bluuebunny/crossref_metadata_2025 huggingface dataset:
Numerical investigation of phase change material integration in structured thermocline systems for concentrated solar power
Authors: Sanmartí Oriol , Vera Jordi , Torras Santiago , Pérez-Segarra Carlos D.
Published: June 2024

The integration of encapsulated PCM in a structured thermal energy storage system is studied. The fluid and filler material are discretized using a one-dimensional approach, while the PCM is discretized two-dimensionally. The accumulated energy for the height percentage of PCM and cutoff temperature differences are obtained for three PCMs, NaNO3, KOH and H380, to obtain the best options to enhance the accumulated energy using encapsulated PCM.
Influence of PCMs on thermal performance of wet fire protective clothing
Authors: Malaquias André Fonseca , Campos J B L M
Published: June 2024

The inclusion of phase change materials (PCMs) in firefighting protective clothing (FPC) has been previously shown to be beneficial during the exposure stage, but detrimental in the post-exposure, mainly due to PCM latent heat release towards the skin, after the exposure. It is unclear whether that is also the case for when the FPC is wet. Hence, in this study, a one-dimensional numerical approach is used to study the effect of PCM parameters (PCM mass, melting temperature) and global heat flux, on the thermal performance of a wet fire protective clothing. It is concluded that under wet conditions, the PCM amount, and its phase change temperature have a significant effect on thermal performance, depending on the heat exposure scenario considered. Great benefits are observed in introducing PCMs to prevent water condensation near the skin, but at the cost of greater PCM re-solidification skin damage.
Analyzing the impact of using phase change materials on energy consumption in buildings: A case study
Authors: Hrnčić B. , Vušanović I.
Published: June 2024

The use of phase change material (PCM) in buildings has been shown to be a promising method for reducing energy consumption. This study investigates the effectiveness of using PCM in reducing energy consumption in a typical residential building located in Podgorica, Montenegro, a city with mild winters and hot and dry summers. EnergyPlus software was used to simulate the thermal performance of a building with and without the incorporation of PCM. Building models were created in a way to incorporate PCM in form of a panel, and simulations were done with five different types of PCM, five different thicknesses and three different positions (outside, inside and middle of building envelope). The simulations were performed over a one-year period to account for seasonal variations in temperature and humidity. The simulation results indicate that the use of PCM in buildings design can significantly reduce energy consumption in buildings located in climates similar to Podgorica. This approach can also lead to a reduction in greenhouse gas emissions associated with energy consumption. These findings provide valuable insights for building designers and policymakers looking to reduce energy consumption and improve the sustainability of buildings. In conclusion, the results of this study support the use of PCM in building design as an effective strategy for reducing energy consumption and greenhouse gas emissions in buildings. Further research is needed to investigate the cost-effectiveness of using PCM in buildings design and to explore the potential for their widespread implementation.
What are sustainable plastics? A review of interrelated problems and solutions to help avoid unintended consequences
Authors: Gonella Sara , de Gooyert Vincent
Published: June 2024

Plastics are affordable and versatile, but there is a growing awareness that they are unsustainable in a number of ways, including concerns about climate, health and biodiversity. A number of solutions are being explored that could enable a more sustainable plastics system. So far, most research has focused on isolated technical solutions that address only one specific sustainability challenge posed by plastics, such as end-of-life management or feedstock alternatives to fossil fuels. Some interventions might mitigate one problem but contribute to another at a different stage of the plastics life cycle. This study is based on a literature review and adopts qualitative system dynamics to analyse the unsustainability of plastics with a holistic, integrative approach. The review shows that there is still no agreed definition of sustainable plastics, so the authors propose one based on inputs from the literature. The paper provides an overview of the impacts of potential solutions on the plastics system, highlighting how some interventions could end up having unintended consequences, perhaps even overshadowing the benefits. The results highlight the need for improved communication transparency between plastics stakeholders and a more vertically integrated, harmonised value chain to effectively implement a sustainability transition in the plastics system.
How suitable are current approaches to simulate flood risk under future urbanization trends?
Authors: Zwirglmaier Veronika , Reimuth Andrea , Garschagen Matthias
Published: June 2024

Flood risk in urban areas will increase massively under future urbanization and climate change. Urban flood risk models have been increasingly applied to assess impacts of urbanization on flood risk. For this purpose, different methodological approaches have been developed in order to reflect the complexity and dynamics of urban growth. To assess the state-of-the art in the application of flood risk models under urbanization scenarios, we conducted a structured literature review and systematically analyzed 93 publications with 141 case studies. Our review shows that hydrological and hydrodynamic flood models are the most commonly used approaches to simulate flood risk. Future urbanization is mostly considered as urban sprawl through the adjustment of land use maps and roughness parameters. A low number of approaches additionally consider transitions of urban structures and densification processes in their urbanization scenarios. High-resolution physically based flood models have been advanced and are well suited for describing quantifiable processes in data-rich contexts. In regions with limited data, we argue that reducing the level of detail in flood models and increasing the level of detail in urbanization patterns should be considered to improve the quality of flood risk projections under future urbanization. For this purpose, we also call for the development of integrative model structures such as causal network models that have greater explanatory power and enable the processing of qualitative data.
Miniature snapshot mid-infrared spectrometer based on metal-insulator-metal metasurface
Authors: Liu Weijun , Wan Yuanqing , Yu Haoxiang , Yuan Quan , Li Tianyue , Xue Fang , Wang Shuming
Published: June 2024

Metasurfaces showcase the performance of light field manipulation at the subwavelength scale, generating tremendous applications in the field of optical imaging and sensing, especially in spectroscopic detection. Here, we demonstrate a spectral detector comprising metal-insulator-metal composite structures working in the mid-infrared band, which can effectively collect and restore target spectral characteristics in the mid-infrared band with a trained reconstruction algorithm. The proposed device consists of snapshot multichannel detection and spectral reconstruction, showing an average spectral reconstruction accuracy approaching 80% of the system. Moreover, we discuss the feasibility of applying this structural design to a miniature spectrometer over a wider infrared wavelength range by proposing a feasible design strategy. Our results provide a novel approach for low-cost and portable mid-infrared spectroscopic detection in ultracompact mid-infrared spectral imaging and sensing elements.
Channel multiplexing of FSO systems based on singular optics approaches
Authors: Mokhun I , Vasnetsov M , Felde Ch , Galushko Y , Karabchiyvskiy M , Viktorovskaya Y
Published: June 2024

The article proposes two new methods for multiplexing-demultiplexing communication channels in the FSO system, based on singular optics approaches. The first makes use of computer generated vortex holograms installed in the transmitting and receiving modules of the systems, which make it possible to generate and separate communication channels formed by vortex beams with different topological charges. The second method, spatial singular multiplexing, is based on the property of singular beams to restore angular momentum when vortex beams propagate in a medium with physical disturbances. The method uses opaque screens installed in the transmitting block of the system, which diaphragm the vortex beams. As a result of this operation, the centers of the vortices in the receiving part of the system are displaced, which makes it possible to separate the beams that are differently blocked in the transmitting unit. Computer simulation data and experimental results are presented.
Introduction
Authors: Krotoszynski, Jr. Ronald J
Published: June 2024

In the contemporary United States, the federal judiciary, notably including the conservative majority on the Supreme Court, embraces “textualist originalism” as the primary interpretative methodology in constitutional adjudication. Coupled with a commitment to the “original public meaning” of the Constitution, Bill of Rights, and Civil War Amendments, in theory this approach constrains judicial discretion by limiting the power of judges to interpret independently constitutional text. In the context of the First Amendment, however, this commitment to textualist originalism gets largely, arguably completely, disregarded in favor of a dynamic, purposive, “living tree” approach that reads all four of the First Amendment’s speech-related clauses as creating a general rule against government censorship of speech that has any arguable connection to the marketplace of political ideas. The actual words of the First Amendment, and the four independent clauses, more or less go out the window. This demonstrates, with convincing clarity, the limited relevance of constitutional text to the protection of expressive freedom. Rather than hewing closely and carefully to the text and original public meaning, judges in the United States use a common law process to develop and refine free speech principles over time and on an interstitial basis. This ongoing process of common law constitutionalism—not the text—serves as the primary means through which the Article III courts define and protect expressive freedom.
Genomic profiling of a skin adnexal carcinomas cohort using a comprehensive high-throughput sequencing approach
Authors: Louveau Baptiste , Nakouri Ines , Jouenne Fanélie , Baroudjian Barouyr , Sadoux Aurélie , Da Meda Laetitia , Osio Amélie , Reinhart Fanny , Robert Julien , Herms Florian , Cribier Bernard , Mortier Laurent , Jouary Thomas , Basset Seguin Nicole , Lebbé Céleste , Mourah Samia , Battistella Maxime
Published: June 2024

We conducted a comprehensive molecular characterization of a cohort of 77 patients with skin adnexal carcinomas and compared our findings with those of other skin carcinomas. We highlighted genomic profiles bringing insights regarding classification, tumorigenesis processes and therapeutic options.
Mosaic EGFR exon 20 in-frame insertion pathogenic variants are associated with papular epidermal naevus with ‘skyline’ basal cell layer (PENS)
Authors: Bessis Didier , Poujade Laura , Cossée Mireille , Boursier Guilaine , Barat-Houari Mouna , Tharreau Mylene , Durand Luc , Aguilar Simon-Cabello , Solassol Jérome , Willems Marjolaine , Vendrell Julie
Published: June 2024

Papular epidermal naevus with ‘skyline’ basal cell layer (PENS) is a type of keratinocytic epidermal naevus for which the molecular genetic mechanism has not yet been identified. EGFR ex20ins could represent a new and specific genetic somatic marker of PENS.
Abdominal CT findings characteristic of Castleman disease: multi-centre review of 76 adult cases with abdominopelvic nodal involvement
Authors: Pickhardt Perry J , Wong Vincenzo K , Mellnick Vincent , Sugi Mark , Aswani Yashant
Published: June 2024

Objective

Characterize the CT findings of abdominopelvic Castleman disease, including a new observation involving the perinodal fat.

Methods

Multi-centre search at 5 institutions yielded 76 adults (mean age, 42.1 ± 14.3 years; 38 women/38 men) meeting inclusion criteria of histopathologically proven Castleman disease with nodal involvement at abdominopelvic CT. Retrospective review of the dominant nodal mass was assessed for size, attenuation, and presence of calcification, and for prominence and soft-tissue infiltration of the perinodal fat. Hypervascular nodal enhancement was based on both subjective and objective comparison with aortic blood pool attenuation.

Results

Abdominal involvement was unicentric in 48.7% (37/76) and multicentric in 51.3% (39/76), including 31 cases with extra-abdominal involvement. Histopathologic subtypes included hyaline vascular variant (HVV), plasma cell variant (PCV), mixed HVV/PCV, and HHV-8 variant in 39, 25, 3 and 9 cases, respectively. The dominant nodal mass measured 4.4 ± 1.9 cm and 3.2 ± 1.7 cm in mean long- and short-axis, respectively, and appeared hypervascular in 58.6% (41/70 with IV contrast). Internal calcification was seen in 22.4% (17/76). Infiltration of the perinodal fat, with or without hypertrophy, was present in 56.6% (43/76), more frequent with hypervascular vs non-hypervascular nodal masses (80.5% vs 20.7%; P < .001). Among HVV cases, 76.9% were unicentric, 71.1% appeared hypervascular, and 69.2% demonstrated perinodal fat infiltration.

Conclusion

Hypervascular nodal masses demonstrating prominence and infiltration of perinodal fat at CT can suggest the specific diagnosis of Castleman disease, especially the HVV.

Advances in knowledge

Abdominopelvic nodal masses that demonstrate hypervascular enhancement and prominent infiltration of the perinodal fat at CT can suggest the diagnosis of Castleman disease, but nonetheless requires tissue sampling.
Diagnostic challenges in a family with dominant dystrophic epidermolysis bullosa and isolated hereditary nail disorder: paternal gonosomal mosaicism for COL7A1 variant and maternal RSPO4 variant
Authors: Öktem Ayşe , Özaydın Berna , Gündüz Kaan , Gökpınar İli Ezgi , Şanlı Hatice , Kaplan İbrahim , Yürür Kutlay Nüket
Published: June 2024

This case series aims to serve as an example for similar cases of genodermatoses and to highlight the importance of detailed genetic analysis guided by comprehensive medical history in reaching a diagnosis.
Penile nodules and ulcer
Authors: Savo Karin , Taimen Pekka , Hieta Niina
Published: June 2024

Primary amyloidosis of the penis is an uncommon variant of localized amyloidosis. The clinical presentation is variable, ranging from waxy or infiltrated nodules or plaques typical for nodular amyloidosis, to hyperpigmented macules in macular amyloidosis, and papules or plaques in lichen amyloidosis. Amyloidosis should be suspected and Congo red staining performed in cases of clinically uncommon penile masses or ulcers, or histologically atypical hyalinization.
Penile melanocytoma
Authors: Rapparini Luca , Vaccari Sabina , Gaspari Valeria , Venturi Federico , Corti Barbara , Misciali Cosimo , Dika Emi
Published: June 2024

Diagnosing mucosal pigmented lesions poses challenges due to the necessity of considering various differential entities. We present the case of an 18-year-old man with a histologically confirmed pigmented epithelioid melanocytoma (PEM) of the penile shaft, describing its clinical presentation, dermoscopy and histology. PEM is a rare neoplasm predominantly observed in young individuals and adults, typically found on the trunk and extremities, but it can also affect oral and genital mucosae. Its diagnosis and management present considerable challenges, necessitating a multidisciplinary approach.
Seeing Beyond the Surface: Superior Performance of Ultrasound Elastography over Milan Ultrasound Criteria in Distinguishing Fibrosis of Ulcerative Colitis
Authors: Zhu Feng , Chen Xin , Qiu Xueni , Guo Wenwen , Wang Xuesong , Cao Junying , Gong Jianfeng
Published: June 2024

Background

Colonic fibrosis has important clinical implications in ulcerative colitis [UC]. Ultrasound imaging has emerged as a convenient and reliable tool in diagnosis of inflammatory bowel disease. We aimed to explore the potential use of ultrasound to evaluate UC fibrosis.

Methods

Consecutive UC patients who had proctocolectomy from July 2022 to September 2023 were enrolled in the study. Patients underwent bowel ultrasound examination and ultrasound elastography imaging prior to surgery. Milan ultrasound criteria [MUC] were calculated and bowel wall stiffness was determined using two mean strain ratios [MSRs]. Degree of colonic fibrosis and inflammation was measured upon histological analysis. Receiver operating characteristic [ROC] analysis was used to evaluate the performance of ultrasound-derived parameters to predict fibrosis.

Results

In all, 56 patients were enrolled with 112 segments included in analysis. The median fibrosis score was 2 [0-4] and the median Geboes score was 5 [0-13] and these two scores were significantly correlated [p < 0.001]. The muscularis mucosa thickness was significantly higher in moderate-severe fibrosis than none-mild fibrosis [p = 0.003] but bowel wall thickness was not [p = 0.082]. The strain ratios [p < 0.001] and MUC [p = 0.010] were significantly higher in involved than non-involved segments. The strain ratios were correlated with fibrosis score [p < 0.001] but not MUC [p = 0.387]. At ROC analysis, mean strain ratio 1 [MSR1] had an area under the curve [AUC] of 0.828 [cutoff value 3.07, 95% CI 0.746-0.893, p < 0.001] to predict moderate-severe fibrosis.

Conclusion

Ultrasound elastography imaging could predict the degree of colonic fibrosis in UC. Application of this technique could help disease monitoring and decision making in UC patients.
Singularity points and their degeneracies in anisotropic media
Authors: Stovas Alexey , Roganov Yuriy , Roganov Vyacheslav
Published: June 2024

We define double (S1S2) and triple (PS1S2) singularity points and their degeneracy classes in triclinic anisotropic media. We derive equations for the group velocity image for all these cases. The degeneracy classes are defined by factorization of quadratic (double singularity point) and cubic (triple singularity point) forms with three variables.
APIR: Aggregating Universal Proteomics Database Search Algorithms for Peptide Identification with FDR Control
Authors: Chen Yiling Elaine , Ge Xinzhou , Woyshner Kyla , McDermott MeiLu , Manousopoulou Antigoni , Ficarro Scott B , Marto Jarrod A , Li Kexin , Wang Leo David , Li Jingyi Jessica
Published: June 2024

Advances in mass spectrometry (MS) have enabled high-throughput analysis of proteomes in biological systems. The state-of-the-art MS data analysis relies on database search algorithms to quantify proteins by identifying peptide–spectrum matches (PSMs), which convert mass spectra to peptide sequences. Different database search algorithms use distinct search strategies and thus may identify unique PSMs. However, no existing approaches can aggregate all user-specified database search algorithms with a guaranteed increase in the number of identified peptides and a control on the false discovery rate (FDR). To fill in this gap, we proposed a statistical framework, Aggregation of Peptide Identification Results (APIR), that is universally compatible with all database search algorithms. Notably, under an FDR threshold, APIR is guaranteed to identify at least as many, if not more, peptides as individual database search algorithms do. Evaluation of APIR on a complex proteomics standard dataset showed that APIR outpowers individual database search algorithms and empirically controls the FDR. Real data studies showed that APIR can identify disease-related proteins and post-translational modifications missed by some individual database search algorithms. The APIR framework is easily extendable to aggregating discoveries made by multiple algorithms in other high-throughput biomedical data analysis, e.g., differential gene expression analysis on RNA sequencing data. The APIR R package is available at https://github.com/yiling0210/APIR.
Risks of regionalized stock assessments for widely distributed species like the panmictic European eel
Authors: Höhne Leander , Briand Cédric , Freese Marko , Marohn Lasse , Pohlmann Jan-Dag , van der Hammen Tessa , Hanel Reinhold
Published: June 2024

In fisheries management, accurate stock assessment is pivotal to determine sustainable harvest levels or the scope of conservation measures. When assessment is decentralized and methods differ regionally, adopted approaches must be subjected to rigorous quality-checking, as biased assessments may mislead management decisions. To enable recovery of the critically endangered European eel, EU countries must fulfill a biomass target of potential spawner (“silver eel”) escapement, while local eel stock assessment approaches vary widely. We summarize local approaches and results of ground-truthing studies based on direct silver eel monitoring, to evaluate the accuracy of eel stock assessments in retrospect and identify bias sources. A substantial fraction of eel habitat is currently unassessed or assessed by unvalidated approaches. Across assessment models for which validation exists, demographic models frequently overestimated actual escapement, while misestimations of extrapolation (“spatial”) models were more balanced, slightly underestimating escapement. Stock size overestimation may lead to overexploitation or insufficient conservation measures, increasing the risk of stock collapse or slow recovery in coordinated frameworks. Underestimations may imply inefficient allocation of conservation efforts or negatively affect socioeconomy. Our work highlights the risks of regionalizing assessment responsibilities along with management decisions, calling for a common assessment toolbox and centralized quality-checking routines for eel.
Barriers Experienced by First Nations Deaf People in the Justice System
Authors: Elder Brent C , Soldatić Karen , Schwartz Michael A , Barney Jody , Howard Damien , McGee Patrick
Published: June 2024

Anecdotal evidence strongly suggests that members of the First Nations Deaf community experience more barriers when engaging with the criminal justice system than those who are not deaf. Therefore, our purpose for writing this article is to highlight legal and policy issues related to First Nations Deaf people, including perspectives of professionals working with these communities, living in Australia who have difficulty in accessing supports within the criminal justice system. In this article, we present data from semi-structured qualitative interviews focused on four key themes: (a) indefinite detention and unfit to plead, (b) a need for an intersectional approach to justice, (c) applying the maximum extent of the law while minimizing social services–related resources, and (d) the need for language access and qualified sign language interpreters. Through this article and the related larger sustaining project, we seek to center the experiences and needs of First Nations Deaf communities to render supports for fair, just, and equitable access in the Australian criminal justice system to this historically marginalized group.
Mitigating the rise of unilateralism: lessons from forestry management
Authors: Messenger Gregory
Published: June 2024

This article responds to the rise in unilateralism in trade policy (particularly from the EU and USA) and considers how its negative effects, especially concerning developing countries, can be mitigated through the use of instruments of trade law in the practice of economic diplomacy. It does this in three steps: first, it challenges the dichotomy between unilateral and plurilateral approaches to trade policy, and reframes this rise in unilateralism as conceptually and practically linked to the increasing plurality of trade law’s actors, sources, and institutions (the plural-unilateral dynamic); second, trade in forest products is used as a case study to examine this dynamic, identifying underlying tensions in the use of unilateral and plurilateral policies as well as potential mechanisms of accommodation; finally, in step three, the article identifies two related avenues of accommodation to improve participation and engagement—leveraging structures of meta-governance in trade (dialogues, committees, and standards bodies). In doing so, this article both reframes debates around unilateralism and plurilateralism in trade law and policy, and places the hitherto underexplored practice of economic diplomacy at the heart of means to improve trade relations.
Past five years on strategies and applications in hybrid brain storm optimization algorithms: a review
Authors: Simić Dragan , Banković Zorana , Villar José R , Calvo-Rolle José Luis , Ilin Vladimir , Simić Svetislav D , Simić Svetlana
Published: June 2024

Optimization, in general, is regarded as the process of finding optimal values for the variables of a given problem in order to minimize or maximize one or more objective function(s). Brain storm optimization (BSO) algorithm solves a complex optimization problem by mimicking the human idea generating process, in which a group of people solves a problem together. The aim of this paper is to present hybrid BSO algorithm solutions in the past 5 years. This study could be divided into two parts: strategies and applications. In the first part, different strategies for the hybrid BSO algorithms intended to improve the various ability of the original BSO algorithm are displayed. In the second part, the real-world applications in the past five years in optimization, prediction and feature selection processes are presented.
Slam dunk statistics
Authors: Ley Christophe , Jack Oliver
Published: June 2024

Despite other countries catching up, the USA remains a global basketball powerhouse and is favourite to win gold in basketball at the Paris 2024 Olympic Games. Oliver Jack and Christophe Ley use cluster analysis to help answer some of its fans’ hottest topics of discussion
Presenting data the Significance way - Part 1
Authors: Rennie Nicola , Krause Andreas
Published: June 2024

Want to be published in Significance? Our data visualisation guide, created by Andreas Krause and Nicola Rennie, offers contributors insights, advice, and examples (with code) to make data outputs more readable, accessible, and impactful. Over the next few issues, we will publish it section by section until you have a complete guide to creating the best data visualisation for the needs of both your article and Significance magazine
It’s not about right and wrong
Authors: Harrison Camille
Published: June 2024

Official statistics affect everyone. But not everyone agrees with them – or even cares about them. Tackling indifference, mistrust and criticism is hard work but, says Camille Harrison, is essential for statistics organisations in our “post-truth” age
Surgical management of spinal intradural metastatic pathologies: a case-based review
Authors: Thoma Constantinos , Englander Zachary K , Prezerakos Georgios
Published: June 2024

Intradural spinal metastases significantly impair neurological function and quality of life, necessitating multimodal, palliative management to preserve mobility and alleviate pain. The effectiveness of systemic chemotherapy and radiotherapy is limited due to the blood-spinal cord barrier and the tumours’ radioresistance, respectively. This highlights the urgency for alternative treatments given the rapid neurological decline. Surgical intervention becomes crucial, focusing on maximum tumour debulking to enhance disease control, restore ambulation, and palliate symptoms without compromising neurological function. Achieving this involves meticulous preoperative planning and aggressive intraoperative neuromonitoring. Combining surgery with adjuvant therapies may improve local control and potentially delay recurrence. This case-based review emphasizes the surgical considerations and outcomes in two cases of intradural spinal metastases, underscoring the value of surgery in multimodal therapy.
Raman-based machine-learning platform reveals unique metabolic differences between IDHmut and IDHwt glioma
Authors: Lita Adrian , Sjöberg Joel , Păcioianu David , Siminea Nicoleta , Celiku Orieta , Dowdy Tyrone , Păun Andrei , Gilbert Mark R , Noushmehr Houtan , Petre Ion , Larion Mioara
Published: June 2024

Background

Formalin-fixed, paraffin-embedded (FFPE) tissue slides are routinely used in cancer diagnosis, clinical decision-making, and stored in biobanks, but their utilization in Raman spectroscopy-based studies has been limited due to the background coming from embedding media.

Methods

Spontaneous Raman spectroscopy was used for molecular fingerprinting of FFPE tissue from 46 patient samples with known methylation subtypes. Spectra were used to construct tumor/non-tumor, IDH1WT/IDH1mut, and methylation-subtype classifiers. Support vector machine and random forest were used to identify the most discriminatory Raman frequencies. Stimulated Raman spectroscopy was used to validate the frequencies identified. Mass spectrometry of glioma cell lines and TCGA were used to validate the biological findings.

Results

Here, we develop APOLLO (rAman-based PathOLogy of maLignant gliOma)—a computational workflow that predicts different subtypes of glioma from spontaneous Raman spectra of FFPE tissue slides. Our novel APOLLO platform distinguishes tumors from nontumor tissue and identifies novel Raman peaks corresponding to DNA and proteins that are more intense in the tumor. APOLLO differentiates isocitrate dehydrogenase 1 mutant (IDH1mut) from wild-type (IDH1WT) tumors and identifies cholesterol ester levels to be highly abundant in IDHmut glioma. Moreover, APOLLO achieves high discriminative power between finer, clinically relevant glioma methylation subtypes, distinguishing between the CpG island hypermethylated phenotype (G-CIMP)-high and G-CIMP-low molecular phenotypes within the IDH1mut types.

Conclusions

Our results demonstrate the potential of label-free Raman spectroscopy to classify glioma subtypes from FFPE slides and to extract meaningful biological information thus opening the door for future applications on these archived tissues in other cancers.
Effects of age, breeding strategy, population density, and number of neighbors on territory size and shape in Passerculus sandwichensis (Savannah Sparrow)
Authors: Suarez Sharma Sarika P , Dobney Sarah L , Norris D Ryan , Doucet Stéphanie M , Newman Amy E M , Burant Joseph B , Moran Ines G , Mueller Sarah D , Spina Hayley A , Mennill Daniel J
Published: June 2024

The size and shape of an animal’s breeding territory are dynamic features influenced by multiple intrinsic and extrinsic factors and can have important implications for survival and reproduction. Quantitative studies of variation in these territory features can generate deeper insights into animal ecology and behavior. We explored the effect of age, breeding strategy, population density, and number of neighbors on the size and shape of breeding territories in an island population of Passerculus sandwichensis (Savannah Sparrow). Our dataset consisted of 407 breeding territories belonging to 225 males sampled over 11 years. We compared territory sizes to the age of the male territorial holder, the male’s reproductive strategy (monogamy vs. polygyny), the number of birds in the study population (population density), and the number of immediate territorial neighbors (local density). We found substantial variation in territory size, with territories ranging over two orders of magnitude from 57 to 5,727 m2 (0.0057–0.57 ha). Older males had larger territories, polygynous males had larger territories, territories were smaller in years with higher population density, and larger territories were associated with more immediate territorial neighbors. We also found substantial variation in territory shape, from near-circular to irregularly shaped territories. Males with more neighbors had irregularly shaped territories, but shape did not vary with male age, breeding strategy, or population density. For males that lived 2 years or longer, we found strong consistent individual differences in territory size across years, but weaker individual differences in territory shape, suggesting that size has high repeatability whereas shape has low repeatability. Our work provides evidence that songbird territories are highly dynamic, and that their size and shape reflect both intrinsic factors (age and number of breeding partners) and extrinsic factors (population density and number of territorial neighbors).
Melt-Rock Reaction in the Lower Oceanic Crust and the Influence on the Evolution of Mid-Ocean Ridge Basalts at the Central Indian Ridge (7°50′–8°30′S)
Authors: Choi Sarang , Park Jung-Woo , Kim Jonguk , Oh Jihye , Park Changkun , Han Seunghee
Published: June 2024

Various crustal processes shape both the lower oceanic crust and mid-ocean ridge basalts (MORBs). To better understand how these crustal processes influence MORB compositions, we conducted comprehensive petrographic and geochemical investigations on gabbroic rocks and erupted lavas dredged from a segment of the Central Indian Ridge (CIR) spanning from 7°50′S to 8°30′S. The petrographic and geochemical analyses of the gabbroic rocks revealed evidence of melt-rock reaction through reactive porous flow in olivine gabbro and gabbro. This process resulted in distinctive features in clinopyroxene, including disequilibrium textures with a troctolite/anorthosite matrix, complex variations in Mg#-Cr-Ti [Mg# = molar Mg/(Mg + Fe2+)] relationships, and considerable enrichment and fractionation of incompatible trace elements. A significant finding of our study is the close resemblance of trace element ratios in MORB and olivine-hosted melt inclusions to those of melts in equilibrium with clinopyroxene from olivine gabbro and gabbro with Sr anomaly (Sr/Sr* = SrN/sqrt[PrN*NdN]; N refers to chondrite-normalized values) greater than ~0.7. This observation strongly indicates that the composition of MORB is influenced by the melt-rock reaction taking place in the lower oceanic crust. Furthermore, our findings suggest that evolved melts in equilibrium with clinopyroxene having Sr/Sr* values lower than ~0.7 are less likely to erupt onto the seafloor and are instead trapped within the lower oceanic crust. Oxide gabbronorite is characterized by coarse-granular, pegmatitic textures and exhibits mineralogically and chemically more evolved characteristics compared to olivine gabbro and gabbro. It is inferred that the oxide gabbronorite formed through the in situ freezing of highly evolved melts within a melt-rich layer. Finally, we present a comprehensive model for melt evolution in the lower oceanic crust at the 7°50′S–8°30′S CIR by integrating all petrological and geochemical data obtained from gabbroic rocks, MORB, and olivine-hosted melt inclusions. This holistic model contributes to a better understanding of the intricate processes governing MORB composition in the context of the lower oceanic crust dynamics at slow-spreading ridges.
Which advanced treatment should be used following the failure of a first-line anti-TNF in patients with rheumatoid arthritis? 15 years of evidence from the Quebec registry RHUMADATA
Authors: Choquette Denis , Haraoui Boulos , Movahedi Mohammad , Bessette Louis , Sauvageau Loïc Choquette , Ferdinand Isabelle , Joly-Chevrier Maxine , Masetto Ariel , Massicotte Frédéric , Nadon Valérie , Pelletier Jean-Pierre , Raynauld Jean-Pierre , Sauvageau Diane , Villeneuve Édith , Coupal Louis
Published: June 2024

Background

Since 2000, advanced therapies (AT) have revolutionized the treatment of moderate to severe RA. Randomized control trials as well as observational studies together with medication availability often determine second-line choices after the failure of first TNF inhibitors (TNFi). This led to the observation that specific sequences provide better long-term effectiveness. We investigated which alternative medication offers the best long-term sustainability following the first TNFi failure in RA.

Methods

Data were extracted from RHUMADATA from January2007. Patients were followed until treatment discontinuation, loss to follow-up or 25 November 2022. Kaplan–Meier and Cox regression models were used to compare discontinuation between groups. Missing data were imputed, and propensity scores were computed to reduce potential attribution bias. Complete, unadjusted and propensity score-adjusted imputed data analyses were produced.

Results

Six hundred eleven patients [320 treated with a TNFi and 291 treated with molecules having another mechanism of action (OMA)] were included. The mean age at diagnosis was 44.5 and 43.9 years, respectively. The median retention was 2.84 and 4.48 years for TNFi and OMAs groups. Using multivariable analysis, the discontinuation rate of the OMA group was significantly lower than TNFi (adjHR: 0.65; 95% CI: 0.44–0.94). This remained true for the PS-adjusted MI Cox models. In a stratified analysis, rituximab (adjHR: 0.39; 95% CI: 0.18–0.84) had better retention than TNFi after adjusting for patient characteristics.

Conclusion

Switching to an OMA, especially rituximab, in patients with failure to a first TNFi appears to be the best strategy as a second line of therapy.
Vascular endothelial growth factor secretion and immunosuppression are distinct potency mechanisms of human bone marrow mesenchymal stromal cells
Authors: Faircloth Tyler U , Temple Sara , Parr Rhett N , Tucker Anna B , Rajan Devi , Hematti Peiman , Kugathasan Subra , Chinnadurai Raghavan
Published: June 2024

Mesenchymal stromal cells (MSCs) are investigated as cellular therapeutics for inflammatory bowel diseases and associated perianal fistula, although consistent efficacy remains a concern. Determining host factors that modulate MSCs’ potency including their secretion of angiogenic and wound-healing factors, immunosuppression, and anti-inflammatory properties are important determinants of their functionality. We investigated the mechanisms that regulate the secretion of angiogenic and wound-healing factors and immune suppression of human bone marrow MSCs. Secretory analysis of MSCs focusing on 18 angiogenic and wound-healing secretory molecules identified the most abundancy of vascular endothelial growth factor A (VEGF-A). MSC viability and secretion of other angiogenic factors are not dependent on VEGF-A secretion which exclude the autocrine role of VEGF-A on MSC’s fitness. However, the combination of inflammatory cytokines IFNγ and TNFα reduces MSC’s VEGF-A secretion. To identify the effect of intestinal microvasculature on MSCs’ potency, coculture analysis was performed between human large intestine microvascular endothelial cells (HLMVECs) and human bone marrow-derived MSCs. HLMVECs do not attenuate MSCs’ viability despite blocking their VEGF-A secretion. In addition, HLMVECs neither attenuate MSC’s IFNγ mediated upregulation of immunosuppressive enzyme indoleamine 2,3-dioxygenase nor abrogate suppression of T-cell proliferation despite the attenuation of VEGF-A secretion. We found that HLMVECs express copious amounts of endothelial nitric oxide synthase and mechanistic analysis showed that pharmacological blocking reverses HLMVEC-mediated attenuation of MSC’s VEGF-A secretion. Together these results suggest that secretion of VEGF-A and immunosuppression are separable functions of MSCs which are regulated by distinct mechanisms in the host.
Analysis of the Genetic Variation and Geographic Distribution Patterns of Xanthomonas citri pv. citri Strains in Citrus Production in Burkina Faso
Authors: Zerbo Kevin Ben Fabrice , Yameogo Florence , Wonni Issa , Somda Irénée
Published: June 2024

It is essential to have a thorough knowledge of the genetic variation among different strains of Xanthomonas citri pv. citri, which is responsible for causing citrus bacterial canker. This understanding is important for studying disease characteristics, population structure, and evolution and ultimately for developing sustainable methods of control. A total of 48 strains obtained from citrus production areas in Burkina Faso in 2012, 2020, and 2021 were subjected to Polymerase Chain reaction (PCR) tests using specific primers. The aim was to examine the distribution of type 3 effectors and determine the geographical origins of the strains. The examination of the distribution of type 3 non-transcription-activator-like effectors (TALEs) revealed a broader range of strains obtained in 2020 and 2021 than in 2012. However, all the strains possessed a shared set of three genes, specifically, XopE2, XopN, and AvrBs2. Furthermore, all examined effectors were observed in the Bobo-Dioulasso region. Regarding the characterization of TALEs, two profiles containing two to three TALEs were discovered. Profile 1, consisting of two TALEs, was found in 37 X. citri pv. citri strains, whereas Profile 2, comprising three TALEs, was detected in 11 strains. Among the three TALEs (A, B, and C) that were identified, TALEs B and C were present in all the strains. The correlation matrix indicated a positive association between the type 3 effector content of strains and the duration of their isolation. Principal component analysis revealed a limited organization of the strains under investigation.

[Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Increased Gremlin1 Expression in Pancreatic Ductal Adenocarcinoma Promotes a Fibrogenic Stromal Microenvironment
Authors: Tindall Rachel R. , Faraoni Erika Y. , Li Jiajing , Zhang Yinjie , Ting Shun-Ming , Okeugo Beanna , Zhao Xiurong , Liu Yuying , Younes Mamoun , Shen Qiang , Bailey-Lundberg Jennifer M. , Cao Yanna , Ko Tien C.
Published: June 2024

Objective

Pancreatic ductal adenocarcinoma (PDAC) microenvironment is primarily composed of cancer-associated fibroblasts and immune cells. Gremlin1 (Grem1) is a profibrogenic factor that promotes tumorigenesis in several cancers. However, the role of Grem1 in the PDAC microenvironment is not defined.

Materials and Methods

We correlated Grem1 levels with activated stroma and immune cells in human PDAC using The Cancer Genome Atlas RNA-sequencing data and characterized expression of Grem1 transcripts and isoforms in pancreatic cell lines and PDAC tissues. We assessed the role of Grem1 in the microenvironment by in vitro studies.

Results

Grem1 expression is associated with an activated stroma and increased M1 and M2 macrophages. Only full length Grem1 variant 1 and isoform 1 were detectable in human pancreatic cells, and remarkably high levels of Grem1 were observed in pancreatic fibroblasts. Immunohistochemistry detected Grem1 protein in PDAC tumor and stromal cells, which correlated with infiltrating macrophages in PDAC tumors. Grem1 knockdown in cancer-associated fibroblasts suppressed transforming growth factor β–induced extracellular matrix proteins. Grem1 recombinant protein treatment in vitro increased M1 and M2 macrophages.

Conclusions

Grem1 acts as a profibrogenic factor in the PDAC microenvironment via modulation of fibroblasts and macrophages. Grem1 may have the potential to be developed as a therapeutic target for PDAC.
The Mediating Effect of Coping Style in the Relationship Between Sleep Quality and Perceived Cognitive Impairment Among Breast Cancer Patients
Authors: Chen Fan , Li Changzai , Zhu Jingwen , Zhao Yaning , Zhang Pan , Gao Jianru , Yang Yuqi , Guo Lin
Published: June 2024

Background

Perceived cognitive impairment is a significant symptom experienced by breast cancer patients and may be affected by sleep quality. Coping styles have potential relevancies with both sleep quality and perceived cognitive impairment. However, the empirical evidence supporting their association among breast cancer patients is limited.

Objective

This study explored the associations between sleep quality, coping styles, and perceived cognitive impairment and tested the mediating role of coping styles in breast cancer patients.

Methods

A total of 294 breast cancer patients were included in this cross-sectional study. Patients were assessed using the Pittsburgh Sleep Index Scale, the Simplified Coping Styles Questionnaire, and the Functional Assessment of Cancer Therapy-Cognitive Functioning (Version 3) Scale. The data were analyzed using SPSS and Process macros.

Results

The direct effect of sleep quality on reported cognitive impairment was significant (β = −0.245, P < .001). Furthermore, sleep quality was found to have a significant indirect effect on perceived cognitive impairment through positive coping style (β = −0.026, P < .05) and negative coping style (β = −0.131, P < .05).

Conclusions

Our research suggests that sleep quality has both a direct effect on perceived cognitive impairment and an indirect effect through positive and negative coping styles in breast cancer patients. Moreover, negative coping style had a more pronounced mediating effect than positive coping style.

Implications for Practice

Clinical medical staff could reduce the perceived cognitive impairment of breast cancer patients by improving their sleep quality and encouraging them to adopt a more positive coping style.
Retracing the horizontal transfer of a novel innate immune factor inDrosophila
Authors: Tarnopol Rebecca L. , Tamsil Josephine , Cinege Gyöngyi , Ha Ji Heon , Verster Kirsten I. , Ábrahám Edit , Magyar Lilla B. , Kim Bernard Y. , Bernstein Susan L. , Lipinszki Zoltán , Andó István , Whiteman Noah K.
Published: June 2024

Immune systems are among the most dynamically evolving traits across the tree of life, and long-lived macroparasites play an outsized role in shaping animal immunity. Even without adaptive immunity, insects have evolved potent innate immune strategies to neutralize such enemies, including nematodes and parasitoid wasps. One such strategy relies on endosymbioses between insects and toxin-expressing bacteria. Here, we use genome editing inDrosophila melanogasterto retrace the evolution of two of such toxins —cytolethal distending toxin B(cdtB) andapoptosis inducing protein of 56kDa(aip56) — that were horizontally transferred from bacteriophages to insects. We found that acdtB::aip56fusion gene (fusionB), which is conserved inDrosophila ananassaesubgroup species, dramatically promoted fly survival and suppressed wasp development when expressed inD. melanogasterimmune tissues. FusionB, a functional nuclease, was secreted into the host hemolymph where it targeted the parasitoid embryo’s serosal tissue and is to our knowledge the first humoral anti-parasitoid toxin inDrosophila. When expressed ubiquitously,fusionBslowed development in late stage fly larvae and eventually killed flies, pointing to the salience of regulatory constraint in preventing autoimmunity. Our findings demonstrate how horizontal gene transfer, in the right regulatory context, can instantly provide new and potent innate immune modules in animals.