bluuebunny/crossref_metadata_2025 huggingface dataset:
HCN1 hyperpolarization-activated cyclic nucleotide–gated channels enhance evoked GABA release from parvalbumin-positive interneurons
Authors: Buss Eric W. , Lofaro Olivia M. , Barnett Anastasia , Leroy Felix , Santoro Bina , Siegelbaum Steven A. , Bock Tobias
Published: October 2024

Hyperpolarization-activated, cyclic nucleotide–gated (HCN) channels generate the cationic I
h
current in neurons and regulate the excitability of neuronal networks. The function of HCN channels depends, in part, on their subcellular localization. Of the four HCN isoforms (HCN1-4), HCN1 is strongly expressed in the dendrites of pyramidal neurons (PNs) in hippocampal area CA1 but also in presynaptic terminals of parvalbumin-positive interneurons (PV+ INs), which provide strong inhibitory control over hippocampal activity. Yet, little is known about how HCN1 channels in these cells regulate the evoked release of the inhibitory transmitter GABA from their axon terminals. Here, we used genetic, optogenetic, electrophysiological, and imaging techniques to investigate how the electrophysiological properties of PV+ INs are regulated by HCN1, including how HCN1 activity at presynaptic terminals regulates the release of GABA onto PNs in CA1. We found that application of HCN1 pharmacological blockers reduced the amplitude of the inhibitory postsynaptic potential recorded from CA1 PNs in response to selective optogenetic stimulation of PV+ INs. Homozygous HCN1 knockout mice also show reduced IPSCs in postsynaptic cells. Finally, two-photon imaging using genetically encoded fluorescent calcium indicators revealed that HCN1 blockers reduced the probability that an extracellular electrical stimulating pulse evoked a Ca
2+
response in individual PV+ IN presynaptic boutons. Taken together, our results show that HCN1 channels in the axon terminals of PV+ interneurons facilitate GABAergic transmission in the hippocampal CA1 region.
Injury-induced myosin-specific tissue-resident memory T cells drive immune checkpoint inhibitor myocarditis
Authors: Kalinoski Hannah , Daoud Abdel , Rusinkevich Vitali , Jurčová Ivana , Talor Monica V. , Welsh Robin A. , Hughes David , Zemanová Kateřina , Stříž Ilja , Hooper Jody E. , Kautzner Josef , Peichl Petr , Melenovský Vojtěch , Won Taejoon , Čiháková Daniela
Published: October 2024

Cardiac myosin-specific (MyHC) T cells drive the disease pathogenesis of immune checkpoint inhibitor–associated myocarditis (ICI-myocarditis). To determine whether MyHC T cells are tissue-resident memory T (T
RM
) cells, we characterized cardiac T
RM
cells in naive mice and established that they have a distinct phenotypic and transcriptional profile that can be defined by their upregulation of CD69, PD-1, and CXCR6. We then investigated the effects of cardiac injury through a modified experimental autoimmune myocarditis mouse model and an ischemia–reperfusion injury mouse model and determined that cardiac inflammation induces the recruitment of autoreactive MyHC T
RM
cells, which coexpress PD-1 and CD69. To investigate whether the recruited MyHC T
RM
cells could increase susceptibility to ICI-myocarditis, we developed a two-hit ICI-myocarditis mouse model where cardiac injury was induced, mice were allowed to recover, and then were treated with anti-PD-1 antibodies. We determined that mice who recover from cardiac injury are more susceptible to ICI-myocarditis development. We found that murine and human T
RM
cells share a similar location in the heart and aggregate along the perimyocardium. We phenotyped cells obtained from pericardial fluid from patients diagnosed with dilated cardiomyopathy and ischemic cardiomyopathy and established that pericardial T cells are predominantly CD69
+
T
RM
cells that up-regulate PD-1. Finally, we determined that human pericardial macrophages produce IL-15, which supports and maintains pericardial T
RM
cells.
Methionine-rich domains emerge as facilitators of copper recruitment in detoxification systems
Authors: Contaldo Umberto , Savant-Aira Dylan , Vergnes Alexandra , Becam Jérôme , Biaso Frédéric , Ilbert Marianne , Aussel Laurent , Ezraty Benjamin , Lojou Elisabeth , Mazurenko Ievgen
Published: October 2024

Copper homeostasis mechanisms are critical for bacterial resistance to copper-induced stress. The
Escherichia coli
multicopper oxidase copper efflux oxidase (CueO) is part of the copper detoxification system in aerobic conditions. CueO contains a methionine-rich (Met-rich) domain believed to interact with copper, but its exact function and the importance of related copper-binding sites remain unclear. This study investigates these open questions by employing a multimodal and multiscale approach. Through the design of various
E. coli
CueO (EcCueO) variants with altered copper-coordinating residues and domain deletions, we employ biological, biochemical, and physico-chemical approaches to unravel in vitro CueO catalytic properties and in vivo copper resistance. Strong correlation between the different methods enables evaluation of EcCueO variants’ activity as a function of Cu+ availability. Our findings demonstrate the Met-rich domain is not essential for cuprous oxidation, but it facilitates Cu+ recruitment from strongly chelated forms, acting as transient copper binding domain thanks to multiple methionines. They also indicate that the Cu6/7 copper-binding sites previously observed within the Met-rich domain play a negligible role. Meanwhile, Cu5, located at the interface with the Met-rich domain, emerges as the primary and sole substrate-binding active site for cuprous oxidation. The Cu5 coordination sphere strongly affects the enzyme activity and the in vivo copper resistance. This study provides insights into the nuanced role of CueO Met-rich domain, enabling the functions of copper-binding sites and the entire domain itself to be decoupled. This paves the way for a deeper understanding of Met-rich domains in the context of bacterial copper homeostasis.
Precision livestock farming in the 21st century: Challenges and opportunities for sustainable agriculture
Authors: Chapagaee Pawan , Nainabasti Anjal , Kunwar Adhiraj , Bist Dipak Raj , Khatri Lokendra , Mandal Ashmita
Published: October 2024

This study aimed to review the recent development of different technologies in precision livestock farming (PLF), along with their scopes and challenges. PLF is an innovative, contemporary, and fast-expanding approach to agriculture that aims to improve sustainable livestock farming. The growing global population has increased the demand for animal products. To meet this demand, farmers have to increase their production, so without the integration of precision technology, this cannot be achieved. PLF currently employs a variety of technologies. Some of these methods include vision-based solutions, load cells, accelerometers, microphones, thermal cameras, photoelectric sensors, and radio-frequency identification (RFID). Despite the availability of different PLF technologies, their adoption by farmers varies widely on the basis of the cost of investment, ease of operation, availability, and accessibility. These technologies are used to track different activities of livestock farming, such as feeding, drinking, physical behavior, temperature regulation, tracking and identification, estrus detection, disease detection, and milking. PLF contributes significantly to technological advancement, human-animal relationships, environmental sustainability, and increased productivity. It does, however, present a number of obstacles and eventual advantages.
A method for quality fault diagnosis based on Bayesian network D-cut set
Authors: Li Ziyan , Tong Shanggao , Wang Zhaowei
Published: October 2024

Quality issues are important factors restricting the development of hydrogen fuel cells. Quality problems in hydrogen fuel cells may stem from various stages, including technology, preparation processes, equipment used, usage environment, and personnel operation. Moreover, different problems are coupled with each other, resulting in the characteristics of one cause with multiple effects and multiple causes with one effect in the quality issues of hydrogen fuel cells. However, there are often similarities between these qualities in high-level information, such as mechanism, object, and behaviour, which are reflected in the similarity of network models in Bayesian diagnostic networks. Therefore, this article discusses how to reuse the Bayesian diagnosis network of previous quality problem cases to construct a Bayesian diagnosis network for hydrogen fuel cell quality problem diagnosis, thereby effectively improving the diagnosis efficiency of hydrogen fuel cell quality problems.
The impact of using predigested feed on growth and molting frequency in blue swimming crab (Portunus pelagicus) enlargement
Authors: Chofifakh U , Khasanah S , Solikhah  , Wildan DM , Nugroho KC , Setioko W , Nugraha BA , Ervinia A , Satria MB , Darmawan D , Taqiyuddin MW
Published: October 2024

Blue swimming crab is one of the leading fishery export commodities which occupies the 3rd largest position after tuna and shrimp. Crab maintenance so far uses rasbora fish feed which has several drawbacks, including inappropriate nutrition, depending on the season, and is difficult to handle. Therefore, simple artificial feed is needed to support crab growth. The purpose of this study was to determine the effect of artificial feeding supplemented with pancreatic extract on crab growth. The research design used in this study was completely randomized design (CRD) with different concentrations of pancreatic extract (0%, 3%, 6%, 9%). Parameters observed included water quality (temperature, dissolved oxygen, pH, salinity, and ammonia), feed proximate, crab biology. The results of this study indicate that the water quality in this study supports the life of blue swimming crabs. The feed proximate results show that the proximate value is in accordance with the crab’s needs. The results of swimming crab biology showed that the highest growth of crab was owned by the artificial feed + 9% pancreas and the lowest was in the trash fish treatment. Based on the results it can be seen that the best treatment to support the life of the blue swimming crab is artificial feed + 9% pancreas. Predigestion feed with the help of pancreatic extract concentrations can increase crab growth compared to ordinary feed or rasbora fish feed.
Morphometric Character of Horseshoe Crab (Tachypleus) at Mempawah Mangrove Park Coastal Area, West Kalimantan, Indonesia
Authors: Anzani YM , Kurniadi B , Rahayu S , Dandayati M
Published: October 2024

In Mempawah Mangrove Park (MMP) coastal area, fishers are still often catch horseshoe crabs as a bycatch. One of its genera is Tachypleus. This research aimed to assess the morphometric character of Tachypleus from MMP Coastal area, West Kalimantan. A total of 14 parameters were measured from samples that were collected using a trammel net. The sampling frequency was three times from July to September 2022. Physical and chemical parameters of the waters are also studied to support the ecological information. Two species of Tachypleus were found in these waters, i.e. Tachypleus gigas (8 males and 4 females) and Tachypleus tridentatus (6 males and 11 females). In terms of size, females were larger than males in both species. Based on morphometric comparison between females and males of T. gigas, there was a significant difference in CL/PW ratio (p<0.05). On the other hand, for T. tridentatus, the ratio of PL/OL differed significantly (p<0.05).
The effectiveness of crab apartment to shelter egg berried female of blue swimming crab (Portunus pelagicus) in Rembang, Central Java, Indonesia
Authors: Mustabiq K , Rizal ES , Nugraha BA , Nugroho KC , Setioko W
Published: October 2024

Blue swimming crab is an Indonesian fishery commodity with high economic value for export to America, Asia, and Europe. The increase in crab fishing activities every year results in diminishing stocks in nature, in addition to predator attacks around spawning areas. The purpose of this study was to determine the growth of blue swimming crabs and identify types of fish in the crab apartment shelters in Rembang Regency, Central Java Province, from March to May 2023. The egg berried female crabs were put in a floating apartment for three months and monitored every 2 weeks to determine the growth of the hatched crab eggs. Our observations showed as many as 50 egg berried female crab with with an average size of 8–10 cm and a weight of 40–65 g. There were other marine organisms found in the shelter, including rabbit fish, shrimp, small crabs, and therapon-perch. Rabbit fish and therapon-perch often result in reduced juveniles. Therefore, add and installing shelter is highly recommended to the entry of these fish. This study found crab apartment brings positive impacts on the survival of hacthing crabs and protected them from the threat of predatory fish.
Impact of steaming and peeling on the weight loss in blue swimming crabs in Pangkajene Islands, South Sulawesi
Authors: Welis M , Cardin M , Taqiyuddin MW , Setioko W
Published: October 2024

The blue swimming crab (Portunus pelagicus) is an important fishery resource in Indonesia because it has a high value and involves a lot of human resources. The pasteurized crab goes through several main stages, namely steaming, stripping, and canning. Steamed crabs will experience weight loss and produce a yield of meat in a certain amount and composition after peeling. This study aims to determine the weight loss during crab steaming and stripping processes on different sizes of crabs. The crabs were classified into three categories, namely small crab (carapace width <10 cm), big crab (carapace width >10 cm), and egg-berried female crabs. Technically, crabs were steamed for 20 minutes after the water boils with temperature of steaming of 80–90 °C. Steaming process wereallowed to stand for 60 minutes, followed by. peeling process where crab meat were separated from the skin. Weight measurements were taken on fresh, warm (shortly after steaming), and cooked crab (adjusted to room temperature) to calculate weight loss due to steaming while considering temperature adjustments and total loss. Results revealed the weight decrease about 16.75% during steaming, 19.61% during relaxation, and 27.47% during overall process. The highest meat yield was obtained from small crab by 30.64%, followed by large crab by 27.25%, and egg berried female by 24.39%.
Dual band high gain circularly polarized frequency tunable silicon-graphene based MIMO antenna for THz wireless applications
Authors: Shukla Neha , Chadhar Ram Milan , Shastri Ravikant , Jain Rakhee , Verma Shashikant
Published: October 2024

The two-port aperture linked silicon-graphene radiator in THz regime is investigated in this study. The primary characteristics of the radiator design are as follows: (i) a perturbed circular aperture that offers two working spectrums, 2.85–3.58 THz and 2.31–2.45 THz, with the support of a circular E-field within the two operating bands; (ii) an aperture mirror arrangement that enhances polarization diversity and raises the isolation level to over 25 dB; and (iii) a graphene layer over the ceramic that allows for tunability in the entire working band as well as a circularly polarized frequency range. The broadsided radiation pattern is produced by the dual hybrid mode, or HEM11δ and HEM12δ. A metallic reflector positioned underneath the radiator enhances the dual working spectrum’s gain value, or around 7.5 dBi. With the aid of CST-MWS software, the final results are confirmed. The developed radiator may be used for a variety of wireless applications in the THz domain thanks to its stable far-field pattern and strong diversity parameter values.
Rigidity for inscribed radius estimate of asymptotically hyperbolic Einstein manifold
Authors: Jin Xiaoshang
Published: October 2024

The inscribed radius of a compact manifold with boundary is bounded above if its Ricci curvature and mean curvature are bounded from below. The rigidity result implies that the upper bound can be achieved only in space form. In this paper, we generalize this result to asymptotically hyperbolic (AH) Einstein manifold. We get an upper bound of the relative volume of AH manifold and if we combine it with the recent work of Wang and Zhou, then the rigidity is obtained.
Cultural Property
Authors: Ho Jean
Published: October 2024

Chapter 2 argues that cultural property is poorly regulated and understood in international law due to uncoordinated overlapping regulatory regimes and a persistent failure to develop and adopt a functional and progressive definition of cultural property. It further explains how transposing the attributes of new property identified in Chapter 1—imputable ownership, responsiveness to contextual factors, separability, and conferral of a benefit to cultural property—imparts credibility and coherence to an umbrella notion of cultural property that lends itself to more predictable regulation. Section 2 examines how cultural property is concurrently regulated by four distinct bodies of international law, none of which appear to absorb newer forms of cultural property. Section 3 critiques the tendency of international lawmakers to favour piecemeal regulatory regimes specific to cultural property when a common regulatory regime could have sufficed. The outcome of their approach is a series of bifurcations, where cultural property is distinguished from cultural heritage, and regulated differently depending on whether it is tangible or intangible, and whether it lies above water or underwater. These divisions have a distortive effect, cultivating the erroneous impression that cultural property is merely one of several discrete objects of regulation when it is, in fact, the principal object of regulation. Section 4 advocates the assimilation of cultural property to new property to mitigate the definitional chaos brought about by uncoordinated and piecemeal regulation outlined in Sections 2 and 3, and discusses the implications of regulating cultural property as new property in international law. Section 5 concludes.
Common Property
Authors: Ho Jean
Published: October 2024

Chapter 3 contends that international law thus far offers no compelling framework for common property regulation because its makers have either advanced or acquiesced in the extension of private, capitalist property regulation to common, communal property regulation. By paying lip service to the multi-state ownership attribute of common property as new property, while crafting regimes that optimize benefit-sharing from common property use only among select states and stakeholders, international lawmakers afford an opportunity to review and rectify the misalignments in common property regulation. Section 2 explains how the current regulatory arrangements for the Antarctic, the Moon and other celestial objects, and the Area reveal a capitalist orientation where commercial, not communal, interests hold sway. Section 3 then elaborates on how these existing arrangements fail to cope with present and projected uses of common property, thereby jeopardizing the prospect of sustainable natural resource consumption. Section 4 recommends turning to common pool resource management principles for guidance on common property regulation, and considers the outlook for stakeholder commitment to a modified regulatory blueprint. Section 5 concludes.
NIGMS Sandbox: a learning platform toward democratizing cloud computing for biomedical research
Authors: Lei Ming , Matukumalli Lakshmi K , Arora Krishan , Weber Nick , Malashock Rachel , Mao Fenglou , Gregurick Susan , Lorsch Jon
Published: October 2024

Biomedical data are growing exponentially in both volume and levels of complexity, due to the rapid advancement of technologies and research methodologies. Analyzing these large datasets, referred to collectively as “big data,” has become an integral component of research that guides experimentation-driven discovery and a new engine of discovery itself as it uncovers previously unknown connections through mining of existing data. To fully realize the potential of big data, biomedical researchers need access to high-performance-computing (HPC) resources. However, supporting on-premises infrastructure that keeps up with these consistently expanding research needs presents persistent financial and staffing challenges, even for well-resourced institutions. For other institutions, including primarily undergraduate institutions and minority serving institutions, that educate a large portion of the future workforce in the USA, this challenge presents an insurmountable barrier. Therefore, new approaches are needed to provide broad and equitable access to HPC resources to biomedical researchers and students who will advance biomedical research in the future.
MultiSC: a deep learning pipeline for analyzing multiomics single-cell data
Authors: Lin Xiang , Jiang Siqi , Gao Le , Wei Zhi , Wang Junwen
Published: October 2024

Single-cell technologies enable researchers to investigate cell functions at an individual cell level and study cellular processes with higher resolution. Several multi-omics single-cell sequencing techniques have been developed to explore various aspects of cellular behavior. Using NEAT-seq as an example, this method simultaneously obtains three kinds of omics data for each cell: gene expression, chromatin accessibility, and protein expression of transcription factors (TFs). Consequently, NEAT-seq offers a more comprehensive understanding of cellular activities in multiple modalities. However, there is a lack of tools available for effectively integrating the three types of omics data. To address this gap, we propose a novel pipeline called MultiSC for the analysis of MULTIomic Single-Cell data. Our pipeline leverages a multimodal constraint autoencoder (single-cell hierarchical constraint autoencoder) to integrate the multi-omics data during the clustering process and a matrix factorization–based model (scMF) to predict target genes regulated by a TF. Moreover, we utilize multivariate linear regression models to predict gene regulatory networks from the multi-omics data. Additional functionalities, including differential expression, mediation analysis, and causal inference, are also incorporated into the MultiSC pipeline. Extensive experiments were conducted to evaluate the performance of MultiSC. The results demonstrate that our pipeline enables researchers to gain a comprehensive view of cell activities and gene regulatory networks by fully leveraging the potential of multiomics single-cell data. By employing MultiSC, researchers can effectively integrate and analyze diverse omics data types, enhancing their understanding of cellular processes.
Outcomes of percutaneous endobiliary radiofrequency ablation in managing resistant benign biliary strictures: a retrospective analysis
Authors: Husnain Ali , Aadam Abdul Aziz , Keswani Rajesh , Sinha Jasmine , Caicedo Juan Carlos , Duarte Andres , Stiff Kristine , Reiland Allison , Cacho Daniel Borja , Salem Riad , Riaz Ahsun
Published: October 2024

Objectives

To assess the safety and effectiveness of percutaneous endobiliary radiofrequency ablation (EB-RFA) in the management of refractory benign biliary strictures.

Methods

Percutaneous EB-RFA was performed in 15 individuals (M/F = 8/7; median age: 57 [33-84]) for benign biliary strictures resistant to traditional methods (transhepatic cholangioplasty and biliary drains). All patients underwent ≥1 unsuccessful cholangioplasty session and upsizing of their transhepatic biliary drains pre-procedure. Technical and clinical success were defined as luminal gain with enhanced flow and a lack of clinically evident recurrent stricture on follow-up after drain/stent removal, respectively.

Results

A total of 16 EB-RFA procedures were performed. Technical success rate was 100% (16/16). Procedure-related complications occurred in 1/16 cases (drain leakage with subsequent cellulitis). Clinical success rate was 87% (13/15) with a median follow-up of 17 (2-24) months. Drain/stent was not removed in one case (1/16) as the patient was lost to follow-up immediately post-procedure. The one-year patency rate was 100%. A significant reduction was observed in the median number of IR visits (8 [1-51] to 1 [0-9]; P = .003) and drain insertion/exchange procedures (5 [1-45] to 0 [0-6]; P = .003) pre- and post-EB-RFA with a median follow-up of 18 (0-26) months.

Conclusion

Percutaneous EB-RFA can safely and effectively treat refractory benign biliary strictures. However, larger prospective studies with extended follow-ups are needed to gather more robust data.

Advances in knowledge

This study contributes to the limited evidence on the role of EB-RFA in addressing refractory benign biliary strictures, enhancing the understanding of its clinical utility.
Revisiting the Global Social Work Definition: How Social Workers Define the Profession a Decade Later?
Authors: Tarshish Noam
Published: October 2024

Social work has struggled to establish a unanimous definition encompassing the full professional scope. In 2014, the International Federation of Social Workers introduced a revised global definition outlining principles, objectives, goals and theories. Now, a decade later, questions have emerged about the definition and its contemporary relevance. This qualitative study interviewed sixty-five Israeli social workers to uncover how they define the profession. Analysis revealed they define social work as a profession that fosters positive change and well-being through tailored interventions. It upholds humanistic values like equality, dignity and participation and assists diverse clients experiencing challenging transitions by utilising different means of support. Findings show continuity in how social workers in Western contexts view the purpose and tools of the profession, whilst also highlighting tensions with the global definition’s macro-orientation. This research then incorporates an inclusive ‘both/and’ perspective, including both micro and macro dimensions, using principles from rights-based social work, to propose small amendments to the global definition.
Last minute cancellation of elective lung cancer surgery is associated with poorer survival
Authors: Nardini Marco , Chaudhuri Nilanjan , Lodhia Joshil , Milton Richard , Tcherveniakov Peter , Teh Elaine , Brunelli Alessandro
Published: October 2024

OBJECTIVES

Our objective was to assess the incidence and reason of last-minute cancellations before surgery for lung cancer and their association with outcomes.

METHODS

Retrospective analysis on all consecutive patients booked for elective lung cancer surgery from January 2017 through December 2022 in a single centre.

Last minute cancellation: a cancellation occurring within the last 24 hours from the planned operation. Cancellation categories: process-related and patient-related.

The short-term and long-term outcomes of patients who experienced a last-minute cancellation were analysed.

RESULTS

197 patients of 1587 (12%) had a last-minute cancellation: 156 (79%) were process-related and 41 (21%) were patient-related.

3% (5/156) of patients cancelled for process reasons did not receive surgery vs 39% (16/41) of those cancelled for patient-related reasons, p < 0.0001.

The 90-day mortality rates of cancelled and non-cancelled patients were similar (4.6% vs 4.7%, p = 1).

Five-year overall survival of patients with cancellation was 58% (95% CI 49–66) vs 69% (95% CI 66–71) of those without cancellations, p = 0.022.

Among those who had a cancellation, the 5-year OS of those with process-related cancellations was 61% (52–60) vs 35% (14–58) of those with patient-related cancellations (adjusted p value for multiple comparisons = 0.14).

Cox regression analysis showed that surgery cancellations within the last 24 hours for patient-related (HR 1.87, 95% CI 1.02–3.42, p = 0.043) reasons remained a factor associated with poorer overall survival after adjusting for clinical stage, type of operation and patient related variables.

CONCLUSIONS

Implementing the patient's preoperative clinical evaluation to reduce the occurrence of related last-minute cancellations might mitigate its negative impact on survival
Temporal enrichment of comammox Nitrospira and Ca. Nitrosocosmicus in a coastal plastisphere
Authors: Yang Qian , Zhong Yin , Feng Shi-wei , Wen Ping , Wang Heli , Wu Junhong , Yang Sen , Liang Jie-Liang , Li Dan , Yang Qiong , Tam Nora F Y , Peng Ping’an
Published: October 2024

Plastic marine debris is known to harbor a unique microbiome (termed the “plastisphere”) that can be important in marine biogeochemical cycles. However, the temporal dynamics in the plastisphere and their implications for marine biogeochemistry remain poorly understood. Here, we characterized the temporal dynamics of nitrifying communities in the plastisphere of plastic ropes exposed to a mangrove intertidal zone. The 39-month colonization experiment revealed that the relative abundances of Nitrospira and Candidatus Nitrosocosmicus representatives increased over time according to 16S rRNA gene amplicon sequencing analysis. The relative abundances of amoA genes in metagenomes implied that comammox Nitrospira were the dominant ammonia oxidizers in the plastisphere, and their dominance increased over time. The relative abundances of two metagenome-assembled genomes of comammox Nitrospira also increased with time and positively correlated with extracellular polymeric substances content of the plastisphere but negatively correlated with NH4+ concentration in seawater, indicating the long-term succession of these two parameters significantly influenced the ammonia-oxidizing community in the coastal plastisphere. At the end of the colonization experiment, the plastisphere exhibited high nitrification activity, leading to the release of N2O (2.52 ng N2O N g−1) in a 3-day nitrification experiment. The predicted relative contribution of comammox Nitrospira to N2O production (17.9%) was higher than that of ammonia-oxidizing bacteria (4.8%) but lower than that of ammonia-oxidizing archaea (21.4%). These results provide evidence that from a long-term perspective, some coastal plastispheres will become dominated by comammox Nitrospira and thereby act as hotspots of ammonia oxidation and N2O production.
Neutrophils on the mast cell menu
Authors: Espinosa Eric
Published: October 2024

A recent article in Cell reported a new peculiar interaction between mast cells (MCs) and neutrophils. Upon IgE/Ag-mediated degranulation, MCs produce leukotriene B4, which attracts migrating neutrophils. Some neutrophils are able to establish close contact with MCs and end up trapped inside the MC, forming a cell-in-cell structure. While the neutrophil eventually dies inside the vacuole, the MC benefits from the remains of its prisoner, using it as a nutrient reserve and reusing its antimicrobial weapons.
The early hormone signaling network underlying wound-induced de novo root regeneration
Authors: Kim Ji Woo , Seo Pil Joon
Published: October 2024

Plants possess a remarkable capability to regenerate new organs after wounding. De novo root regeneration (DNRR) from aboveground tissues after physical wounding is observed in a wide range of plant species. Here, we provide an overview of recent progress in the elucidation of the molecular mechanisms that govern DNRR, with a particular emphasis on the early signaling components. Wound-inducible chemicals and hormones such as jasmonic acid, ethylene, and salicylic acid, which were originally identified as defense hormones, influence DNRR. Ongoing work elucidating the molecular network underlying DNRR provides insight into the coactivating regeneration and defense responses at the early stages of the wound response in plants.
Observational signatures of circumbinary discs - II. Kinematic signatures in velocity residuals
Authors: Calcino Josh , Norfolk Brodie J , Price Daniel J , Hilder Thomas , Speedie Jessica , Pinte Christophe , Garg Himanshi , Teague Richard , Hall Cassandra , Stadler Jochen
Published: October 2024

Kinematic studies of protoplanetary discs are a valuable method for uncovering hidden companions. In the first paper of this series, we presented five morphological and kinematic criteria that aid in asserting the binary nature of a protoplanetary disc. In this work, we study the kinematic signatures of circumbinary discs in the residuals of their velocity maps. We show that Doppler-flips, spiral arms, eccentric gas motion, fast flows inside of the cavity, and vortex-like kinematic signatures are commonly observed. Unlike in the planetary mass companion case, Doppler-flips in circumbinary discs are not necessarily centred on a companion, and can extend towards the cavity edge. We then compare the kinematic signatures in our simulations with observations and see similarities to the Doppler-flip signal in HD 100546 and the vortex-like kinematic signatures in HD 142527. Our analysis also reveals kinematic evidence for binarity in several protoplantary discs typically regarded as circumstellar rather than circumbinary, including AB Aurigae and HD 100546.
Mitigating calibration errors from mutual coupling with time-domain filtering of 21 cm cosmological radio observations
Authors: Charles N , Kern N S , Pascua R , Bernardi G , Bester L , Smirnov O , Acedo E D L , Abdurashidova Z , Adams T , Aguirre J E , Baartman R , Beardsley A P , Berkhout L M , Billings T S , Bowman J D , Bull P , Burba J , Byrne R , Carey S , Chen K , Choudhuri S , Cox T , DeBoer D R , Dexter M , Dillon J S , Dynes S , Eksteen N , Ely J , Ewall-Wice A , Fritz R , Furlanetto S R , Gale-Sides K , Garsden H , Gehlot B K , Ghosh A , Gorce A , Gorthi D , Halday Z , Hazelton B J , Hewitt J N , Hickish J , Huang T , Jacobs D C , Josaitis A , Kerrigan J , Kittiwisit P , Kolopanis M , Lanman A , Liu A , Ma Y -Z , MacMahon D H E , Malan L , Malgas K , Malgas C , Marero B , Martinot Z E , McBride L , Mesinger A , Mohamed-Hinds N , Molewa M , Morales M F , Murray S , Nikolic B , Nuwegeld H , Parsons A R , Patra N , Plante P L , Qin Y , Rath E , Razavi-Ghods N , Riley D , Robnett J , Rosie K , Santos M G , Sims P , Singh S , Storer D , Swarts H , Tan J , Wilensky M J , Williams P K G , Wyngaarden P v , Zheng H
Published: October 2024

The 21 cm transition from neutral Hydrogen promises to be the best observational probe of the Epoch of Reionization (EoR). This has led to the construction of low-frequency radio interferometric arrays, such as the Hydrogen Epoch of Reionization Array (HERA), aimed at systematically mapping this emission for the first time. Precision calibration, however, is a requirement in 21 cm radio observations. Due to the spatial compactness of HERA, the array is prone to the effects of mutual coupling, which inevitably lead to non-smooth calibration errors that contaminate the data. When unsmooth gains are used in calibration, intrinsically spectrally smooth foreground emission begins to contaminate the data in a way that can prohibit a clean detection of the cosmological EoR signal. In this paper, we show that the effects of mutual coupling on calibration quality can be reduced by applying custom time-domain filters to the data prior to calibration. We find that more robust calibration solutions are derived when filtering in this way, which reduces the observed foreground power leakage. Specifically, we find a reduction of foreground power leakage by 2 orders of magnitude at $k_\parallel \approx 0.5$ h Mpc$^{-1}$.
Integrated multi-omics analysis of PBX1 in mouse adult neural stem- and progenitor cells identifies a transcriptional module that functionally links PBX1 to TCF3/4
Authors: Laub Vera , Nan Elisabeth , Elias Lena , Donaldson Ian J , Bentsen Mette , Rusling Leona A , Schupp Jonathan , Lun Jennifer H , Plate Karl H , Looso Mario , Langer Julian D , Günther Stefan , Bobola Nicoletta , Schulte Dorothea
Published: October 2024

Developmental transcription factors act in networks, but how these networks achieve cell- and tissue specificity is still poorly understood. Here, we explored pre-B cell leukemia homeobox 1 (PBX1) in adult neurogenesis combining genomic, transcriptomic, and proteomic approaches. ChIP-seq analysis uncovered PBX1 binding to numerous genomic sites. Integration of PBX1 ChIP-seq with ATAC-seq data predicted interaction partners, which were subsequently validated by mass spectrometry. Whole transcriptome spatial RNA analysis revealed shared expression dynamics of Pbx1 and interacting factors. Among these were class I bHLH proteins TCF3 and TCF4. RNA-seq following Pbx1, Tcf3 or Tcf4 knockdown identified proliferation- and differentiation associated genes as shared targets, while sphere formation assays following knockdown argued for functional cooperativity of PBX1 and TCF3 in progenitor cell proliferation. Notably, while physiological PBX1-TCF interaction has not yet been described, chromosomal translocation resulting in genomic TCF3::PBX1 fusion characterizes a subtype of acute lymphoblastic leukemia. Introducing Pbx1 into Nalm6 cells, a pre-B cell line expressing TCF3 but lacking PBX1, upregulated the leukemogenic genes BLK and NOTCH3, arguing that functional PBX1-TCF cooperativity likely extends to hematopoiesis. Our study hence uncovers a transcriptional module orchestrating the balance between progenitor cell proliferation and differentiation in adult neurogenesis with potential implications for leukemia etiology.
Real-world pan-tumor comprehensive genomic profiling sample adequacy and success rates in tissue and liquid specimens
Authors: Lin Douglas I , Pasquina Lincoln W , Mavares Estefany , Elvin Julia A , Huang Richard S P
Published: October 2024

Real-world success rate of liquid and tissue-based comprehensive genomic profiling (CGP) is unknown. We analyzed real-world pan-tumor cohorts that underwent CGP during clinical care via FoundationOne CDx (F1CDx) and FoundationOne Liquid CDx (F1LCDx) to determine tissue and liquid sample adequacy based on tumor type. Pan-tumor presequencing adequacy was high (>90%) by both tissue-based F1CDx (median: 92.3%; range: 88.2%-96.9%) and liquid-based F1LCDx (median: 94.8%; range: 86.6%-96.7%). Similarly, postsequencing analysis revealed that most tissue and liquid samples yielded successful sequencing results with a median sequencing success rate of 97.9% and 98.1% for F1CDx and F1LCDx, respectively. One exception is central nervous system (CNS) tumors, for which F1CDx had dramatically higher sample sufficiency (96.9%) and postsequencing success rate (97.0%) compared with F1LCDx (86.6% and 92.9%, respectively). The pan-tumor median sample-to-success rate was 90.4% (range: 84.8%-94.4%) for F1CDx. The equivalent rate for F1LCDx was slightly higher at 93.2% (range: 80.4%-95.7%). Conversely, when examining the prevalence of F1LCDx results with high tumor fraction (TF≥1%), the sample-to-high TF results rate was dramatically lower (median: 37.7%, range: 2.1% [CNS tumors]-46.0%). In conclusion, except in CNS tumors or when accounting for liquid TF, success rates of F1CDx and F1LCDx are equivalently high. These results may guide informed decision on when to pursue tissue vs liquid testing of patients with cancer.
A rapid review of nutrition and exercise approaches to managing unintentional weight loss, muscle loss, and malnutrition in cancer
Authors: Baguley Brenton J , Edbrooke Lara , Denehy Linda , Prado Carla M , Kiss Nicole
Published: October 2024

Purpose

This narrative review summarizes the evidence for nutrition, exercise, and multimodal interventions to maintain weight and muscle mass and prevent malnutrition from meta-analysis, systematic reviews, and randomized controlled trials published within the last 5 years, and in comparison to future research priority areas identified by international guidelines.

Recent findings

Dietary counseling with oral nutrition support (ONS), escalated to enteral nutrition if weight loss continues, is the gold standard treatment approach to maintaining weight and preventing malnutrition. Recent ONS trials with dietary counseling show promising findings for weight maintenance, extending the literature to include studies in chemoradiotherapy, however, change in body composition is rarely evaluated. Emerging trials have evaluated the impact of isolated nutrients, amino acids, and their derivatives (ie, β-hydroxy β-methylbutyrate) on muscle mass albeit with mixed effects. There is insufficient evidence evaluating the effect of exercise interventions on unintentional weight loss, muscle mass, and malnutrition, however, our knowledge of the impact of multimodal nutrition and exercise interventions is advancing. Prehabilitation interventions may attenuate weight and muscle loss after surgery, particularly for patients having gastrointestinal and colorectal surgery. Multimodal trials that commence during treatment show mixed effects on weight and muscle mass when measured.

This review highlights that the evidence for preventing unintentional weight loss and malnutrition from cancer treatment is strong within nutrition. Multimodal interventions are emerging as effective interventions to prevent unintentional weight loss. Promising interventions are demonstrating improvements in muscle mass, however further exploration through studies designed to determine the effect on muscle is required.
Nursing Professional Identity
Authors: Payne Alayna , Lalonde Michelle , Vanderspank-Wright Brandi , Perron Amélie
Published: October 2024

Heroism is an immutable and quintessential part of what gives rise to the phenomenon that is nurse. This altruistic discourse comes with profound consequences for the nursing profession, particularly in relation to nursing’s professional identity. This critical review explores nursing’s professional identity against the backdrop of gendered and heroic discourses. Two concept analyses of nursing’s professional identity are critically reviewed and juxtaposed with literature on the topic amidst COVID-19. Using poststructural feminism and critical discourse analysis, the review provides valuable insights into the evolutionary significance of the concept and raises key questions around knowledge-power structures and discursive constructions of nurse.
THREE-YEAR CLINICAL OUTCOMES IN GEOGRAPHIC ATROPHY
Authors: Shughoury Aumer , Boucher Nick , Aggarwal Nitika , Ciulla Thomas A.
Published: October 2024

Purpose:

To assess visual outcomes and rate of neovascular age-related macular degeneration (nAMD) development in eyes with geographic atrophy (GA).

Methods:

Retrospective analysis of 18,712 eyes with GA using the CorEvitas Vestrum Health Retina Database.

Results:

Mean age at index was 78.6 years (SD = 7.9) and mean visual acuity was 67.5 letters (SD = 13.0, Snellen equivalent 20/45). In total, 18.9% of eyes developed nAMD within 36 months. Eyes with fellow-eye nAMD developed nAMD at over twice the rate of eyes with fellow-eye GA (relative risk 2.34, 95% confidence interval [2.20–2.49]). Mean visual acuity of eyes that did not develop nAMD declined by 12.4 letters (95% confidence interval [12.0–12.9]) within 36 months. Older age and moderate baseline visual impairment (visual acuity <20/40–20/100) independently correlated with accelerated rate of decline. Eyes of patients in the oldest quartile with moderate visual impairment experienced the worst outcomes, losing an average of 19.7 letters over 36 months (95% confidence interval [18.1–21.3]). By 36 months, 70% of eyes had vision below threshold for driving (visual acuity ≤20/40), 42% had low vision (visual acuity ≤20/70), and 23% were legally blind (visual acuity ≤20/200).

Conclusion:

Geographic atrophy is associated with significant disease burden. Eyes with GA lose an average of two to three lines of visual acuity within 36 months of follow-up. Older age and moderate baseline visual impairment independently correlate with poorer visual outcomes. Presence of nAMD in the fellow eye is associated with 2-fold higher risk of exudative conversion within 36 months.
Requesting Relatives’ Consent for Intensive Care for Organ Donation: An Empirical Analysis of Spanish Transplant Coordinators’ Practices
Authors: García-Sánchez Rubén , Soria-Oliver María , López Jorge S. , Martínez José M. , Martín María J. , Barceló-Soler Alberto , Coll Elisabeth , Roldán José , Uruñuela David , Fernández-Carmona Alberto
Published: October 2024

Background.

Intensive care to facilitate organ donation (ICOD) involves the initiation or continuation of intensive care for patients with devastating brain injury for donation purposes. In the Spanish system, relatives undergo an early interview to request consent for this procedure. If they consent, a waiting time is agreed upon in the expectation that death by neurological criteria occurs and donation after brain death takes place. Otherwise, relatives can decide on donation after circulatory determination of death or withdrawal of life support. This study analyzes how Spanish transplant coordinators interact with relatives in early interviews and follow-ups on potential donation pathways.

Methods.

Semistructured interviews were conducted with a random stratified sample of 23 Spanish transplant coordination teams to explore strategies, practices, and perceptions of ICOD consent requests. The interviews were recorded, transcribed, and analyzed using content analysis.

Results.

Previous coordination with other units and information retrieval regarding patient and relatives’ situations is crucial. The development of early interviews includes an introduction to the family, identification of decision makers, empathizing with relatives and offering condolences, reaffirming the fatal prognosis, explaining the possibility of donating based on the patient’s will, confirming the family’s understanding and resolving doubts, and ensuring comfort and assessing family needs.

Conclusions.

Approaching families to obtain ICOD consent is a regular practice for Spanish coordination teams. It involves a highly professional and diversified set of strategies based on establishing a support relationship for relatives. Our study provides strategies that serve as a reference for obtaining ICOD consent from families in other settings.
Inverse spectral Love problem via Weyl–Titchmarsh function
Authors: Sottile Samuele
Published: October 2024

In this paper, we prove an inverse resonance theorem for the half-solid with vanishing stresses on the surface via Weyl–Titchmarsh function. Using a semi-classical approach, it is possible to simplify this three-dimensional problem of the elastic wave equation for the half-solid as a Schrödinger equation with Robin boundary conditions on the half-line. The goal of the paper is to establish a method to recover the potential from eigenvalues and resonances through the Weyl–Titchmarsh function for non-self-adjoint problems and to establish a one-to-one and onto map between suitable function spaces. Moreover, we produce an algorithm in order to retrieve the shear modulus from the eigenvalues and resonances, via the spectral data.