bluuebunny/crossref_metadata_2025 huggingface dataset:
High-Resolution CT Patterns of Anti-PD1 Checkpoint Inhibitor-Related Pneumonitis in Patients With Lung Cancer
Authors: Pan Xiaohuan , Xie Xiaohong , Chen Xiaojuan , Chen Huai
Published: August 2024

Background

Lung cancer has the highest morbidity and mortality in the world, and immunotherapies have been developed for this disease in recent years. However, activation of the immune system can cause immune-related adverse events (irAEs), and checkpoint inhibitor-related pneumonitis (CIP), can be the most severe and fatal. But few reports have systematically examined the spectrum of imaging findings of this condition. Therefore, the objective of this paper is to investigate the high-resolution computed tomography (HRCT) characteristics of CIP in patients with lung cancer.

Objective

To investigate the HRCT characteristics of CIP in patients with lung cancer.

Methods

HRCT patterns in 41 lung cancer patients who developed CIP after treatment with immune checkpoint inhibitors were retrospectively characterized by interstitial lung disease classification, and their severity was graded. Specific HRCT characteristics related to CIP were identified.

Results

There are 4 types of immunotherapy-induce pneumonitis patterns (organizing pneumonia OP 19 cases, nonspecific interstitial pneumonia NSIP 8 cases, acute interstitial pneumonia AIP 7 cases, 7 cases of undetermined type) and image grade (13 cases of grade 1, 17 cases of grade 2, 11 cases of grade 3, 0 cases of grade 4) were identified. Spatial distribution characteristics of these lesions were noted (17 cases predominantly distributed in tumor-containing lobes, 6 cases predominantly distributed in non–tumor-containing lobes, and no specific predilection in 18 cases). Specific CT imaging features found in CIP included, in the order of prevalence, the following: ground glass opacities (38 cases), subpleural/vertical line (37 cases), interstitial thickening around the bronchovascular bundles (36 cases), reticulation (34 cases), fine reticular shadow (31 cases), consolidation (31 cases), small cystic shadow (24 cases, may not having honeycombing), small nodules (17 cases), bronchiectasis (15 cases), honeycombing (11 cases), mosaic sign (11 cases), and pleural effusion (18 cases).

Conclusion

HRCT of CIP predominantly manifests as ground glass opacities, reticulation, subpleural/vertical line, interstitial thickening around the bronchovascular bundle, and consolidation.
Improved Pulmonary Artery Evaluation Using High-Pitch Photon-Counting CT Compared to High-Pitch Conventional or Routine-Pitch Conventional Dual-Energy CT
Authors: Yalon Mariana , Hoodeshenas Safa , Chan Alex , Horst Kelly K. , Crum Isaac , Thorne Jamison E. , Lee Yong S. , Yu Lifeng , McCollough Cynthia H. , Fletcher Joel G. , Rajiah Prabhakar Shantha
Published: August 2024

Objective

Pulmonary CT angiography (CTA) to detect pulmonary emboli can be performed using conventional dual-source CT with single-energy acquisition at high-pitch (high-pitch conventional CT), which minimizes motion artifacts, or routine-pitch, dual-energy acquisitions (routine-pitch conventional DECT), which maximize iodine signal. We compared iodine signal, radiation dose, and motion artifacts of pulmonary CTA between these conventional CT modalities and dual-source photon-counting detector CT with high-pitch, multienergy acquisitions (high-pitch photon-counting CT).

Methods

Consecutive clinically indicated pulmonary CTA exams were collected. CT number/noise was measured from the main to right lower lobe segmental pulmonary arteries using 120 kV threshold low, 120 kV, and mixed kV (0.6 linear blend) images. Three radiologists reviewed anonymized, randomized exams, rating them using a 4- or 5-point Likert scale (1 = worst, and 4/5 = best) for contrast enhancement in pulmonary arteries, motion artifacts in aortic root to subsegmental pulmonary arteries, lung image quality; pulmonary blood volume (PBV) map image quality (for multienergy or dual-energy exams), and contribution to reader confidence.

Results

One hundred fifty patients underwent high-pitch photon-counting CT (n = 50), high-pitch conventional CT (n = 50), and routine-pitch conventional DECT (n = 50). High-pitch photon-counting CT had lower radiation dose (CTDIvol: 8.1 ± 2.5 vs 9.6 ± 6.8 and 16.2 ± 8.5 mGy, respectively; P < 0.001), and routine-pitch conventional DECT had significantly less contrast (P < 0.009). CT number and CNR measurements were significantly greater at high-pitch photon-counting CT (P < 0.001). Across readers, high-pitch photon-counting CT demonstrated significantly higher subjective contrast enhancement in the pulmonary arteries compared to the other modalities (4.7 ± 0.6 vs 4.4 ± 0.7 vs 4.3 ± 0.7; P = 0.011) and lung image quality (3.4 ± 0.5 vs 3.1 ± 0.5 vs 3.1 ± 0.5; P = 0.013). High-pitch photon-counting CT and high-pitch conventional CT had fewer motion artifacts at all levels compared to DECT (P < 0.001). High-pitch photon-counting CT PBV maps had superior image quality (P < 0.001) and contribution to reader confidence (P < 0.001) compared to routine-pitch conventional DECT.

Conclusion

High-pitch photon-counting pulmonary CTA demonstrated higher contrast in pulmonary arteries at lower radiation doses with improved lung image quality and fewer motion artifacts compared to high-pitch conventional CT and routine-pitch conventional dual-energy CT.
Clinical Diagnostic Value of Shear-Wave Elastography in Detecting Malignant Nipple Retraction
Authors: Tan Rong , Liu Jie , Tang Qi , Chen Hui , Zhang Zhenhui
Published: August 2024

Objectives

In recent years, the use of shear-wave elastography (SWE) as a diagnostic tool for detecting malignant breast lesions has shown promising results. This study aims to determine the clinical diagnostic value of SWE in detecting malignant nipple retraction.

Methods

Both US and SWE (Philips EPIQ7 system) were performed for 41 consecutive patients with nipple retraction (56 nipples). The mean, median, and maximum tissue elasticity values (in kilopascals) were determined for each nipple by using SWE. The sensitivity, specificity, and overall accuracy of each measurement was determined by using the surgical pathology results or clinical diagnosis as the gold standard.

Results

Of the 56 retracted nipples, 32 were due to benign lesions, and 24 were due to malignant lesions. No significant differences in dimensions or echo features were found between the benign and malignant groups. The sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of the color Doppler flow imaging (CDFI) pattern were 63.89% (23/36), 95% (19/20), 95.83 (23/24), 59.38 (19/32), and 75% (42/56), respectively; the corresponding values for median elasticity on SWE were 88.46% (23/26), 96.67% (29/30), 95.83 (23/24), 90.63 (29/32), and 92.85 (52/56), respectively.

Conclusions

The addition of SWE to conventional US could help differentiate benign from malignant lesions associated with nipple retraction.
IGF1 and CXCR4 Respectively Related With Inhibited M1 Macrophage Polarization in Keloids
Authors: Liu Ying , Han Bing , Tan Liuchang , Ji Dongshuo , Chen Xiaofang
Published: August 2024

Purpose:

The pathophysiology of keloid remains unclear. Exploring the immune heterogeneity and new biomarkers of keloids can help design new therapeutic targets for keloid treatments and prevention.

Methods:

The authors performed single-cell RNA sequencing analysis and bulk data differential gene expression analysis of public datasets(GSE92566 and GSE163973). They used Gene Ontology (GO), Gene Set Enrichment Analysis (GSEA), and immune infiltration analysis to identify the function of the differential expressed genes. Besides, the authors performed qt-PCR on keloid tissue and adjacent normal tissues from 3 patients for further verification.

Results:

M2 macrophage increased in keloid samples than M1 macrophage. The authors identified 2 potential novel biomarkers of keloid, IGF1 and CXCR4, which could inhibit M1 macrophage polarization. The potential mechanism could be inhibiting immune responses and anti-inflammatory activities through INF signaling and E2F targeting. The differential expression of the 2 genes was verified by clinical samples.

Conclusions:

The authors identified 2 immune signaling molecules associated with keloid formation (IGF1 and CXCR4) and analyzed their potential pathogenic mechanisms.
A Novel Interdisciplinary Approach for the Management of Micrognathia (Brodie Syndrome)
Authors: Behnia Parsa , Tehranchi Azita , Dehghani Soltani Anahita , Rezayian Vida , Tabrizi Reza
Published: August 2024

This study describes a multidisciplinary approach for correcting a severe Class II malocclusion with reduced mandibular transverse dimension. A 35-year-old woman presented with an increased overjet, complaining chiefly of forwardly placed upper front teeth and unpleasant smile esthetics. The patient had a convex profile with severe mentalis strain on lip closure. Intraoral examination indicated a bilateral Class II canine relationship, scissor bite, and narrow lower arch. The skull lateral view assessment revealed a skeletal Class II relationship with reduced lower facial height. According to the diagnostic records and after consultation with the patient, surgically assisted expansion of the mandibular symphysis with a bone distractor, comprehensive orthodontic treatment, and combined jaw surgery were planned, followed by dental implant placement and prosthetic full-mouth rehabilitation. Restorative dentistry, orthodontics, and orthognathic surgery were the 3 disciplines that helped in achieving the best esthetic and functional results in this patient.
Ex-vivo Liver Resection and Autotransplantation for Liver Malignancy
Authors: Aini Abudusalamu , Lu Qian , Chen Zhiyu , Yang Zhanyu , Liu Zhipeng , Zhang Leida , Dong Jiahong
Published: August 2024

Objective:

To assess the effectiveness of optimized ex-vivo liver resection and autotransplantation (ELRA) for treating liver malignancies.

Background:

ELRA is a promising surgery for radical resection of conventionally unresectable tumors, despite the disappointing long-term prognosis during its developmental stages. A recent multicenter study reported 5-year overall and disease-free survival rates of 28% and 20.8%, respectively.

Methods:

We retrospectively analyzed data of patients who underwent ELRA for advanced liver cancers between 2009 and 2022. We applied ELRA via our novel surgical indication classification system where the surgical risk with curative intent for advanced liver malignancy was controllable using the ex-vivo approach. The ELRA was optimized for determinacy, predictability, and controllability via the precision liver surgery paradigm.

Results:

Thirty-seven cases with liver malignancies were enrolled. The operative time and anhepatic phase duration were 649.6±200.0 and 261.2±74.5 minutes, respectively, while the intraoperative blood loss was 1902±1192 mL. Negative resection margins were achieved in all patients, and the 90-day morbidity at Clavien-Dindo IIIa/IIIb and mortality rates were 27.0% and 24.3%. Post-ELRA 1-, 3-, and 5-year actual overall survival rates were 62.2%, 37.8%, and 35.1%, respectively, and 1-, 3-, and 5-year actual disease-free survival rates were 43.2%, 24.3%, and 18.9%, respectively.

Conclusions:

Long-term outcomes of ELRA under precision liver surgery for advanced liver malignancy were favorable. Appropriate criteria for disease selection and surgical indications and optimized procedures together can improve surgical treatment and patient prognosis.
Effectiveness and predictors of psychotherapy in eating disorders: state-of-the-art and future directions
Authors: Monteleone Alessio Maria , Abbate-Daga Giovanni
Published: August 2024

Purpose of review

Psychotherapy is the cornerstone of the multidisciplinary treatment approach for eating disorders. This review examines recent evidence regarding effectiveness, predictors, and mechanisms of change of psychotherapy in eating disorders, providing a road map for clinicians and researchers.

Recent findings

Family-based treatments (FBT) are effective in adolescents with anorexia nervosa and bulimia nervosa. Evidence-based psychotherapies for anorexia nervosa have no evidence of superiority compared with treatment as usual (TAU) in adults with anorexia nervosa. Cognitive–behavioural therapy (CBT) is the first-choice psychotherapy recommended for adults with bulimia nervosa and binge-eating disorder (BED). Self-help interventions have some evidence of effectiveness in nonunderweight individuals with eating disorders. Early symptom improvement and adolescent age predict more favourable outcomes.

Evidence-based psychotherapies can be suggested for eating disorders, although follow-up data are needed. Beyond anorexia nervosa, bulimia nervosa, and BED, there is no evidence of psychotherapy effectiveness in other eating disorders. The effectiveness of novel (e.g. ‘third-wave’) psychotherapies, treatment delivery modality (e.g. internet-delivered), and adjunctive interventions (e.g. virtual reality) needs to be further explored. A broader definition of recovery is recommended, including behavioural, physical, and psychological criteria. Predictors and mechanisms of changes have not been studied enough: quantitative and qualitative studies are needed to promote more tailored and individualized psychotherapy interventions.
Early intervention for eating disorders
Authors: Mills Regan , Hyam Lucy , Schmidt Ulrike
Published: August 2024

Purpose of review

Research on early intervention for eating disorders has started to gain traction and examples of this in practice are increasing. This review summarizes findings over the past 3 years, focusing on the clinical effectiveness of early intervention in practice and the barriers and facilitators to its implementation.

Recent findings

Recent developments in early intervention for eating disorders can be divided into three broad themes: research that has examined the efficacy of early intervention pathways in practice, research that has informed understanding of the target patient groups of early intervention (via clinical staging models, e.g.), and research that has suggested new ways to progress early intervention, towards becoming a standard part of best practice care.

Early intervention pathways have shown promising clinical outcomes and are viewed positively by patients, clinicians and other stakeholders. However, more robust trials of their efficacy, effectiveness and cost-effectiveness are needed. Additionally, barriers to early intervention have been identified (e.g. delayed help-seeking); research must now develop and evaluate strategies to address these. Finally, the early intervention models in practice are underpinned partly by clinical staging models for eating disorders, which require further development, especially for eating disorders other than anorexia nervosa.
Age-Related Cerebral Ventriculomegaly occurs in Patients with Primary Ciliary Dyskinesia
Authors: Eisenhuth Franziska , Agbonze Joy E. , Groh Adam M.R. , Rudko David A. , Stratton Jo Anne , Shapiro Adam J.
Published: August 2024

Primary ciliary dyskinesia (PCD) is a genetic disorder causing motile ciliary dysfunction primarily affecting the respiratory and reproductive systems. However, the impact of PCD on the central nervous system, through dysfunction of motile cilia in multiciliated ependymal cells, remains poorly understood. We hypothesized that patients with PCD exhibit sub-clinical ventriculomegaly due to ependymal ciliary dysfunction, which may influence neuropsychiatric diagnoses.

We demonstrated highly specific expression levels of known PCD-related genes in human brain ependymal cells (p<0.0001), supporting their potential role in regulating ependymal ciliary function. Computed tomography sinus images from patients with PCD (n=33) and age/sex-matched controls (n=64) were analysed. Patients with PCD displayed significantly larger ventricular areas (p<0.0001) and Evans index (p<0.01), indicating ventriculomegaly that was consistent across all genetic subgroups. Ventricular enlargement correlated positively with increasing age in patients with PCD compared to controls (p<0.001). Chart review demonstrated a high prevalence (39%) of neuropsychiatric/neurological disorders in adult PCD patients that did not correlate with degree of ventriculomegaly.

Our findings suggest that patients with PCD may have unrecognized, mild ventriculomegaly potentially due to ependymal ciliary dysfunction which correlates with ageing. Further study is required to determine if ventricular enlargement contributes to neuropsychiatric/neurological or other morbidity in PCD.
EMhub: a web platform for data management and on-the-fly processing in scientific facilities
Authors: De la Rosa-Trevin Jose M. , Sharov Grigory , Fleischmann Stefan , Morado Dustin , Bollinger John C. , Miller Darcie J. , Terry Daniel S. , Blanchard Scott C. , Fernandez Israel S. , Carroni Marta
Published: August 2024

Most scientific facilities produce large amounts of heterogeneous data at a rapid pace. Managing users, instruments, reports, and invoices presents additional challenges. To address these challenges, we introduce EMhub, a web platform designed to support the daily operations and record-keeping of a scientific facility. EMhub enables easy management of user information, instruments, bookings, and projects. The application was initially developed to meet the needs of a CryoEM facility, but its functionality and adaptability have proven broad enough to be extended to other data-generating centers. The expansion of EMHub is enabled by the modular nature of its core functionalities. The application allows external processes to be connected via a REST API, automating tasks such as folder creation, user and password generation, and execution of real-time data processing pipelines. EMhub has been used for several years at the Swedish National CryoEM Facility and installed in the CryoEM center at the Structural Biology Department at St. Jude Children’s Research Hospital. A fully automated single-particle pipeline has been implemented for on-the-fly data processing and analysis. At St. Jude, the X-Ray Crystallography Center and the Single-Molecule Imaging Center have already expanded the platform to support their operational and data management workflows.
Under Cover of Darkness: Refuge from Artificial Light at Night may Mitigate Risks to Stranded Seabirds
Authors: Brown Taylor M. , Baker Kaitlyn , Wilhelm Sabina I. , Burness Gary
Published: August 2024

Artificial light at night is an anthropogenic pollutant that has wide-ranging effects on wildlife. Fledgling seabirds of the order Procellariiformes exhibit phototaxis toward artificial lights on their first flights from the nest, causing them to become grounded in human settlements where they are subject to increased risk of predation. Limited evidence suggests that certain light types may be less attractive than others, yet there is also evidence for an aversion to light under certain circumstances. We investigated differences in phototactic behaviour, activity level, and shelter-seeking behaviour of groundedHydrobates leucorhous(Leach’s storm-petrel) fledglings exposed to artificial light in three experiments: a Y-maze choice experiment, an open field test, and a modified open field test with a hide box provided (“Safe Haven test”). When provided with combinations of different light types in the Y-maze, storm-petrels typically remained stationary in the darkest part of the apparatus and exhibited no response toward one light type over another. This was consistent with results from the open field test, in which individuals were less active in darkness than when exposed to two out of three light conditions (Warm White Light-Emitting Diode and High Pressure Sodium). More than half of birds entered the hide box in light conditions, compared to none in the dark. Considered together, our results indicate Leach’s storm-petrel fledglings exhibit photophobic behaviour after stranding, which may be part of a behavioural strategy to avoid predation. Further, we demonstrate the utility of providing hide boxes to protect stranded seabird fledglings in locations where lighting cannot be eliminated or where rescue efforts may be limited in spatial or temporal coverage. However, hide boxes would have limited utility in dark locations. Hide boxes constitute a novel mitigation measure that merits future testing for its ability to reduce stranding-induced mortality, especially in imperiled procellariiform species.

LAY SUMMARY

Globally, fledglings of many seabird species become stranded in towns and at industrial sites near their breeding colonies

Strandings are thought to be caused by attraction to lights, although some species appear to avoid light

We tested behavioural responses and activity levels of Leach’s storm-petrel fledglings toward several different light types

When presented with different types of light in a choice experiment, most birds remained stationary

Fledglings were more active in warm-hued lights than in darkness

Birds sought shelter when it was provided in light conditions, but not when provided in darkness

Our results suggest that rescue programs targeting Leach’s storm-petrels should include searches in dark, hidden locations where fledglings are likely to hide, and support the use of small shelters to protect stranded seabirds when lights cannot be turned off
DNA damage-associated protein co-expression network in cardiomyocytes informs on tolerance to genetic variation and disease
Authors: Johnson Omar D. , Paul Sayan , Gutierrez Jose A. , Russell William K. , Ward Michelle C.
Published: August 2024

Cardiovascular disease (CVD) is associated with both genetic variants and environmental factors. One unifying consequence of the molecular risk factors in CVD is DNA damage, which must be repaired by DNA damage response proteins. However, the impact of DNA damage on global cardiomyocyte protein abundance, and its relationship to CVD risk remains unclear. We therefore treated induced pluripotent stem cell-derived cardiomyocytes with the DNA-damaging agent Doxorubicin (DOX) and a vehicle control, and identified 4,178 proteins that contribute to a network comprising 12 co-expressed modules and 403 hub proteins with high intramodular connectivity. Five modules correlate with DOX and represent distinct biological processes including RNA processing, chromatin regulation and metabolism. DOX-correlated hub proteins are depleted for proteins that vary in expression across individuals due to genetic variation but are enriched for proteins encoded by loss-of-function intolerant genes. While proteins associated with genetic risk for CVD, such as arrhythmia are enriched in specific DOX-correlated modules, DOX-correlated hub proteins are not enriched for known CVD risk proteins. Instead, they are enriched among proteins that physically interact with CVD risk proteins. Our data demonstrate that DNA damage in cardiomyocytes induces diverse effects on biological processes through protein co-expression modules that are relevant for CVD, and that the level of protein connectivity in DNA damage-associated modules influences the tolerance to genetic variation.
New viruses infecting hyperthermophilic bacteriumThermus thermophilus
Authors: Kolesnik Matvey , Pavlov Constantine , Demkina Alina , Samolygo Aleksei , Karneyeva Karyna , Trofimova Anna , Sokolova Olga S. , Moiseenko Andrei V. , Kirsanova Maria , Severinov Konstantin
Published: August 2024

Highly diverse phages infecting thermophilic bacteria of theThermusgenus have been isolated over the years from hot springs around the world. Many of these phages are unique, rely on highly unusual developmental strategies, and encode novel enzymes. The variety ofThermusphages is clearly undersampled, as evidenced, for example, by a paucity of phage-matching spacers inThermusCRISPR arrays. Using water samples collected from hot springs in the Kunashir Island from the Kuril archipelago and from the Tsaishi and Nokalakevi districts in the Republic of Georgia we isolated several distinct phages infecting laboratory strains ofThermus thermophilus. Genomic sequence analysis of 11 phages revealed both close relatives of previously describedThermusphages isolated from geographically distant sites, as well as phages with very limited similarity to earlier isolates. Comparative analysis allowed us to predict several accessory phage genes whose products may be involved in host defense/interviral warfare, including a putative Type V CRISPR-cassystem.
An ecological, phenotypic and genomic survey of duckweeds with their associated aquatic environments in the United Kingdom
Authors: Smith Kellie E. , Cowan Laura , Flis Paulina , Moore Chris , Heatley Matthew , Robles-Zazueta Carlos A. , Lee Adam , Yant Levi
Published: August 2024

The duckweeds feature global distributions and diverse applications in phytoremediation and nutrition, as well as use in fundamental studies of development. Existing collections have minimal environmental data linked to natural habitats. Thus, there is a lack of understanding of natural variation in the context of native habitats. Here, a novel collection of 124 duckweed accessions from 115 sites across the United Kingdom were characterised by genome sequencing and ionomics. In nutrient-replete conditions all accessions hyperaccumulated P, K, Mg and Ca. Local but not large-scale associations were revealed between elemental composition of duckweed in common, replete conditions and native water profiles.Lemna minorwas the most prevalent species in the UK, with a closely related hybridL. japonicafrequently found in waters with higher micronutrient concentrations. InvasiveL. minutawas common in the southern and midland regions, but restricted in Scotland.Lemnaaccessions accumulated heavy metal contaminants typically together with macronutrients, suggesting phytoremediation potential, but some limitations as food. Furthermore, monitoring the ecological interactions between native, hybrid and invasiveLemnaspecies should be ongoing in the interest of biodiversity.
Unveiling Mechanistic and Structural Insights of EstS1 Esterase: A Potent Broad-Spectrum Phthalate Diester Degrading Enzyme
Authors: Verma Shalja , Choudhary Shweta , Kumar K Amith , Mahto Jai Krishna , Vamsi K Anil Kumar , Mishra Ishani , Prakash Vellanki Bhanu , Sircar Debabrata , Tomar Shailly , Sharma Ashwani Kumar , Singla Jitin , Kumar Pravindra
Published: August 2024

The ubiquitous presence of plastics and plasticizers around the globe has raised an alarming condition. Phthalate diesters are high-priority pollutants that mimic natural hormones and act as endocrine disruptors upon entering living systems. While certain bacterial esterases have been identified for their role in phthalate diester degradation, their structural and mechanistic characteristics remain largely unexplored. A thermostable and pH-tolerant EstS1 esterase fromSulfobacillus acidophiluscatalyzes the conversion of low molecular weight phthalate diesters to monoesters. This study highlights the unique potential of EstS1 to degrade high molecular weight bis(2-ethylhexyl) phthalate (DEHP) by employing biophysical and biochemical approaches along with in-depth structural analysis utilizing high-resolution crystal structures in both apo and complex forms, with various substrates, products, and their analogs to elucidate mechanistic details. The catalytic tunnel mediating entry and exit of the substrate and product, respectively, centralized the Ser-His-Asp triad performing catalysis by bi-bi ping-pong mechanism, forming a tetrahedral intermediate. Additionally, structural analysis of the polypropylene analog jeffamine with EstS1 revealed effective covalent binding, demonstrating its multifunctional capability. Mutation analysis showed that the Met207Ala mutation abolished DEHP binding at the active site, confirming its essential role in supporting catalysis. These findings underscore the potential of EstS1 as a key tool for advancing technologies aimed at phthalate diesters biodegradation.
Territoriality and resource availability modulate the effect of conspecific encounters on the foraging behaviours of a mammalian predator
Authors: Clermont Jeanne , Dulude-de Broin Frédéric , Poulin Marie-Pier , Berteaux Dominique
Published: August 2024

The probability of encountering conspecifics shapes multiple dimensions of animal behaviour. For example, territorial individuals increase vigilance, scent marking and alarm calling when approaching home range boundaries. Whether territorial predators modify their foraging behaviours with respect to the probability of encountering neighbouring territory owners is poorly understood. However, this could strongly influence the landscape of predation risk and therefore modulate predator-prey interactions. We studied the movements and behaviours of 23 resident Arctic foxes occupying neighbouring home ranges during two years of contrasting resource availability (abundant resources in 2019, scarce resources in 2022) on Bylot Island, Nunavut, Canada. First, based on simultaneous GPS tracking of individuals, we established which individuals used a territory (an exclusive area) by estimating the spatial distribution of the probability of encountering a neighbour within their home range. Second, using GPS and accelerometry data, we evaluated if the probability of encountering a neighbour influenced the spatial distribution of foraging behaviours, and whether this relationship differed between territorial and non-territorial individuals. When resources were abundant, only breeding individuals excluded other foxes from a part of their home range and were thus territorial. When resources were rare, none of the foxes reproduced and all but one were territorial. Non-territorial individuals in 2019 were less likely to cache prey in areas with a high probability of encounter, possibly reducing the risk of cache pilfering. We found no effect of the probability of encounter on the behaviours of the non-territorial individual in 2022. The probability to cache prey of territorial individuals however did not depend on the probability of encountering a neighbour, suggesting they have no benefit of modulating the distribution of their caches according to potential encounters in a partly exclusive area. Our results thus suggest that Arctic foxes use different tactics to secure resources based on their degree of territoriality and the availability of resources. We highlight how the presence of resident, but non-territorial predators, whose home ranges overlap those of their territorial neighbours, may influence the distribution of predation risk by creating zones where predator density is high, potentially influencing predator-prey interactions.
Evolutionary Origins and Functional Diversification of Auxin Response Factors
Authors: Hernández-García Jorge , Carrillo-Carrasco Vanessa Polet , Rienstra Juriaan , Tanaka Keita , de Roij Martijn , Dipp-Álvarez Melissa , Freire-Ríos Alejandra , Crespo Isidro , Boer D. Roeland , van den Berg Willy A.M. , Lindhoud Simon , Weijers Dolf
Published: August 2024

The Auxin Response Factors (ARFs) family of transcription factors are the central mediators of auxin-triggered transcriptional regulation. Functionally different classes of extant ARFs operate as antagonistic auxin-dependent and -independent regulators. While part of the evolutionary trajectory to the present auxin response functions has been reconstructed, it is unclear how ARFs emerged, and how early diversification led to functionally different proteins. Here, we usein silicoandin vivoanalyses to revisit the molecular events that led to the origin and subsequent evolution of the ARFs. We reveal the shared origin of ARFs from preexisting domains, uncovering a protein fold homologous to the ARF DNA-binding fold in a conserved eukaryotic chromatin regulator. Building on this, we reconstruct the complete evolutionary history of ARFs, including the divergence events leading to the appearance of the ARF classes and defining the main molecular targets for their functional diversification. We derive a complete evolutionary trajectory that led to the emergence of the nuclear auxin signalling pathway.
Hierarchical Working Memory and a New Magic Number
Authors: Zhong Weishun , Katkov Mikhail , Tsodyks Misha
Published: August 2024

The extremely limited working memory span, typically around four items, contrasts sharply with our everyday experience of processing much larger streams of sensory information concurrently. This disparity suggests that working memory can organize information into compact representations such as chunks, yet the underlying neural mechanisms remain largely unknown. Here, we propose a recurrent neural network model for chunking within the framework of the synaptic theory of working memory. We showed that by selectively suppressing groups of stimuli, the network can maintain and retrieve the stimuli in chunks, hence exceeding the basic capacity. Moreover, we show that our model can dynamically construct hierarchical representations within working memory through hierarchical chunking. A consequence of this proposed mechanism is a new limit on the number of items that can be stored and subsequently retrieved from working memory, depending only on the basic working memory capacity when chunking is not invoked. Predictions from our model were confirmed by analyzing single-unit responses in epileptic patients and memory experiments with verbal material. Our work provides a novel conceptual and analytical framework for understanding the on-the-fly organization of information in the brain that is crucial for cognition.
Protein Carrier AAV
Authors: Hoffmann Mareike D. , Sorensen Ryan J. , Extross Ajay , He Yungui , Schmidt Daniel
Published: August 2024

AAV is widely used for efficient delivery of DNA payloads. The extent to which the AAV capsid can be used to deliver a protein payload is unexplored. Here, we report engineered AAV capsids that directly package proteins – Protein Carrier AAV (pcAAV). Nanobodies inserted into the interior of the capsid mediate packaging of a cognate protein, including Green Fluorescent Protein (GFP),Streptococcus pyogenesCas9, Cre recombinase, and the engineered peroxidase APEX2. We show that protein packaging efficiency is affected by the nanobody insertion position, the capsid protein isoform into which the nanobody is inserted, and the subcellular localization of the packaged protein during recombinant AAV capsid production; each of these factors can be rationally engineered to optimize protein packaging efficiency. We demonstrate that proteins packaged within pcAAV retain their enzymatic activity and that pcAAV can bind and enter the cell to deliver the protein payload. Establishing pcAAV as a protein delivery platform may expand the utility of AAV as a therapeutic and research tool.
NOK promotes tumorigenesis through coordinating epidermal growth factor receptor to boost the downstream signaling in breast cancer
Authors: Wang Yinyin , Zhang Bingdong , He Chunhua , Tian Bo , Liu Sihan , Li Jianghua , Wang Jiayu , Yang Shigao , Zhu Bingtao , Wang Xiaoguang , Chang Zhijie , Cao Chenxi
Published: August 2024

BACKGROUND

Epidermal growth factor receptor (EGFR) forms a homodimer or heterodimer with other ErbB receptor family members to activate different downstream cytoplasmic signaling proteins during tumorigenesis.

METHODS

Adenovirus and lentivirus were used to overexpress or deplete NOK and/or EGFR to evaluate the phosphorylation of EGFR, the interaction of NOK-EGFR and their role in cell proliferation and metastasis.

RESULTS

EGFR heterodimerizes with NOK (also known as STYK1), a novel tyrosine kinase with a transmembrane domain, to promote tumorigenesis and metastasis of breast cancer cells. We found that NOK directly interacted with EGFR and formed a heterodimer complex. Depletion of NOK impaired, but over-expression of NOK increased, the phosphorylation of EGFR. NOK enhanced EGF signaling activation, in particular, the phosphorylation of STAT3, STAT5 and Erk1/2 via its juxtamembrane (JM) domain in promoting the proliferation and migration of breast cancer cells. Overexpression of NOK and EGFR synergistically induced the tumorigenesis of NIH-3T3 normal cells. We finally demonstrated that co-expression of NOK and EGFR correlated with tumor malignant stages in breast cancer patients.

CONCLUSIONS

Our findings uncover a mechanism by which NOK coordinates EGFR to enhance EGF signaling during tumorigenesis and metastasis and propose a potential strategy for targeting NOK-EGFR in breast cancer treatment.

GRAPHICAL ABSTRACT

EGFR heterodimerizes with NOK/STYK1, a novel tyrosine kinase with a transmembrane domain, in a manner of cross interaction via their juxtamembrane (JM) domains and kinase domains.

NOK enhances EGF signaling activation, in particular, the phosphorylation of STAT3, STAT5 and Erk1/2 via its JM domain.

NOK and EGFR synergistically promote proliferation and migration of breast cancer cells and induce tumorigenesis of normal cells.

Co-expression of NOK and EGFR correlates with tumor malignant stages in breast cancer patients.
Synchronization of bowhead whales
Authors: Podolskiy Evgeny A. , Teilmann Jonas , Heide-Jørgensen Mads Peter
Published: August 2024

Inferring animal behavior from irregular tracking data is a challenging area of research. It is particularly difficult to determine if whales, who intermittently explore different depths while staying in the same acoustic medium, synchronize their days with their prey and each other over kilometer-scale distances. Here, we aim to better understand the diving behavior of bowhead whales () in Disko Bay, West Greenland, using the largest high-frequency dive-depth dataset to date (144 days at 1 Hz from 12 different whales) and nonlinear dynamics, whereby we consider the whales to be chaotic (aperiodic) oscillators. We find that foraging whales dive deeper during the daytime in spring, with this diving behavior being in apparent synchrony with their vertically migrating prey. Furthermore, we demonstrate that bowhead whales can synchronize their behavior with each other for up to a week while staying within a range of up to ∼100km. This discovery agrees with the acoustic herd theory of long-range signaling in baleen whales. On the other hand, the synchrony might emerge when animals experience similar ecological conditions, which are, however, difficult to name because targeted depths and locations were separated for hundreds of meters and tens of kilometers, respectively. In this paper, we identify a framework for studying the sociality and behavior of such chaotically moving, unrestrained marine animals and call for more simultaneous tagging campaigns.

Published by the American Physical Society
2024
Decoherence induced by a sparse bath of two-level fluctuators: Peculiar features of
1/f
noise in high-quality qubits
Authors: Mehmandoost M. , Dobrovitski V. V.
Published: August 2024

Progress in fabrication of semiconductor and superconductor qubits has greatly diminished the number of decohering defects, thus decreasing the devastating low-frequency 1/f noise and extending the qubits' coherence times (dephasing time T2* and the echo decay time T2). However, large qubit-to-qubit variation of the coherence properties remains a problem, making it difficult to produce a large-scale register where all qubits have a uniformly high quality. In this work, we show that large variability is a characteristic feature of a qubit dephased by a sparse bath made of many (n≫1) decohering defects, coupled to the qubit with similar strength. We model the defects as two-level fluctuators (TLFs) whose transition rates γ are sampled from a log-uniform distribution over an interval [γm,γM], which is a standard model for 1/f noise. We investigate decoherence by such a bath in the limit of high-quality qubit, i.e., when the TLF density d is small (the limit of sparse bath, with d=n/w≪1, where n is the number of TLFs and w=ln[γM/γm] is the log-width of the distribution). We show that different realizations of the bath produce very similar noise power spectra S(f)∼1/f, but lead to drastically different coherence times T2* and T2. Thus the spectral density

S

(

f

)

does not determine coherence of a qubit coupled to a sparse TLF bath, as opposed to a dense bath; instead, decoherence is controlled by only a few exceptional fluctuators, determined by their value of γ. We show that removing only two of these TLFs greatly increases T2 and T2* times. Our findings help theoretical understanding and further improvements in the coherence properties of semiconductor and superconductor qubits, battling the 1/f noise in these platforms.

Published by the American Physical Society
2024
On the structure refinement of metal complexes against 3D electron diffraction data using multipolar scattering factors
Authors: Pacoste Laura , Ignat'ev Vladislav Mikhailovich , Dominiak Paulina Maria , Zou Xiaodong
Published: August 2024

This study examines various methods for modelling the electron density and, thus, the electrostatic potential of an organometallic complex for use in crystal structure refinement against 3D electron diffraction (ED) data. It focuses on modelling the scattering factors of iron(III), considering the electron density distribution specific for coordination with organic linkers. We refined the structural model of the metal–organic complex, iron(III) acetylacetonate (FeAcAc), using both the independent atom model (IAM) and the transferable aspherical atom model (TAAM). TAAM refinement initially employed multipolar parameters from the MATTS databank for acetylacetonate, while iron was modelled with a spherical and neutral approach (TAAM ligand). Later, custom-made TAAM scattering factors for Fe—O coordination were derived from DFT calculations [TAAM-ligand-Fe(III)]. Our findings show that, in this compound, the TAAM scattering factor corresponding to Fe3+ has a lower scattering amplitude than the Fe3+ charged scattering factor described by IAM. When using scattering factors corresponding to the oxidation state of iron, IAM inaccurately represents electrostatic potential maps and overestimates the scattering potential of the iron. In addition, TAAM significantly improved the fitting of the model to the data, shown by improved R
1 values, goodness-of-fit (GooF) and reduced noise in the Fourier difference map (based on the residual distribution analysis). For 3D ED, R
1 values improved from 19.36% (IAM) to 17.44% (TAAM-ligand) and 17.49% (TAAM-ligand-Fe3+), and for single-crystal X-ray diffraction (SCXRD) from 3.82 to 2.03% and 1.98%, respectively. For 3D ED, the most significant R
1 reductions occurred in the low-resolution region (8.65–2.00 Å), dropping from 20.19% (IAM) to 14.67% and 14.89% for TAAM-ligand and TAAM-ligand-Fe(III), respectively, with less improvement in high-resolution ranges (2.00–0.85 Å). This indicates that the major enhancements are due to better scattering modelling in low-resolution zones. Furthermore, when using TAAM instead of IAM, there was a noticeable improvement in the shape of the thermal ellipsoids, which more closely resembled those of an SCXRD-refined model. This study demonstrates the applicability of more sophisticated scattering factors to improve the refinement of metal–organic complexes against 3D ED data, suggesting the need for more accurate modelling methods and highlighting the potential of TAAM in examining the charge distribution of large molecular structures using 3D ED.
Analysis of smart warehouse in the context of India’s National Logistics Policy and digital-push: an ISM-MICMAC technique
Authors: Singh Shalini , Singh Ram
Published: August 2024

Purpose

India’s rapid economic growth has triggered a significant transformation in its logistics sector, fueled by comprehensive reforms and digital initiatives outlined in the National Logistics Policy. Smart warehouses, equipped with cutting-edge technologies such as IoT, AI and automation, have taken center stage in this evolution. They play a pivotal role in India’s digital journey, revolutionizing supply chains, reducing costs and boosting productivity. This AI-driven transformation, in alignment with the “Digital India” campaign, positions India as a global logistics leader poised for success in the industry 4.0 era. In this context, this study highlights the significance of smart warehouses and their enablers in the broader context of supply chain and logistics.

Design/methodology/approach

This paper utilized the ISM technique to suggest a multi-tiered model for smart warehouse ecosystem enablers in India. Enablers are also graphically categorized by their influence and dependence via MICMAC analysis.

Findings

The study not only identifies the 17 key enablers fostering a viable ecosystem for smart warehouses in India but also categorizes them as linkage, autonomous, dependent and independent enablers.

Research limitations/implications

This research provides valuable insights for practitioners aiming to enhance technological infrastructure, reduce costs, minimize wastage and enhance productivity. Moreover, it addresses critical academic and research gaps contributing to the advancement of knowledge in this domain, thus paving the way forward for more research and learning in the field of smart warehouses.

Originality/value

The qualitative modeling is done by collecting experts' opinions using the ISM technique solicits substantial value to this research.
The European Union and China's geoeconomic tools in a multipolar world
Authors: Gómez‐Hernández Unai
Published: August 2024

This paper analyzes what the geoeconomic tools of the European Union (EU) and China are and examines their nature from a comparative perspective. To this end, a literature review is conducted, accounting for the tools known as geoeconomic, and this is complemented by a content analysis of official documents, which include lesser‐known geoeconomic tools. The results indicate that although a similar number of geoeconomic tools have been identified, their salience and nature vary. While the EU's usage of these tools has lately been reactive to external developments and is not very often researched by academics, the Chinese usage takes a proactive stance. The paper concludes by pointing out that the development and relevance of these tools mirrors the systemic rivalry between the EU and China and indicates the geoeconomic shift that is taking place in international relations. Similarly, it also shows that the literature does not address all the geoeconomic tools there are and therefore this paper contributes to the literature by providing a comprehensive list of the instruments mentioned.
Does the Publication or the Implementation of IAS 19(R) Have Real Economic Consequences?
Authors: Chircop Justin , Kiosse Paraskevi Vicky
Published: August 2024

IAS 19 revised (IAS 19(R)) abolished the corridor approach and replaced the expected rate of return (ERR) on pension plan assets with the discount rate. While the abolition of the corridor method did not have a significant impact on UK firms, which were historically using a different method to recognize actuarial gains or losses, the elimination of the ERR was anticipated to have a major impact. We examine whether the elimination of the ERR had real economic consequences for UK firms around the publication and implementation dates of IAS 19(R). Our findings suggest that UK firms shifted pension investments away from equities following the publication and implementation of IAS 19(R). In addition, we find evidence that firms with higher pension deficits and firms that used higher ERRs reduced equity investments to a greater extent following the publication of IAS 19(R); interestingly, firms with larger differences between the expected and actual rates of return on pension plan assets reduced equity investments to a greater extent only following the implementation of IAS 19(R). These findings may be of interest to regulators in the context of standard‐setting, investment professionals, and other stakeholders.