bluuebunny/crossref_metadata_2025 huggingface dataset:
The mechanics of male courtship display behaviour in the Ptiloris riflebirds (Aves: Paradisaeidae)
Authors: MacGillavry Thomas , Frith Clifford B , Fusani Leonida
Published: September 2024

Sexual selection through female choice has driven the evolution of some of the most elaborate signalling behaviours in animals. These displays often require specialized morphological adaptations and may incorporate signals in multiple sensory modalities. Visual and acoustic signals are often precisely choreographed in temporally structured courtship performances, though the precise mechanics of such signalling behaviours are often enigmatic. We find that riflebirds (genus Ptiloris)—a bird of paradise clade—achieve their remarkable display postures by hyperextending the wrist joint, vastly exceeding the maximal wrist extension capabilities of any other known bird. Using video collected in the field, we then show that this hypermobility is required for a sonation unique to riflebirds, and find that the yellow interior of the mouth is displayed in the dynamic phase of display. As this sonation cannot be produced when the mouth is exposed, it represents a mechanical constraint to signal design. Finally, we used a large morphometric dataset to describe patterns of sexual dimorphism in wing length across diverse bird of paradise species, and find evidence of sexual selection for large and structurally modified wings used in riflebird displays. Our study highlights nuanced choreographic differences in the display behaviours of different riflebird species, and sheds light on the intricate design features of sexual signals in this fascinating taxon.
Mitogenomics of a declining species, the Rio Grande silvery minnow (Hybognathus amarus), with boom–bust population dynamics
Authors: Osborne Megan J , Caeiro-Dias Guilherme , Turner Thomas F
Published: September 2024

Large mitochondrial DNA fragments and nearly complete mitogenomes were obtained from nextera-tagmented reductively amplified DNA (nextRAD) data from the Rio Grande silvery minnow (Hybognathus amarus). We used these data to characterize variation across the mitogenome and to evaluate changes in mitochondrial diversity across a 20 year time series punctuated by marked species decline. We observed different evolutionary rates among protein-coding genes and inflated values of the ratio of non-synonymous change to non-synonymous sites to synonymous changes per synonymous site for several protein-coding genes, violating assumptions of selective neutrality. Analyses suggested that non-synonymous substitutions are effectively neutral, and our results were not consistent with genetic draft. Mitogenomes revealed large long-term effective population size for Rio Grande silvery minnow, and time-series data indicated recent reductions in mitochondrial diversity via genetic drift associated with population bottlenecks. The results presented in this study show that in some cases, nextRAD sequences contain informative mitochondrial DNA data.
Management and outcomes of hidradenitis suppurativa in solid organ transplant recipients
Authors: Imhof Reese L , Dai Christina , Alavi Afsaneh , Sokumbi Olayemi
Published: September 2024

This case series includes patients with hidradenitis suppurativa (HS) who underwent solid organ transplant with subsequent transplant-related immunosuppression. Most patients in this case series experienced improvement of their HS following the initiation of transplant immunosuppressive treatment, particularly with the majority on tacrolimus and mycophenolate mofetil.
Deep learning-assisted distinguishing breast phyllodes tumours from fibroadenomas based on ultrasound images: a diagnostic study
Authors: Yan Yuqi , Liu Yuanzhen , Yao Jincao , Sui Lin , Chen Chen , Jiang Tian , Liu Xiaofang , Wang Yifan , Ou Di , Chen Jing , Wang Hui , Feng Lina , Pan Qianmeng , Su Ying , Wang Yukai , Wang Liping , Zhou Lingyan , Xu Dong
Published: September 2024

Objectives

To evaluate the performance of ultrasound-based deep learning (DL) models in distinguishing breast phyllodes tumours (PTs) from fibroadenomas (FAs) and their clinical utility in assisting radiologists with varying diagnostic experiences.

Methods

We retrospectively collected 1180 ultrasound images from 539 patients (247 PTs and 292 FAs). Five DL network models with different structures were trained and validated using nodule regions annotated by radiologists on breast ultrasound images. DL models were trained using the methods of transfer learning and 3-fold cross-validation. The model demonstrated the best evaluation index in the 3-fold cross-validation was selected for comparison with radiologists’ diagnostic decisions. Two-round reader studies were conducted to investigate the value of DL model in assisting 6 radiologists with different levels of experience.

Results

Upon testing, Xception model demonstrated the best diagnostic performance (area under the receiver-operating characteristic curve: 0.87; 95% CI, 0.81-0.92), outperforming all radiologists (all P < .05). Additionally, the DL model enhanced the diagnostic performance of radiologists. Accuracy demonstrated improvements of 4%, 4%, and 3% for senior, intermediate, and junior radiologists, respectively.

Conclusions

The DL models showed superior predictive abilities compared to experienced radiologists in distinguishing breast PTs from FAs. Utilizing the model led to improved efficiency and diagnostic performance for radiologists with different levels of experience (6-25 years of work).

Advances in knowledge

We developed and validated a DL model based on the largest available dataset to assist in diagnosing PTs. This model has the potential to allow radiologists to discriminate 2 types of breast tumours which are challenging to identify with precision and accuracy, and subsequently to make more informed decisions about surgical plans.
Assessing fat fraction and R2* value of lumbar spine based on MRI as a marker of bone mineral density
Authors: Zhou Feng , Sheng Bo , Lv Furong
Published: September 2024

Objectives

The study aimed to investigate the correlation between fat fraction (FF), R2* value of vertebrae based on IDEAL-IQ sequence and bone mineral density (BMD) based on QCT, and their diagnostic value for low BMD and osteoporosis.

Methods

Subgroups were divided according to different gender, age, BMI, and bone mass to compare the differences in parametric variables. One-way ANOVA, independent samples t-test, correlation coefficient analysis, linear regression analysis, and ROC curve analysis were performed.

Results

Significant differences were found in FF among different bone mass groups, and between different gender and age groups. While R2* only had a significant difference between different gender groups and males with different ages. BMD was significantly negatively correlated with FF, especially in women, and FF significantly negatively affected BMD after controlling for gender, age, and BMI. There was mildly positive correlation between BMD and R2* in men, and R2* significantly positively influenced BMD controlling for the confounders. In addition, FF was positively correlated with age, whereas R2* was negatively correlated with age in men. FF had high diagnostic efficacy for low bone mass and osteoporosis, while R2* alone was weakly diagnostic.

Conclusions

Vertebral FF can be served as a potentially important imaging biomarker for assessing low BMD and osteoporosis, and R2* of males can be utilized as a complementary parameter for evaluating osteoporosis.

Advances in knowledge

The IDEAL-IQ sequence has the potential to be used as an accessory examination in the diagnosis of osteoporosis, assessment of treatment efficacy, and prediction of fracture risk.
Lifetime history of head injury is associated with reduced perivascular space number in acute mild traumatic brain injury
Authors: Garcia Kiersten J , Brolly Grace , Ng Daniel , Bederson Maria , Martinez Pedro , Whiting Mark D
Published: September 2024

Traumatic brain injury impairs function of the glymphatic system, a perivascular network involved in waste clearance. Enlarged perivascular spaces visible on MRI are an emerging biomarker of glymphatic function. This study characterized enlarged perivascular spaces in acute head injury with 7 T MRI. Healthy controls (n = 8) and patients (n = 11) with mild traumatic brain injury underwent MRI within 7 days of injury and were evaluated for lifetime history of head injury, neurobehavioral symptoms and sleep disturbances. MRI-visible perivascular spaces were quantified and assessed according to published criteria. The number of enlarged perivascular spaces was significantly higher in traumatic brain injury patients than controls (P = 0.015). Among healthy controls, 6/8 scored ‘none’ or ‘mild’ on the perivascular space rating scale, while 10/11 patients scored ‘moderate’, ‘frequent’ or ‘severe’. There was an inverse relationship between perivascular space number and number of lifetime head injuries. Patients with more prior head injuries exhibited fewer enlarged perivascular spaces (P = 0.014). These results indicate that mild head injury results in acute alterations in perivascular space number, and this effect is mediated by previous head injury history. Enlarged perivascular spaces may reflect a glymphatic response that is diminished after multiple head injuries, although this will require further study.
Highly efficient direct air capture using solid–liquid phase separation in aqueous diamine solution as sorbent
Authors: Cao Furong , Kikkawa Soichi , Yamada Hidetaka , Yamazoe Seiji
Published: September 2024

To reduce climate change, absorbing CO2 directly from the air (DAC) with high-efficient CO2 absorption, low-cost, and environmentally friendly system has been attracted much attention for several decades. In this work, a series of aqueous diamine solutions was examined for 400 ppm CO2 absorption at ambient temperature. The absorbents exhibited CO2 absorption with molar ratio of 1 molCO2/molamine, and aqueous isophorone diamine (IPDA) in particular showed >99% CO2 removal even under a 500 mL min−1 flow of 400 ppm CO2–N2 with the contact rate of 13,761.5 h−1 between CO2 and IPDA aqueous solution and the CO2 absorption rate of 4.46 mmol/L min. A precipitate of carbamic acid of IPDA was formed by reaction with CO2, and the CO2 removal efficiency was enhanced by increasing the solution viscosity by the formation of this precipitate. The CO2 was absorbed in aqueous IPDA solution as carbamic acid of IPDA and bicarbonate/carbonate species, and the absorbed CO2 could desorb by heating under O2-containing gas flow, which indicates our system is applicable to the CO2 condensation for a plant growth. This work provides fundamental information to establishing a solid–liquid phase change system with a high-efficient and environmentally friendly DAC system using aqueous solvent.
High- and low-social-anxiety individuals process the outcomes of ability comparisons differently: an event-related potential study
Authors: Liu Siqi , Chen Peiqi , Qin Shaozhen , Mai Xiaoqin
Published: September 2024

Individuals engage in upward or downward comparisons with superiors or inferiors, respectively. Social comparison is associated with social anxiety. Utilizing event-related potentials, we investigated how individuals with high social anxiety (HSA) and low social anxiety (LSA) evaluate self- versus other-outcomes in upward and downward comparison contexts. We found significant valence effects of self- or other-outcomes on feedback-related negativity (FRN) and P300 for both groups, with loss inducing larger FRN and smaller P300 than gain. In the early stage, the valence effect of other-outcomes was significant when LSA participants gained money, but not when they lost money, revealing a social comparison effect on FRN. Conversely, this valence effect was significant whether HSA participants gained or lost money. At the late stage, the valence effect of other-outcomes was significant when HSA or LSA participants gained money but not when they lost, revealing social comparison effects on the P300. Notably, only the social comparison effect in the LSA group was further moderated by comparison direction. These findings suggest that LSA participants engaged in social comparison throughout all evaluation stages, whereas HSA participants started at the late stage. Moreover, LSA participants were more sensitive to different comparison directions in the late stage.
Cerebral white matter injury in haemodialysis patients: a cross-sectional tract-based spatial statistics and fixel-based analysis
Authors: Qi Yu , Song Lijun , Liu Xu , Xu Boyan , Yang Wenbo , Li Mingan , Li Min , Zhu Zhengyang , Liu Wenhu , Yang Zhenghan , Wang Zhenchang , Wang Hao
Published: September 2024

Background

End-stage renal disease (ESRD) patients on maintenance haemodialysis (HD) often have damage to brain white matter (WM) and cognitive impairment. However, whether this damage is caused by maintenance HD or renal dysfunction is unclear. Herein we investigate the natural progression of WM damage in patients with ESRD and the effects of HD on WM using tract-based spatial statistics (TBSS) and fixel-based analysis (FBA).

Methods

Eighty-one ESRD patients, including 41 with no dialysis (ND) and 40 on HD, and 46 healthy controls (HCs) were enrolled in this study. The differences in WM among the three groups [ESRD patients with HD (ESRD-HD), ESRD patients without HD (ESRD-ND) and HCs] were analysed using TBSS and FBA. Pairwise comparison was then used to compare the differences in WM between two groups. The relationships between WM and neurocognitive assessments/clinical data were analysed in ESRD patients with and without HD.

Results

The damage to WM in ESRD-ND and ESRD-HD appeared around the lateral ventricles in TBSS, while FBA reflected that the changes had extended to adjacent WM in the anterior hemisphere, with a larger region in ESRD-HD compared with ESRD-ND and the brainstem was also widely affected in ESRD-HD. The Montreal Cognitive Assessment (MoCA) scores were lower in the ESRD-HD group. RD in the body of the corpus callosum were negatively correlated with MoCA scores in both groups. Fiber density and cross-section (FDC) in the left thalamo-prefrontal projection (T_PREFL) and left and right cingulum (CGL and CGR) were positively correlated with MoCA scores in both groups. Creatinine (Cr) was positively correlated with FDC in some frontal projection fibres in the striatum and thalamus, CG and fronto-pontine tract and was positively correlated with FD mainly in premotor projection fibres in the striatum and thalamus in the ESRD-HD group. Cr was negatively correlated with mean and radial diffusivity in regions of the corona radiata in the ESRD-ND group.

Conclusions

FBA is more sensitive in detecting differences between ESRD patients and HCs. When ESRD patients receive maintenance HD, the degree of WM damage may not be aggravated, but the range of damaged WM may be expanded, especially in the anterior hemisphere and brainstem. Some of these changes in the anterior hemisphere may contribute to cognitive decline.
Silent severe aortic regurgitation due to blunt chest trauma: ignore it at your peril—a case report
Authors: Markides Rafaella I L , Rosendahl Ulrich P , Roussin Isabelle
Published: September 2024

Background

Blunt chest trauma (BCT) presenting to the emergency department is common and may cause life-threatening cardiac complications. Whilst complications causing haemodynamic instability are generally detected promptly, others may present late with long-term consequences. We describe a rare, serious complication of BCT presenting five years after a road traffic accident (RTA).

Case summary

A 23-year-old man was incidentally found to have a murmur. Past history was notable only for BCT with rib fracture sustained in a RTA 5 years prior. Examination revealed a hyperdynamic pulse, loud decrescendo diastolic murmur, and Duroziez’s sign over the femoral arteries. Echocardiography showed severe valvular aortic regurgitation (AR) from a hole in the left coronary cusp and holodiastolic flow reversal in the descending aorta. The left ventricle (LV) showed marked dilatation in diastole, mild dilatation in systole, and preserved systolic function. The aorta was normal. Severe AR was attributed to his previous BCT, with AR causing subsequent LV dilatation. He underwent aortic valve replacement (AVR) with rapid recovery. He remains well, and his echo shows a well-functioning AVR with normalization of LV dimensions.

Discussion

Aortic regurgitation following BCT is rare but well-recognized, most often resulting from RTAs. Only a third of cases are diagnosed acutely. In others, lack of haemodynamic instability means that emergency echocardiography is not routinely performed, such that this may go unrecognized with long-term consequences. Clinicians should be aware of possible valve damage following BCT. Prompt echocardiography should be routinely performed for all BCT at initial presentation, even without haemodynamic instability.
The phenotype of the pediatric patient with Cushing syndrome but without obesity
Authors: Padilla Cameron , Stratakis Constantine A , Tatsi Christina
Published: September 2024

Objective

Cushing syndrome (CS) often presents with obesity that is not as severe in children as it is in adults. The role of obesity in the severity of metabolic syndrome in children with CS has not been studied. This study evaluates whether pediatric patients with CS have obesity-specific differences in their demographic, biochemical, and presenting findings.

Design

Cohort study.

Participants and Methods

We analyzed 273 patients with young onset of CS at ≤18 years old and who were classified as patients with or without obesity based on their BMI z scores.

Results

Patients without obesity (n = 84, 31%) were more frequently females with an older age of onset compared with patients with obesity (n = 189, 69%). Consistent with their older age, patients without obesity were also more likely to have advanced Tanner stages. Patients with and without obesity had a similar duration of disease, but patients with obesity showed higher markers of hypercortisolemia (urinary free cortisol, UFC). A higher prevalence of hypertension and insulin resistance was seen in patients with obesity than those without obesity, adjusting for UFC (P < .05 for all comparisons). While fatty liver disease was not statistically different among the entire cohort, elevated alanine transaminase and metabolic dysfunction–associated steatotic liver disease scores were more common in ACTH-dependent CS patients with obesity (P < .05).

Conclusions

Weight gain appears to mediate some but not all the cortisol-associated complications in pediatric CS. Therefore, obesity may be a modifiable risk factor among these patients.
Risk of sleep-disordered breathing in orthodontic patients: comparison between children and adolescents
Authors: Jost Patrícia , Conte Ana Lurdes , Lira Adriana de Oliveira , Pugliese Fernando , Palomo Juan Martin , Quevedo Beatriz , Garib Daniela
Published: September 2024

Objective

The aim of this study was to assess the risk of sleep-disordered breathing (SDB) in orthodontic patients and to evaluate the influence of sex, age, and orthodontic treatment in a cohort of subjects using the Pediatric Sleep Questionnaire (PSQ) screening tool.

Methods

Parents of 245 patients aged 5–18 years (11.4 ± 3.3 years) were invited to participate in the study by answering the PSQ, which has 22 questions about snoring, sleepiness, and behavior. The frequency of high and low risk was calculated for the full sample. Multiple logistic regression was used to assess the association among sex, age, orthodontic treatment, rapid maxillary expansion (RME), and body mass index (BMI) with SDB. A significance level of 5% (P < .05) was adopted in all tests.

Results

A high risk of SDB was found in 34.3% of the sample. No sex and BMI difference was found for the risk of SDB. The high risk of SDB was significantly associated with younger ages (OR = 1.889, P = .047), pre-orthodontic treatment phase (OR = 3.754, P = .02), and RME (OR = 4.157, P = .001).

Limitations

Lack of ear, nose and throat-related medical history.

Conclusion

Children showed a 1.8 higher probability of having a high risk of SDB compared with adolescents. Patients before orthodontic treatment and patients submitted to RME showed a high risk of SDB.
What is known about the challenges people with Parkinson’s disease experience with their medicines and what solutions have been explored to overcome them? A scoping review
Authors: Jones Shelley , Patel Jignesh P , Twigg Michael J , Chaudhuri Kallol Ray
Published: September 2024

Background

The symptomatic management of Parkinson’s disease (PD) relies heavily on medications, which increase in complexity as the disease progresses.

Objectives

To describe (i) the extent, range, and nature of research describing the experience and challenges people with PD and their carers have with their medicines for symptomatic treatment, and (ii) any interventions that have been reported in a community setting that address medicine-related challenges experienced by people with PD.

Methods

The scoping review searched electronic databases (EMBASE, PubMed, and CINAHL). The studies included were full-text articles in English only, including conference abstracts that focussed on patients with PD or their carers and discussed medicines in the primary care setting, even where this was not the primary focus.

Results

Thirty-nine papers were taken forward for data extraction. Twenty described patient experience and challenges. Although none were explicitly focussed on medications, they did highlight challenges including the work of taking multiple medications and a desire for non-oral formulations. Nineteen described or tested interventions to support people with PD with their medication including community pharmacist-led reviews, medication compliance aids, and the use of text message reminders. These were all small-scale feasibility and pilot studies, and none were grounded in a methodological framework. Positive outcomes were reported against various scales, but no evidence of scaling up any of the interventions was found.

Conclusion

There is very little published research surrounding the challenges people with PD have with their medicines. The published research that does exist alludes to challenges with medicines taking in people with PD but identifies a gap in the detail and understanding. Further work is required to improve our understanding and allow the development of sustainable interventions that support people with PD and their carers.
Real-world data on long-acting intramuscular maintenance therapy with cabotegravir and rilpivirine mirror Phase 3 results
Authors: Serris Alexandra , Ferre Valentine Marie , Le Hingrat Quentin , Bachelard Antoine , Charpentier Charlotte , Exarchopoulos Marina , Damond Florence , Phung Bao-Chau , Landman Roland , Yazdanpanah Yazdan , Descamps Diane , Joly Véronique , Peytavin Gilles , Ghosn Jade
Published: September 2024

Introduction

Cabotegravir, an integrase strand transfer inhibitor, and rilpivirine, an NNRTI, constitute the first long-acting (LA), injectable, two-drug ART regimen approved for the maintenance of virological suppression in persons living with HIV-1 (PLHIV). The aim of this study was to assess clinical effectiveness and tolerability of LA cabotegravir/rilpivirine in a real-world setting.

Patients and methods

We conducted a retrospective, single centre study, including all PLHIV receiving LA cabotegravir/rilpivirine as standard-of-care in our tertiary centre even if initiated in clinical trials.

Results

Between 2014 and 2022, 126 PLHIV initiated LA cabotegravir/rilpivirine. All were ART-experienced, and 98.4% had a viral load (VL) of <50 copies/mL before LA cabotegravir/rilpivirine initiation. Median BMI at cabotegravir/rilpivirine initiation was 24 IQR (23–28). During a median follow-up of 9 months IQR (7–24), 27 patients discontinued cabotegravir/rilpivirine: 5 because of virological failure, 6 for adverse events, 11 for personal reasons unrelated to treatment tolerance and 5 for other reasons. Virological failure was not associated with a higher BMI, nor with weight gain during LA intramuscular (IM) cabotegravir/rilpivirine treatment, inadequate cabotegravir and rilpivirine concentrations, VL blips or the use of oral lead-in (OLI) or not. No drug resistance-associated mutation emerged. Adverse events leading to treatment interruption were injection-site pain (n = 3) and neuropsychological side effects (n = 3). A correlation between BMI and both cabotegravir and rilpivirine concentrations at 1 month post-initiation of LA-IM cabotegravir/rilpivirine was observed, with no impact of OLI.

Conclusions

Data from this real-world cohort of PLHIV who received cabotegravir/rilpivirine LA injections suggest that this regimen is effective and well tolerated. Virological failures were not associated with the acquisition of resistance mutations.
Genome analysis of tigecycline-resistant Acinetobacter baumannii reveals nosocomial lineage shifts and novel resistance mechanisms
Authors: Qian Changrui , Hu Panjie , Guo Wenhui , Han Yijia , Yu Pingting , Zhang Yi , Ma Zhexiao , Chen Lijiang , Zhou Tieli , Cao Jianming
Published: September 2024

Objectives

To investigate the characteristics and clonal dynamics of tigecycline-resistant Acinetobacter baumannii (TRAB) isolates from a Chinese hospital from 2016 to 2021.

Methods

A total of 64 TRAB isolates were screened and WGS was performed. Phylogenetic analysis and non-polymorphic mutation analysis were used to analyse their clonal dynamics and tigecycline resistance-related mutations. RT-PCR was used to analyse the expression of the resistance-nodulation cell-division (RND) efflux pump genes adeB and adeJ. Gene cloning was used to explore the effect of tet(39) variants on tigecycline resistance.

Results

Most TRAB isolates were found to be MDR, with 95% (61/64) of the isolates showing resistance to carbapenems. These TRAB isolates were classified into three primary genetic clusters based on core-genome SNPs. The KL2 cluster persisted throughout the study period, whereas the KL7 cluster emerged in 2019 and became the dominant clone. The KL7 cluster carried more antimicrobial resistance genes than the other two clusters. The predominant tigecycline resistance mechanism of the KL2 cluster and KL7 cluster was IS insertion in adeN (82.1%, 23/28) and genetic alterations in adeS (76.2%, 16/21), respectively. Eleven novel AdeS mutations were identified associated with elevated AdeB expression and tigecycline resistance. Moreover, we characterized a plasmid-borne tet(39) variant with an Ala-36-Thr substitution that synergizes with the RND efflux pump to confer high-level tigecycline resistance.

Conclusions

This work provides important insights into the diverse mechanisms associated with tigecycline resistance in A. baumannii, highlighting a pressing need for further monitoring of ST2-KL7 A. baumannii in clinical settings.
COVID-19 in patients receiving treatment at an outpatient chemotherapy unit
Authors: Kinoshita Shiori , Takemoto Masashi , Asaoka Minami , Haraguchi Yoko , Adachi Tamami , Iida Shinsuke , Komatsu Hirokazu
Published: September 2024

During the COVID-19 pandemic period, many patients who required outpatient chemotherapy developed COVID-19, requiring chemotherapy interruption. However, there are no clear guidelines regarding the safe timing for restarting chemotherapy. We conducted a retrospective study to assess when such patients can safely recommence chemotherapy. Of the 40 patients included in this study, 34 restarted anticancer drug therapy after COVID-19 infection. Six patients, four with multiple myeloma, and one each with follicular lymphoma and glioma, remained SARS-CoV-2 antigen positive >20 days after COVID-19 onset. Multiple myeloma patients recorded significantly higher frequencies of SARS-CoV-2 antigen positivity >20 days after COVID-19 onset compared with solid tumor patients, with no significant differences in the frequency of SARS-CoV-2 positivity during 5–20 days from COVID-19 onset between them. According to our data, most solid tumor patients achieved SARS-CoV-2 antigen negativity after 20 days from COVID-19 onset. On the other hand, multiple myeloma patients might need serial antigen tests before restarting anticancer therapy in the outpatient chemotherapy setting.
A Bayesian complex-valued latent variable model applied to functional magnetic resonance imaging
Authors: Sakitis Chase J , Brown D Andrew , Rowe Daniel B
Published: September 2024

In linear regression, the coefficients are simple to estimate using the least squares method with a known design matrix for the observed measurements. However, real-world applications may encounter complications such as an unknown design matrix and complex-valued parameters. The design matrix can be estimated from prior information but can potentially cause an inverse problem when multiplying by the transpose as it is generally ill-conditioned. This can be combat by adding regularizers to the model but does not always mitigate the issues. Here, we propose our Bayesian approach to a complex-valued latent variable linear model with an application to functional magnetic resonance imaging (fMRI) image reconstruction. The complex-valued linear model and our Bayesian model are evaluated through extensive simulations and applied to experimental fMRI data.
Jones & Sufrin's EU Competition Law
Authors: Brenda Sufrin , Niamh Dunne , Alison Jones
Published: September 2024

EU Competition Law: Text, Cases, and Materials provides a complete guide to European competition law in a single authoritative volume. Carefully selected extracts from key cases, academic articles, and statutory materials are accompanied by in-depth author commentary from three experienced academics in the field. Thorough footnoting and referencing give a tour of the available literature, making this an ideal text and stand-alone resource for undergraduate and postgraduate students, as well as for competition law scholars engaged in specialised study. This eighth edition has been fully updated with detailed coverage and commentary on recent developments. These include contemporary concerns about the objectives, interpretation, and application of competition law in the light of sustainability imperatives including the EU’s Green Deal, worldwide economic and political upheaval stemming in particular from the Covid-19 pandemic and the war in Ukraine, and continuing developments in the digital economy; the EU Courts’ judgments on Articles 101, 102, and mergers including Intel (RENV), Google and Alphabet, Google (Android), Slovak Telekom, Generics, Lundbeck, and CK Telecoms; cases on the Commission’s enforcement powers and judicial review, including Sped-Pro and Slovak Telekom; new legislation, guidelines, and notices (in final form or draft) on vertical agreements, horizontal agreements, and market definition; Commission actions in the pharmaceutical, energy, and financial sectors, including interaction with regulatory rules, liberalisation programmes, and intellectual property law; private litigation in the wake of the directive on damages, including the Court’s judgments in Sumal and Paccar; and thorough discussion of ongoing developments in competition law such as the Commission’s enforcement policy against cartels, the appraisal of mergers, the use of commitments decisions, the use of comfort letters during Covid-19 and the Commission’s revised notice on informal guidance, and the increasing activity by national competition authorities. The eighth edition contains an entirely new chapter on the digital economy, including detailed coverage of the Digital Markets Act.
Investigating temporary capture in the Sun–Jupiter three-body system via Lagrangian coherent structures
Authors: Li Zhenyu , Qiao Dong , Li Xiangyu
Published: September 2024

The temporary capture (TC) of Jupiter-family objects has long been a pivotal focus in celestial mechanics research. This study investigates the TC of objects near Jupiter within the context of the planar circular restricted three-body problem (PCRTBP), employing Lagrangian coherent structures (LCSs) and periapsis Poincaré maps. Initially, LCSs are identified via periapsis Poincaré maps and applied to segment the phase space. Parameter scanning enables a detailed analysis, classifying the orbital behaviours of objects in the proximity of Jupiter into three distinct categories: TC, low-energy flyby, and collision, each designating specific regions in phase space. Subsequently, a novel method for screening potential TC objects within the Jupiter system is proposed and validated, informed by the dynamic characteristics of TC motions. The efficacy of this method is illustrated by the re-identification of six known TC comets and the prediction of a prospective TC asteroid, 2002 GV28. Within the framework of the PCRTBP, analogous TC trajectories for these comets and asteroids are identified, offering novel insights into the dynamics of TC events.
Functional Characterization Supports Multiple Evolutionary Origins of Pheromone Receptors in Bark Beetles
Authors: Biswas Twinkle , Sims Cassie , Yuvaraj Jothi Kumar , Roberts Rebecca E , Löfstedt Christer , Andersson Martin N
Published: September 2024

Chemical communication using pheromones is thought to have contributed to the diversification and speciation of insects. The species-specific pheromones are detected by specialized pheromone receptors (PRs). Whereas the evolution and function of PRs have been extensively studied in Lepidoptera, only a few PRs have been identified in beetles, which limits our understanding of their evolutionary histories and physiological functions. To shed light on these questions, we aimed to functionally characterize potential PRs in the spruce bark beetle Ips typographus (“Ityp”) and explore their evolutionary origins and molecular interactions with ligands. Males of this species release an aggregation pheromone comprising 2-methyl-3-buten-2-ol and (4S)-cis-verbenol, which attracts both sexes to attacked trees. Using two systems for functional characterization, we show that the highly expressed odorant receptor (OR) ItypOR41 responds specifically to (4S)-cis-verbenol, with structurally similar compounds eliciting minor responses. We next targeted the closely related ItypOR40 and ItypOR45. Whereas ItypOR40 was unresponsive, ItypOR45 showed an overlapping response profile with ItypOR41, but a broader tuning. Our phylogenetic analysis shows that these ORs are present in a different OR clade as compared to all other known beetle PRs, suggesting multiple evolutionary origins of PRs in bark beetles. Next, using computational analyses and experimental validation, we reveal two amino acid residues (Gln179 and Trp310) that are important for ligand binding and pheromone specificity of ItypOR41 for (4S)-cis-verbenol, possibly via hydrogen bonding to Gln179. Collectively, our results shed new light on the origins, specificity, and ligand binding mechanisms of PRs in beetles.
Genomic Signatures of Domestication in a Fungus Obligately Farmed by Leafcutter Ants
Authors: A Leal-Dutra Caio , Vizueta Joel , Baril Tobias , Kooij Pepijn W , Rødsgaard-Jørgensen Asta , Conlon Benjamin H , Croll Daniel , Shik Jonathan Z
Published: September 2024

The naturally selected fungal crop (Leucoagaricus gongylophorus) farmed by leafcutter ants shows striking parallels with artificially selected plant crops domesticated by humans (e.g., polyploidy, engorged nutritional rewards, dependence on cultivation). To date, poorly resolved L. gongylophorus genome assemblies based on short-read sequencing have constrained hypotheses about how millions of years under cultivation by ants shaped the fungal crop genome and potentially drove domestication. We use PacBio HiFi sequencing of L. gongylophorus from the leafcutter ant Atta colombica to identify 18 putatively novel biosynthetic gene clusters that likely cemented life as a cultivar (e.g., plant fragment degradation, ant-farmer communication, antimicrobial defense). Comparative analyses with cultivated and free-living fungi showed genomic signatures of stepwise domestication transitions: 1) free-living to ant-cultivated: loss of genes conferring stress response and detoxification, 2) hyphal food to engorged nutritional rewards: expansions of genes governing cellular homeostasis, carbohydrate metabolism, and siderophore biosynthesis, and 3) detrital provisioning to freshly cut plant fragments: gene expansions promoting cell wall biosynthesis, fatty acid metabolism, and DNA repair. Comparisons across L. gongylophorus fungi farmed by three leafcutter ant species highlight genomic signatures of exclusively vertical clonal propagation and widespread transposable element activity. These results show how natural selection can shape domesticated cultivar genomes towards long-term ecological resilience of farming systems that have thrived across millennia.
Maturational competence of equine oocytes is associated with alterations in their ‘cumulome’
Authors: Walter Jasmin , Colleoni Silvia , Lazzari Giovanna , Fortes Claudia , Grossmann Jonas , Roschitzki Bernd , Laczko Endre , Naegeli Hanspeter , Bleul Ulrich , Galli Cesare
Published: September 2024

Assisted reproductive technologies are an emerging field in equine reproduction, with species-dependent peculiarities, such as the low success rate of conventional IVF. Here, the ‘cumulome’ was related to the developmental capacity of its corresponding oocyte. Cumulus–oocyte complexes collected from slaughterhouse ovaries were individually matured, fertilized by ICSI, and cultured. After maturation, the cumulus was collected for proteomics analysis using label-free mass spectrometry (MS)-based protein profiling by nano-HPLC MS/MS and metabolomics analysis by UPLC-nanoESI MS. Overall, a total of 1671 proteins and 612 metabolites were included in the quantifiable ‘cumulome’. According to the development of the corresponding oocytes, three groups were compared with each other: not matured (NM; n = 18), cleaved (CV; n = 15), and blastocyst (BL; n = 19). CV and BL were also analyzed together as the matured group (M; n = 34). The dataset revealed a closer connection within the two M groups and a more distinct separation from the NM group. Overrepresentation analysis detected enrichments related to energy metabolism as well as vesicular transport in the M group. Functional enrichment analysis found only the KEGG pathway ‘oxidative phosphorylation’ as significantly enriched in the NM group. A compound attributed to ATP was observed with significantly higher concentrations in the BL group compared with the NM group. Finally, in the NM group, proteins related to degradation of glycosaminoglycans were lower and components of cumulus extracellular matrix were higher compared to the other groups. In summary, the study revealed novel pathways associated with the maturational and developmental competence of oocytes.
4CAC: 4-class classifier of metagenome contigs using machine learning and assembly graphs
Authors: Pu Lianrong , Shamir Ron
Published: September 2024

Microbial communities usually harbor a mix of bacteria, archaea, plasmids, viruses and microeukaryotes. Within these communities, viruses, plasmids, and microeukaryotes coexist in relatively low abundance, yet they engage in intricate interactions with bacteria. Moreover, viruses and plasmids, as mobile genetic elements, play important roles in horizontal gene transfer and the development of antibiotic resistance within microbial populations. However, due to the difficulty of identifying viruses, plasmids, and microeukaryotes in microbial communities, our understanding of these minor classes lags behind that of bacteria and archaea. Recently, several classifiers have been developed to separate one or more minor classes from bacteria and archaea in metagenome assemblies. However, these classifiers often overlook the issue of class imbalance, leading to low precision in identifying the minor classes. Here, we developed a classifier called 4CAC that is able to identify viruses, plasmids, microeukaryotes, and prokaryotes simultaneously from metagenome assemblies. 4CAC generates an initial four-way classification using several sequence length-adjusted XGBoost models and further improves the classification using the assembly graph. Evaluation on simulated and real metagenome datasets demonstrates that 4CAC substantially outperforms existing classifiers and combinations thereof on short reads. On long reads, it also shows an advantage unless the abundance of the minor classes is very low. 4CAC runs 1–2 orders of magnitude faster than the other classifiers. The 4CAC software is available at https://github.com/Shamir-Lab/4CAC.
Crystal structure and nucleic acid binding mode of CPV NSP9: implications for viroplasm in Reovirales
Authors: Wang Yeda , Guo Hangtian , Lu Yuhao , Yang Wanbin , Li Tinghan , Ji Xiaoyun
Published: September 2024

Cytoplasmic polyhedrosis viruses (CPVs), like other members of the order Reovirales, produce viroplasms, hubs of viral assembly that shield them from host immunity. Our study investigates the potential role of NSP9, a nucleic acid-binding non-structural protein encoded by CPVs, in viroplasm biogenesis. We determined the crystal structure of the NSP9 core (NSP9ΔC), which shows a dimeric organization topologically similar to the P9-1 homodimers of plant reoviruses. The disordered C-terminal region of NSP9 facilitates oligomerization but is dispensable for nucleic acid binding. NSP9 robustly binds to single- and double-stranded nucleic acids, regardless of RNA or DNA origin. Mutagenesis studies further confirmed that the dimeric form of NSP9 is critical for nucleic acid binding due to positively charged residues that form a tunnel during homodimerization. Gel migration assays reveal a unique nucleic acid binding pattern, with the sequential appearance of two distinct complexes dependent on protein concentration. The similar gel migration pattern shared by NSP9 and rotavirus NSP3, coupled with its structural resemblance to P9-1, hints at a potential role in translational regulation or viral genome packaging, which may be linked to viroplasm. This study advances our understanding of viroplasm biogenesis and Reovirales replication, providing insights into potential antiviral drug targets.
Constitutional mosaicism of pathogenic variants in SMARCB1 in a subset of patients with sporadic rhabdoid tumors
Authors: Fleischmann Lara S , Nemes Karolina , Glaser Selina , Kouroukli Alexandra G , Boros Matej , Bens Susanne , Dahlum Sonja , Kretzmer Helene , Oyen Florian , Gerss Joachim , Hasselblatt Martin , Frühwald Michael C , Siebert Reiner
Published: September 2024

Background

Malignant rhabdoid tumors (RT) are aggressive malignancies predominantly affecting very young children. The characteristic genetic alteration is the biallelic inactivation of SMARCB1. In approximately 30% of patients, one SMARCB1 allele is constitutionally altered conferring a particularly unfavorable prognosis. Constitutional mosaicism for pathogenic SMARCB1 mutations has recently been reported in distinct cases of allegedly sporadic RT. We aimed to systematically investigate the frequency and clinical impact of constitutional mosaicism in patients with sporadic RT included in the EU-RHAB registry.

Methods

We selected 29 patients with RT displaying at least one pathogenic small variant in SMARCB1 in the tumor DNA and the absence of a germline mutation. We re-screened blood-derived patients and controlled DNA for the respective small variant by polymerase chain reaction with unique molecular identifiers and ultra-deep next-generation sequencing. Clinical data in patients with and without mosaicism and 174 EU-RHAB controls were compared.

Results

Employing an ultra-deep sequencing approach, we detected tumor-associated SMARCB1 variants in blood-derived DNA in 9/29 patients. In 6/29 patients (21%), whose variant allele frequency (VAF) exceeded 2%, constitutional mosaicism was assumed whereas tumor DNA contamination was documented in 1/3 of patients with VAF below 1%. No significant differences were observed between 6 mosaic-positive and 20 -negative patients regarding age at diagnosis, presence of metastases, event-free or overall survival.

Conclusions

Constitutional mosaicism for pathogenic small SMARCB1 variants is recurrent in patients with allegedly sporadic RT. The clinical implications of such variants need to be determined in larger, prospective cohorts also including detection of structural variants of SMARCB1.
Global decline in microbial-derived carbon stocks with climate warming and its future projections
Authors: Liang Yuting , Hu Han , Crowther Thomas W , Jörgensen Rainer Georg , Liang Chao , Chen Ji , Sun Yishen , Liu Chaoyang , Ding Jixian , Huang Aidi , Zhou Jizhong , Zhang Jiabao
Published: September 2024

Soil organic carbon (SOC) represents the largest terrestrial pool of organic carbon and is indispensable for mitigating climate change and sustaining soil fertility. As a major component of stable SOC, microbial-derived carbon (MDC) accounts for approximately half of the total SOC and has repercussions on climate feedback. However, our understanding of the spatial and temporal dynamics of MDC stocks is limited, hindering assessments of the long-term impacts of global warming on persistent SOC sequestration in the soil‒atmosphere carbon cycle. Here, we compiled an extensive global dataset and employed ensemble machine learning techniques to forecast the spatial-temporal dynamics of MDC stocks across 93.4% of the total global land area from 1981 to 2018. Our findings revealed that for every 1°C increase in temperature, there was a global decrease of 6.7 Pg in the soil MDC stock within the predictable areas, equivalent to 1.4% of the total MDC stock or 0.9% of the atmospheric C pool. Tropical regions experienced the most substantial declines in MDC stocks. We further projected future MDC stocks for the next century based on shared socioeconomic pathways, showing a global decline in MDC stocks with a potential 6–37 Pg reduction by 2100 depending on future pathways. We recommend integrating the response of MDC stocks to warming into socioeconomic models to enhance confidence in selecting sustainable pathways.