bluuebunny/crossref_metadata_2025 huggingface dataset:
GDmicro: classifying host disease status with GCN and deep adaptation network based on the human gut microbiome data
Authors: Liao Herui , Shang Jiayu , Sun Yanni
Published: December 2023

Motivation

With advances in metagenomic sequencing technologies, there are accumulating studies revealing the associations between the human gut microbiome and some human diseases. These associations shed light on using gut microbiome data to distinguish case and control samples of a specific disease, which is also called host disease status classification. Importantly, using learning-based models to distinguish the disease and control samples is expected to identify important biomarkers more accurately than abundance-based statistical analysis. However, available tools have not fully addressed two challenges associated with this task: limited labeled microbiome data and decreased accuracy in cross-studies. The confounding factors, such as the diet, technical biases in sample collection/sequencing across different studies/cohorts often jeopardize the generalization of the learning model.

Results

To address these challenges, we develop a new tool GDmicro, which combines semi-supervised learning and domain adaptation to achieve a more generalized model using limited labeled samples. We evaluated GDmicro on human gut microbiome data from 11 cohorts covering 5 different diseases. The results show that GDmicro has better performance and robustness than state-of-the-art tools. In particular, it improves the AUC from 0.783 to 0.949 in identifying inflammatory bowel disease. Furthermore, GDmicro can identify potential biomarkers with greater accuracy than abundance-based statistical analysis methods. It also reveals the contribution of these biomarkers to the host’s disease status.

Availability and implementation

https://github.com/liaoherui/GDmicro.
tANCHOR fast and cost-effective cell-based immunization approach with focus on the receptor-binding domain of SARS-CoV-2
Authors: Bernauer Hubert , Schlör Anja , Maier Josef , Bannert Norbert , Hanack Katja , Ivanusic Daniel
Published: December 2023

Successful induction of antibodies in model organisms like mice depends strongly on antigen design and delivery. New antigen designs for immunization are helpful for developing future therapeutic monoclonal antibodies (mAbs). One of the gold standards to induce antibodies in mice is to express and purify the antigen for vaccination. This is especially time-consuming when mAbs are needed rapidly. We closed this gap and used the display technology tetraspanin anchor to develop a reliable immunization technique without the need to purify the antigen. This technique is able to speed up the immunization step enormously and we have demonstrated that we were able to induce antibodies against different proteins with a focus on the receptor-binding domain of SARS-CoV-2 and the extracellular loop of canine cluster of differentiation 20 displayed on the surface of human cells.
Novel variants in ABCA12 cause erythrokeratodermia variabilis
Authors: Liu Yihe , Mo Ran , Chen Zhiming , Yang Yong
Published: December 2023

We present a patient clinically diagnosed with erythrokeratodermia variabilis harbored compound heterozygous variants in the ABCA12 gene, including an unreported c.3653A>G variant and c.7247C>T, both of which were predicted to be pathogenic.

This finding provide evidence that ABCA12 pathogenic variants were associated with recessive erythrokeratodermia variabilis, an otherwise dominant disorder.

This case highlighted the clinical diversity of ABCA12 variants and the genetic heterogeneity underlying the erythrokeratodermia variabilis, which is significant for genetic counseling and prenatal diagnosis.
The immunobiology of herpes simplex virus encephalitis and post-viral autoimmunity
Authors: Cleaver Jonathan , Jeffery Katie , Klenerman Paul , Lim Ming , Handunnetthi Lahiru , Irani Sarosh R , Handel Adam
Published: December 2023

Herpes simplex virus encephalitis (HSE) is the leading cause of non-epidemic encephalitis in the developed world and, despite antiviral therapy, mortality and morbidity is high. The emergence of post-HSE autoimmune encephalitis reveals a new immunological paradigm in autoantibody-mediated disease. A reductionist evaluation of the immunobiological mechanisms in HSE is crucial to dissect the origins of post-viral autoimmunity and supply rational approaches to the selection of immunotherapeutics.

Herein, we review the latest evidence behind the phenotypic progression and underlying immunobiology of HSE including the cytokine/chemokine environment, the role of pathogen-recognition receptors, T- and B-cell immunity and relevant inborn errors of immunity. Second, we provide a contemporary review of published patients with post-HSE autoimmune encephalitis from a combined cohort of 110 patients. Third, we integrate novel mechanisms of autoimmunization in deep cervical lymph nodes to explore hypotheses around post-HSE autoimmune encephalitis and challenge these against mechanisms of molecular mimicry and others. Finally, we explore translational concepts where neuroglial surface autoantibodies have been observed with other neuroinfectious diseases and those that generate brain damage including traumatic brain injury, ischaemic stroke and neurodegenerative disease.

Overall, the clinical and immunological landscape of HSE is an important and evolving field, from which precision immunotherapeutics could soon emerge.
Effects of multiple anesthetic exposures on rhesus macaque brain development: a longitudinal structural MRI analysis
Authors: Kim Jeongchul , Barcus Richard , Lipford Megan E , Yuan Hongyu , Ririe Douglas G , Jung Youngkyoo , Vlasova Roza M , Styner Martin , Nader Michael A , Whitlow Christopher T
Published: December 2023

Concerns about the potential neurotoxic effects of anesthetics on developing brain exist. When making clinical decisions, the timing and dosage of anesthetic exposure are critical factors to consider due to their associated risks. In our study, we investigated the impact of repeated anesthetic exposures on the brain development trajectory of a cohort of rhesus monkeys (n = 26) over their first 2 yr of life, utilizing longitudinal magnetic resonance imaging data. We hypothesized that early or high-dose anesthesia exposure could negatively influence structural brain development. By employing the generalized additive mixed model, we traced the longitudinal trajectories of brain volume, cortical thickness, and white matter integrity. The interaction analysis revealed that age and cumulative anesthetic dose were variably linked to white matter integrity but not to morphometric measures. Early high-dose exposure was associated with increased mean, axial, and radial diffusivities across all white matter regions, compared to late-low-dose exposure. Our findings indicate that early or high-dose anesthesia exposure during infancy disrupts structural brain development in rhesus monkeys. Consequently, the timing of elective surgeries and procedures that require anesthesia for children and pregnant women should be strategically planned to account for the cumulative dose of volatile anesthetics, aiming to minimize the potential risks to brain development.
Viral Dynamics of the SARS-CoV-2 Omicron Variant in Pediatric Patients: A Prospective Cohort Study
Authors: Science Michelle , Orkin Julia , Maguire Bryan , Bitnun Ari , Bourns Laura , Corbeil Antoine , Johnstone Jennie , Macdonald Liane , Schwartz Kevin L , Bruce Barrett Cindy , Reinprecht Jessica , Heisey Alice , Nasso Stephanie , Jüni Peter , Campigotto Aaron
Published: December 2023

Background

There are limited data on the viral dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in children. Understanding viral load changes over the course of illness and duration of viral shedding may provide insight into transmission dynamics to inform public health and infection-control decisions.

Methods

We conducted a prospective cohort study of children aged 18 years and younger with polymerase chain reaction–confirmed SARS-CoV-2 between 1 February 2022 and 14 March 2022. SARS-CoV-2 testing occurred on daily samples for 10 days; a subset of participants completed daily rapid antigen tests (RATs). Viral RNA trajectories were described in relation to symptom onset and resolution. The associations between both time since symptom onset/resolution and non-infectious viral load were evaluated using a Cox proportional hazards model.

Results

Among 101 children aged 2 to 17 years, the median time to study-defined non-infectious viral load was 5 days post–symptom onset, with 75% meeting this threshold by 7 days and 90% by 10 days. On the day of and day after symptom resolution, 43 (49%) and 52 (60%) of 87 had met the non-infectious thresholds, respectively. Of the 50 participants completing a RAT, positivity at symptom onset and on the day after symptom onset was 67% (16/24) and 75% (14/20). On the first day where the non-infectious threshold was met, 61% (n = 27/44) of participant RAT results were positive.

Conclusions

Children often met the study-defined non-infectiousness threshold on the day after symptom resolution. The RATs were often negative early in the course of illness and should not be relied on to exclude infection.

Clinical Trials Registration. clinicaltrials.org; NCT05240183.
Effectiveness of Prophylactic Oral and/or Vaginal Probiotic Supplementation in the Prevention of Recurrent Urinary Tract Infections: A Randomized, Double-Blind, Placebo-Controlled Trial
Authors: Gupta Varsha , Mastromarino Paola , Garg Ritu
Published: December 2023

Background

Widespread antibiotic resistance has sparked interest in the identification of nonantibiotic strategies, particularly probiotics for the prevention of recurrent urinary tract infections (UTIs). We evaluated the effectiveness of prophylactic probiotic supplementation through oral and intravaginal routes in the prevention of recurrent UTIs.

Methods

This double-blind, placebo-controlled study enrolled 174 premenopausal women with a history of recurrent UTIs and randomized them to 1 of the 4 treatment groups: placebo (G1, oral placebo + vaginal placebo), oral probiotic (G2, oral lactic acid bacteria and bifidobacteria + vaginal placebo), vaginal probiotic (G3, oral placebo + vaginal lactobacilli), and probiotic combination (oral lactic acid bacteria and bifidobacteria + vaginal lactobacilli), for 4 months. Participants were followed up for symptomatic UTIs for 1 year. The primary end points were the number of symptomatic UTIs at 4 months, the proportion of participants with at least 1 symptomatic UTI, and the time to the first symptomatic UTI.

Results

The incidence of UTI at 4 months in G1, G2, G3, and G4 was 70.4%, 61.3%, 40.9%, and 31.8%, respectively. The mean number of symptomatic UTI recurrences at 4 months was significantly lower (P < .05) in G3 (1.06) and G4 (1.07) compared with G1 (2.1) and G2 (1.63). Further, the time to first symptomatic UTI (days) was significantly longer (P < .05) in G3 (123.8) and G4 (141.8) compared with G1 (69.3) and G2 (71.9). Probiotic supplementations were well tolerated with no serious adverse events.

Conclusions

Prophylactic supplementation with either vaginal probiotics or in combination with oral probiotics demonstrated effectiveness in preventing recurrent symptomatic UTI episodes.

Clinical Trials Registration

Registered at Clinical Trials Registry India (CTRI): CTRI/2014/02/004425 (https://ctri.nic.in).
Novel biomarkers and pathophysiology of membranous nephropathy: PLA2R and beyond
Authors: Murtas Corrado , Bruschi Maurizio , Spinelli Sonia , Kajana Xhuliana , Verrina Enrico E , Angeletti Andrea , Caridi Gianluca , Candiano Giovanni , Feriozzi Sandro , Prunotto Marco , Ghiggeri Gian Marco
Published: December 2023

Research on membranous nephropathy truly exploded in the last 15 years. This happened because of the application of new techniques (laser capture microdissection, mass spectrometry, protein G immunoprecipitation, arrays) to the study of its pathogenesis. After the discovery of PLA2R as the major target antigen, many other antigens were identified and others are probably ongoing. Clinical and pathophysiology rebounds of new discoveries are relevant in terms of diagnosis and prognosis and it is time to make a first assessment of the innovative issues. In terms of classification, target antigens can be divided into: ‘membrane antigens’ and ‘second wave’ antigens. The first group consists of antigens constitutionally expressed on the podocyte membrane (as PLA2R) that may become a target of an autoimmune process because of perturbation of immune-tolerance. ‘Second wave’ antigens are antigens neo-expressed by the podocyte or by infiltrating cells after a stressing event: this allows the immune system to produce antibodies against them that intensify and maintain glomerular damage. With this abundance of target antigens it is not possible, at the moment, to test all antibodies at the bedside. In the absence of this possibility, the role of histological evaluation is still irreplaceable.
DFS70 Autoantibodies: Clinical Utility in Antinuclear Antibody Testing
Authors: Bossuyt Xavier
Published: December 2023

Background

Screening for antinuclear antibodies (ANA) by indirect immunofluorescence (IIF) on HEp-2 cells is helpful for the diagnosis and classification of ANA-associated rheumatic diseases, including systemic lupus erythematosus, Sjögren syndrome, mixed connective tissue disease, systemic sclerosis, and inflammatory myopathies. The dense fine speckled (DFS) pattern is a special HEp-2 IIF pattern (produced by anti-DFS70 antibodies) because it is not associated with a specific medical condition and therefore can obfuscate interpretation.

Content

In this paper, detection methods for and clinical associations of anti-DFS70 antibodies are reviewed.

The target antigen of the antibodies that cause the DFS pattern is a 70 kDa protein (DFS70). Commercial methods that detect antibodies to full-length or truncated DFS70 are available for use in clinical laboratories (ELISA, chemiluminescence, dot/line blot). Anti-DFS70 can be found in (apparently) healthy individuals (with a higher frequency in young individuals and in females), in several (inflammatory) conditions and in malignancy. There is no clinical association that is well-established. Special attention (and critical reflection) is given to the observation that monospecific anti-DFS70 (i.e., in the absence of antibodies that are linked to ANA-associated rheumatic diseases) is rarely found in ANA-associated rheumatic diseases.
Even mild mitral regurgitation is associated with incident atrial fibrillation in the general population
Authors: Yafasov Marat , Olsen Flemming Javier , Shabib Ali , Skaarup Kristoffer Grundtvig , Lassen Mats Christian Højbjerg , Johansen Niklas Dyrby , Jensen Magnus T , Jensen Gorm Boje , Schnohr Peter , Møgelvang Rasmus , Biering-Sørensen Tor
Published: December 2023

Aims

Mitral regurgitation (MR) can be difficult to quantify. We sought to investigate whether the MR jet area to left atrial (LA) area ratio (MR/LA ratio) method for quantifying MRs can be used to predict incident atrial fibrillation (AF) in the general population.

Methods and results

The study included 4466 participants from the 5th Copenhagen City Heart Study, a prospective general population study, who underwent transthoracic echocardiography. MR jet area was measured and indexed to LA area. The endpoint was incident AF. MR was quantified in 4042 participants (mean age: 57 years, 43% men). Of these, 198 (4.9%) developed AF during a median follow-up period of 5.3 years (interquartile range: 4.4–6.1 years). MR was present in 1938 participants (48%) including 1593 (39%) trace/mild MRs (MR/LA ratio ≤ 20% and ≤4 cm2). In unadjusted analysis, MR/LA ratio was associated with incident AF [HR: 1.06 (1.00–1.13), P = 0.042 per 5% increase] but not after adjusting for CHARGE-AF score. However, the association was modified by age (P for interaction = 0.034), such that MR/LA ratio was associated with AF only in participants ≤ 73 years. In these participants, MR/LA ratio ‘was’ independently associated with AF after adjusting for CHARGE-AF score [HR: 1.14 (1.06–1.24), P = 0.001, per 5% increase]. This finding persisted when restricting the analysis to participants without moderate or severe MR and normal LA size [HR: 1.35 (1.09–1.68), P = 0.005, per 5% increase].

Conclusion

MR, including even trace regurgitations quantified by MR/LA ratio, is independently associated with incident AF in individuals ≤ 73 years of age.
ELT teachers’ agency for wellbeing
Authors: Sulis Giulia , Mairitsch Astrid , Babic Sonja , Mercer Sarah , Resnik Pia
Published: December 2023

Wellbeing is crucial for teachers, not only for themselves but also for ensuring that they teach to the best of their abilities. Thus, identifying ways of empowering teachers to take action to boost or maintain their wellbeing is vital. In this article, an ecological lens is adopted to understand what determines language teachers’ agency for wellbeing. A thematic analysis of in-depth interviews with 30 EFL teachers based in Austria revealed four key themes which help to explain how teachers exercise their agency for wellbeing. These are: triggers, reflection, affordances, and action. The results show that critical incidents in their personal and professional domains act as triggers drawing teachers’ attention towards their wellbeing and starting a process of deeper reflection. However, a prerequisite for taking action following this reflection appears to be a perceived sense of control about their ability to change things in their personal and professional lives.
Myocardial infarction drives trained immunity of monocytes, accelerating atherosclerosis
Authors: Dong Zheng , Hou Lei , Luo Wei , Pan Li-Hong , Li Xiao , Tan Hai-Peng , Wu Run-Da , Lu Hao , Yao Kang , Mu Man-Di , Gao Chen-Shan , Weng Xin-Yu , Ge Jun-Bo
Published: December 2023

Background and Aims

Survivors of acute coronary syndromes face an elevated risk of recurrent atherosclerosis-related vascular events despite advanced medical treatments. The underlying causes remain unclear. This study aims to investigate whether myocardial infarction (MI)-induced trained immunity in monocytes could sustain proatherogenic traits and expedite atherosclerosis.

Methods

Apolipoprotein-E deficient (ApoE−/−) mice and adoptive bone marrow transfer chimeric mice underwent MI or myocardial ischaemia–reperfusion (IR). A subsequent 12-week high-fat diet (HFD) regimen was implemented to elucidate the mechanism behind monocyte trained immunity. In addition, classical monocytes were analysed by flow cytometry in the blood of enrolled patients.

Results

In MI and IR mice, blood monocytes and bone marrow-derived macrophages exhibited elevated spleen tyrosine kinase (SYK), lysine methyltransferase 5A (KMT5A), and CCHC-type zinc finger nucleic acid-binding protein (CNBP) expression upon exposure to a HFD or oxidized LDL (oxLDL) stimulation. MI-induced trained immunity was transmissible by transplantation of bone marrow to accelerate atherosclerosis in naive recipients. KMT5A specifically recruited monomethylation of Lys20 of histone H4 (H4K20me) to the gene body of SYK and synergistically transactivated SYK with CNBP. In vivo small interfering RNA (siRNA) inhibition of KMT5A or CNBP potentially slowed post-MI atherosclerosis. Sympathetic denervation with 6-hydroxydopamine reduced atherosclerosis and inflammation after MI. Classical monocytes from ST-elevation MI (STEMI) patients with advanced coronary lesions expressed higher SYK and KMT5A gene levels.

Conclusions

The findings underscore the crucial role of monocyte trained immunity in accelerated atherosclerosis after MI, implying that SYK in blood classical monocytes may serve as a predictive factor for the progression of atherosclerosis in STEMI patients.
Global epidemiology of lower extremity artery disease in the 21st century (2000–21): a systematic review and meta-analysis
Authors: Adou Caroline , Magne Julien , Gazere Nana , Aouida Maissa , Chastaingt Lucie , Aboyans Victor
Published: December 2023

Aims

The epidemiology of lower extremity artery disease (LEAD) is evolving. This meta-analysis of aggregate data aimed to (i) determine the global prevalence of LEAD and by regions in the 21st century and (ii) update the associated risk factors in this period.

Methods and results

A systematic literature review was performed through PubMed, Cochrane, Scopus, Science Direct, and Google Scholar databases, restricted to general population studies between January 2000 and September 2021, with LEAD defined by a low (</≤0.90) ankle–brachial index. The Newcastle–Ottawa Scale was used to evaluate the quality of the articles before data extraction. Due to high heterogeneity, the random effect model was applied to this meta-analysis. Among 1418 references, 38 studies (127 961 participants) were retained. The global prevalence in adults, mostly ≥40 years, was estimated at 9.7% [95% confidence interval (CI): 7.1–12.4], higher in women (10.2%) than in men (8.8%), increasing sharply with age. The highest prevalence was found in South–Central Asia (14.5%) and the lowest in North America (5.6%). Significant associations were found between LEAD and current [odds ratio (OR) = 1.9, 95% CI: 1.4–2.5] and past smoking (OR = 1.6, 95% CI: 1.3–1.9) and between LEAD and diabetes (OR = 2.3, 95% CI: 2.0–2.8). Hypertension was significantly associated with LEAD (OR = 2.3, 95% CI: 1.9–2.8) and in particular in South America (OR = 4.0). Obesity (OR = 1.5, 95% CI: 1.2–1.8) and hypercholesterolaemia ≥200 mg/dL (OR = 1.9, 95% CI: 1.3–2.8) were also significantly associated with LEAD.

Conclusion

This meta-analysis highlights a currently high prevalence of LEAD worldwide, with substantial differences in global regions and between sexes. The strongest associations were found with metabolic risk factors.
A synthesis of coevolution across levels of biological organization
Authors: Dixit Tanmay
Published: December 2023

In evolutionary ecology, coevolution is typically defined as reciprocal evolution of interacting species. However, outside the context of interacting species, the term “coevolution” is also used at levels of biological organization within species (e.g., between males and females, between cells, and between genes or proteins). Furthermore, although evolution is typically defined as “genetic change over time”, coevolution need not involve genetic changes in the interacting parties, since cultures can also evolve. In this review, I propose that coevolution be defined more broadly as “reciprocal adaptive evolution at any level of biological organisation”. The classification of reciprocal evolution at all levels of biological organization as coevolution would maintain consistency in terminology. More importantly, the broader definition should facilitate greater integration of coevolution research across disciplines. For example, principles usually discussed only in the context of coevolution between species or coevolution between genes (e.g., tight and diffuse coevolution, and compensatory coevolution, respectively) could be more readily applied to new fields. The application of coevolutionary principles to new contexts could also provide benefits to society, for instance in deducing the dynamics of coevolution between cancer cells and cells of the human immune system.
Seismic wave dispersion and attenuation resulting from multiscale wave-induced fluid flow in partially saturated porous media
Authors: Shi Zhiqi , He Xiao , Chen Dehua , Wang Xiuming
Published: December 2023

Sedimentary rocks are typical heterogeneous porous media induced by fluid patches and pore fabric. It is well acknowledged that the wave-induced fluid flow (WIFF) at different scales will cause seismic wave dispersion and attenuation in a wide frequency range. Consequently, modelling wave dispersion and attenuation due to multiscale WIFF is of significance for reservoir characterization from multiscale geophysical measurement and interpretation. In this study, the multiscale WIFF in partially saturated porous media, including global, 3-D mesoscopic and squirt flows, are investigated. And we derive the wave equations by introducing the Rayleigh's spherical bubble oscillation and the porous grain models into Santos poroelasticity theory. Numerical simulations demonstrate that the multiscale model can interpret the transition of rock states as frequency increases and capture the broad-band seismic wave dispersion and attenuation characteristics, which are directly associated with the heterogeneity scale. Besides, the multiscale model can be degraded to a single- or dual-scale model under specific parameters. We validate the proposed model with board-band experimental data of partially saturated sandstones, confirming its comprehensive characterization of velocity dispersion and attenuation over a wider range of frequencies. Moreover, the model successfully interprets the unrelaxed state of partially saturated rock at ultrasound frequencies.
Suppliers’ entry, upgrading, and innovation in mining GVCs: lessons from Argentina, Brazil, and Peru
Authors: Pietrobelli Carlo , Calzada Olvera Beatriz , Iizuka Michiko , Mazzi Caio Torres
Published: December 2023

This paper studies whether the mining sector can represent a true engine of growth for selected Latin American countries through the suppliers’ entry and upgrading within mining value chains. We start by using international trade data to study where mining value is added and how rents are distributed across countries. Despite their importance in the production and exports of copper ores and concentrate, the participation of the selected Latin American countries in copper value chains is still confined to the upstream segment. Moreover, their share of innovation relevant for the sector remains very limited, although new data on patenting and publications show that the sector is becoming increasingly innovative worldwide. Then, we use new microeconomic evidence from case-studies in Latin America to explore the specific opportunities and obstacles faced by mining suppliers in entering the value chain and upgrading within it, and how the regulatory and innovation systems have influenced this process. We show that barriers related to the contractual practices, lead firms’ attitudes, and the hierarchical industrial organization of the sector, coupled with the countries’ weaknesses in local innovation and regulatory systems, have been contributing to hamper suppliers’ entry into mining value chains and upgrading.
A paradigm for understanding whole ecosystem effects of offshore wind farms in shelf seas
Authors: Isaksson Natalie , Scott Beth E , Hunt Georgina L , Benninghaus Ella , Declerck Morgane , Gormley Kate , Harris Caitlin , Sjöstrand Sandra , Trifonova Neda I , Waggitt James J , Wihsgott Juliane U , Williams Charlotte , Zampollo Arianna , Williamson Benjamin J
Published: December 2023

With the rapid expansion of offshore windfarms (OWFs) globally, there is an urgent need to assess and predict effects on marine species, habitats, and ecosystem functioning. Doing so at shelf-wide scale while simultaneously accounting for the concurrent influence of climate change will require dynamic, multitrophic, multiscalar, ecosystem-centric approaches. However, as such studies and the study system itself (shelf seas) are complex, we propose to structure future environmental research according to the investigative cycle framework. This will allow the formulation and testing of specific hypotheses built on ecological theory, thereby streamlining the process, and allowing adaptability in the face of technological advancements (e.g. floating offshore wind) and shifting socio-economic and political climates. We outline a strategy by which to accelerate our understanding of environmental effects of OWF development on shelf seas, which is illustrated throughout by a North Sea case study. Priorities for future studies include ascertaining the extent to which OWFs may change levels of primary production; whether wind energy extraction will have knock-on effects on biophysical ecosystem drivers; whether pelagic fishes mediate changes in top predator distributions over space and time; and how any effects observed at localized levels will scale and interact with climate change and fisheries displacement effects.
Broadband target strength of arabesque greenling, Pacific sand lance, and pointhead flounder
Authors: Yan Naizheng , Mukai Tohru , Hasegawa Kohei , Yamamoto Jun , Fukuda Yoshiaki
Published: December 2023

Measurement of target strength (TS) is important for estimating the abundance of species using fisheries acoustics. However, most researchers have only used a limited number of representative frequencies for acoustic measurements of fish without a swim bladder (bladderless fish). Here, we measured the broadband TS of three bladderless fish species, arabesque greenling (Pleurogrammus azonus), Pacific sand lance (Ammodytes personatus), and pointhead flounder (Cleisthenes pinetorum), using two broadband echosounders. TS measurements were conducted in a seawater tank over frequency ranges of 45–90 and 80–120 kHz using a tether method. Higher TS and directivity were observed at higher frequencies than at lower frequencies for pointhead flounder and arabesque greenling. However, the TS for Pacific sand lance was relatively flat over the measured frequency spectra. Additionally, the TS of pointhead flounder and Pacific sand lance could be expressed as a function of body length and the TS of arabesque greenling could be expressed as a function of body length and frequency, which could be used in fish species discriminations and size estimations.
Exact Mobility Edges for Almost-Periodic CMV Matrices via Gauge Symmetries
Authors: Cedzich Christopher , Fillman Jake , Li Long , Ong Darren C , Zhou Qi
Published: December 2023

We investigate the symmetries of the so-called generalized extended Cantero–Moral–Velázquez (CMV) matrices. It is well-documented that problems involving reflection symmetries of standard extended CMV matrices can be subtle. We show how to deal with this in an elegant fashion by passing to the class of generalized extended CMV matrices via explicit diagonal unitaries in the spirit of Cantero–Grünbaum–Moral–Velázquez. As an application of these ideas, we construct an explicit family of almost-periodic CMV matrices, which we call the mosaic unitary almost-Mathieu operator, and prove the occurrence of exact mobility edges. That is, we show the existence of energies that separate spectral regions with absolutely continuous and pure point spectrum and exactly calculate them.
RNA Landscapes of Brain and Brain-Derived Extracellular Vesicles in Simian Immunodeficiency Virus Infection and Central Nervous System Pathology
Authors: Huang Yiyao , Abdelgawad Ahmed , Turchinovich Andrey , Queen Suzanne , Abreu Celina Monteiro , Zhu Xianming , Batish Mona , Zheng Lei , Witwer Kenneth W
Published: December 2023

Background

Brain tissue-derived extracellular vesicles (bdEVs) act locally in the central nervous system (CNS) and may indicate molecular mechanisms in human immunodeficiency virus (HIV) CNS pathology. Using brain homogenate (BH) and bdEVs from a simian immunodeficiency virus (SIV) model of HIV disease, we identified RNA networks in SIV infection and neuroinflammation.

Methods

Postmortem occipital cortex samples were obtained from uninfected controls and SIV-infected subjects (acute and chronic phases with or without CNS pathology [SIV encephalitis]). bdEVs were separated and characterized per international consensus guidelines. RNAs from bdEVs and BH were sequenced and quantitative polymerase chain reaction (qPCR)-amplified to detect levels of small RNAs (sRNAs, including microRNAs [miRNAs]) and longer RNAs including messenger RNAs (mRNAs) and circular RNAs (circRNAs).

Results

Dysregulated RNAs in BH and bdEVs were identified in acute and chronic infection with pathology groups, including mRNAs, miRNAs, and circRNAs. Most dysregulated mRNAs in bdEVs reflected dysregulation in source BH. These mRNAs are disproportionately involved in inflammation and immune responses. Based on target prediction, several circRNAs that were differentially abundant in source tissue might be responsible for specific differences in sRNA levels in bdEVs during SIV infection.

Conclusions

RNA profiling of bdEVs and source tissues reveals potential regulatory networks in SIV infection and SIV-related CNS pathology.
Developing quality measures for non-pharmacological prevention and rehabilitation in primary health care for chronic conditions: a consensus study
Authors: Svendsen Marie Louise , Andersen Tina Veje , Soendergaard Hanne
Published: December 2023

Poor health-related behaviours are root causes of a large number of chronic conditions; however, this study is the first to develop guideline-based quality measures targeting health-related behaviours through generic non-pharmacological secondary prevention and rehabilitation in municipal primary health care for persons with chronic conditions.

From January 2020 to September 2021, a consensus study was conducted in accordance with the current scientific recommendations for developing guideline-based quality measures. A clinical expert panel (n = 11) was established and included a patient representative, health care professionals, researchers, and key specialists. The process for developing quality measures was led by methodologists and encompassed a modified Research and Development/University of California at Los Angeles (RAND/UCLA) study to evaluate consensus in the expert panel. The consensus recommendations were directed to a steering group including the Danish Ministry of Health, the Danish Regions, and the Local Government Denmark.

The expert panel rated 102 clinical practice recommendations. Consensus was demonstrated on 13 quality measures assessing whether the patients are offered participation in and adhere to: self-management, smoking cessation, physical exercise training, nutritional efforts, and preventive consultation on excessive alcohol consumption; whether the patients participate in a closing meeting, whether they are offered follow-up, and whether reasons for dropout are documented.

The identified quality measures constitute a framework for assessing the quality of non-pharmacological prevention and rehabilitation in municipal primary health care for persons with chronic conditions. The next steps focus on field testing of the quality measures to refine measure criteria and assess implementation. A close link between clinical practice, the evidence and practice recommendations, the data infrastructure, economic considerations, and national priorities was a key to the consensus process.
Textiling World Politics: Towards an extended epistemology, methodology, and ontology
Authors: Andrä Christine , Bliesemann de Guevara Berit , Querejazu Amaya , Santos Victória M S
Published: December 2023

This article argues that textiling—a particular kind of making that simultaneously constitutes a concept, a metaphor, and a practice—can facilitate a radical rethinking and redoing of the study of world politics. Specifically, we suggest three ways in which textiling, and the relationality it enables, facilitates this innovation: as a different way of theorizing in the discipline of international relations (IR), as a creative method and methodology for the empirical study of world politics, and as ontological world-making through cosmopraxis. These three ways open up possibilities of engaging the world and its politics differently by enabling an extended epistemology that accounts not only for propositional (abstract and textual) knowledge, but also for experiential, presentational, and practical ways of knowing. Thereby, textiling is not only an innovative practical instrument by means of which different research traditions within IR can cultivate non-propositional ways of knowing; it can also entangle these new insights with the propositional knowledge traditionally privileged by IR and interweave theory and practice in IR scholarship.
The Empire Strikes Back: Comparing US and China’s Structural Power in Outer Space
Authors: Morin Jean-Frédéric , Tepper Eytan
Published: December 2023

This article assesses the structural power of the United States and China in the field of space governance. While much of the literature on space power focuses on their technologies and capabilities, we take a complementary approach and explore their capacity to shape the regulatory landscape. Possessing structural power has far-reaching implications for global power projection as well as for various industries, such as telecommunications, transportation, and remote sensing. To assess structural power, we gathered and analyzed three types of data: a dataset featuring 1,709 space organizations, a second dataset comprising 1,764 international space arrangements connecting them, and insights from fifty-two interviews with key space actors. Our findings indicate that the United States holds significant structural power thanks to its thriving commercial space sector and extensive international network. This has enabled the global diffusion of its preferred norms while simultaneously constraining China’s space cooperation network. Despite its remarkable technological capabilities, China has not been able to translate them into substantial global structural power. To encourage further exploration in this domain, we make available our original dataset of 1,764 space arrangements, including 970 in full-text format, inviting fellow researchers to investigate other facets of outer space governance.
Impact of antibiotic allergy labels on timely and appropriate antibiotics for sepsis in the emergency department
Authors: Rush Lily , Rashidzada Zohal , Cairns Kelly , Roman Cristina , Bourne Thomas , Orosz Judit , Poole Susan , Lee Sue J , Peel Trisha
Published: December 2023

Objectives

Time to initiation of effective antibiotic therapy is a strong predictor of survival for patients with sepsis presenting to the Emergency Department (ED). Antibiotic allergy labels (AALs) are a known barrier to timely sepsis management. The aim was to evaluate the influence of AALs on timely sepsis management for ED sepsis presentations in an Australian hospital.

Methods

A retrospective cohort study was conducted for ED presentations requiring direct ICU admission for suspected sepsis, comparing patients with and without an AAL using propensity scores.

Results

Between November 2018 and June 2021, 377 patients were included. The prevalence of an AAL was 29.6% (86/377). The median time to antibiotic administration was similar in the AAL versus non-AAL groups (51 versus 60 min, P = 0.11); there was no difference in mortality (14.1% versus 14.0%, P = 0.98) and length of stay (9.21 versus 10.10 days). The median time to antibiotic administration was shorter in those with Emergency Medicine (EM) pharmacist attendance versus those without (50 versus 92 min, P = 0.0001). Appropriateness of antibiotic prescription was 91.0% (343/377) for the overall cohort and was not associated with AALs, possibly due to our clear antimicrobial sepsis guidelines; however, EM pharmacist involvement was associated with increased antibiotic appropriateness (97.3% versus 88.4%, P = 0.00048).

Conclusions

In our Australian ED, AALs were not found to impact timeliness of antibiotic administration in patients with sepsis. EM pharmacist involvement was associated with improved timeliness and appropriateness of antibiotic selection in patients presenting with sepsis.
In vitro activity of tebipenem and comparator agents against bacterial pathogens isolated from patients with cancer
Authors: Gerges Bahgat , Rosenblatt Joel , Shellburne Samuel A , Chaftari Anne-Marie , Hachem Ray , Raad Issam
Published: December 2023

Background

Tebipenem is a broad-spectrum orally administered carbapenem antibiotic that could be an alternative to IV carbapenems. The current study evaluated in vitro activity of tebipenem against bacterial isolates recovered from patients with cancer.

Methods

A total of 611 bacterial pathogens recently isolated from patients with cancer were tested for susceptibility to tebipenem and comparators. CLSI-approved broth microdilution methods were used. MIC50, MIC90, MIC range and percentage susceptibility calculations were made using FDA breakpoints when available.

Results

Tebipenem had a low MIC90 for most Gram-positive and Enterobacterales isolates. Tebipenem MIC90 ranged from 0.06 to 0.25 mg/L for all tested Enterobacterales.

Conclusions

Oral tebipenem has promising activity against clinically significant bacterial pathogens isolated from patients with cancer. Further clinical evaluation of tebipenem for the treatment of bacterial infections in patients with cancer is warranted.
Effects of 12 Months’ Treatment with Testosterone Undecanoate on Markers for Erythropoietic Activity and Safety Aspects in Transgender and Cisgender Hypogonadal Men
Authors: Lethin Kajsa , Aardal Elisabeth , Lood Yvonne , Ekman Bertil , Wahlberg Jeanette
Published: December 2023

Background

To investigate the erythropoietic activity and safety aspects of testosterone undecanoate (TU) injections in transgender men, assigned female at birth.

Methods

Twenty-three men (13 hypogonadal cisgender men and 10 transgender men) who initiated TU at the study start (naïve) and 15 men (10 hypogonadal cisgender men and 5 transgender men) on steady-state treatment with TU (non-naïve) were included in this prospective 1-year observational study. A control group of 32 eugonadal cisgender men was investigated once at baseline. Complete blood count, testosterone in serum and saliva, and plasma lipids, and liver enzymes were assessed.

Results

For naïve transgender men, a significant increase in hemoglobin concentration was noted (mean (SD)), 141 (8) g/L to 151 (13) g/L, while no increase was seen in naïve hypogonadal cisgender men. At the end of the study, naïve transgender men exhibited comparable levels of hemoglobin, hematocrit, and testosterone levels in serum and saliva to hypogonadal cisgender men, as well as to the eugonadal cisgender men. During the study, HDL-cholesterol decreased significantly in naïve transgender men, 1.4 (0.4) mmol/L to 1.2 (0.4) mmol/L, P = 0.03, whereas no significant change was noted in naïve hypogonadal cisgender men. Liver enzymes remained unchanged in all groups.

Conclusions

After 12 months of treatment with TU in naïve transgender men, hemoglobin and hematocrit increased to levels within the cisgender male reference range. A slight decrease in HDL-cholesterol was seen in naïve transgender men but liver enzymes remained unchanged.
Strategy and Subterfuge: Billy Graham’s Political Machinations from Montreux to the Mayflower Hotel and Beyond
Authors: Balmer Randall
Published: December 2023

One of the turning points in the 1960 presidential campaign was a gathering of 150 Protestant ministers at the Mayflower Hotel in Washington on September 7, 1960, two days after Labor Day. During the closed-door gathering, Protestant leaders, including Norman Vincent Peale, unanimously adopted a statement warning about the dangers to the First Amendment and the separation of church and state should a Roman Catholic be elected president. Drawing on newly available archival sources, this article examines the role of religion in the 1960 campaign, including John F. Kennedy’s long struggle to neutralize the issue and the significance of Paul Blanshard’s 1949 best-seller, American Freedom and Catholic Power. Although Peale was roundly criticized for his role in the Mayflower gathering, the real force behind the meeting was Billy Graham, who did not attend. After assuring Kennedy in a letter dated August 10, 1960, that he, Graham, would not raise the religious issue in the campaign, Graham, at Peale’s behest, convened a group of Protestant ministers at the Montreux Palace Hotel in Switzerland eight days later to discuss how they could deny Kennedy’s election in November. The direct consequence of the Montreux meeting was the Mayflower Hotel gathering. While Peale took the heat for the meeting, Graham continued to play both sides, insisting publicly that he was neutral in the presidential race while working behind the scenes to advance Nixon’s candidacy, a strategy he employed again twenty years later in an attempt to jettison the reelection of a fellow evangelical, Jimmy Carter.
Prostate cancer risk stratification using magnetic resonance imaging–ultrasound fusion vs systematic prostate biopsy
Authors: Khajir Ghazal , Press Benjamin , Lokeshwar Soum , Ghabili Kamyar , Rahman Syed , Gardezi Mursal , Washington Samuel , Cooperberg Matthew R , Sprenkle Preston , Leapman Michael S
Published: December 2023

Background

Image-guided approaches improve the diagnostic yield of prostate biopsy and frequently modify estimates of clinical risk. To better understand the impact of magnetic resonance imaging–ultrasound fusion targeted biopsy (MRF-TB) on risk assessment, we compared the distribution of National Comprehensive Cancer Network (NCCN) risk groupings, as calculated from MRF-TB vs systematic biopsy alone.

Methods

We performed a retrospective analysis of 713 patients who underwent MRF-TB from January 2017 to July 2021. The primary study objective was to compare the distribution of National Comprehensive Cancer Network risk groupings obtained using MRF-TB (systematic + targeted) vs systematic biopsy.

Results

Systematic biopsy alone classified 10% of samples as very low risk and 18.7% of samples as low risk, while MRF-TB classified 10.5% of samples as very low risk and 16.1% of samples as low risk. Among patients with benign findings, low-risk disease, and favorable/intermediate-risk disease on systematic biopsy alone, 4.6% of biopsies were reclassified as high risk or very high risk on MRF-TB. Of 207 patients choosing active surveillance, 64 (31%), 91 (44%), 42 (20.2%), and 10 (4.8%) patients were classified as having very low-risk, low-risk, and favorable/intermediate-risk and unfavorable/intermediate-risk criteria, respectively. When using systematic biopsy alone, 204 patients (28.7%) were classified as having either very low-risk and low-risk disease per NCCN guidelines, while 190 men (26.6%) received this classification when using MRF-TB.

Conclusion

The addition of MRF-TB to systematic biopsy may change eligibility for active surveillance in only a small proportion of patients with prostate cancer. Our findings support the need for routine use of quantitative risk assessment over risk groupings to promote more nuanced decision making for localized cancer.
Variable selection in latent variable models via knockoffs: an application to international large-scale assessment in education
Authors: Xie Zilong , Chen Yunxiao , von Davier Matthias , Weng Haolei
Published: December 2023

International large-scale assessments (ILSAs) play an important role in educational research and policy making. They collect valuable data on education quality and performance development across many education systems, giving countries the opportunity to share techniques, organisational structures, and policies that have proven efficient and successful. To gain insights from ILSA data, we identify non-cognitive variables associated with students’ academic performance. This problem has three analytical challenges: (a) academic performance is measured by cognitive items under a matrix sampling design; (b) there are many missing values in the non-cognitive variables; and (c) multiple comparisons due to a large number of non-cognitive variables. We consider an application to the Programme for International Student Assessment, aiming to identify non-cognitive variables associated with students’ performance in science. We formulate it as a variable selection problem under a general latent variable model framework and further propose a knockoff method that conducts variable selection with a controlled error rate for false selections.