bluuebunny/crossref_metadata_2025 huggingface dataset:
Extensive Population Structure Highlights an Apparent Paradox of Stasis in the Impala (Aepyceros melampus)
Authors: Garcia‐Erill Genís , Wang Xi , Rasmussen Malthe S. , Quinn Liam , Khan Anubhab , Bertola Laura D. , Santander Cindy G. , Balboa Renzo F. , Ogutu Joseph O. , Pečnerová Patrícia , Hanghøj Kristian , Kuja Josiah , Nursyifa Casia , Masembe Charles , Muwanika Vincent , Bibi Faysal , Moltke Ida , Siegismund Hans R. , Albrechtsen Anders , Heller Rasmus
Published: October 2024

Impalas are unusual among bovids because they have remained morphologically similar over millions of years—a phenomenon referred to as evolutionary stasis. Here, we sequenced 119 whole genomes from the two extant subspecies of impala, the common (Aepyceros melampus melampus) and black‐faced (A. m. petersi) impala. We investigated the evolutionary forces working within the species to explore how they might be associated with its evolutionary stasis as a taxon. Despite being one of the most abundant bovid species, we found low genetic diversity overall, and a phylogeographic signal of spatial expansion from southern to eastern Africa. Contrary to expectations under a scenario of evolutionary stasis, we found pronounced genetic structure between and within the two subspecies with indications of ancient, but not recent, gene flow. Black‐faced impala and eastern African common impala populations had more runs of homozygosity than common impala in southern Africa, and, using a proxy for genetic load, we found that natural selection is working less efficiently in these populations compared to the southern African populations. Together with the fossil record, our results are consistent with a fixed‐optimum model of evolutionary stasis, in which impalas in the southern African core of the range are able to stay near their evolutionary fitness optimum as a generalist ecotone species, whereas eastern African impalas may struggle to do so due to the effects of genetic drift and reduced adaptation to the local habitat, leading to recurrent local extinction in eastern Africa and re‐colonisation from the South.
Divide and conquer: using RhizoVision Explorer to aggregate data from multiple root scans using image concatenation and statistical methods
Authors: Seethepalli Anand , Ottley Chanae , Childs Joanne , Cope Kevin R. , Fine Aubrey K. , Lagergren John H. , Kalluri Udaya , Iversen Colleen M. , York Larry M.
Published: October 2024

Roots are important in agricultural and natural systems for determining plant productivity and soil carbon inputs. Sometimes, the amount of roots in a sample is too much to fit into a single scanned image, so the sample is divided among several scans, and there is no standard method to aggregate the data.

Here, we describe and validate two methods for standardizing measurements across multiple scans: image concatenation and statistical aggregation. We developed a Python script that identifies which images belong to the same sample and returns a single, larger concatenated image. These concatenated images and the original images were processed with RhizoVision Explorer, a free and open‐source software. An R script was developed, which identifies rows of data belonging to the same sample and applies correct statistical methods to return a single data row for each sample. These two methods were compared using example images from switchgrass, poplar, and various tree and ericaceous shrub species from a northern peatland and the Arctic.

Most root measurements were nearly identical between the two methods except median diameter, which cannot be accurately computed by statistical aggregation.

We believe the availability of these methods will be useful to the root biology community.
Emergency of oral haemorrhage: Retrospective study over 2 years
Authors: Pinana M. , Rodriguez‐Perron I. , Lescaille G. , Toledo R. , Mondoloni M. , Rochefort J.
Published: October 2024

Introduction

Oral haemorrhages (OH) represent a relatively rare reason for an emergency consultation, among dental pain, infectious processes and traumas. Various haemorrhagic risk factors are described, particularly those related to a general medical context or local factors. It is common to associate OH with haemorrhagic risk patients. Current studies mainly focus on patients considered at risk, but there is limited data on the characteristics of OH in patients without known haemorrhagic risk.

Method

We conducted a 2‐year retrospective study in a dental emergency department to identify OH occurring in patients without known haemorrhagic risk and to study their characteristics.

Results

OH accounted for approximately 2% of the reasons for consultation among all consultations carried out for dental emergencies. Their frequency was similar in the population of patients without hemorrhagic risk and those with a confirmed risk. They mainly occurred in young patients, without medical history. They also led to the diagnosis of an underlying pathology in about 1% of cases.

Conclusion

This study underscores the importance of accurately documenting patients' medical history during preoperative consultations, as well as identifying associated risk factors. It also highlights that OH can be an early sign of a systemic disorder.
Dysphagia and Dysphonia After Head and Neck Cancer
Authors: Parsons Aaron , Dewan Karuna
Published: October 2024

Objective

The purpose of this work is to synthesize the latest developments in diagnosis and management of acute and late dysphagia and dysphonia in oral cavity cancer.

Methods

A literature search was conducted using PubMed, Web of Science, Embase and Google Scholar in May 2024 of articles published between 2021 and 2024. Keywords in the search terms included oral cavity cancer, dysphagia, dysphonia, deglutition, swallowing, voice, oral cavity cancer treatment, oral cavity radiation, chemotherapy, dysgeusia, xerostomia, swallow preservation.

Results

Twenty‐seven pertinent studies fit the inclusion criteria. The most common dysphagic complaints following head and neck cancer are trismus, xerostomia, mucositis and dysphagia. Dysphonia, change in voice is reported by half of head and neck cancer survivors. Fibrosis and neuropathy following radiation therapy to the oral cavity, tongue, oropharynx and its surrounding structures is the most common etiology of post‐treatment dysphonia.

Conclusions

Oral cavity cancers cause speech and swallowing dysfunction due to both anatomic and post‐treatment changes. These sequalae can be detrimental to the quality of life of the head and neck cancer survivor. For both dysphagia and dysphonia after head and neck cancer early speech and swallow therapy with a Speech Language Pathologist are essential to restoring and maintaining function.
‘I'm ruined’: Young people's and their mothers' experiences of living with, and receiving a diagnosis of, borderline personality disorder: An interpretative phenomenological analysis
Authors: Marriner L. , Larkin M. , Urquhart Law G. , Kaur Bhogal S.
Published: October 2024

Background

The adolescent borderline personality disorder (BPD) diagnosis has been widely debated for many years. Strikingly, young people's experiences of both receiving a diagnosis of BPD, and of living with BPD, are largely under‐explored. The current study seeks to address these gaps in the literature in a multi‐perspectival design utilising young people–parent dyads.

Methods

Young people (aged 16–18 years) with a diagnosis of BPD (n = 5) and their mothers (n = 5) were recruited from two NHS Community Mental Health Services in the West Midlands and participated in semi‐structured interviews. Data were analysed using interpretative phenomenological analysis [IPA].

Findings

Analysis identified two superordinate themes with five subthemes: (1) The “ugly” reality of living with BPD (providing a stark insight into what it is like to live with the unpredictable nature of experiences labelled as BPD), and (2) The diagnosis that dare not speak its name (highlighting the complexities of how the diagnosis itself is experienced by participants as a symbol of personal and permanent defectiveness and danger).

Discussion

Findings highlight a clear commonality of experience centred around the intensity of the young people's emotional distress and the accompanying pressure on parents to keep young people safe, both of which services must strive to do more to contain. Ultimately, the costs of receiving a BPD diagnosis appear to outweigh the benefits, and this paper adds support to calls for change in respect to how we conceptualise difficulties labelled as BPD and how we communicate about these difficulties, in order to avoid causing harm.
Information is cheap, but filtering is costly: Congressional investment in reference resources
Authors: Craig Alison , Russell Annelise
Published: October 2024

Lawmakers who can supply themself with information to manage complex problems are at an advantage, but equally important is the filtering and contextualizing of applicable information. Members of Congress manage a deluge of policy and political information, and this short paper examines one strategy members of Congress use to mitigate that burden—by investing in reference material and news media to filter and summarize the policymaking environment. Using congressional disbursement data from the 116th and 117th Congress, I explain how institutional experience is associated with an office's choice to invest in more information filtering. Freshman members of the House are more likely to turn to news media or publications to provide insight into the congressional agenda, offer political context, and prioritize issues of importance. Reference investment is not tied to partisanship, ideology, lawmaking capacity, or previous office, but those junior offices who need to get up to lawmaking speed invest in external information filtering. These results illuminate how central institutional knowledge is to lawmaking in Congress, and how much an office is willing to invest to mitigate that weakness.
Turn to the right, turn away from the green?—A nuanced analysis on how a populist radical right party affects environmental policy making in Sweden
Authors: Berker Lars E.
Published: October 2024

Populist radical right parties are on the rise all over Europe. Recent literature investigates their effects on environmental policy, however, often applying an overly broad perspective on the policy area and neglecting causal mechanisms. This article addresses both gaps in an in‐depth case study of partisan effects on Swedish environmental policy in the wake of increasing populist radical right influence. A novel data approach deriving party positions and policy output from the hard figures of budget proposals between 2001 and 2023, allows a nuanced analysis of environmental policy and its subsectors (e.g., nature conservation and climate mitigation). In summary, a traditional partisan effect is confirmed as a major explaining factor for environmental policy change, while the effect unfolds through altered coalition formation strategies leading to the exclusion of “green voices.” This brings to the fore interactive environmental policy effects of the populist radical right and center‐right parties in the context of changing party competition constellations more generally.
Perceptions of Beneficiaries of Informal Social Protection Initiatives in Uganda: An Exploratory Factor Analysis Approach
Authors: Lubinga Stellah , Lubinga Moses H. , Tyanai Masiya , Asilla Rodney
Published: October 2024

Informal social protection interventions are instrumental in improving people's welfare through fostering income growth and enabling self‐sufficiency. Whereas the success of some informal social protection initiatives has been acknowledged and documented, there is limited knowledge of the factors influencing the performance of informal social protection initiatives, especially in developing countries like Uganda. In this study, we identify and isolate the perceived factors influencing the performance of informal social protection initiatives. We use exploratory factor analysis on a sample of 130 beneficiaries of two informal social protection interventions in the Alebtong and Kampala districts of Uganda. Findings reveal that the performance of informal social protection interventions is perceived to be influenced by three categories of factors, collectively accounting for 62.4% of the total dataset variance which is more than the threshold of 50%. The factors are beneficiary empowerment, welfare enhancement and coverage and equality. Each factor encompasses a cluster of variables that collectively capture the essential dimensions of individual perceptions concerning the effect of informal social protection initiatives. This research offers valuable insights into how the beneficiaries perceive informal social protection initiatives, shedding light on the nuanced factors contributing to their effectiveness in Uganda.
Relationships of Physical Activity and Type 2 Diabetes With Cognition in Mexican Americans and Non-Hispanic Whites
Authors: Yu Fang , Pituch Keenan , Maxfield Molly , Joseph Rodney P. , Pruzin Jeremy J. , Ashish Dev , Coon David W. , Shaibi Gabriel , _ _
Published: October 2024

Problem, Research Strategy, and Findings: Low physical activity (PA) and Type 2 diabetes are associated with cognitive aging and Alzheimer’s disease, but the evidence is inconsistent and particularly limited by ethnicity. The purpose of this study was to examine the relationships of PA and Type 2 diabetes with cognition in Mexican Americans and non-Hispanic Whites. The study was a cross-sectional analysis of the Health and Aging Brain Study-Health Disparities (n = 1,982–2,000 after removing outliers). Predictors included Rapid Assessment of Physical Activity and hemoglobin A1c (HbA1c). Episodic memory was assessed by Weschler Memory Scale–Third Edition Logical Memory and Spanish-English Verbal Learning Test, executive function by Weschler Memory Scale–Third Edition Digit Span and Digit Symbol Substitution Test, verbal fluency by FAS and animal naming, and global cognition by the Mini-Mental State Examination. Results show that aerobic PA and HbA1c were not associated with domain-specific, or global cognition, but strength/flexibility PA was associated with FAS (b = 0.404, 95% CI [0.023, 0.761]). Higher aerobic PA was associated with greater verbal fluency for Mexican Americans (b = 0.294, 95% CI [0.96, 0.497]) only. HbA1c was negatively associated with Mini-Mental State Examination (b = 0.838, 95% CI [0.008, 1.656]). For low HbA1c, the association between aerobic PA and Digit Symbol Substitution Test was significant for non-Hispanic Whites (b = 0.838, 95% CI [0.008, 1.656]) in comparison to Mexican Americans. Takeaway for Practice: The relationships between PA, Type 2 diabetes, and cognition vary by cognitive domains and ethnicity. Increasing aerobic activities may be particularly important for Mexican Americans who have elevated HbA1c to potentially improve fluency or executive function.
Preservice Teachers’ Content Knowledge in Physical Education Teacher Education Programs
Authors: Tsuda Emi , Ward Phillip , Santiago José A. , Hastie Peter , Kim Insook , Ko Bomna , Kim Junyoung
Published: October 2024

Purpose: This study examined changes in common content knowledge (CCK) among preservice teachers in tennis and volleyball over time from entry to completion of physical education teacher education (PETE) programs in a convenient sample in the United States. Method: Six PETE programs for tennis and five for volleyball were the sites of the study. Participants (tennis n = 245; volleyball n = 238) were preservice teachers who had just entered a PETE program and who finished the first, second, and third years in a PETE program (sophomores and juniors). A demographic background survey and valid and reliable tennis and volleyball CCK tests were the instruments used for the study. Results: Descriptive statistics showed that preservice teachers scored well below the expected level of CCK (80%) in both content areas across the years. Discussion/Conclusion: PETE programs need to do a better job of teaching CCK.
Developing a Universal Design for Learning Pedagogy: Perspectives of Students With and Without Disabilities
Authors: Lieberman Lauren J. , Bean Lauren , Grenier Michelle
Published: October 2024

Introduction: Universal design for learning (UDL) is a pedagogical approach utilized to eliminate barriers. Often, UDL has been seen as a strategy implemented solely to benefit students with disabilities. However, recent research on the voices of students with and without disabilities in physical education illuminates a clear need for this educational approach. Purpose: While UDL has been utilized across a variety of subjects, this manuscript identifies the need for UDL implementation in physical education for all students. Method: A document analysis of 69 articles illuminated the voices of children with and without disabilities in physical education related to the components of UDL. Careful analysis of these studies identified voices related to each component of UDL. Results/Conclusions: The results illustrate the need for a call-to-action to promote an inclusive pedagogy that addresses learner variability. The infusion of the UDL approach can alleviate the negative experiences currently impacting children’s experiences in the schools.
Supplemental Material: Underplating-induced trans-crustal melting and maturation of Neoarchean continental crust in the North China Craton
Authors: Yu Yang , al. et
Published: October 2024

Supplemental Texts S1–S2, Figures S1–S4, and Tables S1–S4.  
Chemical synthesis, in vitro testing, and in silico Nampt-based molecular docking of novel aniline aromatic ring-substituted 2-aminothiazole analogs
Authors: Husain Ali A. , Manickam Ravikumar , Gordon Jonah , Santhana Sandhya , Mizgalska Katarzyna , Guida Wayne C. , Tipparaju Srinivas M. , Bisht Kirpal S.
Published: October 2024

The heterocyclic 2-aminothiazoles scaffolds are used in a wide range of therapeutic applications against various diseases for its antioxidant, anti-inflammatory, antimicrobial and anticancer actions. In this study, we synthesized novel aniline aromatic ring-substituted 2-aminothiazole derivatives. Molecular docking was performed using Glide module of the Schrödinger Suite to fit compounds JG-49, JG-62, and KBA-18 against the Nicotinamide phosphoribosyl transferase (Nampt) enzyme, an intracellular regulator of nicotinamide adenine dinucleotide (NAD) redox cofactor involved in energy metabolism and epigenetics and are implicated in aging and metabolic diseases. The three compounds viz. JG-49, JG-62, and KBA-18 showed an increase in Nampt enzymatic activity in vitro. All three substituted derivatives of 2-aminothiazole showed no cytotoxicity with the mouse C2C12 myoblasts cultures assessed with the MTT cell viability assay. Moreover, the wound closure of the mouse C2C12 myoblasts in vitro displayed no significant difference between the treatment groups of the 2-aminothiazole derivatives compared with the control naïve and DMSO treated myoblasts cultures, except for the 2-aminothiazole substituted derivatives JG-62 and KBA-18, which showed a significant increase in the wound closure compared with the control cells at different concentrations. Taken together, we demonstrated that 2-aminothiazole substituted derivatives provide enhanced Nampt activity, wound closure, and no cytotoxic effects in vitro. Further studies will allow to improve the substitution of 2-aminothiazole derivatives and test their potential therapeutic applications.
Revisiting Buchdahl transformations: new static and rotating black holes in vacuum, double copy, and hairy extensions
Authors: Barrientos José , Cisterna Adolfo , Hassaine Mokhtar , Oliva Julio
Published: October 2024

This paper investigates Buchdahl transformations within the framework of Einstein and Einstein-Scalar theories. Specifically, we establish that the recently proposed Schwarzschild–Levi-Civita spacetime can be obtained by means of a Buchdahl transformation of the Schwarschild metric along the spacelike Killing vector. The study extends Buchdahl’s original theorem by combining it with the Kerr–Schild representation. In doing so, we construct new vacuum-rotating black holes in higher dimensions which can be viewed as the Levi-Civita extensions of the Myers–Perry geometries. Furthermore, it demonstrates that the double copy scheme within these new generated geometries still holds, providing an example of an algebraically general double copy framework. In the context of the Einstein-Scalar system, the paper extends the corresponding Buchdahl theorem to scenarios where a static vacuum seed configuration, transformed with respect to a spacelike Killing vector, generates a hairy black hole spacetime. We analyze the geometrical features of these spacetimes and investigate how a change of frame, via conformal transformations, leads to a new family of black hole spacetimes within the Einstein-Conformal-Scalar system.
A brain-network operator for modeling disease: a first data-based application for Parkinson’s disease
Authors: Mannone Maria , Fazio Peppino , Kurths Jürgen , Ribino Patrizia , Marwan Norbert
Published: October 2024

The complexity of our brains can be described as a multi-layer network: neurons, neural agglomerates, and lobes. Neurological diseases are often related to malfunctions in this network. We propose a conceptual model of the brain, describing the disease as the result of an operator affecting and disrupting the network organization. We adopt the formalism of operators, matrices, and tensor products adapted from theoretical physics. This novel approach can be tested and instantiated for different diseases, balancing mathematical formalism and data-driven findings, including pathologies where aging is included as a risk factor. We quantitatively model the K-operator from real data of Parkinson’s Disease, from the Parkinson’s Progression Markers Initiative (PPMI) upon concession by the University of Southern California. The networks are reconstructed from fMRI analysis, resulting in a matrix acting on the healthy brain and giving as output the diseased brain. We finally decompose the K-operator into the tensor product of its submatrices and we are able to assess its action on each region of interest (ROI) characterizing the brain for the specific considered samples. We also approximate the time-dependent K-operator from the fMRI of the same patient at the baseline and at the first follow-up. Our results confirm the findings of the literature on the topic. Also, these applications confirm the feasibility of the proposed analytic technique. Further research developments can compare operators for different patients and for different diseases, looking for commonalities and aiming to develop a comprehensive theoretical approach.
Computer Models Assist Innovative Design of Graphic Arts
Authors: Xu Jing , Zhu Qi
Published: October 2024

In order to study the theory and application of computer aided design (CAD) related to the composition of art, the theory of symbolic matrix was introduced to realize the purpose of the study of the interaction between perceptual and rational problems. In this paper, the original image was extracted from the design object, and the transformation between the original image and the symbol matrix was realized by the correspondence with the elements in the matrix. Based on the research route, four kinds of mathematical models were established, namely random distribution, symmetric distribution, central diffusion, and reorganization. By applying the mathematical model constructed in this paper, the picture was transformed, the combination of various styles of graphics was added, and how to put the simple image picture into a meaningful integrated image picture was discussed. The computer-aided design method of the existing verification examples was summarized in this paper, and the design method was accurate and effective. Compared with traditional graphic art design methods, the computer-aided design method mentioned in the paper has the following advantages. Computer-aided design can quickly process and analyze images, convert and combine them through mathematical models and algorithms, greatly saving designers time and energy. By introducing symbol matrix theory and establishing various mathematical models, computer-aided design can provide diverse graphic combinations and style transformations, helping designers explore more innovative design solutions.
Observable signatures of no-scale supergravity in NANOGrav
Authors: Basilakos Spyros , Nanopoulos Dimitri V. , Papanikolaou Theodoros , Saridakis Emmanuel N. , Tzerefos Charalampos
Published: October 2024

In light of NANOGrav data, we provide for the first time possible observational signatures of Superstring theory. First, we work with inflection-point inflationary potentials naturally realized within Wess–Zumino-type no-scale Supergravity, which give rise to the formation of microscopic primordial black holes (PBHs) triggering an early matter-dominated era (eMD) and evaporating before big bang nucleosynthesis (BBN). Remarkably, we obtain an abundant production of primordial gravitational waves (PGW) at the frequency ranges of nHz, Hz and kHz and in strong agreement with pulsar time array (PTA) gravitational wave (GW) data. This PGW background could serve as a compelling observational signature for the presence of quantum gravity via no-scale Supergravity.
EARLY VIRAL TRANSMISSIONS MAY PROVIDE A POSITIVE IMPACT ON THE QUASISPECIES MUTATIONAL FITNESS LANDSCAPE
Authors: FURUYAMA TAIMÁ NAOMI , DE CARVALHO ISABEL MARIA VICENTE GUEDES , JANINI LUIZ MARIO RAMOS , ANTONELI FERNANDO
Published: October 2024

It is known that for RNA viruses, such as HIV and HCV, the early or acute infection period may be correlated to higher transmissibility regarding chronic or late stages. However, studies of the impact of fitness effects caused by mutations on viral particles over transmission events are lacking. Our goal is to verify whether the passing of time can change the quality of viral particles and promote impact on an epidemic. We propose to address this question through a two-level mathematical model based on RNA viral population dynamics. The first level of the model represents the intra-host viral population dynamics and the second level represents the host-to-host dynamics of transmission events. The intra-host dynamics model uses the fitness of viral particles to track the presence of highly infective particles during transmission bottlenecks. More specifically, the intra-host dynamics is described by stochastic quasispecies, based on a multivariate branching process. The host-to-host dynamics of transmission events are emulated by a putative transmission tree with a ‘host zero’ at the root and a fixed number of branches emanating from each internal node. A Monte Carlo Markov Chain strategy was adopted to explore the tree by sampling random walks along transmission chains along the tree. Viral infections of a single host and several transmission events among hosts were simulated in early and late infection stages scenarios. The results show that the early infection stages may represent a key factor in a viral epidemic. Over the evolution of the viral population within each host the mean fitness decreases due to the occurrence of mutations (most of them causing deleterious effects). Despite the small opportunity interval, early-stage transmissions could infect new hosts at a higher rate than in late stages. It was observed that a very early transmission scenario could reach a transmission chain 20 times longer than a very late transmission scenario. This indicates that the quality of the viral particles is a relevant factor for transmission events.
FRACTIONAL ANALYSIS OF ONE-DIMENSIONAL SCHRÖDINGER MODEL IN THE CONTEXT OF CAPUTO-TYPE FRACTIONAL DERIVATIVES BASED ON RESIDUAL POWER SERIES METHOD
Authors: NADEEM MUHAMMAD , SHAO YABIN , ALNFIAI MRIM M. , DEEBANI WEJDAN , SHUTAYWI MESHAL
Published: October 2024

This research presents a novel analytical approach to explore the fractional analysis of the one-dimensional time-fractional Schrödinger model (TFSM) using Caputo fractional derivatives. By integrating the Mohand transform (MT) with the residual power series method (RPSM), we develop the Mohand residual power series method (MT-RPSM) that provides results in the form of convergent series without assumptions on variables. Initially, we employ MT to reduce the fractional order, and then we transfer the fractional problem into the Mohand space formulation. Second, we use the RPSM concept to derive the iterative series formula for the Mohand space formulation. We analyze these findings using visual layouts to show the physical representation of the TFSM, which matches the precise results very well. The results indicate that the proposed technique is a reliable and practical method for identifying and analyzing various nonlinear models of physical phenomena.
Passages
Authors: Groce Alex
Published: October 2024

Peter Seibel's Coders at Work: Reflections on the Craft of Programming is 600-odd pages of extraordinary software engineering wisdom and insight. It is also self-contradictory; these pages often disagree with each other, and sometimes actually argue with each other. As Donald Knuth says, near the end of this book, "the key is usually to have a stereo view instead of a one-dimensional view."
First International Workshop on Quantum SoftwareEngineering: The Next Evolution (QSE-NE) Summary 2024
Authors: Khan Arif Ali , Azeem Akbar Muhammad , Liang Peng
Published: October 2024

As we enter the new quantum age, tech giants like IBM, Google, and Microsoft are leading the way. But, there is a major challenge: we need to turn exciting quantum possibilities into real, practical tools. That's where Quantum Software Engineering (QSE) comes in, and it's why "Quantum Software Engineering: The next Evolution (QSE-NE)" workshop is proposed. This workshop is conducted to help guide this change. It aims to highlight the latest ideas in QSE and get people from different fields talking, from university researchers to big tech companies. Our main goals were to share new QSE methods, tools, and studies and to tackle the tough problems we face in developing quantum software. This workshop is all about setting the direction for the future of building quantum software, at a time when it is really crucial. More details can be found at: https://sites.google.com/view/qse-ne/ home.
Epigenetic Regulation in Insect–Microbe Interactions
Authors: Lai Yiling , Wang Sibao
Published: October 2024

Insects have evolved diverse interactions with a variety of microbes, such as pathogenic fungi, bacteria, and viruses. The immune responses of insect hosts, along with the dynamic infection process of microbes in response to the changing host environment and defenses, require rapid and fine-tuned regulation of gene expression programs. Epigenetic mechanisms, including DNA methylation, histone modifications, and noncoding RNA regulation, play important roles in regulating the expression of genes involved in insect immunity and microbial pathogenicity. This review highlights recent discoveries and insights into epigenetic regulatory mechanisms that modulate insect–microbe interactions. A deeper understanding of these regulatory mechanisms underlying insect–microbe interactions holds promise for the development of novel strategies for biological control of insect pests and mitigation of vector-borne diseases.
Cysteinyl Leukotrienes in Allergic Inflammation
Authors: Lee Minkyu , Boyce Joshua A. , Barrett Nora A.
Published: October 2024

The cysteinyl leukotrienes (CysLTs), LTC4, LTD4, and LTE4, are potent lipid mediators derived from arachidonic acid through the 5-lipoxygenase pathway. These mediators produce both inflammation and bronchoconstriction through three distinct G protein–coupled receptors (GPCRs)—CysLT1, CysLT2, and OXGR1 (also known as CysLT3 or GPR99). While CysLT-mediated functions in the effector phase of allergic inflammation and asthma have been established for some time, recent work has demonstrated novel roles for these mediators and their receptors in the induction and amplification of type 2 inflammation. Additionally, in vitro studies and murine models have uncovered diverse regulatory mechanisms that restrain or amplify CysLT receptor activation and CysLT receptor function. This review provides an overview of CysLT biosynthesis and its regulation, the molecular and functional pharmacology of CysLT receptors, and an overview of the established and emerging roles of CysLTs in asthma, aspirin-exacerbated respiratory disease, and type 2 inflammation.
The Shadow Economy, an Enigma, in the Agriculture of 15 EU Member States over the Period 1996–2019
Authors: Quendler Erika , Schneider Friedrich
Published: October 2024

The focus of this review is the shadow economy (SE) in agriculture. Our research aim is to empirically quantify the SE in the agricultural sector based on data collected in the EU-15 member states from 1996 to 2019. We apply the multiple indicators multiple causes model to estimate the levels and development of the SE in these countries. Furthermore, we investigate how the size of the agricultural SE differs between the EU-15 member states and how it affects the economy overall. The results show that (a) the main potential for SE lies in agricultural subsidies, the effects of taxation, the share of imports, and factor income in agriculture; (b) certain patterns and differences exist among the countries, which can be associated with the north-south-west divide; and (c) there are higher levels of SEs in agriculture compared to in the overall economies. This review emphasizes the potential for measuring the SE in agriculture, while recognizing current methodological limitations. Recommendations include diversifying methods, standardizing definitions internationally, and enhancing theoretical foundations. Furthermore, expanding research to include more regions and improve visibility and transparency in measurements is crucial if informed policy is to be made to benefit agriculture globally.
Metabolic and ionic control of T cells in asthma endotypes
Authors: Franz Tobias , Stegemann-Koniszewski Sabine , Schreiber Jens , Müller Andreas , Bruder Dunja , Dudeck Anne , Boehme Julia D. , Kahlfuss Sascha
Published: October 2024

CD4+ T cells play a central role in orchestrating the immune response in asthma, with dysregulated ion channel profiles and altered metabolic signatures contributing to disease progression and severity. An important classification of asthma is based on the presence of T-helper cell type 2 (Th2) inflammation, dividing patients into Th2-high and Th2-low endotypes. These distinct endotypes have implications for disease severity, treatment response, and prognosis. By elucidating how ion channels and energy metabolism control Th cells in asthma, this review contributes to the pathophysiological understanding and the prospective development of personalized therapeutic treatment strategies for patients suffering from distinct asthma endotypes.
Maternal-fetal interfaces transcriptome changes associated with placental insufficiency and a novel gene therapy intervention
Authors: Jones Helen N. , Davenport Baylea N. , Wilson Rebecca L.
Published: October 2024

Placental insufficiency at midpregnancy, established through moderate maternal nutrient restriction, is characterized with fewer maternal spiral arteries lined by trophoblast, shallower trophoblast invasion, and downregulation of genelists involved in the regulation of cell migration. Treatment of placenta insufficiency with a hIGF1 nanoparticle results in marked changes to transporter activity and increases our mechanistic understanding of how therapies designed to improve fetal growth may impact the placenta.
Profiling Circular RNA Expression Across 11 Tissues in the Marine Gastropod Rapana venosa
Authors: Hong Mingwei , Huang Zixia
Published: October 2024

The carnivorous marine gastropod, Rapana venosa, also known as the veined rapa whelk, has recently gained considerable attention due to its dual significance as both a valuable commercial seafood resource and a biological invader with widespread ecological implications. Significant efforts have been made to investigate the molecular pathways governing the specific adaptations in R. venosa. However, the regulatory mechanisms of these pathways remain largely unclear. Circular RNA (circRNA), a newly‐recognized class of non‐coding molecules, plays crucial roles in post‐transcriptional regulation, impacting various fundamental bioprocesses including development, cell cycle, immunity and disease pathogenesis. In this study, we conducted a comprehensive genome wide profiling of circRNAs across 11 tissues of R. venosa. We identified a total of 1214 circRNA genes across tissues, with 640 regarded as high‐confidence candidates. circRNAs displayed overall low expression levels, diverse isoform types and dynamic expression patterns across various tissues. Our comparative analyses revealed a few circRNA genes with a great diversity of isoforms and abundant expression in the salivary gland, suggesting potential roles in the feeding process of R. venosa. Furthermore, Gene Ontology (GO) enrichment analysis indicated the potential involvement of commonly expressed circRNAs in fundamental cellular processes, including cell division, amide biosynthesis and cellular response to hormone stimuli. Our study describes a preliminary examination of circRNAs across various tissues of R. venosa, offering a foundation for future research into the molecular mechanisms that influence the biology, ecology and behaviour of marine gastropods.
Supplementary Fig 2 from Steroid Ligands, the Forgotten Triggers of Nuclear Receptor Action; Implications for Acquired Resistance to Endocrine Therapy
Authors: Bleach Rachel , Madden Stephen F. , Hawley James , Charmsaz Sara , Selli Cigdem , Sheehan Katherine M. , Young Leonie S. , Sims Andrew H. , Souček Pavel , Hill Arnold D. , McIlroy Marie
Published: October 2024

Steroid profiles of breast cancer patient serum (recurrent versus non-recurrent).
Supplementary Figure 1-9 from Inhibition of DNA-PK with AZD7648 Sensitizes Tumor Cells to Radiotherapy and Induces Type I IFN-Dependent Durable Tumor Control
Authors: Nakamura Kyoko , Karmokar Ankur , Farrington Paul M. , James Neil H. , Ramos-Montoya Antonio , Bickerton Susan J. , Hughes Gareth D. , Illidge Timothy M. , Cadogan Elaine B. , Davies Barry R. , Dovedi Simon J. , Valge-Archer Viia
Published: October 2024

Supplementary Figure 1-9
Supplementary Figure 8 from Identification of a Novel Inflamed Tumor Microenvironment Signature as a Predictive Biomarker of Bacillus Calmette-Guérin Immunotherapy in Non–Muscle-Invasive Bladder Cancer
Authors: Damrauer Jeffrey S. , Roell Kyle R. , Smith Markia A. , Sun Xuezheng , Kirk Erin L. , Hoadley Katherine A. , Benefield Halei C. , Iyer Gopakumar , Solit David B. , Milowsky Matthew I. , Kim William Y. , Nielsen Matthew E. , Wobker Sara E. , Dalbagni Guido , Al-Ahmadie Hikmat A. , Olshan Andrew F. , Bochner Bernard H. , Furberg Helena , Troester Melissa A. , Pietzak Eugene J.
Published: October 2024

Supplemental Figure 8 shows the relationship between the Fraction of Genome Altered by UROMOL subgroups within the MSK cohort.
Supplementary Figure 7 from Identification of a Novel Inflamed Tumor Microenvironment Signature as a Predictive Biomarker of Bacillus Calmette-Guérin Immunotherapy in Non–Muscle-Invasive Bladder Cancer
Authors: Damrauer Jeffrey S. , Roell Kyle R. , Smith Markia A. , Sun Xuezheng , Kirk Erin L. , Hoadley Katherine A. , Benefield Halei C. , Iyer Gopakumar , Solit David B. , Milowsky Matthew I. , Kim William Y. , Nielsen Matthew E. , Wobker Sara E. , Dalbagni Guido , Al-Ahmadie Hikmat A. , Olshan Andrew F. , Bochner Bernard H. , Furberg Helena , Troester Melissa A. , Pietzak Eugene J.
Published: October 2024

Supplemental Figure 7 shows PDL1 (CD274) Expression, PD1 (PDCD1) Expression, and CTLA4 Expression by UROMOL Subclasses in MSK and UNC cohorts and RFS (by high, medium, low tertiles) in MSK, UROMOL, & Northwestern Cohorts.
Supplementary Figure 3 from Identification of a Novel Inflamed Tumor Microenvironment Signature as a Predictive Biomarker of Bacillus Calmette-Guérin Immunotherapy in Non–Muscle-Invasive Bladder Cancer
Authors: Damrauer Jeffrey S. , Roell Kyle R. , Smith Markia A. , Sun Xuezheng , Kirk Erin L. , Hoadley Katherine A. , Benefield Halei C. , Iyer Gopakumar , Solit David B. , Milowsky Matthew I. , Kim William Y. , Nielsen Matthew E. , Wobker Sara E. , Dalbagni Guido , Al-Ahmadie Hikmat A. , Olshan Andrew F. , Bochner Bernard H. , Furberg Helena , Troester Melissa A. , Pietzak Eugene J.
Published: October 2024

Supplemental Figure 3 shows the relationship for UROMOL Subclasses in MSK and UNC cohorts between expression of Proliferation markers and FOXM1.
Data from Regorafenib-Avelumab Combination in Patients with Microsatellite Stable Colorectal Cancer (REGOMUNE): A Single-arm, Open-label, Phase II Trial
Authors: Cousin Sophie , Cantarel Coralie , Guegan Jean-Philippe , Gomez-Roca Carlos , Metges Jean-Philippe , Adenis Antoine , Pernot Simon , Bellera Carine , Kind Michèle , Auzanneau Céline , Le Loarer François , Soubeyran Isabelle , Bessede Alban , Italiano Antoine
Published: October 2024

AbstractPurpose:
Regorafenib is synergistic with immune checkpoint inhibition in colorectal cancer preclinical models.
Patients and Methods:
This was a single-arm, multicentric phase II trial. Regorafenib was given 3 weeks on/1 week off, 160 mg every day; avelumab 10 mg/kg i.v. was given every 2 weeks, beginning at cycle 1, day 15 until progression or unacceptable toxicity. The primary endpoint was the confirmed objective response rate under treatment, as per RECIST 1.1. The secondary endpoints included a 1-year nonprogression rate, progression-free survival (PFS), and overall survival (OS), safety and biomarkers studies performed on sequential tumor samples obtained at baseline and at cycle 2 day 1.
Results:
Forty-eight patients were enrolled in four centers. Forty-three were assessable for efficacy after central radiological review. Best response was stable disease for 23 patients (53.5%) and progressive disease for 17 patients (39.5%). The median PFS and OS were 3.6 months [95% confidence interval (CI), 1.8–5.4] and 10.8 months (95% CI, 5.9–NA), respectively. The most common grade 3 or 4 adverse events were palmar-plantar erythrodysesthesia syndrome (n = 14, 30%), hypertension (n = 11, 23%), and diarrhea (n = 6, 13%). High baseline infiltration by tumor-associated macrophages was significantly associated with adverse PFS (1.8 vs. 3.7 months; P = 0.002) and OS (3.7 months vs. not reached; P = 0.002). Increased tumor infiltration by CD8+ T cells at cycle 2, day 1 as compared with baseline was significantly associated with better outcome.
Conclusions:
The combination of regorafenib + avelumab mobilizes antitumor immunity in a subset of patients with microsatellite stable colorectal cancer. Computational pathology through quantification of immune cell infiltration may improve patient selection for further studies investigating this approach.
Data from Opening of the Blood–Brain Barrier Using Low-Intensity Pulsed Ultrasound Enhances Responses to Immunotherapy in Preclinical Glioma Models
Authors: Sabbagh Aria , Beccaria Kevin , Ling Xiaoyang , Marisetty Anantha , Ott Martina , Caruso Hillary , Barton Emily , Kong Ling-Yuan , Fang Dexing , Latha Khatri , Zhang Daniel Yang , Wei Jun , DeGroot John , Curran Michael A. , Rao Ganesh , Hu Jian , Desseaux Carole , Bouchoux Guillaume , Canney Michael , Carpentier Alexandre , Heimberger Amy B.
Published: October 2024

AbstractPurpose:
The blood–brain barrier (BBB) inhibits adequate dosing/penetration of therapeutic agents to malignancies in the brain. Low-intensity pulsed ultrasound (LIPU) is a safe therapeutic method of temporary BBB disruption (BBBD) to enhance chemotherapeutic delivery to the tumor and surrounding brain parenchyma for treatment of glioblastoma.
Experimental Design:
We investigated if LIPU could enhance therapeutic efficacy of anti–PD-1 in C57BL/6 mice bearing intracranial GL261 gliomas, epidermal growth factor receptor variant III (EGFRvIII) chimeric antigen receptor (CAR) T cells in NSG mice with EGFRvIII-U87 gliomas, and a genetically engineered antigen-presenting cell (APC)-based therapy producing the T-cell attracting chemokine CXCL10 in the GL261-bearing mice.
Results:
Mice treated with anti–PD-1 and LIPU-induced BBBD had a median survival duration of 58 days compared with 39 days for mice treated with anti–PD-1, and long-term survivors all remained alive after contralateral hemisphere rechallenge. CAR T-cell administration with LIPU-induced BBBD resulted in significant increases in CAR T-cell delivery to the CNS after 24 (P < 0.005) and 72 (P < 0.001) hours and increased median survival by greater than 129%, in comparison with CAR T cells alone. Local deposition of CXCL10-secreting APCs in the glioma microenvironment with LIPU enhanced T-cell glioma infiltration during the therapeutic window (P = 0.004) and markedly enhanced survival (P < 0.05).
Conclusions:
LIPU increases immune therapeutic delivery to the tumor microenvironment with an associated increase in survival and is an emerging technique for enhancing novel therapies in the brain.
Data from Identification of a Novel Inflamed Tumor Microenvironment Signature as a Predictive Biomarker of Bacillus Calmette-Guérin Immunotherapy in Non–Muscle-Invasive Bladder Cancer
Authors: Damrauer Jeffrey S. , Roell Kyle R. , Smith Markia A. , Sun Xuezheng , Kirk Erin L. , Hoadley Katherine A. , Benefield Halei C. , Iyer Gopakumar , Solit David B. , Milowsky Matthew I. , Kim William Y. , Nielsen Matthew E. , Wobker Sara E. , Dalbagni Guido , Al-Ahmadie Hikmat A. , Olshan Andrew F. , Bochner Bernard H. , Furberg Helena , Troester Melissa A. , Pietzak Eugene J.
Published: October 2024

AbstractPurpose:
Improved risk stratification and predictive biomarkers of treatment response are needed for non–muscle-invasive bladder cancer (NMIBC). Here we assessed the clinical utility of targeted RNA and DNA molecular profiling in NMIBC.
Experimental Design:
Gene expression in NMIBC samples was profiled by NanoString nCounter, an RNA quantification platform, from two independent cohorts (n = 28, n = 50); targeted panel sequencing was performed in a subgroup (n = 50). Gene signatures were externally validated using two RNA sequencing datasets of NMIBC tumors (n = 438, n = 73). Established molecular subtype classifiers and novel gene expression signatures were assessed for associations with clinicopathologic characteristics, somatic tumor mutations, and treatment outcomes.
Results:
Molecular subtypes distinguished between low-grade Ta tumors with FGFR3 mutations and overexpression (UROMOL-class 1) and tumors with more aggressive clinicopathologic characteristics (UROMOL-classes 2 and 3), which were significantly enriched with TERT promoter mutations. However, UROMOL subclasses were not associated with recurrence after bacillus Calmette-Guérin (BCG) immunotherapy in two independent cohorts. In contrast, a novel expression signature of an inflamed tumor microenvironment (TME) was associated with improved recurrence-free survival after BCG. Expression of immune checkpoint genes (PD-L1/PD-1/CTLA-4) was associated with an inflamed TME, but not with higher recurrence rates after BCG. FGFR3 mutations and overexpression were both associated with low immune signatures.
Conclusions:
Assessment of the immune TME, rather than molecular subtypes, is a promising predictive biomarker of BCG response. Modulating the TME in an immunologically “cold” tumor warrants further investigation. Integrated transcriptomic and exome sequencing should improve treatment selection in NMIBC.