) has emerged as a groundbreaking option in the management of burns, linked to quicker wound healing and more effective infection resolution. However, its impact on LOS remains uncertain. This article introduces a series of burn injuries managed with NPWTi-d, using the Solventum V.A.C. Veraflo Cleanse Choice Dressing. Severely burned patients with deep burns were selected for treatment with NPWTi-d using Solventum V.A.C. Veraflo Cleanse Choice Dressing and were treated after skin grafts with Solventum V.A.C. Granufoam Dressing. We calculated the predictive LOS, with the formulas developed by Taylor et al and compared them with the actual LOS. NPWTi-d was administered to three patients. The age of the patients ranged from 16 to 42 years, with an average of 28.6 years (SD, 10.84) and an average total burn area of 48.16% (SD, 1.4%). We observed an average reduction in hospital stay of 23.2% (SD, 19.83%) All burn injuries either healed completely or demonstrated adequate skin graft survival and recovery in follow-ups. All the patients exhibited a decrease in the LOS, despite experiencing systemic complications arising from distributive shock.
Cervical Cancer Prevention in Individuals With Criminal Legal System Involvement
Authors: Ramaswamy Megha , Hall Bianca , Cejtin Helen , Sufrin Carolyn , Moore Shawana , Nattell Noah , Jodry Dominique , Flowers Lisa
Published: August 2024

Objectives

Women with a history of criminal legal system involvement have cervical cancer rates that are 4–5 times higher than the general population—a disparity that has persisted for nearly 50 years. Our objective is to describe the intersection of mass incarceration in the United States and risk factors for cervical cancer to offer equitable prevention and treatment strategies for the field.

Results

A group was convened by American Society for Colposcopy and Cervical Pathology members and experts in the field to address a topic of importance relevant to cervical cancer elimination in underserved groups. This topic has received consistent attention from the American Society for Colposcopy and Cervical Pathology. After convening multiple times to discuss salient issues on the topic, the group proposed 12 specific recommendations related to vaccination, screening, treatment, practice, research, and policy to address the burden of cervical cancer among individuals with criminal legal system involvement.

Discussion

At least 10% of the incarcerated population is at risk for cervical cancer. Clinicians in all areas of practice will encounter patients with incarceration histories or current incarceration, regularly throughout their careers.

Conclusions

Clinicians who provide preventive care for people at risk of cervical cancer can play a critical role in eliminating disparities for this vulnerable population, by drawing on these expert recommendations.
Combined Endoscopic Ultrasonography and Endoscopic Retrograde Cholangiopancreatography in Patients With Malignant Distal Biliary Obstruction Is Associated With Reduced Time to Oncological Therapy Compared With ERCP and Sampling Alone
Authors: Gauci James , On Wei , Paranandi Bharat , Huggett Matthew Thomas , Everett Simon
Published: August 2024

Objectives

Standard endoscopic retrograde cholangiopancreatography (ERCP) sampling techniques for pancreaticobiliary malignancy have modest yields that could lead to delays in treatment. We evaluated whether combining EUS-guided tissue acquisition (EUS-TA) with ERCP improved time to first outpatient evaluation and treatment.

Materials and Methods

All patients without a prior pathological diagnosis who underwent index ERCP at Leeds Teaching Hospitals NHS Trust, United Kingdom, for malignant distal biliary obstruction from 2015 to 2020 were considered.

Results

A total of 292 patients were included, of whom 74.7% (n = 202) underwent EUS-TA/ERCP. A combined approach was more likely to establish a positive diagnosis (96.5% [n = 195] vs 57.8% [n = 52], P < 0.01) and less likely to require further sampling procedures (2.0% [n = 4] vs 17.8% [n = 16], P < 0.01). Mean times to first outpatient evaluation (16.9 vs 24.5 days [P = 0.01]) and oncological treatment (55.1 vs 79.3 days [P = 0.03]) were significantly shorter. A third (n = 86) of patients with a positive diagnosis did not receive oncological/surgical treatment.

Conclusions

A combined approach was associated with improved yield and reduced time to evaluation/treatment, with similar success and adverse event rates. Careful multidisciplinary discussion is recommended to avoid performing unnecessary EUS procedures.
Incidence of postoperative pneumonia in various surgical subspecialties: a retrospective study
Authors: Alrefaei Mariya Ibrahim , Ahmed Reem Anees , Al thoubaity FATMA
Published: August 2024

Postoperative pneumonia (POP) can be defined as either hospital-acquired pneumonia (HAP, pneumonia developing 48–72 h after admission) or ventilator-associated pneumonia (VAP, pneumonia developing 48–72 h after endotracheal intubation)‘ or within 30 days in postoperative patients. POP accounts for 2.7–3.4% of postoperative complications. Few studies have evaluated the incidence and the risk factors of POP. This study aimed to estimate the incidence of POP and identify the predictive factors of POP in King Abdul-Aziz University Hospital (KAUH), Jeddah, Saudi Arabia. This retrospective record review included all patients diagnosed with POP at KAUH between 2011 and 2021. Patients younger than 18 years of age and those diagnosed with congenital heart or lung disease were excluded from the study. Data were analyzed using the SPSS program version 26. Of the 2350 patients, 236 met the inclusion criteria. The mean age of patients was 58.12± 17.66 years; 82.6% had comorbidities. ENT (6.4%) and cardiothoracic surgeries associated with POP were the most common surgeries (4.2%). Comorbidities were found as an independent predictor of pneumonia among the studied patients (P = 0.024). The incidence of developing POP was (19.9%). Therefore, Physicians should be aware of POP. Especially when treating patients with comorbidities and patients on corticosteroids.