bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temporal colonization of macadamia tree roots by Phytophthora cinnamomi based on a newly developed quantitative real‐time PCR assay
Authors: McLeod Adele , Hamza Zizipho , Schoeman Maritha H. , Moyo Lindani , Akinsanmi Olufemi A. 
Published: November 2023

AbstractPhytophthora cinnamomi is an important soilborne pathogen causing root rot and stem cankers on macadamia in South Africa and other countries. It is unknown whether a temporal pattern exists in the colonization of macadamia tree roots by P. cinnamomi. To investigate this, three macadamia orchards were studied bimonthly for 2 years. The study also examined whether two types of feeder roots contained varying levels of P. cinnamomi DNA. A new sensitive P. cinnamomi‐specific quantitative real‐time PCR (qPCR) assay was used to conduct the assessments. Only symptomatic trees were studied in two of the orchards (ZC and ZD), while symptomatic and asymptomatic trees were assessed in the third orchard (ZA). In the ZC and ZD orchards, white non‐suberized feeder roots from a new root flush had higher levels of P. cinnamomi DNA than suberized feeder roots. In orchard ZD, autumn and winter yielded the highest P. cinnamomi root quantities in suberized roots. The symptomatic and asymptomatic trees in orchard ZA generally contained higher P. cinnamomi root quantities in winter than in summer. However, in orchard ZC, no significant temporal pattern was evident, although a trend was noticeable towards higher P. cinnamomi root colonization in autumn, winter and spring. Principal component analyses supported autumn and winter as the months yielding the highest P. cinnamomi root colonization levels. The study has contributed to a better understanding of the temporal nature of P. cinnamomi root colonization, and feeder root types that are optimal for qPCR quantifying the pathogen in macadamia.
Isothermal microcalorimetry improves accuracy and time to bacterial detection of periprosthetic joint infection after total joint arthroplasty
Authors: Cichos Kyle H. , Ruark Randall J. , Ghanem Elie S. 
Published: November 2023

ABSTRACT

Isothermal microcalorimetry (IMC) was evaluated compared to conventional cultures to determine the clinical performance for diagnosing periprosthetic joint infection (PJI) of hip/knee replacements. We prospectively collected three to five deep tissue samples per patient from 152 patients undergoing conversion or revision hip/knee arthroplasty from July 2020 to November 2022. Cultures and IMC for each sample were compared for concordance, median time to detection (TTD), and diagnostic performance based on 2013 Musculoskeletal Infection Society criteria. Secondary analyses involved patients on antibiotics at sampling. The 152 total patients had 592 tissue samples (mean 3.9 ± 0.3) with sample concordance between cultures and IMC of 90%. IMC demonstrated a sensitivity of 83%, specificity of 100%, negative predictive value (NPV) of 89%, and positive predictive value (PPV) of 100% for PJI. Cultures resulted in 69% sensitivity, 100% specificity, 81% NPV, and 100% PPV. The accuracy of IMC was 93% compared to 87% for cultures (
P
< 0.001). The median TTD of PJI by cultures was 51 (21–410) hours compared to 10 (0.5–148) hours for IMC (
P
< 0.001). For 39 patients on chronic antibiotics, sensitivity in PJI detection was 93%, specificity 100%, NPV 85%, and PPV 100% by IMC compared to 79% sensitivity, 100% specificity, 65% NPV, and 100% PPV for cultures. The accuracy was 95% for IMC compared to 85% for cultures (
P
< 0.001) with median TTD of 12 (0.5–127) hours compared to 52 (21–174) hours (
P
< 0.001). Utilizing IMC for PJI detection improves TTD by nearly 2 days while improving diagnostic accuracy compared to cultures, particularly in patients on chronic antibiotics.
Draft genome sequence of soil isolate
Mycolicibacterium fortuitum
DVD-1301
Authors: Bragin Eugeny Y. , Dovbnya Dmitry V. , Ivashina Tanya V. , Donova Marina V. 
Published: November 2023

ABSTRACT

Some strains of
Mycolicibacterium
possess high sterol-oxidizing activity and are used in the pharmaceutical industry for the production of steroid precursors. Herein, we report a draft genome sequence of the soil-dwelling
Mycolicibacterium fortuitum
DVD-1301 isolated in the floodplain of the river Oka. The genome contains a full set of steroid catabolic genes.
Flexible changes to the Heliothis virescens ascovirus 3h (HvAV-3h) virion components affect pathogenicity against different host larvae species
Authors: Yu Huan , Chen Hong , Li Ni , Yang Chang-Jin , Xiao Hua-Yan , Chen Gong , Huang Guo-Hua 
Published: November 2023

ABSTRACT

The pathogenicity of a virus to a specific host species is an inerratic and describable ability of a virus to cause infection but is generally shaped by a variety of abiotic and biotic factors. In this investigation, the variations in pathogenicity of Heliothis virescens ascovirus 3h (HvAV-3h) to five noctuid pests were assessed based on mass spectrometry analysis on the virion compositions. Twenty-nine common HvAV-3h proteins were shared across all hosts, and different flexible proteins were identified in the virions of each specific host. Different host proteins were identified as HvAV-3h virion-associated proteins, including different detoxification enzyme proteins. Furthermore, a relatively fixed relationship between viral replication and changes in host detoxification enzyme activity caused by deficiencies in various viral structural proteins was found in the host larvae using a correlation matrix analysis: the host larval carboxylesterase and cytochrome P450 monooxygenases generally had highly similar responses to the viruses blocked by different structural proteins’ antisera and their effects on viral DNA replication. Different interaction patterns for the virion structural proteins were found in different host larvae-produced virions, and the interactions between
Spodoptera litura
glutathione S-transferases and viral structural proteins were confirmed. The different host responses after viral infection could be the reason for the changes in viral pathogenicity, while the virus responses gradually adapted to the different hosts and there were flexible changes in the virion structures.

IMPORTANCE
Different pathogenic processes of a virus in different hosts are related to the host individual differences, which makes the virus undergoes different survival pressures. Here, we found that the virions of an insect virus, Heliothis virescens ascovirus 3h (HvAV-3h), had different protein composition when they were purified from different host larval species. These “adaptive changes” of the virions were analyzed in detail in this study, which mainly included the differences of the protein composition of virions and the differences in affinity between virions and different host proteins. The results of this study revealed the flexible changes of viruses to help themselves adapt to different hosts. Also, these interesting findings can provide new insights to improve our understanding of virus adaptability and virulence differentiation caused by the adaptation process.
Evolution of SARS-CoV-2 Spikes shapes their binding affinities to animal ACE2 orthologs
Authors: Yao Weitong , Li Yujun , Ma Danting , Hou Xudong , Wang Haimin , Tang Xiaojuan , Cheng Dechun , Zhang He , Du Chengzhi , Pan Hong , Li Chao , Lin Hua , Sun Mengsi , Ding Qiang , Wang Yingjie , Gao Jiali , Zhong Guocai 
Published: November 2023

ABSTRACT
Spike-receptor interaction is a critical determinant for the host range of coronaviruses. Here, we investigated all the five World Health Organization-designated variants of concern (VOC), including Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.1.529), for their Spike receptor-binding domain (RBD)’s interactions with ACE2 orthologs of 18 animal species. We found that, compared to the RBD of an early isolate WHU01, the Alpha RBD has markedly increased affinity to cattle and pig ACE2 proteins and decreased affinity to horse and donkey ACE2 proteins. The RBDs of Beta and Gamma variants have almost completely lost affinity to bat, horse, and donkey ACE2 orthologs. Mainly due to the Q493R and N501Y mutations, the Omicron RBD showed markedly enhanced affinity to mouse ACE2. Molecular dynamic simulations further suggest that Omicron RBDs are optimal for electrostatic interactions with mouse ACE2. Interestingly, the Omicron RBD also showed decreased or complete loss of affinity to eight tested animal ACE2 orthologs, including that of horse, donkey, pig, dog, cat, pangolin, American pika, and bat. The K417N, G496S, and Y505H substitutions were identified as three major contributors that commonly have negative impact on RBD binding to these eight ACE2 orthologs. These findings show that Spike mutations have been continuously shaping SARS-CoV-2’s binding affinities to animal ACE2 orthologs and suggest the importance of surveillance of animal infection by circulating SARS-CoV-2 variants.

IMPORTANCE

Spike-receptor interaction is a critical determinant for the host range of coronaviruses. In this study, we investigated the SARS-CoV-2 WHU01 strain and five WHO-designated SARS-CoV-2 variants of concern (VOCs), including Alpha, Beta, Gamma, Delta, and the early Omicron variant, for their Spike interactions with ACE2 proteins of 18 animal species. First, the receptor-binding domains (RBDs) of Alpha, Beta, Gamma, and Omicron were found to display progressive gain of affinity to mouse ACE2. More interestingly, these RBDs were also found with progressive loss of affinities to multiple ACE2 orthologs. The Omicron RBD showed decreased or complete loss of affinity to eight tested animal ACE2 orthologs, including that of some livestock animals (horse, donkey, and pig), pet animals (dog and cat), and wild animals (pangolin, American pika, and
Rhinolophus sinicus
bat). These findings shed light on potential host range shift of SARS-CoV-2 VOCs, especially that of the Omicron variant.
Microporous and Hierarchical ZSM-5 Zeolites in Friedländer Synthesis
Authors: Grigor’eva N. G. , Bubennov S. V. , Artem’eva A. S. , Serebrennikov D. V. , Filippova N. A. , Kutepov B. I. 
Published: November 2023

Abstract
The study investigates the catalytic performance of microporous and granular micro–meso–macroporous zeolites (H-ZSM-5 and H-ZSM-5h, respectively) in synthesis of quinolines by the reaction of 2-aminoacetophenone with diketones (2,4-pentanedione or dimedone), known as the Friedländer synthesis. In the presence of H-ZSM-5h, 1-(2,4-dimethylquinolin-3-yl)ethanone (1a) and 3,4-dihydro-3,3,9-trimethyl-1(2H)-acridinone (1b) were produced in 82 and 93% yields, respectively.
Awareness and knowledge of diabetic ketoacidosis in people with type 1 diabetes: a cross-sectional, multicenter survey
Authors: Hepprich Matthias , Roser Pia , Stiebitz Sebastian , Felix Barbara , Schultes Bernd , Schmitz Daniela , Rutishauser Jonas , Schubert Sabine , Aberle Jens , Rudofsky Gottfried 
Published: November 2023

IntroductionTo evaluate awareness and knowledge of diabetic ketoacidosis (DKA), a common and potentially life-threatening complication in people living with type 1 diabetes (T1D).Research design and methodsA survey was developed to assess individuals’ current knowledge, management, and unmet needs regarding DKA. The study was conducted in six Swiss and three German endocrine outpatient clinics specialized in the treatment of diabetes.ResultsA total of 333 participants completed the questionnaire (45.7% female, mean age of 47 years, average duration of T1D at 22 years). Surprisingly, 32% of individuals were not familiar with the term ‘diabetic ketoacidosis’. Participants rated their own knowledge of DKA significantly lower than their physicians (p<0.0001). 46% of participants were unable to name a symptom of DKA, and 45% were unaware of its potential causes. 64% of participants did not test for ketones at all. A significant majority (67%) of individuals expressed the need for more information about DKA.ConclusionsIn patients treated in specialized centers, knowledge of DKA was found to be inadequate, with a lack of understanding regarding symptoms and causes. Healthcare professionals tended to overestimate individuals’ knowledge. Future efforts should focus on addressing these knowledge gaps and incorporating protective factors into the treatment of T1D.
Association between infection and the onset of giant cell arteritis and polymyalgia rheumatica: a systematic review and meta-analysis
Authors: Pacoureau Lucas , Barde François , Seror Raphaele , Nguyen Yann 
Published: November 2023

ObjectiveWe aimed to analyse the association between infections and the subsequent risk of giant cell arteritis (GCA) and/or polymyalgia rheumatica (PMR) by a systematic review and a meta-analysis of observational studies.MethodsTwo databases (Medline and Embase) were systematically reviewed. Epidemiological studies studying the association between any prior infection and the onset of GCA/PMR were eligible. Risk of bias was assessed using the Newcastle-Ottawa quality assessment scale. Outcomes and pooled statistics were reported as OR and their 95% CI.ResultsEleven studies (10 case–control studies and one cohort study) were analysed, seven of them were included in the meta-analysis. Eight were at low risk of bias. A positive and significant association was found between prior overall infections and priorHerpes Zoster(HZ) infections with pooled OR (95% CI) of 1.27 (1.18 to 1.37) and 1.20 (1.08 to 1.21), respectively. When analysed separately, hospital-treated and community-treated infections, were still significantly associated with the risk of GCA, but only when infections occurring within the year prior to diagnosis were considered (pooled OR (95% CI) 1.92 (1.67 to 2.21); 1.67 (1.54 to 1.82), respectively). This association was no longer found when infections occurring within the year prior to diagnosis were excluded.ConclusionOur study showed a positive association between the risk of GCA and prior overall infections (occurring in the year before), and prior HZ infections. Infections might be the reflect of an altered immunity of GCA patients or trigger the disease. However, reverse causation cannot be excluded.CRD42023404089.
Pharmacodynamic effects of filgotinib treatment driving clinical improvement in patients with active psoriatic arthritis enrolled in the EQUATOR trial
Authors: Chandran Vinod , Malkov Vladislav A , Ito Kaori L , Liu Yihua , Vestergaard Lene , Yoon Oh Kyu , Liu Jinfeng , Trivedi Mona , Hertz Angie , Gladman Dafna 
Published: November 2023

ObjectivesThe goal of this study was to identify protein and transcriptional biomarkers and pathways associated with baseline disease state, the effect of filgotinib (FIL) treatment on these biomarkers, and to investigate the mechanism of action of FIL on clinical improvement in patients with active psoriatic arthritis (PsA).MethodsThe phase II EQUATOR (NCT03101670) trial evaluated the efficacy of FIL, a Janus kinase 1-preferential inhibitor, in patients with PsA. Peripheral protein and gene expression levels in association with clinical state at baseline and post-treatment were assessed in 121 patients using linear mixed effects models for repeated measures analyses. Mediation analysis and structural equation modelling (SEM) were performed to investigate the mechanism of action of FIL at week 4 on downstream clinical improvement at week 16.ResultsBaseline analyses showed that markers of inflammation were significantly associated with multiple PsA clinical metrics, except for Psoriasis Area and Severity Index (PASI), which corresponded to Th17 markers. FIL treatment resulted in sustained transcriptional inhibition of immune genes and pathways, a sustained increase in B-cell fraction and mature B-cells in circulation, and a transient effect on other cell fractions. Mediation analysis revealed that changes in B cells, systemic inflammatory cytokines and neutrophils at week 4 were associated with changes in clinical metrics at week 16. SEM suggested that FIL improved PASI through reduction of IL-23 p19 and IL-12 p40 proteins.ConclusionsOur results revealed that FIL treatment rapidly downregulates inflammatory and immune pathways associated with PsA disease activity corresponding to clinical improvement in PsA.Trial registration numberNCT03101670.
Significance of the auditory meatus inferior wall cartilage in the surgical treatment of congenital first branchial cleft anomalies in children
Authors: Yu Bo , Zhu Ruiyang , Fu Yong , Xu Bin , Yu Lulu , Bi Jing 
Published: November 2023

ObjectiveTo investigate the clinical significance of the inferior wall cartilage of the auditory meatus in surgical treatment of congenital first branchial cleft anomalies (CFBCAs) in children.MethodsTwenty children diagnosed with CFBCAs who underwent surgery between December 2018 and June 2022 at our hospital were retrospectively analyzed and classified according to their Work lesion type. The guiding significance of the inferior wall cartilage in the surgical treatment of CFBCAs was summarized by investigating the adjacent relationships of the surgical lesions with the external auditory canal and facial nerve.ResultsOf the 20 patients, 16 were classified as Work type I and 4 as Work type II. The lesions were adjacent to the inferior wall cartilage of the auditory meatus in all children. Work type I lesions were located in the upper lateral aspect and were not adjacent to the facial nerve. Work type II lesions were located in the inferior-medial region of the facial nerve. The lesions were completely resected in all children. One patient experienced recurrence 3 months postoperatively because of a residual endochondral fistula. No patients developed facial paralysis or other complications.ConclusionsThe inferior wall cartilage of the auditory meatus may help to the identify the initial lesion of the CFBCAs and can be regarded as a guiding anatomical structure. These lesions can be completely resected. For resection of Work type II first branchial cleft lesions, the surgical incision can be narrower, and can be precisely positioned with the assistance of endoscope.
The Burgess Shale lagerstätte at the Walcott Quarry, Yoho National Park, Canada
Authors: Anderson Thomas B. , James Matthew J. , McNeil Paul 
Published: November 2023

Abstract
The Walcott Quarry was discovered in 1909 by the Smithsonian Institute's Charles Doolittle Walcott (1850–1927). The Cambrian Burgess Shale (505 Ma, Miaolingian) crops out in the quarry and the lagerstätte is the nexus of ongoing vigorous debate about fossil preservation (including taphonomy and diagenesis), taxonomy, classification, phylogeny, and the origin of phyla and baupläne. Smithsonian Institute's field crews collected from 1909–24, and the quarry was subsequently expanded by Harvard University (1930), the Canadian Geological Survey (1966–67), and the Royal Ontario Museum (1992–2000). Approximately 250 000 fossils, including soft-bodied forms, have been collected, making the Walcott Quarry with exposures of the Middle Cambrian Burgess Shale, a significant geoheritage site and an important representation of the Cambrian Explosion.
Social Networks and Cardiovascular Disease Events in the Jackson Heart Study
Authors: Glover LáShauntá , Sutton Janiyah , O'Brien Emily , Sims Mario 
Published: November 2023

Background
Cardiovascular disease (CVD) disproportionately affects Black adults. Greater social networks (SNs), or social connectedness, may lower the risk of CVD events. This study determined the association of SNs and incident CVD and tested mediation by depressive symptoms, hypertension control, and diabetes control.

Methods and Results
We used the Social Network Index at exam 1 (2000–2004) to develop a continuous standardized SN score and binary categories (high versus low) among participants in the Jackson Heart Study (n=4686; mean age, 54.8 years). Surveillance of coronary heart disease, stroke, and heart failure events occurred after exam 1 (2005 for HF) until 2016. Using Cox proportional hazards regression, we estimated the association of SNs and CVD events by sex and tested the mediation of depressive symptoms, hypertension control, and diabetes control. Models adjusted for age, education, health behaviors, CVD comorbidities, and depressive symptoms. Among women, the SN score was associated with a lower hazard of stroke, coronary heart disease, and heart failure after full adjustment (hazard ratio [HR], 0.78 [95% CI, 0.64–0.95]; HR, 0.79 [95% CI, 0.71–0.88]; and HR, 0.78 [95% CI, 0.66–0.92], respectively). SN scores were also associated with a lower hazard of coronary heart disease in men (HR, 0.84 [95% CI, 0.75–0.94]) after full adjustment. High versus low SNs were associated with a lower hazard of coronary heart disease and heart failure among women after full adjustment. There was no evidence of mediation by depressive symptoms, diabetes control, and hypertension control.

Conclusions
Higher SNs may lower the risk of CVD events, especially in women.
Association of Bypass Surgery and Mortality in Moyamoya Disease
Authors: Park Hyunjun , Han Minkyung , Jang Dong‐Kyu , Kim Dal‐Soo , Huh Pil‐Woo , Park Hae‐Kwan , Park Ik Seong , Han Young‐Min , Sung Jae Hoon , Lee Kwan‐Sung , Lee Hyung‐Jin , Kim Young Woo 
Published: November 2023

Background
Patients with moyamoya disease (MMD) have a high risk of stroke or death. We investigated whether extracranial to intracranial bypass surgery can reduce mortality by preventing strokes in patients with MMD.

Methods and Results

This nationwide retrospective cohort study encompassed patients with MMD registered under the Rare Intractable Diseases program via the Relieved Co‐Payment Policy between 2006 and 2019, using the Korean National Health Insurance Service database. Following a 4‐year washout period, landmark analyses were employed to assess mortality and stroke occurrence between the bypass surgery group and the nonsurgical control group at specific time points postindex date (1 month and 3, 6, 12, and 36 months). The study included 18 480 patients with MMD (mean age, 40.7 years; male to female ratio, 1:1.86) with a median follow‐up of 5.6 years (interquartile range, 2.5–9.3; mean, 6.1 years [SD, 4.0 years]). During 111 775 person‐years of follow‐up, 265 patients in the bypass surgery group and 1144 patients in the nonsurgical control group died (incidence mortality rate of 618.1 events versus 1660.3 events, respectively, per 10
5
person‐years). The overall adjusted hazard ratio (HR) revealed significantly lower all‐cause mortality in the bypass surgery group from the 36‐month landmark time point, for any stroke mortality from 3‐ and 6‐month landmark time points, and for hemorrhagic stroke mortality from the 6‐month landmark time point. Furthermore, the overall adjusted HRs for hemorrhagic stroke occurrence were beneficially maintained from all 5 landmark time points in the bypass surgery group.

Conclusions
Bypass surgery in patients with MMD was associated with a lower risk of all‐cause and hemorrhagic stroke mortality and hemorrhagic stroke occurrence compared with nonsurgical control.