bluuebunny/crossref_metadata_2025 huggingface dataset:
Detection of Live Attenuated Measles Virus in the Respiratory Tract Following Subcutaneous Measles-Mumps-Rubella Vaccination
Authors: Watkins Timothy A , Brockhurst Jacqueline K , Germain Gregory , Griffin Diane E , Foxman Ellen F
Published: November 2024

The live attenuated measles vaccine is extremely effective in preventing measles and induces mucosal immunity in the respiratory tract; however, the mechanism is not known. We show that live attenuated measles virus (LAMV) RNA is frequently detected in the respiratory tract 7–21 days after subcutaneous measles-mumps-rubella (MMR) vaccination in healthy children (n = 5/20) and macaques (n = 6/8). Replicating LAMV was isolated from the lungs of 2 macaques, with no evidence of transmission to unvaccinated individuals. These observations suggest that LAMV in the respiratory tract may play a role in the development of robust mucosal immunity following MMR vaccination.
Impact of a multifaceted antibiotic stewardship programme in a paediatric acute care unit over 8 years
Authors: Brigadoi Giulia , Gres Emelyne , Barbieri Elisa , Liberati Cecilia , Rossin Sara , Chiusaroli Lorenzo , Demarin Giulia Camilla , Tesser Francesca , Maestri Linda , Tirelli Francesca , Carrara Elena , Tacconelli Evelina , Bressan Silvia , Giaquinto Carlo , Da Dalt Liviana , Donà Daniele
Published: November 2024

Background

Antibiotics are the most prescribed drugs for children worldwide, but overuse and misuse have led to an increase in antibiotic resistance. Antimicrobial stewardship programmes (ASPs) have proven feasible in reducing inappropriate antimicrobial use. The study aimed at evaluating the impact and sustainability of an ASP with multiple interventions over 8 years.

Methods

This quasi-experimental study was conducted between 2014 and 2022 in the paediatric acute care unit of Padua University Hospital. Demographic and clinical data were retrieved from the electronic clinical records. Daily prescriptions were collected and analysed based on the AWaRe classification and using days of therapy (DOT) out of 1000 patient days (DOT/1000PDs). The primary outcome was to assess the change in overall antibiotic consumption and of access and watch antibiotics, stratifying patients with and without comorbidities. Trends in antibiotic consumption (DOTs/1000PD) were assessed using joinpoint regression analysis.

Findings

A total of 3118 children were included. Total antibiotic consumption remained stable and low in patients without comorbidities, ∼300 DOT/1000PDs, whereas a statistically significant constant reduction was observed in children with comorbidities, from almost 500 DOT/1000PPDs to <400 DOT/1000PDs. Access consumption increased in both groups of patients, whereas watch consumption constantly decreased, although statistically significant only in children with comorbidities.

Interpretation

Implementing a multistep ASP has proven feasible and sustainable in improving antibiotic prescriptions for previously healthy and fragile children. All the implemented interventions were low cost, and with efficient use of resources, ensuring an ASP that was effective, practical, and easily replicable and implementable in various healthcare settings.
Enhancement efficiency of flow and irreversibility system for MHD Buongiorno’s nanofluid in complex peristaltic tapered channel with electroosmosis forces
Authors: Alsemiry Reima Daher , Abo-Elkhair Rabea E , Eid Mohamed R , Elsaid Essam M
Published: November 2024

Magnetohydrodynamic flow efficiency and irreversibility improvement research are multiple problems that arise when electroosmosis forces affect Buongiorno’s nanofluid in a complicated peristaltic tapered channel. Thermal energy and temperature gradients cause nanoparticles to migrate randomly, affecting flow efficiency and irreversibility. Sometimes the infected veins generate complex peristaltic waves on its walls. The mathematical model that characterizes the motion of Jeffrey magnetohydrodynamic Buongiorno’s nanofluid inside a complex tapered peristaltic channel, considering the effects of electroosmotic forces, is discussed. The long wavelength and low Reynolds numbers approximation is considered. The approximate solution of the nonlinear system of partial differential formulas is obtained using the Adomian decomposition method. Also, the irreversibility of the system and entropy generation are being studied. Flow characteristics with biophysical and thermal parameters are plotted and discussed. The improvement in the interstitial distances that make up the nanofluid in turn enhances the Bejan numbers. So, one of the important results is that when the increment of Brownian motion and thermophoresis of the nanoparticles, the Bejan numbers are raised significantly. Both the Jeffrey parameter and Debye–Huckel parameter work to upsurge the loss of kinetic energy within the molecules, which reduces the temperatures inside the nanofluid and thus reduces the entropy rate, in contrast to the rest of the parameters that raise the kinetic energy inside the molecules that make up the nanofluid.
Study protocol: randomized phase III trial of neo-adjuvant and adjuvant chemotherapy vs. immediate surgery and adjuvant chemotherapy for localized soft tissue sarcoma: Japan Clinical Oncology Group study JCOG2102 (NACLESS)
Authors: Funauchi Yuki , Tsukushi Satoshi , Hiraga Hiroaki , Sakamoto Akio , Kunisada Toshiyuki , Nagano Akihito , Hiraoka Koji , Kikuta Kazutaka , Yonemoto Tsukasa , Ae Keisuke , Kawai Akira , Endo Makoto , Sano Yusuke , Machida Ryunosuke , Sekita Tetsuya , Fukuda Haruhiko , Oda Yoshinao , Ozaki Toshifumi , Tanaka Kazuhiro ,   JCOG Bone Soft Tissue Tumor Study Group
Published: November 2024

The optimal timing of surgery and the number of courses of perioperative chemotherapy for high-risk soft tissue sarcoma patients are still controversial. Tumour growth during neoadjuvant chemotherapy led to limb amputation in some patients. This study aims to confirm the non-inferiority of surgery and three courses of adjuvant chemotherapy with adriamycin (30 mg/m2, days 1 and 2) plus ifosfamide (2 g/m2, days 1–5) compared with our standard treatment of three courses of neoadjuvant chemotherapy and surgery followed by two courses of adjuvant chemotherapy with adriamycin plus ifosfamide for localized high-risk soft tissue sarcoma patients. This is a multi-center, two-arm, open-label, randomized phase III trial. The primary aim is to confirm the non-inferiority in overall survival (margin: hazard ratio of 1.61). This is the first randomized controlled trial to compare neoadjuvant chemotherapy and immediate surgery for soft tissue sarcoma. This trial was initiated on 16 November 2022 and registered with the Japan Clinical Trials Registry (jRCTs031220446).
Entomological surveillance of container-breeding mosquitoes focusing on Aedes (Stegomyia) (Diptera: Culicidae) vectors along altitudinal range in Nepal
Authors: Sukupayo Punya Ram , Poudel Ram Chandra , Ghimire Tirth Raj
Published: November 2024

Mosquitoes are a significant public health concern due to their role in transmitting various diseases. This study aimed to investigate mosquitoes’ diversity, abundance, and ecological aspects, mainly focusing on Aedes (Diptera: Culicidae) mosquitoes, in central Nepal. The research explored variations across regions, seasons, altitudes, and years. Fieldwork for mosquito collection was conducted between May 2022 and October 2023. Dipping and pipetting methods were employed to collect larvae and pupae, whereas Biogents-Mosquitaire trap captured adult mosquitoes. A total of 7,223 (3,640 larvae and 3,583 adults) mosquitoes, belonging to 8 genera and 18 species, were collected and analyzed. Additionally, a survey examined 5,941 wet containers of 20 different types to assess potential breeding sites. The study revealed Culex pipiens (Linnaeus, 1758) (34.13%) and Aedes albopictus (Skuse, 1895) (27.36%) as the most abundant species. Interestingly, larvae were predominantly Aedes spp. (66.13%), whereas only 13.76% of adults belonged to this genus. Mosquito abundance varied across locations and altitudes, with Siwalik region (331–700 m asl) exhibiting the highest numbers. The monsoon season showed the highest overall abundance (1,492). Used tires were identified as significant breeding sites for Aedes mosquitoes, and infestation rates were higher in shaded containers. Seasonal analysis showed the House Index (HI) reaching its peak (10.92%) and the Breteau Index (BI) reaching 23.08% during the monsoon. Conversely, the Container Index (CI) reached its highest point (37.67%) in the post-monsoon season. The results emphasize the need for comprehensive disease prevention strategies at local and national levels, including public awareness campaigns, to address mosquito-borne illnesses in this famous tourist region.
Sexual function and satisfaction in young women with breast cancer: a 5-year prospective study
Authors: Ferrigno Guajardo Ana , Vaca-Cartagena Bryan F , Mesa-Chavez Fernanda , Platas Alejandra , Fonseca Alan , Cruz-Ramos Marlid , Miaja Avila Melina , Rodriguez Ana Laura , Cabrera-Galeana Paula , Mohar Alejandro , Villarreal-Garza Cynthia
Published: November 2024

Background

Young women with breast cancer (YWBC) face unique challenges that can affect their sexual health. This study aimed to identify factors associated with sexual activity, function, and satisfaction in YWBC up to 5 years postdiagnosis.

Methods

We conducted a prospective cohort study of 474 women 40 years of age or younger diagnosed with nonmetastatic breast cancer in Mexico. Sexual function and satisfaction were assessed using the Female Sexual Function Index and the Sexual Satisfaction Inventory, respectively. Factors associated with sexual health outcomes were examined using mixed-effects models.

Results

The prevalence of sexual dysfunction increased from 33.6% at baseline to 52.9% at 4-5 years postdiagnosis. Factors associated with worse sexual function included older age (mean predicted FSFI score = −1.35, P = .037), treatment-induced amenorrhea (−2.86, P < .001), depression (−4.11, P < .001), and anxiety (−2.13, P < .001). Lower sexual satisfaction was associated with lower educational attainment (mean predicted SSI score = −5.61, P = .002), being single (−6.41, P < .001), treatment-induced amenorrhea (−3.76, P = .004), bilateral oophorectomy (−8.21, P = .017), depression (−11.29, P < .001), and anxiety (−7.50, P < .001). Quality of life, body image, and systemic therapy side effects significantly affected both outcomes. Three distinct trajectories of sexual function were identified: high (62.2%), intermediate (24.3%), and markedly declining (13.5%). Four trajectories of sexual satisfaction were found, ranging from intermediate-to-high (57.3%) to progressively worsening (27.5%).

Conclusion

Sexual dysfunction is prevalent and persistent among YWBC. Multiple biological, psychological, and social factors influence sexual health outcomes in this population. These findings highlight the importance of routine screening and tailored interventions to address the sexual health of YWBC throughout survivorship.
Surgical management of delayed mucosal cyst after rhinoplasty: a case report
Authors: Kubilay Utku , Yaramis Huseyin Berk
Published: November 2024

Mucosal cysts are rare late complications of rhinoplasty, appearing anywhere from weeks to years post-surgery. The cyst’s location can cause both cosmetic and functional issues. Definitive treatment requires complete surgical excision of the cyst and its capsule to prevent recurrence. A 32-year-old man presented with a 2 × 2-cm painless, soft nasal mass 3 years after open rhinoplasty. The mass had gradually enlarged over 6 months, leading to breathing difficulties. Physical examination revealed a pollybeak deformity. Imaging confirmed a well-defined cystic lesion. The cyst was excised through an open rhinoplasty approach, followed by reconstruction using a costal cartilage graft. The postoperative period was uneventful, with no recurrence or issues at 12 months follow-up. We highlight the importance of meticulous surgical techniques in rhinoplasty to reduce mucosal cyst formation. For cysts >1 cm, open rhinoplasty is preferred due to better reconstruction and lower recurrence rates.
Cosmology in modified f (𝒢) gravity: a late-time cosmic phenomena
Authors: Lohakare Santosh V , Niyogi Soumyadip , Mishra B
Published: November 2024

In this work, we present a method for numerically solving the Friedmann equations of modified $f(\mathcal {G})$ gravity in the presence of pressureless matter. This method enables us to predict the redshift behaviour of the Hubble expansion rate. To evaluate the credibility of the model, we applied a Bayesian MCMC technique using late-time cosmic observations to impose limitations on the free parameters of the Gauss–Bonnet model. Our results suggest that the $f(\mathcal {G})$ model can reproduce the low-redshift behaviour of the standard Lambda cold dark matter ($\Lambda$CDM) model, but there are significant differences at high redshifts, leading to the absence of a standard matter-dominated epoch. We also examined the profiles of cosmographic parameters using the model parameter values from the standard range to verify the intermediate epochs. Our analysis shows that the highly promising $f(\mathcal {G})$ model is a feasible candidate for explaining the current epochs. We presented a dynamical system analysis framework to examine the stability of the model. Our study identified critical points depicting various phases of the Universe and explained the evolutionary epochs. We demonstrated that the model effectively captures the evolution of energy components over cosmic time, supporting its validity as an alternate explanation for the observed acceleration of the Universe.
Hawai‘i Supernova Flows: a peculiar velocity survey using over a Thousand Supernovae in the near-infrared
Authors: Do Aaron , Shappee Benjamin J , Tonry John L , Tully R Brent , de Jaeger Thomas , Rubin David , Ashall Chris , Burns Christopher R , Desai Dhvanil D , Hinkle Jason T , Hoogendam Willem B , Huber Mark E , Jones David O , Mandel Kaisey S , Payne Anna V , Peterson Erik R , Scolnic Dan , Tucker Michael A
Published: November 2024

We introduce the Hawai‘i Supernova Flows project and present summary statistics of the first 1217 astronomical transients observed, 668 of which are spectroscopically classified Type Ia Supernovae (SNe Ia). Our project is designed to obtain systematics-limited distances to SNe Ia while consuming minimal dedicated observational resources. To date, we have performed almost 5000 near-infrared (NIR) observations of astronomical transients and have obtained spectra for over 200 host galaxies lacking published spectroscopic redshifts. In this survey paper, we describe the methodology used to select targets, collect/reduce data, calculate distances, and perform quality cuts. We compare our methods to those used in similar studies, finding general agreement or mild improvement. Our summary statistics include various parametrizations of dispersion in the Hubble diagrams produced using fits to several commonly used SN Ia models. We find the lowest dispersions using the SNooPy package’s EBV_model2, with a root mean square deviation of 0.165 mag and a normalized median absolute deviation of 0.123 mag. The full utility of the Hawai‘i Supernova Flows data set far exceeds the analyses presented in this paper. Our photometry will provide a valuable test bed for models of SN Ia incorporating NIR data. Differential cosmological studies comparing optical samples and combined optical and NIR samples will have increased leverage for constraining chromatic effects like dust extinction. We invite the community to explore our data by making the light curves, fits, and host galaxy redshifts publicly accessible.
Iron-sulfur cluster-dependent enzymes and molybdenum-dependent reductases in the anaerobic metabolism of human gut microbes
Authors: Zahn Leah E , Gannon Paige M , Rajakovich Lauren J
Published: November 2024

Metalloenzymes play central roles in the anaerobic metabolism of human gut microbes. They facilitate redox and radical-based chemistry that enables microbial degradation and modification of various endogenous, dietary, and xenobiotic nutrients in the anoxic gut environment. In this review, we highlight major families of iron-sulfur (Fe–S) cluster-dependent enzymes and molybdenum cofactor-containing enzymes used by human gut microbes. We describe the metabolic functions of 2-hydroxyacyl-CoA dehydratases, glycyl radical enzyme activating enzymes, Fe–S cluster-dependent flavoenzymes, U32 oxidases, and molybdenum-dependent reductases and catechol dehydroxylases in the human gut microbiota. We demonstrate the widespread distribution and prevalence of these metalloenzyme families across 5000 human gut microbial genomes. Lastly, we discuss opportunities for metalloenzyme discovery in the human gut microbiota to reveal new chemistry and biology in this important community.
Design of a Trustworthy Cloud-Native National Digital Health Information Infrastructure for Secure Data Management and Use
Authors: Zao John Kar-Kin , Wu Joseph Tsung-Shu , Kanyimbo Kennedy , Delizy Florian , Gan Tchin-Tze , Kuo Hung-I , Hsia Chih-Hao , Lo Chuan-Hsi , Yang Shang-Hui , Richard Clément Jean Alexandre , Rajab Billy , Monawe Maganizo , Kamanga Blessings , Mtambalika Nikotelhe , Yu Kwong-Leung Joseph , Chou Chih-Feng , Neoh Choo-Aun , Gallagher Joseph , O'Donoghue John , Mtegha Rebecca , Lee Hsin-Yi , Mbewe Alinafe
Published: November 2024

Since 2022, Malawi Ministry of Health (MoH) designated the development of a National Digital Health Information System (NDHIS) as one of the most important pillars of its national health strategy. This system is built upon a distributed computing infrastructure employing the following state-of-art technologies: (i) digital healthcare devices to capture medical data; (ii) Kubernetes-based Cloud-Native Computing architecture to simplify system management and service deployment; (iii) Zero-Trust Secure Communication to protect confidentiality, integrity and access rights of medical data transported over the Internet; (iv) Trusted Computing to allow medical data to be processed by certified software without compromising data privacy and sovereignty. Trustworthiness, including reliability, security, privacy and business integrity, of this system was ensured by a peer-to-peer network of trusted medical information guards deployed as the gatekeepers of the computing facility on this system. This NDHIS can facilitate Malawi to attain universal health coverage by 2030 through its scalability and operation efficiency. It shall improve medical data quality and security by adopting a paperless approach. It will also enable MoH to offer data rental services to healthcare researchers and AI model developers around the world. This project is spearheaded by the Digital Health Division (DHD) under MoH. The trustworthy computing infrastructure was designed by a taskforce assembled by the DHD in collaboration with Luke International in Norway, and a consortium of hardware and software solution providers in Taiwan. A prototype that can connect community clinics with a district hospital has been tested at Taiwan Pingtung Christian Hospital.
Commentary on ‘the interplay of the innovation cycle, build time, lifetime, and deployment rate of new energy technologies: a case study of nuclear fusion energy’ designing innovation strategies for rapid feasible technological change
Authors: Jewell Jessica
Published: November 2024

How fast can new technologies come online and what is the most effective policy strategy to accelerate their growth? A recent article by Lopes Cardozo and Ward contribute to shedding light on this very interesting question particularly tricky to answer for technologies which are not yet commercial. Taking the case of nuclear fusion, the authors aim to identify the best innovation strategy for the technology. They embed this analysis in a useful concept of a `forced transition' which echoes the general belief that energy transitions will need to be driven by policies rather than pure market forces. Their work introduces two significant theoretical advances: the Fastest Feasible Growth (FFG) model and foregrounding generational changes for analyzing technological deployment. While the authors' insights offer valuable contributions to both growth modeling and experience curve analysis, their work raises important questions for future research. These include the empirically validating of the relationship between technological generations and growth; identifying the conditions under which technological expansion would be faster then their FFG model; the duration of the exponential growth phase; the applicability of the model beyond the global scale; and conceptualising technological generations.
An undiscovered circadian clock to regulate phytoplankton photosynthesis
Authors: Su Yixi , Hu Jingyan , Xia Mengsheng , Chen Jiwei , Meng Weizhao , Qian Cheng , Shu Yuexuan , Wang Chao , Wang Xianwei , Salehi-Ashtiani Kourosh , Brynjólfsson Sigurður , Lin Jianping , Li Yongquan , Zhang Haisheng , Wang Lizhong , Fu Weiqi
Published: November 2024

Circadian clocks exist in all types of organisms and coordinate key biological processes, e.g. photosynthesis in phytoplankton (microalgae) and land plants. We asked whether a circadian rhythm sustains in phytoplankton when living under constant illumination without environmental cues. Here, we report the first transcriptomic architecture of persistent oscillatory gene expression in the model marine diatom, Phaeodactylum tricornutum living under constant illumination and temperature without environmental cues. We show that cyclic expression of a considerable number of genes involved in light harvesting and carbon fixation sustained after 24 h of constant illumination (free-running), which could pose additional constraints on cell growth under constant light conditions. Over long-term adaptation to constant illumination, the majority of the rhythmic genes identified under diel light conditions lose their oscillatory expression in the absence of external entrainers, and the genes potentially controlled by persistent circadian clocks are primarily involved in transcriptional regulation and cell division. We find constant illumination leads to an increased average expression of transcription factors and cell division genes, while genes involved in the Calvin–Benson cycle and pigment biosynthesis are kept at low expression levels, which plays a role in the down-regulation of photosynthetic efficiency. By manipulation of the dark rest period, we confirm a fine-tuned light/dark cycle could dramatically improve photosynthetic efficiency in microalgae. Our results unveil a novel persistent circadian rhythm on photosynthetic regulation in marine phytoplankton and provide critical insights into the interaction between environmental signals and inheritable internal circadian clocks in diatoms.
Over-the-scope clips for Nonvariceal upper gastrointestinal bleeding: a systematic review and meta-analysis of randomized studies
Authors: Ni Yuanzhi , Ali Kamran , Tang Penghao , Hayat Khizar , Cheng Zhiwen , Xu Benfeng , Qin Zhiwen , Zhang Wu
Published: November 2024

Background & Aims

Nonvariceal upper gastrointestinal bleeding (NVUGIB) is a common and potentially life-threatening condition. Over-the-scope clips (OTSCs) have emerged as a promising endoscopic treatment option for NVUGIB. We aimed to analyze the efficacy and safety of OTSCs compared to standard endoscopic treatments (ST) in patients with NVUGIB.

Methods

We conducted a comprehensive search of PubMed, Embase, Scopus, and Cochrane Library databases from inception to June 2024 for randomized controlled trials (RCTs) comparing OTSCs with ST for NVUGIB. The primary outcomes were initial hemostasis and persistent bleeding. Secondary outcomes included rebleeding rates, mortality, hospital stays and others. Pooled odds ratios (ORs) with 95% confidence intervals (CIs) were calculated using random/fixed-effects models.

Results

Six RCTs involving 621 patients were included in the meta-analysis. OTSCs demonstrated significantly higher initial hemostasis (OR 4.80, 95% CI 1.78–12.96; P = 0.002) and lower persistent bleeding rates (OR 0.17, 95% CI 0.05–0.56; P = 0.003) compared to ST group. The rebleeding rate was significantly lower in the OTSC group 7-days re-bleeding (OR 0.27, 95% CI 0.14–0.53; P = 0.001); 30-days rebleeding (OR 0.40, 95%CI 0.22, 0.70; P = 0.002). No significant differences were observed in mortality (OR 0.65, 95% CI 0.31–1.33; P = 0.38) and hospital stay (mean difference 0.79 days 95%CI -0.57, 2.15) between the two groups.

Conclusions

OTSCs are more effective than ST for achieving hemostasis and preventing rebleeding in patients with NVUGIB, without increasing mortality.

Key message What is Already Known  Previous studies have shown that nonvariceal upper gastrointestinal bleeding (NVUGIB) is a serious medical condition that needs effective endoscopic interventions. The success rates of standard treatments for achieving hemostasis and preventing rebleeding are not consistent. What This Study Adds  According to this study, over-the-scope clips (OTSCs) have the same mortality rate as standard endoscopic treatments, but they significantly improve initial hemostasis and lower rebleeding rates. Impact on Research, Practice, or Policy  The findings support the use of OTSCs as a preferred intervention for NVUGIB, which could affect clinical guidelines and encourage additional research focused on improving endoscopic techniques and patient outcomes in the management of gastrointestinal bleeding.
CONTExT-RA: a cross-sectional study evaluating disease activity, quality of life and the socio-demographic profile of Irish patients with rheumatoid arthritis
Authors: Murphy Grainne , O’Rourke Killian , Camon Angela , Kane David , O’Shea Finbar , Conway Richard , Sheehy Claire , Saddiq Moneeb , Moran Deirdre
Published: November 2024

Objectives

CONTExT-RA is a cross-sectional, non-interventional multicentre study which enrolled patients diagnosed with RA and receiving DMARD treatment in a secondary care setting. The study evaluated disease control and associated disease burden amongst this Irish population.

Methods

Patients with RA attending six Irish rheumatology centres were invited to participate. Each consented patient attended a single routine study visit. Disease activity was assessed using Clinical Disease Activity Index (CDAI). The primary endpoint was EuroQol-5 dimensions (EQ-5D-5L) stratified by CDAI, compared using a non-parametric Wilcoxon Rank-Sum test.

Results

130 patients were included. Using CDAI, 34 (26.2%) patients were in clinical remission (CR), 42 (32.3%) had low disease activity (LDA), 41 (31.5%) had moderate disease activity (MDA) and 13 (10.0%) had high disease activity (HDA). QoL (EQ-5D-5L index (median)) scores were significantly (P < 0.001) greater for patients in CR or CR/LDA than for those with MDA/HDA, 0.866 (0.920), 0.777 (0.822) vs 0.578 (0.691), respectively. Patients in CR reported higher levels of work productivity, mean (s.d.) rating of 1.7 (2.52) vs those in MDA/HDA of 4.2 (3.28) (higher rating indicates greater impairment). Similar findings were observed for non-work-related activities.

Conclusion

Disease control for many patients with RA, treated in secondary care in Ireland, is sub-optimal with only 1 in 4 in CDAI remission. The impact of poor disease control on QoL is significant, and the superior outcomes for patients in CR provide compelling evidence that by achieving greater disease control, the burden of disease on patients can be greatly reduced.
Interrater reliability of RheuMetric checklist scales for physician global assessment, inflammation, damage and patient distress
Authors: Schmukler Juan , Castrejon Isabel , Li Tengfei , Block Joel A , Pincus Theodore
Published: November 2024

Objective

To analyse interrater reliability of four RheuMetric checklist 0–10 visual numerical scales (VNSs) of physician global assessment (DOCGL), inflammation or reversible findings (DOCINF), organ damage or irreversible findings (DOCDAM) and patient distress or findings explained by fibromyalgia, depression or anxiety (DOCDIS).

Methods

A retrospective study was performed of data from a rheumatology fellows’ continuity clinic at Rush University. Each rheumatology patient seen in routine care with any diagnosis completed a multidimensional health assessment questionnaire (MDHAQ). Both the rheumatology fellow and attending rheumatologist independently completed RheuMetric estimates at the same visit for DOCGL, DOCINF, DOCDAM, DOCDIS and the proportion of DOCGL explained by each subglobal estimate (totalling 100%). Agreement between the two assessors was compared using paired t-tests, Spearman correlation coefficients, intraclass correlation coefficients (ICCs), Lin’s concordance correlation coefficients (LCCCs) and Bland–Altman plots.

Results

In 112 patients, mean levels of DOCINF were highest in inflammatory diseases, DOCDAM in osteoarthritis (OA) and DOCDIS in primary fibromyalgia (FM). However, mean DOCDAM was as high as DOCINF in inflammatory diseases. No statistically significant differences were seen between scores from attending rheumatologists and fellows. Agreement within 2/10 ranged from 60% for DOCGL to 71% for DOICINF and DOCDAM. Spearman correlations were 0.49–0.65, ICCs were 0.46–0.63 and LCCCs were 0.46–0.62 between rheumatologist and fellow, indicating moderate agreement; reliability was slightly higher for each subglobal VNS than for DOCGL.

Conclusion

RheuMetric 0–10 DOCGL, DOCINF, DOCDAM and DOCDIS have moderate interrater reliability and are feasible in routine care to estimate patient status beyond DOCGL for improved management decisions.
A virus associated with the zoonotic pathogen Plasmodium knowlesi causing human malaria is a member of a diverse and unclassified viral taxon
Authors: Petrone Mary E , Charon Justine , Grigg Matthew J , William Timothy , Rajahram Giri S , Westaway Jacob , Piera Kim A , Shi Mang , Anstey Nicholas M , Holmes Edward C
Published: November 2024

The Apicomplexa are a phylum of single-celled eukaryotes that can infect humans and include the mosquito-borne parasite Plasmodium, the cause of malaria. Viruses that infect non-Plasmodium spp. disease-causing protozoa affect the pathogen life cycle and disease outcomes. However, only one RNA virus (Matryoshka RNA virus 1) has been identified in Plasmodium, and none have been identified in zoonotic Plasmodium species. The rapid expansion of the known RNA virosphere via metagenomic sequencing suggests that this dearth is due to the divergent nature of RNA viruses that infect protozoa. We leveraged newly uncovered data sets to explore the virome of human-infecting Plasmodium species collected in Sabah, east (Borneo) Malaysia. From this, we identified a highly divergent RNA virus in two human-infecting P. knowlesi isolates that is related to the unclassified group ‘ormycoviruses’. By characterizing 15 additional ormycoviruses identified in the transcriptomes of arthropods, we show that this group of viruses exhibits a complex ecology as noninfecting passengers at the arthropod–mammal interface. With the addition of viral diversity discovered using the artificial intelligence–based analysis of metagenomic data, we also demonstrate that the ormycoviruses are part of a diverse and unclassified viral taxon. This is the first observation of an RNA virus in a zoonotic Plasmodium species. By linking small-scale experimental data to advances in large-scale virus discovery, we characterize the diversity and confirm the putative genomic architecture of an unclassified viral taxon. This approach can be used to further explore the virome of disease-causing Apicomplexa and better understand how protozoa-infecting viruses may affect parasite fitness, pathobiology, and treatment outcomes.
Hierarchical meta-porous materials as sound absorbers
Authors: Kuznetsova Svetlana , Deleplanque Samuel , Allein Florian , Dubus Bertrand , Miniaci Marco
Published: November 2024

The absorption of sound has great significance in many scientific and engineering applications, from room acoustics to noise mitigation. In this context, porous materials have emerged as a viable solution towards high absorption performance and lightweight designs. However, their performance is somewhat limited in the low-frequency regime. Inspired by the concept of recursive patterns over multiple length scales, typical of many natural materials, here, we propose a hierarchical organization of multilayered porous media and investigate their performance in terms of sound absorption. Two types of designs are considered: a hierarchical periodic (HP) and a hierarchical gradient (HG). In both cases, it is found that in some frequency ranges the introduction of multiple levels of hierarchy simultaneously allows for: (i) an increase in the level of absorption compared with the corresponding bulk block of porous material (or to the previous hierarchical levels (HLs)), and (ii) a reduction in the quantity of porous material required. Another advantage of using this approach is on the fabrication, since only one porous material is required. The performances are examined for both normal and oblique incidences, as well as for different values of the static air-flow resistivity. The methodological approach is based on the transfer-matrix method, optimization algorithms such as the metaheuristic greedy randomized adaptive search procedure (GRASP), finite-element calculations and measurements performed in an impedance tube.
Periodic dynamics in viscous fingering
Authors: Lawless Jack , Hazel Andrew , Juel Anne
Published: November 2024

The displacement of a viscous liquid by air inside a Hele-Shaw channel is an archetype for nonlinear pattern-forming systems. Typically, bubbles or fingers of air propagate steadily at low values of the capillary number

Ca

=
μ

U
*

/
σ

, where

μ

is the viscosity of the liquid,

U
*

is the speed of the bubble or finger and

σ

is the surface tension at the air–liquid interface. However, as the capillary number increases, the advancing interface can exhibit disordered pattern-forming dynamics. We demonstrate experimentally that a sustained, remote perturbation of the bubble tip can drive time-periodic dynamics. We exploit the propensity of a group of bubbles to propagate in steady spatial arrangements inside a Hele-Shaw channel with a centralized depth-reduction to apply a sustained pressure perturbation ahead of the bubble as it propagates. The oscillation cycle is initiated by the splitting of the bubble tip, via the Saffman–Taylor instability, which is promoted by the local flow-field conditions. The restoral of the bubble tip follows naturally because the system is driven by a fixed flow rate and the perturbed bubble is attracted to the weakly unstable, steadily propagating state that is set by the ratio of imposed viscous and capillary forces. The splitting and restoral mechanisms do not rely on the specific perturbation used in this study, suggesting a generic mechanism for periodic dynamics of propagating curved fronts subject to steady flow-field perturbations.
Resistance to age-related hearing loss in the echolocating big brown bat (
Eptesicus fuscus
)
Authors: Capshaw Grace , Diebold Clarice A. , Adams Danielle M. , Rayner Jack G. , Wilkinson Gerald S. , Moss Cynthia F. , Lauer Amanda M.
Published: November 2024

Hearing mediates many behaviours critical for survival in echolocating bats, including foraging and navigation. Although most mammals are susceptible to progressive age-related hearing loss, the evolution of biosonar, which requires the ability to hear low-intensity echoes from outgoing sonar signals, may have selected against the development of hearing deficits in bats. Many echolocating bats exhibit exceptional longevity and rely on acoustic behaviours for survival to old age; however, relatively little is known about the ageing bat auditory system. In this study, we used DNA methylation to estimate the ages of wild-caught big brown bats (
Eptesicus fuscus
) and measured hearing sensitivity in young and ageing bats using auditory brainstem responses (ABRs) and distortion product otoacoustic emissions (DPOAEs). We found no evidence for hearing deficits in bats up to 12.5 years of age, demonstrated by comparable thresholds and similar ABR and DPOAE amplitudes across age groups. We additionally found no significant histological evidence for cochlear ageing, with similar hair cell counts, afferent and efferent innervation patterns in young and ageing bats. Here, we demonstrate that big brown bats show minimal evidence for age-related hearing loss and therefore represent informative models for investigating mechanisms that may preserve hearing function over a long lifetime.
Investigating the hemiretinal asymmetry in emotion processing as a function of spatial frequency
Authors: Moses Eleanor , Yu Zhou , Taubert Jessica , Pegna Alan J.
Published: November 2024

The subcortical visual pathway to the amygdala has long been considered a rapid and crude stream for processing emotionally salient information that is reliant on low spatial frequency (LSF) information. Recently, research has called this LSF dependency into question. To resolve this debate, we take advantage of an anatomical hemiretinal asymmetry, whereby the nasal hemiretina sends a higher proportion of information through the subcortical pathway than the temporal hemiretina. We recorded brain activity using electroencephalography (EEG) in human participants (N= 40) while they completed a monocular viewing paradigm. Pairs of faces (one fearful and one neutral, or both neutral) were projected simultaneously to the nasal and temporal hemiretina in three contrast-equated blocks; faces filtered to display only (i) LSF, (ii) high spatial frequency (HSF), or (iii) unfiltered information (broadband spatial frequency; BSF). BSF fearful faces were found to produce a greater naso-temporal asymmetry, with greater N170 amplitudes evoked by BSF faces in the nasal field, compared to HSF faces. Conversely, the naso-temporal asymmetry for LSF fearful faces did not differ between BSF and HSF. Collectively, these findings provide crucial evidence that the subcortical pathway carries combined spatial frequency visual signals, with a potential bias against HSF content.
Present and future suitability of invasive and urban vectors through an environmentally driven mosquito reproduction number
Authors: Pardo-Araujo Marta , Eritja Roger , Alonso David , Bartumeus Frederic
Published: November 2024

Temperature and water availability significantly influence mosquito population dynamics. We have developed a method, integrating experimental data with insights from mosquito and thermal biology, to calculate the basic reproduction number (

R
M

) for urban mosquito species
Aedes albopictus
and
Aedes aegypti
.

R
M

represents the number of female mosquitoes produced by one female during her lifespan, indicating suitability for growth. Environmental conditions, including temperature, rainfall and human density, influence

R
M

by altering key mosquito life cycle traits. Validation using data from Spain and Europe confirms the approach’s reliability. Our analysis suggests that temperature increases may not uniformly benefit
Ae. albopictus
proliferation but could boost
Ae. aegypti
expansion. We suggest using vector

R
M

maps, leveraging climate and environmental data, to predict areas susceptible to invasive mosquito population growth. These maps aid resource allocation for intervention strategies, supporting effective vector surveillance and management efforts.
Diversity and plant growth-promoting traits of endophytic bacteria isolated from maize cropped in organic and low-input agricultural systems in southern Brazil
Authors: Fagotti Dafila Santos Lima , Fukami Josiane , Cerezini Paula , Martinez Oliveira Andre Luiz , Andrade Galdino , Klepa Milena , Ferraz Helene Luisa Carolina , Chueire Ligia Maria Oliveira , Ribeiro Renan Augusto , Hungria Mariangela , Nogueira Marco Antonio
Published: November 2024

Plant growth-promoting bacteria (PGPB) may enhance plant growth and health through several mechanisms, contributing for sustainable agriculture. We isolated and characterized endophytic bacteria from stems of landrace maize (Zea mays L.) grown under low-input and organic systems in southern Brazil. The 16S rRNA analysis revealed 83 isolates within 14 genera, including α-Proteobacteria, β-Proteobacteria, γ-Proteobacteria, Actinomycetia, and Bacilli classes. The synthesis of indolic compounds was widespread among the strains, as well as the enhancement of N concentration in N-free media, a putative capacity for biological nitrogen fixation. Phosphate solubilization prevailed in Burkholderia and Paraburkholderia strains, while siderophores production was observed in all genera, except Microbacterium. Inoculation with selected strains confirmed growth-promotion on maize plantlets, particularly Sphingomonas sp. CNPSo 2378 and Bacillus velezensis CNPSo 2384, whose genomes were sequenced and revealed PGPB features and evolutionary relationships, shedding light on the diversity, functional traits, and occurrence in low-input and organic agricultural systems.

Data summary

The 16S rRNA gene sequences have been deposited in the NCBI GenBank database, with accession numbers provided in supplementary material (Table S1). The genomic sequences have also been deposited in the GenBank database, with the following accession numbers: JAXCMJ000000000 for CNPSo 2378 and JAXCMK000000000 for CNPSo 2384. Raw data on the effects of bacterial isolates on the plant growth-promoting of maize plantlets are available at figshare database, with the following DOI: 10.6084/m9.figshare.27610290.
Functional determinants and evolutionary consequences of pleiotropy in complex and Mendelian traits
Authors: Barbitoff Yury A. , Bogaichuk Polina M. , Pavlova Nadezhda S. , Predeus Alexander V.
Published: November 2024

Pleiotropy, a phenomenon of multiple phenotypic effects of the same genetic alteration, is one of the most important features of genotype-to-phenotype networks. Over the last century, biologists have actively debated the prevalence, mechanisms, and consequences of pleiotropy. In this work, we employed data on genotype-to-phenotype associations from the Human Phenotype Ontology and Mouse Genome Database, as well as genome-wide associations from the UK Biobank cohort to investigate the similarities and dissimilarities in the patterns of pleiotropy between species and different trait types (i.e., Mendelian traits and complex traits). We found that the pleiotropic effects of genes correlate well between species, but have a much weaker correlation when different data sources are compared for the same species. In all cases, however, highly pleiotropic genes possessed a common set of features, such as the broad expression across tissues, involvement in many biological processes, or a high number of protein-protein interactions of the respective gene products. Furthermore, we observed a universal tendency of highly pleiotropic genes to be under greater negative selection pressure combined with a significant enrichment of recent positive selection signals at pleiotropic loci. Taken together, our results pinpoint a common mechanism underlying pleiotropic effects in different trait domains, and suggest that high degree of pleiotropy plays a role in adaptation, despite imposing additional constraint on genetic variation.
DistortCorrect Stitcher: Microscopy Image Stitching with Integrated Optical Distortion Correction
Authors: Cang Hu , Fan Huaxun , Sun Sha , Zhang Kai
Published: November 2024

The rapidly advancing field of imaging-based spatial transcriptomics demands microscopy images with larger fields of view (FOV) and high spatial resolution to accurately and efficiently quantify RNA molecules at the single-cell level. This challenge requires advanced image processing algorithms to seamlessly stitch multiple microscopic images while overcoming the inherent FOV limitations of microscopes. However, image stitching accuracy is often compromised by optical distortions, which are typically uncorrected or require cumbersome hardware-based calibration. Here, we present DistortCorrect Stitcher, a powerful software package that simultaneously estimates and corrects optical distortion during the stitching process. By iteratively integrating image stitching with distortion correction, our method significantly enhances alignment accuracy without relying on external calibration, providing a robust solution for processing spatial transcriptomics data. DistortCorrect Stitcher maintains high stitching fidelity across large tissue areas, ensuring that the molecular data remain reliable and biologically meaningful. This integrated approach has broad implications for improving spatial biology analysis and enabling more accurate high-throughput assays, thereby accelerating advancements in the field.
GreedyMini: Generating low-density DNA minimizers
Authors: Golan Shay , Tziony Ido , Kraus Matan , Orenstein Yaron , Shur Arseny
Published: November 2024

Minimizers is the most populark-mer selection scheme in algorithms and data structures analyzing high-throughput sequencing (HTS) data. In a minimizers scheme, the smallestk-mer by some predefined order is selected as the representative of a sequence window containingwconsecutivek-mers, which results in overlapping windows often selecting the samek-mer. Minimizers that achieve the lowest frequency of selectedk-mers over a random DNA sequence, termed the expected density, are desired for improved performance of HTS analyses. Yet, no method to date exists to generate minimizers that achieve minimum expected density. Moreover, forkandwvalues used by common HTS algorithms and data structures there is a gap between the densities achieved by existing selection schemes and a recent theoretical lower bound. Here, we presentGreedyMini, a toolkit of methods to generate minimizers with low expected or particular density, to improve minimizers, to extend minimizers to larger alphabets,k, andw, and to measure the expected density of a given minimizer efficiently. We demonstrate over various combinations ofkandwvalues, including those of popular HTS methods, thatGreedyMinican generate DNA minimizers that achieve expected densities very close to the lower bound, and both expected and particular densities much lower compared to existing selection schemes. Additionally, we show that thek-mer rank-retrieval time byGreedyMiniis comparable to that of commonk-mer hash functions. We expectGreedyMinito improve the performance of many HTS algorithms and data structures and advance the research ofk-mer selection schemes.
To impute or not to impute in untargeted metabolomics - that is the compositional question
Authors: Krutkin Dennis Dimitri , Thomas Sydney , Zuffa Simone , Rajkumar Prajit , Knight Rob , Dorrestein Pieter C. , Kelley Scott T.
Published: November 2024

Untargeted metabolomics often produce large datasets with missing values, arising from biological or technical factors, which can undermine statistical analyses and lead to biased biological interpretations. Imputation methods, such as k-Nearest Neighbors (kNN) and Random Forest (RF) regression are commonly used but their effects vary depending on the type of missing data e.g. Missing Completely At Random (MCAR) and Missing Not At Random (MNAR). Here, we determined the impacts of degree and type of missing data on the accuracy of kNN and RF imputation using two datasets: a targeted metabolomic dataset with spiked-in standards and an untargeted metabolomic dataset. We also assessed the effect of compositional data approaches (CoDA), such as the centered log-ratio (CLR) transform, on data interpretation, since these methods are increasingly being used in metabolomics.

Overall, we found that kNN and RF performed more accurately when the proportion of missing data across samples for a metabolic feature was low. However, these imputations could not handle MNAR data and generated wildly inflated values or imputed values where none should exist. Furthermore, we show that the proportion of missing values had a strong impact on the accuracy of imputation which affected the interpretation of the results. Our results suggest extreme caution should be used with imputation even with modestly levels of missing data or when the type of missingness is unknown.