bluuebunny/crossref_metadata_2025 huggingface dataset:
Global, Regional, and National Survey on Burden and Quality of Care Index (QCI) of Orofacial Clefts: Global Burden of Disease Systematic Analysis 1990–2019
Authors: Sofi-Mahmudi Ahmad , Shamsoddin Erfan , Khademioore Sahar , Khazaei Yeganeh , Tovani-Palone Marcos Roberto
Published: March 2024

Background

Orofacial clefts are the most common craniofacial anomalies that include a variety of conditions affecting the lips and oral cavity. They remain a significant global public health challenge. Despite this, the quality of care for orofacial clefts has not been investigated in global and country level.

Objective

We aimed to measure the quality of care index (QCI) for orofacial clefts worldwide.

Methods

We used the 2019 Global Burden of Disease data to create a multifactorial index (QCI) to assess orofacial clefts globally and nationally. By utilizing data on incidence, prevalence, years of life lost, and years lived with disability, we defined four ratios aimed at indirectly reflecting the quality of healthcare. Subsequently, we conducted a principal component analysis to identify the most critical variables that could account for the observed variability. The outcome of this analysis was defined as the QCI for orofacial clefts. Following this, we tracked the QCI trends among males and females worldwide, across various regions and countries, considering factors such as the socio-demographic index and World Bank classifications.

Results

Globally, the QCI for orofacial clefts exhibited a consistent upward trend from 1990 to 2019 (66.4 to 90.2) overall and for females (82.9 to 94.3) and males (72.8 to 93.6). In the year 2019, the top five countries with the highest QCI scores were as follows: Norway (QCI=99.9), Ireland (99.4), France (99.4), Germany (99.3), the Netherlands (99.3), and Malta (99.3). Conversely, the five countries with the lowest QCI scores on a global scale in 2019 were Somalia (59.1), Niger (67.6), Burkina Faso (72.6), Ethiopia (73.0), and Mali (74.4). Gender difference showed a converging trend from 1990 to 2019 (optimize gender disparity ratio (GDR): 123 vs. 163 countries), and the GDR showed a move toward optimization (between 0.95 and 1.05) in the better and worse parts of the world.

Conclusion

Despite the positive results regarding the QCI for orofacial clefts worldwide, some countries showed a slight negative trend.
Cross sectional study on behavioral determinants associated with sugary foods and beverages and its corelates with body mass index among adolescents
Authors: Gautam Laxmi , Thapa Milan , Pokhrel Poonam , Sapkota Parash Mani , Bhatt Anjali , Paudel Kiran
Published: March 2024

Background

Adolescence is the period that demands high nutrients with changes in dietary habits making them vulnerable. Foods high in calories and deficit in essential nutrients increases risk for overweight. The habits are guided by multiple factors including behavioral determinants. Therefore, this study aims to identify the status of and factors associated with behavioral determinants on adolescents in regard to sugary items.

Methods

A cross-sectional study was conducted among 768 adolescents of Nagarjun Municipality, Kathmandu from September 2022 to January 2023. This study used a multistage random sampling. The chi square test and logistic regression were applied to analyze the results in SPSS V.16 and p-value ≤ 0.05 was considered as statistically significance.

Result

Adequate level of knowledge was found among 84.11% (95% CI: 81.52 to 86.70) of the adolescents. Positive attitude was seen among 60% of the adolescents (95% CI: 56.55 to 63.49). The percentage of adolescent consuming items was 84.50% (95% CI: 81.94 to 87.07). Odds of having adequate knowledge among respondents was twice (AOR=2.05, 95% CI: 1.12 to 3.76) more likely for those who were living with their parents. Female adolescents (AOR=2.51, 95% CI: 1.61 to 3.89), whose mother are homemaker (AOR=1.99, 95% CI: 1.04 to 3.58) and father are engaged in foreign employment (AOR = 2.09, 95% CI: 1.04 to 4.21) were more likely to consume sugary items. Prevalence of overweight was seen among 6.38% (95% CI: 4.64 to 8.11) of respondents. Consumption was seen to be significant to the model overweight versus normal [OR=11.95 (95% CI: 1.61 to 88.42)].

Conclusion

Presence of adequate knowledge wasn’t the only and adequate factor for food selection. Family indulged interventions can be useful as familial factors seem to be affecting behavioral characteristics. Sugary foods and beverages are associated with overweight. Hence interventions focusing on dietary discipline is also recommended.

STRENGTHS AND LIMITATIONS OF THE STUDY

This study deviates the primary focus from range of processed foods items to sugary foods and beverages only. No such studies with sole focus on high calorie sugary foods have been found conducted in Nepal.

Study was limited to a single municipality, whose results cannot be generalized for national context. However, it can apply in case of urban settings.

Majority of the findings are based on self-reporting, which leaves enough space for under-reporting and recall bias. On the other hand, anthropometric measurements taken by research team was positive part of the study.

Difficult to gauge the impact of the findings, because weight gain in adolescence phase varies as a function of age, maturation, and growth velocity not just consumption of sugary foods and beverages.
Using electronic health records to evaluate the adherence to cervical cancer prevention guidelines: a cross-sectional study
Authors: Mooses Kerli , Šavrova Aleksandra , Pajusalu Maarja , Oja Marek , Tamm Sirli , Haug Markus , Padrik Lee , Laanpere Made , Uusküla Anneli , Kolde Raivo
Published: March 2024

Objective

The fight against cervical cancer requires effective screening together with optimal and on-time treatment along the care continuum. We aimed to examine the impact of cervical cancer screening and treatment guidelines on screening, and follow-up adherence to guidelines.

Methods

Data from electronic health records and healthcare provision claims for 50 702 women was used. The annual rates of PAP tests, HPV tests and colposcopies during two guideline periods (2nd version 2012–2014 vs 3rd version 2016–2019) were compared. To assess the adherence to guidelines, the subjects were classified as adherent, over- or undertested based on the timing of the appropriate follow-up test.

Results

The number of PAP tests decreased and HPV tests increased during the 3rd guideline period (p < 0.01). During the 3rd guideline period, among 21–29-year-old women, the adherence to guidelines ranged from 38.7% (44.4…50.1) for ASC-US to 73.4% (62.6…84.3) for HSIL, and among 30–59-year-old from 49.0% (45.9…52.2) for ASC-US to 65.7% (58.8…72.7) for ASC-H. The highest rate of undertested women was for ASC-US (21–29y: 25.7%; 30–59y: 21.9%). The rates of over-tested women remained below 12% for all cervical pathologies observed. There were 55.2% (95% CI 49.7…60.8) of 21–24-year-old and 57.1% (95% CI 53.6…60.6) of 25–29-year-old women who received an HPV test not adherent to the guidelines.

Conclusions

Our findings highlighted some shortcomings in the adherence to guidelines, especially among women under 30. The insights gained from this study helps to improve the quality of care and thus, reduce cervical cancer incidence and mortality.
Differential inclusion ofNEBexons 143 and 144 provides insight intoNEB-related myopathy variant interpretation and disease manifestation
Authors: Silverstein Sarah , Orbach Rotem , Syeda Safoora , Reghan Foley A , Gorokhova Svetlana , Meilleur Katherine G. , Leach Meganne E. , Uapinyoying Prech , Chao Katherine R , Donkervoort Sandra , Bönnemann Carsten G.
Published: March 2024

Biallelic pathogenic variants in the gene encoding nebulin (NEB) are a known cause of congenital myopathy. We present two individuals with congenital myopathy and compound heterozygous variants (NM_001271208.2: c.2079C>A; p.(Cys693Ter) and c.21522+3A>G) inNEB.Transcriptomic sequencing on patient muscle revealed that the extended splice variant c.21522+3A>G causes exon 144 skipping. Nebulin isoforms containing exon 144 are known to be mutually exclusive with isoforms containing exon 143, and these isoforms are differentially expressed during development and in adult skeletal muscles. Patients MRIs were compared to the known pattern of relative abundance of these two isoforms in muscle. We propose that the pattern of muscle involvement in these patients better fits the distribution of exon 144-containing isoforms in muscle than with previously published MRI findings inNEB-related disease due to other variants. To our knowledge this is the first report hypothesizing disease pathogenesis through the alteration of isoform distributions in muscle.
Results of a nationally representative seroprevalence survey of chikungunya virus in Bangladesh
Authors: Allen Sam W. , Dos Santos Gabriel Ribeiro , Paul Kishor K , Paul Repon , Rahman Ziaur , Alam Mohammad Shafiul , Rahman Mahmudur , Al-Amin Hasan Mohammad , Vanhomwegen Jessica , Smull Taylor , Lee Kyu Han , Gurley Emily S. , Salje Henrik
Published: March 2024

Chikungunya virus (CHIKV) is responsible for a rapidly increasing but poorly understood infection burden globally. Bangladesh experienced its first reported outbreak in 2008. Despite a number of subsequent isolated outbreaks, culminating in an enormous nationwide epidemic in 2017, very little is known about the burden or dynamics of chikungunya within the country, and the risk factors for infection. We conducted a nationally representative seroprevalence survey in 2016 in 70 randomly selected communities across the country. Individuals provided blood samples, which were tested for the presence of IgG antibodies to CHIKV. We also trapped and speciated mosquitoes. We found that 69/2,938 (2.4%) of individuals were seropositive to CHIKV. Seropositive individuals were concentrated in the centre and south of the country. We found that being seropositive to dengue virus (aOR 3.11 [95% CIs: 1.17 – 24.45]) and male sex (aOR 0.29 [95% CIs: 0.01 – 0.96]), were significantly associated with CHIKV seropositivity, however,Aedespresence, income, and travel history were not. Using a spatial prediction model, we estimate that at the time of the study, 4.99 million people in the country had been infected with CHIKV. These findings highlight high population susceptibility prior to the major outbreak in 2017 and that historic outbreaks must have been spatially isolated.
Unraveling the shared genetics of common epilepsies and general cognitive ability.
Authors: Karadag Naz , Hagen Espen , Shadrin Alexey A. , Van Der Meer Dennis , O'Connell Kevin S. , Rahman Zillur , Kutrolli Gleda , Parker Nadine , Bahrami Shahram , Fominykh Vera , Heuser Kjell , Tauboll Erik , Ueland Torill , Steen Nils Eiel , Djurovic Srdjan , Dale Anders M. , Frei Oleksandr , Andreassen Ole A. , Smeland Olav B.
Published: March 2024

Objective:Cognitive impairment is prevalent among individuals with epilepsy, and it is possible that genetic factors can underlie this relationship. Here, we investigated the potential shared genetic basis of common epilepsies and general cognitive ability (COG).Methods:We applied linkage disequilibrium score (LDSC) regression, MiXeR and conjunctional false discovery rate (conjFDR) to analyze different aspects of genetic overlap between COG and epilepsies. We used the largest available genome–wide association study data on COG (n= 269,867) and common epilepsies (n= 27,559 cases, 42,436 controls), including the broad phenotypes ′all epilepsy ′, focal epilepsies and genetic generalized epilepsies (GGE), and as well as specific subtypes. We functionally annotated the identified loci using a variety of biological resources and validated the results in independent samples.Results:Using MiXeR, COG (11.2k variants) was estimated to be almost four times more polygenic than ′all epilepsy′, GGE, juvenile myoclonic epilepsy (JME), and childhood absence epilepsy (CAE) (2.5k — 2.9k variants). The other epilepsy phenotypes were insufficiently powered for analysis. We show extensive genetic overlap between COG and epilepsies with significant negative genetic correlations (-0.23 to -0.04). COG was estimated to share 2.9k variants with both GGE and ′all epilepsy′, and 2.3k variants with both JME and CAE. Using conjFDR, we identified 66 distinct loci shared between COG and epilepsies, including novel associations for GGE (27), ′all epilepsy′ (5), JME (5) and CAE (5). The implicated genes were significantly expressed in multiple brain regions. The results were validated in independent samples (COG:p= 1.0 × 10-14; ′all epilepsy′:p= 5.6 × 10-3).Significance:Our study demonstrates a substantial genetic basis shared between epilepsies and COG and identifies novel overlapping genomic loci. Enhancing our understanding of the relationship between epilepsies and COG may lead to the development of novel comorbidity–targeted epilepsy treatments.
Risk of Inflammatory Bowel Disease Following Hospitalisation with Infectious Mononucleosis: A Danish Nationwide Cohort Study (1977-2021)
Authors: Ebert Anthony , Harper Shania , Vestergaard Marie V. , Mitchell Wayne , Jess Tine , Elmahdi Rahma
Published: March 2024

Background

Infectious mononucleosis (IM) is a largely self-limiting syndrome mainly affecting adolescents and young adults but can present as a more severe disease requiring hospitalisation. The infectious agent most commonly causing IM, Epstein-Barr virus (EBV) has been associated with the development of several immune-mediated and inflammatory diseases.

Objective

To investigate the risk of inflammatory bowel disease (IBD) following hospitalisation with severe IM.

Methods

Danish nationwide registries were used to identify severe IM patients and sex-, age- and municipality-matched non-IM hospitalised controls, from 1st January 1977 to 31st December 2022. We undertook Cox regression modelling to calculate the hazards (HR) and 95% CI of IBD diagnosis, including Crohn’s disease (CD) and ulcerative colitis (UC). Analyses were stratified by sex and age at IM hospitalisation.

Results

We identified 39,684 patients with severe IM who were sex-, age-, and municipality-matched to 396,840 non-IM hospitalised controls. Severe IM was significantly associated with the development of IBD (HR:1.35; 95% CI: 1.22-1.49) and this was seen particularly in CD (HR: 1.56; 95% CI: 1.34-1.83) and to a lesser extent in UC (HR: 1.23; 95% CI: 1.08-1.40). Sex at severe IM diagnosis was not found to be a significant modifier to the risk of IBD development with risk increased in both females (HR: 1.36; 95% CI: 1.20-1.55) and males (HR: 1.34; 95% CI: 1.17-1.54). Only those receiving a severe IM diagnosis at 10-16 years (HR: 1.42; 95% CI:1.22-1.64) or 17-29 years (HR: 1.34; 95% CI:1.15-1.56) were at increased risk of IBD development.

Conclusion

This study demonstrated an association between IM hospitalisation and later IBD development, indicating an association between severe EBV disease and IBD development. Further exploration of factors contributing to IBD susceptibility following EBV infection is warranted.
A Three-Year Retrospective Review of Gynecologic Oncology Referrals to the Specialist Palliative Care Team in a Tertiary Referral Centre: Population, Characteristics, and Outcomes
Authors: Goodings Anthony James , Pastrak Mila , Kajitani Sten , Cunningham Elaine , O’Brien Hannah , Weadick Catherine , Dennehy Karie
Published: March 2024

Background

The early integration of a specialist palliative care team is demonstrated to have numerous benefits for patients. These extend beyond end-of-life care to include reducing depressive symptoms, improving quality of life, and reducing unnecessary interventions.

Aims

This study aims to characterize the patient population referred to the specialist palliative care service with a diagnosis of gynecological cancer. It also assesses referral frequency and response time in order to understand palliative care utilization in an acute hospital setting.

Methods

A retrospective chart review and database analysis was performed to extract data on demographics, cancer diagnoses, and referral reasons for patients referred to the specialist palliative care service over three years. The study focuses on identifying patterns in the characteristics of the referred patient population.

Results

Analysis of 162 patients revealed a distribution across cancer subtypes: 62% ovarian, 22% endometrial, 12% cervical, and 4% vulvar. A notable finding was that the outcomes for patients with ovarian cancer were more likely to be discharged home with or without community care (61.8%) compared to those with endometrial cancer (41.0%). A rapid response to referrals was observed, with 70% reviewed within three days and 98% within a week. This highlights the service’s efficiency and the demographic and diagnostic profile of the patient served.

Conclusions

This study gives insight into the demographic and diagnostic profiles of gynecological cancer patients referred for palliative care, alongside demonstrating rapid response to such referrals. Despite the rapid assessment times, the research importantly identifies differences in outcomes among different cancer subtypes, with a particular emphasis on the variance in discharge destinations. These findings reflect both patient preference and medical need, demonstrating the role of tailoring palliative care approaches to meet the individual needs and desires of this diverse patient population.
Algorithmic Individual Fairness and Healthcare: A Scoping Review
Authors: Anderson Joshua W. , Visweswaran Shyam
Published: March 2024

Objective

Statistical and artificial intelligence algorithms are increasingly being developed for use in healthcare. These algorithms may reflect biases that magnify disparities in clinical care, and there is a growing need for understanding how algorithmic biases can be mitigated in pursuit of algorithmic fairness. Individual fairness in algorithms constrains algorithms to the notion that “similar individuals should be treated similarly.” We conducted a scoping review on algorithmic individual fairness to understand the current state of research in the metrics and methods developed to achieve individual fairness and its applications in healthcare.

Methods

We searched three databases, PubMed, ACM Digital Library, and IEEE Xplore, for algorithmic individual fairness metrics, algorithmic bias mitigation, and healthcare applications. Our search was restricted to articles published between January 2013 and September 2023. We identified 1,886 articles through database searches and manually identified one article from which we included 30 articles in the review. Data from the selected articles were extracted, and the findings were synthesized.

Results

Based on the 30 articles in the review, we identified several themes, including philosophical underpinnings of fairness, individual fairness metrics, mitigation methods for achieving individual fairness, implications of achieving individual fairness on group fairness and vice versa, fairness metrics that combined individual fairness and group fairness, software for measuring and optimizing individual fairness, and applications of individual fairness in healthcare.

Conclusion

While there has been significant work on algorithmic individual fairness in recent years, the definition, use, and study of individual fairness remain in their infancy, especially in healthcare. Future research is needed to apply and evaluate individual fairness in healthcare comprehensively.
Resonant breathing improves self-reported symptoms and wellbeing in people with Long COVID
Authors: Polizzi Jessica , Tosto-Mancuso Jenna , Tabacof Laura , Wood Jamie , Putrino David
Published: March 2024

Introduction

Long COVID involves debilitating symptoms, many of which mirror those observed with dysautonomia, and care must be taken with traditional autonomic rehabilitation to avoid post-exertional malaise/post-exertional symptom exacerbation. Resonant breathing exercises require less exertion and can potentially improve autonomic function. The objective of this work was to report on the impact of a resonant breathing program on self-reported symptoms and wellbeing in people with Long COVID.

Methods

A retrospective analysis of de-identified data was completed in a convenience sample of people with Long Covid, who participated in the Meo Health (formerly known as Stasis HP) resonant breathing program. Participants completed baseline and follow up surveys.

Results

Data were available for 99 participants. Most measures of symptoms and wellbeing improved at follow up, with the largest differences per participant seen in sense of wellness (47.3%, p<0.0001), ability to focus (57.5%, p<0.0001), ability to breathe (47.5%, p<0.0001), ability to control stress (61.8%, p<0.0001) and sleep quality (34.9%, p=0.0002). Most (92%) participants reported improvement at follow up on the Patient Global Impression of Change Scale.

Conclusion

Self-reported symptoms and wellbeing improved in people with Long COVID completing resonant breathing. Resonant breathing can be considered as an option within the broader treatment plan of people with Long COVID.
Humoral Immunity Elicited by the XBB.1.5 Monovalent COVID-19 Vaccine
Authors: Nguyenla Xammy Huu , Bates Timothy A. , Trank-Greene Mila , Wahedi Mastura , Tafesse Fikadu G. , Curlin Marcel
Published: March 2024

As novel SARS-CoV-2 variants continue to emerge, the updated XBB.1.5 monovalent vaccines remain to be evaluated in terms of immunogenicity against live clinical isolates. We report boosting of IgG(2.1X), IgA(1.5X), and total IgG/A/M(1.7X) antibodies targeting the spike receptor-binding domain and neutralizing titers against WA1(2.2X), XBB.1.5(7.4X), EG.5.1(10.5X), and JN.1(4.7X) variants.
Prospective study ofCandida aurisnucleic-acids in wastewater solids in 190 wastewater treatment plants in the United States suggests widespread occurrence
Authors: Zulli Alessandro , Chan Elana M. G. , Shelden Bridgette , Duong Dorothea , Xu Xiang-Ru S. , White Bradley J. , Wolfe Marlene K. , Boehm Alexandria B.
Published: March 2024

Candida aurisis an emerging, multidrug-resistant fungal pathogen that poses a significant public health threat in healthcare settings. Despite yearly clinical cases rapidly increasing from 77 to 8,131 in the last decade, surveillance data on its distribution and prevalence remains limited. We implemented a novel assay forC. aurisdetection on a nationwide scale prospectively from September 2023 to March 2024, analyzing a total of 13,842 samples from 190 wastewater treatment plants across 41 U.S. states. Assays were extensively validated through comparison to other known assays and internal controls. Of these 190 wastewater treatment plants,C. auriswas detected in the wastewater solids of 65 of them (34.2%) with 1.45% of all samples having detectable levels ofC. auris. Detections varied seasonally, with 2.00% of samples positive in autumn versus 1.01% in winter (p<0.0001). The frequency of detection in wastewater was significantly associated with states having older populations (p<0.001), sewersheds containing more hospitals (p<0.0001), and sewersheds containing more nursing homes (p<0.001). These associations are in agreement with knownC. aurisepidemiology. This nationwide study demonstrates the viability of wastewater surveillance forC. aurissurveillance, and further highlights the value of wastewater surveillance when clinical testing is constrained.
Defensive fungal symbiosis on insect hindlegs
Authors: Nishino Takanori , Mukai Hiromi , Moriyama Minoru , Hosokawa Takahiro , Tanahashi Masahiko , Tachikawa Shuji , Nikoh Naruo , Koga Ryuichi , Fukatsu Takema
Published: March 2024

Tympanal organs as “insect ears” have evolved repeatedly. Dinidorid stinkbugs were reported to possess a conspicuous tympanal organ on female’s hindlegs. Here we report an unexpected discovery that the stinkbug’s “tympanal organ” is actually a novel symbiotic organ. The stinkbug’s “tympanum” is not membranous but a porous cuticle, where each pore connects to glandular secretory cells. In reproductive females, the hindleg organ is covered with fungal hyphae growing out of the pores. Upon oviposition, the females skillfully transfer the fungi from the organ to the eggs. The eggs are quickly covered with hyphae and physically protected against wasp parasitism. The fungi are mostly benign Cordycipitaceae entomopathogens and show considerable diversity among insect individuals and populations, indicating environmental acquisition of specific fungal associates. These results uncover a novel external fungal symbiosis in which host’s elaborate morphological, physiological and behavioral specializations underpin the selective recruitment of benign entomopathogens for a defensive purpose.
Widespread Horizontal Gene Transfer Among Animal Viruses
Authors: Buck Christopher B. , Welch Nicole , Belford Anna K. , Varsani Arvind , Pastrana Diana V. , Tisza Michael J. , Starrett Gabriel J.
Published: March 2024

The initial objective of this study was to shed light on the evolution of small DNA tumor viruses by analyzingde novoassemblies of publicly available deep sequencing datasets. The survey generated a searchable database of contig snapshots representing more than 100,000 Sequence Read Archive records. Using modern structure-aware search tools, we iteratively broadened the search to include an increasingly wide range of other virus families. The analysis revealed a surprisingly diverse range of chimeras involving different virus groups. In some instances, genes resembling known DNA-replication modules or known virion protein operons were paired with unrecognizable sequences that structural predictions suggest may represent previously unknown replicases and novel virion architectures. Discrete clades of an emerging group called adintoviruses were discovered in datasets representing humans and other primates. As a proof of concept, we show that the contig database is also useful for discovering RNA viruses and candidate archaeal phages. The ancillary searches revealed additional examples of chimerization between different virus groups. The observations support a gene-centric taxonomic framework that should be useful for future virus-hunting efforts.
Peptides from non-immune proteins target infections through antimicrobial and immunomodulatory properties
Authors: Torres Marcelo D. T. , Cesaro Angela , de la Fuente-Nunez Cesar
Published: March 2024

Encrypted peptides have been recently described as a new class of antimicrobial molecules. They have been proposed to play a role in host immunity and as alternatives to conventional antibiotics. Intriguingly, many of these peptides are found embedded in proteins unrelated to the immune system, suggesting that immunological responses may extend beyond traditional host immunity proteins. To test this idea, here we synthesized and tested representative peptides derived from non-immune proteins for their ability to exert antimicrobial and immunomodulatory properties. Our experiments revealed that most of the tested peptides from non-immune proteins, derived from structural proteins as well as proteins from the nervous and visual systems, displayed potentin vitroantimicrobial activity. These molecules killed bacterial pathogens by targeting their membrane, and those originating from the same region of the body exhibited synergistic effects when combined. Beyond their antimicrobial properties, nearly 90% of the peptides tested exhibited immunomodulatory effects, modulating inflammatory mediators such as IL-6, TNF-α, and MCP-1. Moreover, eight of the peptides identified, collagenin 3 and 4, zipperin-1 and 2, and immunosin-2, 3, 12, and 13, displayed anti-infective efficacy in two different preclinical mouse models, reducing bacterial infections by up to four orders of magnitude. Altogether, our results support the hypothesis that peptides from non-immune proteins may play a role in host immunity. These results potentially expand our notion of the immune system to include previously unrecognized proteins and peptides that may be activated upon infection to confer protection to the host.
Pseudo-pac site sequences used by phage P22 in generalized transduction ofSalmonella
Authors: Maier Jessie L. , Gin Craig , Callahan Ben , Sheriff Emma K. , Duerkop Breck A. , Kleiner Manuel
Published: March 2024

Salmonella entericaSerovar Typhimurium (Salmonella) and its bacteriophage P22 are a model system for the study of horizontal gene transfer by generalized transduction. Typically, the P22 DNA packaging machinery initiates packaging when a short sequence of DNA, known as the pac site, is recognized on the P22 genome. However, sequences similar to the pac site in the host genome, called pseudo-pac sites, lead to erroneous packaging and subsequent generalized transduction ofSalmonellaDNA. While the general genomic locations of theSalmonellapseudo-pac sites are known, the sequences themselves have not been determined. We used visualization of P22 sequencing reads mapped to hostSalmonellagenomes to define regions of generalized transduction initiation and the likely locations of pseudo-pac sites. We searched each genome region for the sequence with the highest similarity to the P22 pac site and aligned the resulting sequences. We built a regular expression (sequence match pattern) from the alignment and used it to search the genomes of two P22-susceptibleSalmonellastrains-LT2 and 14028S- for sequence matches. The final regular expression successfully identified pseudo-pac sites in both LT2 and 14028S that correspond with generalized transduction initiation sites in mapped read coverages. The pseudo-pac site sequences identified in this study can be used to predict locations of generalized transduction in other P22-susceptible hosts or to initiate generalized transduction at specific locations in P22-susceptible hosts with genetic engineering. Furthermore, the bioinformatics approach used to identify theSalmonellapseudo-pac sites in this study could be applied to other phage-host systems.

Importance

Bacteriophage P22 has been a genetic tool and a key model for the study of generalized transduction inSalmonellasince the 1950s, yet certain components of the generalized transduction molecular mechanism remain unknown. Specifically, the locations and sequences of pseudo-pac sites, hypothesized to facilitate packaging ofSalmonellaDNA by P22, to date have not been determined. In this study, we identified the specific locations and sequences of the pseudo-pac sites frequently recognized by P22 inSalmonellagenomes. The identification of highly efficient pseudo-pac sites inSalmonellaprovides fundamental insights into the sequence specificity necessary for P22 pac site recognition and opens the door to more targeted use of generalized transduction with P22.
Beam dynamics driven design of powerful energy recovery linac for experiments
Authors: Bogacz S. A. , André K. D. J. , Brüning O. , Holzer B. J. , Hounsell B. R. , Klein M. , Militsyn B. L. , Williams P. H. , Segurana G. Pérez , Bailey I. , Apsimon R. , Setiniyaz S. , Abukeshek R. , Barbagallo C. , Abdillah M. Ben , Bruni C. , Duchesne P. , Duthil P. , Fomin A. , Guyot C. , Kaabi W. , Michaud J. , Olry G. , Perrot L. , Reynet D. , Roux R. , Stocchi A. , Wurth S. , Abualrob H. , Baylac M. , Bouly F. , Jacquot B.
Published: March 2024

Powerful ERL for experiments (PERLE) is a novel energy recovery linac (ERL) test facility [1], designed to validate choices for a 50 GeV ERL foreseen in the design of the Large Hadron Electron Collider and the Future Circular Collider and to host dedicated nuclear and particle physics experiments. Its main goal is to demonstrate the high current, continuous wave, multipass operation with superconducting cavities at 802 MHz. With very high beam power (10 MW), PERLE offers an opportunity for controllable study of every beam dynamic effect of interest in the next generation of ERLs and becomes a “stepping stone” between the present state-of-the-art 1 MW ERLs and the future 100 MW scale applications.

Published by the American Physical Society
2024
Spectroscopy of hot electron pair emission from a driven quantum dot
Authors: Schulenborg Jens , Fletcher Jonathan D. , Kataoka Masaya , Splettstoesser Janine
Published: March 2024

On-demand emission of individual electrons for the implementation of flying qubits and quantum electron-optics experiments requires precise knowledge and tunability of emission times and energies. Crucially, for confined electron sources such as driven quantum dots, the effect of local Coulomb interaction on these emission properties needs to be understood, in particular if multiple particles are emitted close in time or near simultaneously. This paper theoretically analyzes electron pair emission from an ac driven quantum dot, detailing the competing effects of the electron-electron interaction, the time-dependent potential forming the quantum dot, and of the quantum-state properties, such as degeneracy, on the emission times and energies. We complement a numerical analysis of the coherent Schrödinger evolution of two particles in a driven potential with a master-equation description for strongly interacting electrons tunneling stochastically into a weakly coupled conductor. This captures a broad range of different influences on the emitted particles and thereby guides the development of single-electron sources with higher control over two-particle emission properties.

Published by the American Physical Society
2024
Kinetic theory formulation of the
P
- and
CP
-odd terms in the photon self-energy in a medium
Authors: Nieves José F. , Verges John D.
Published: March 2024

In an optically active medium, such as a plasma that contains a neutrino background, the left-handed and right-handed polarization photon modes acquire different dispersion relations. We study the propagation of photons in such a medium, which is otherwise isotropic, within the framework of the covariant collissionless Boltzmann equation incorporating a term that parametrizes the optical activity. Using the linear response approximation, we obtain the formulas for the components of the photon polarization tensor, expressed in terms of integrals over the momentum distribution function of the background particles. The main result here is the formula for the P- and CP-breaking component of the photon polarization tensor in terms of the parameter involved in the new term we consider in the Boltzmann equation to describe the effects of optical activity. We discuss the results for some particular cases, such as long-wavelength and nonrelativistic limits, for illustrative purposes. We also discuss the generalizations of the P- and CP-breaking term we included in the Boltzmann equation. In particular we consider the application to a plasma with a neutrino background and establish contact with calculations of the photon self-energy in those systems in the framework of thermal field theory.

Published by the American Physical Society
2024
Refined renormalization group improvement for thermally resummed effective potential
Authors: Funakubo Koichi , Senaha Eibun
Published: March 2024

We newly develop a renormalization group (RG) improvement for thermally resummed effective potentials. In this method, β-functions are consistently defined in resummed perturbation theories, so that order-by-order RG invariance is not spoiled after thermal resummation. With this improvement, scale dependences of phase transition quantities such as a critical temperature, which are known to be notoriously large at the one-loop order, are greatly reduced compared to calculations with the conventional MS¯ scheme. By taking advantage of the RG invariance, we also devise a resummation method that can incorporate potentially harmful large logarithmic terms and temperature-dependent power corrections in a generic form. We point out that a resummed one-loop effective potential refined by the method can give results that agree with those obtained by resummed two-loop effective potentials within errors.

Published by the American Physical Society
2024
Nonlinear mechanosensation in fiber networks
Authors: Berthier Estelle , Yang Haiqian , Guo Ming , Ronceray Pierre , Broedersz Chase P.
Published: March 2024

In the extracellular matrix, eukaryotic cells exert forces that deform their surroundings. By doing so, they can perform mechanosensation: Cells measure the mechanics of their environment, and adapt their behavior accordingly. Extracellular matrices are, however, disordered nonlinear media: How can a mechanosensor at the cellular scale reliably measure the surroundings mechanics through local probing? Here, we develop a model for nonlinear mechanosensation in disordered fiber networks. At low forces, the linear response of the matrix combined with its extreme mechanical heterogeneity precludes reliable mechanosensation. In contrast, we find that this heterogeneity is strongly suppressed in the physiologically relevant nonlinear mechanical regime where fibers buckle. Conceptually, nonlinearity increases the range of mechanosensation, thereby enhancing disorder averaging and providing more accurate nonlinear mechanical measurements. We support our model using microrheology experiments and show theoretically that this nonlinear mechanosensation is generic to all fiber networks. This contrasts with the collagen-specific observation that nonlinear macroscopic elastic moduli are independent of network density, which we show to originate from the fiber's constitutive nonlinearity. Together, our theoretical study disentangles the micro- and macrorheological nonlinearities of fiber networks, and shows how mechanosensors such as cells can take advantage of these nonlinearities to robustly measure their mechanical environment despite heterogeneities.

Published by the American Physical Society
2024
Scattered high-energy synchrotron radiation at the KARA visible-light diagnostic beamline
Authors: Batchelor David R. , Blomley Edmund , Huttel Erhard , Hagelstein Michael , Mochihashi Akira , Schuh Marcel , Simon Rolf
Published: March 2024

To characterize an electron beam, visible synchrotron light is often used and dedicated beamlines at synchrotron sources are becoming a more common feature as instruments and methods for the diagnostics are, along with the accelerators, further developed. At KARA (Karlsruhe Research Accelerator), such a beamline exists and is based on a typical infrared/visible-light configuration. From experience at such beamlines no significant radiation was expected (dose rates larger than 0.5 µSv h−1). This was found not to be the case and a higher dose was measured which fortunately could be shielded to an acceptable level with 0.3 mm of aluminium foil or 2.0 mm of Pyrex glass. The presence of this radiation led to further investigation by both experiment and calculation. A custom setup using a silicon drift detector for energy-dispersive spectroscopy (Ketek GmbH) and attenuation experiments showed the radiation to be predominantly copper K-shell fluorescence and is confirmed by calculation. The measurement of secondary radiation from scattering of synchrotron and other radiation, and its calculation, is important for radiation protection, and, although a lot of experience exists and methods for radiation protection are well established, changes in machine, beamlines and experiments mean a constant appraisal is needed.
The effect of living wall systems’ variables on the energy consumption of buildings
Authors: Yanardag Erdener Hatice Merve , Edis Ecem
Published: March 2024

Purpose

Living walls (LWs), vegetated walls with an integrated growth layer behind, are being increasingly incorporated in buildings. Examining plant characteristics’ comparative impacts on LWs’ energy efficiency-related thermal behavior was aimed, considering that studies on their relative effects are limited. LWs of varying leaf albedo, leaf transmittance and leaf area index (LAI) were studied for Antalya, Turkey for typical days of four seasons.

Design/methodology/approach

Dynamic simulations run by Envi-met were used to assess the plant characteristics’ influence on seasonal and orientation-based heat fluxes. After model calibration, a sensitivity analysis was conducted through 112 simulations. The minimum, mean and maximum values were investigated for each plant characteristic. Energy need (regardless of orientation), temperature and heat flux results were compared among different scenarios, including a building without LW, to evaluate energy efficiency and variables’ impacts.

Findings

LWs reduced annual energy consumption in Antalya, despite increasing energy needs in winter. South and west facades were particularly advantageous for energy efficiency. The impacts of leaf albedo and transmittance were more significant (44–46%) than LAI (10%) in determining LWs’ effectiveness. The changes in plant characteristics changed the energy needs up to ca 1%.

Research limitations/implications

This study can potentially contribute to generating guiding principles for architects considering LW use in their designs in hot-humid climates.

Originality/value

The plant characteristics’ relative impacts on energy efficiency, which cannot be easily determined by experimental studies, were examined using parametric simulation results regarding three plant characteristics.
A novel time-varying grey Fourier model for variable amplitude seasonal fluctuation sequences
Authors: Liu Xiaomei , Ma Bin , Gao Meina , Chen Lin
Published: March 2024

Purpose

A time-varying grey Fourier model (TVGFM(1,1,N)) is proposed for the simulation of variable amplitude seasonal fluctuation time series, as the performance of traditional grey models can't catch the time-varying trend well.

Design/methodology/approach

The proposed model couples Fourier series and linear time-varying terms as the grey action, to describe the characteristics of variable amplitude and seasonality. The truncated Fourier order N is preselected from the alternative order set by Nyquist-Shannon sampling theorem and the principle of simplicity, then the optimal Fourier order is determined by hold-out method to improve the robustness of the proposed model. Initial value correction and the multiple transformation are also studied to improve the precision.

Findings

The new model has a broader applicability range as a result of the new grey action, attaining higher fitting and forecasting accuracy. The numerical experiment of a generated monthly time series indicates the proposed model can accurately fit the variable amplitude seasonal sequence, in which the mean absolute percentage error (MAPE) is only 0.01%, and the complex simulations based on Monte-Carlo method testify the validity of the proposed model. The results of monthly electricity consumption in China's primary industry, demonstrate the proposed model catches the time-varying trend and has good performances, where MAPEF and MAPET are below 5%. Moreover, the proposed TVGFM(1,1,N) model is superior to the benchmark models, grey polynomial model (GMP(1,1,N)), grey Fourier model (GFM(1,1,N)), seasonal grey model (SGM(1,1)), seasonal ARIMA model seasonal autoregressive integrated moving average model (SARIMA) and support vector regression (SVR).

Originality/value

The parameter estimates and forecasting of the new proposed TVGFM are studied, and the good fitting and forecasting accuracy of time-varying amplitude seasonal fluctuation series are testified by numerical simulations and a case study.
Religion, personality traits and the nature of entrepreneurial activities: insights from Scottish Muslim entrepreneurs
Authors: Rahman Md Zillur , Ullah Farid , Thompson Piers
Published: March 2024

Purpose

Previous studies have shown how the nature of businesses and the strategies pursued by their owners are affected by the personality traits of their owners. These personality traits can be formed in the early stages of life due to experiences and the surrounding context, where religion is a particularly important aspect of this context. This study aims to explore how religion affects entrepreneurial activities through the personality traits created.

Design/methodology/approach

This study uses interviews with 43 Muslim entrepreneurs in Scotland to examine the role played by religion. This ensures that the national institutional context is kept consistent but also allows an in-depth examination of relationships, which are likely to be interlinked and recursive.

Findings

The traits created influence the nature of the entrepreneurial activities undertaken with the potential to harm and support the entrepreneurial endeavours. It is the combination of personality traits that are formed which have the greatest effect. As such, it is found that Muslim entrepreneurs display less openness and creativity associated with new ideas, but this does not reflect risk aversion rather hard work in itself is valued, and patience combined with an external locus of control mean entrepreneurial behaviours are not altered to boost poorly performing business activities.

Originality/value

For Muslim entrepreneurs in Scotland, their traits explain why growth may not be a foremost consideration of these entrepreneurs rather they may value hard work and meeting the ideals of formal and informal institutions associated with religion. For those seeking to support minority groups through the promotion of entrepreneurship, either they must seek to overcome these ingrained traits or alter support to complement the different objectives held by Muslim entrepreneurs.
Exploring the impact of family and organisational values on competence diversity reluctance in rural family SMEs
Authors: Sabel Kristin , Kallmuenzer Andreas , Von Friedrichs Yvonne
Published: March 2024

Purpose

This paper aims to examine how organisational values affect diversity in terms of different competencies in rural family Small and Medium-sized Enterprises (SMEs). Recruiting a diverse workforce in rural family SMEs can be particularly difficult due to the prevalence of internal family values and the lack of available local specialised competencies. A deficiency of diversity in employment and competence acquisition and development can create problems, as it often prevents rural family SMEs from recruiting employees with a wide variety of qualifications and skills.

Design/methodology/approach

The study takes on a multi-case method of Swedish rural family SMEs, applying a qualitative content analysis approach. In total, 20 in-depth structured interviews are conducted with rural family SME owners and 2 industries were investigated and compared – the tourism and the manufacturing industries.

Findings

Rural family SMEs lack long-term employment strategies, and competence diversity does not appear to be a priority for rural family SMEs, as they often have prematurely decided who they will hire rather than what competencies are needed for their long-term business development. It is more important to keep the team of employees tight and the family spirit present than to include competence diversity and mixed qualifications in the employment acquisition and development.

Originality/value

Contrary to prior research, our findings indicate that rural family SMEs apply short-term competence diversity strategies rather than long-term prospects regarding competence acquisition and management, due to their family values and rural setting, which strictly narrows the selection of employees and competencies. Also, a general reluctance towards competence diversity is identified, which originates from the very same family values and rural context.