bluuebunny/crossref_metadata_2025 huggingface dataset:
Integrating satellite-based forest disturbance alerts improves detection timeliness and confidence
Authors: Reiche Johannes , Balling Johannes , Pickens Amy Hudson , Masolele Robert N , Berger Anika , Weisse Mikaela J , Mannarino Daniel , Gou Yaqing , Slagter Bart , Donchyts Gennadii , Carter Sarah
Published: April 2024

Satellite-based near-real-time forest disturbance alerting systems have been widely used to support law enforcement actions against illegal and unsustainable human activities in tropical forests. The availability of multiple optical and radar-based forest disturbance alerts, each with varying detection capabilities depending mainly on the satellite sensor used, poses a challenge for users in selecting the most suitable system for their monitoring needs and workflow. Integrating multiple alerts holds the potential to address the limitations of individual systems. We integrated radar-based RAdar for Detecting Deforestation (RADD) (Sentinel-1), and optical-based Global Land Analysis and Discovery Sentinel-2 (GLAD-S2) and GLAD-Landsat alerts using two confidence rulesets at ten 1° sites across the Amazon Basin. Alert integration resulted in faster detection of new disturbances by days to months, and also shortened the delay to increased confidence. An increased detection rate to an average of 97% when combining alerts highlights the complementary capabilities of the optical and cloud-penetrating radar sensors in detecting largely varying drivers and environmental conditions, such as fires, selective logging, and cloudy circumstances. The most improvement was observed when integrating RADD and GLAD-S2, capitalizing on the high temporal observation density and spatially detailed 10 m Sentinel-1 and 2 data. We introduced the highest confidence class as an addition to the low and high confidence classes of the individual systems, and showed that this displayed no false detection. Considering spatial neighborhood during alert integration enhanced the overall labeled alert confidence level, as nearby alerts mutually reinforced their confidence, but it also led to an increased rate of false detections. We discuss implications of this study for the integration of multiple alert systems. We demonstrate that alert integration is an important data preparation step to make use of multiple alerts more user-friendly, providing stakeholders with reliable and consistent information on new forest disturbances in a timely manner. Google Earth Engine code to integrate various alert datesets is made openly available.
Bilayer ion trap design for 2D arrays
Authors: Nop Gavin N , Smith Jonathan D H , Stick Daniel , Paudyal Durga
Published: April 2024

Junctions are fundamental elements that support qubit locomotion in two-dimensional ion trap arrays and enhance connectivity in emerging trapped-ion quantum computers. In surface ion traps they have typically been implemented by shaping radio frequency (RF) electrodes in a single plane to minimize the disturbance to the pseudopotential. However, this method introduces issues related to RF lead routing that can increase power dissipation and the likelihood of voltage breakdown. Here, we propose and simulate a novel two-layer junction design incorporating two perpendicularly rotoreflected (rotated, then reflected) linear ion traps. The traps are vertically separated, and create a trapping potential between their respective planes. The orthogonal orientation of the RF electrodes of each trap relative to the other provides perpendicular axes of confinement that can be used to realize transport in two dimensions. While this design introduces manufacturing and operating challenges, as now two separate structures have to be precisely positioned relative to each other in the vertical direction and optical access from the top is obscured, it obviates the need to route RF leads below the top surface of the trap and eliminates the pseudopotential bumps that occur in typical junctions. In this paper the stability of idealized ion transfer in the new configuration is demonstrated, both by solving the Mathieu equation analytically to identify the stable regions and by numerically modeling ion dynamics. Our novel junction layout has the potential to enhance the flexibility of microfabricated ion trap control to enable large-scale trapped-ion quantum computing.
Evaluation of the standard test methods for optical coherence tomograph for the posterior segment of the human eye
Authors: Zhao Xiaowei , Liu Wenli , Hu Zhixiong , Duan Liangcheng , Wang Qingqing , Wei Xing , Li Fei , Hong Baoyu
Published: April 2024

Optical Coherence Tomography (OCT) has revolutionized retinal imaging by offering non-invasive high-resolution three-dimensional visualization capabilities. OCT has become the standard of care in routine ophthalmological practice, especially for the posterior segment. Given its widespread clinical applications, establishing standardized test devices and methods for key OCT parameters is imperative to ensure both optimal imaging performance and diagnostic accuracy and treatment effectiveness. As a widely applied standard, ISO 16971:2015 published by the International Organization for Standardization specifies the minimum requirements, test device, and methods for OCT for the posterior segment of the human eye. Notably, these standards lacked experimental validation. In the present study, we implement the test device according to ISO 16971:2015, and assess a commercially available ophthalmic OCT instrument with the suggested test device and methods. Results show that the test device and methods could facilitate a rudimentary evaluation of OCT key parameters. Nevertheless, refinements of the test device and methods are requisite to enhance measurement accuracy, reliability, traceability, and practicability, catering to the diverse needs of manufacturers, end-users, and regulatory entities.
Output feedback command filtered fuzzy controller design for uncertain strict-feedback nonlinear systems with unmodeled dynamics and event-triggered strategy
Authors: Sun Yue , Chen Ming , Gao Chuang , Wu Libing
Published: April 2024

An adaptive control problem is considered for a class of nth-order uncertain nonlinear systems with unmodeled dynamics. Compared with the traditional backstepping method, this article improves the systems performance by introducing command filtered and event-triggered. The former primarily enhances the flexibility of controller design, while the latter employs a variable threshold triggering mechanism to achieve savings in communication resources. Simultaneously, the estimation error is compensated by the introduced hyperbolic tangent function. In addition, fuzzy logic system (FLS) is primarily used for observer design and approximation of unknown functions. The conclusion that the closed-loop signals are bounded is obtained through stability analysis. Finally, the numerical simulation results provide a comparative validation of the effectiveness of the proposed control scheme.
Improved restricted Boltzmann machine-based optimization model for the network security system in cloud environment
Authors: R Manivannan , S Senthil kumar , T Senthil Kumar
Published: April 2024

This paper introduces a novel approach to enhancing computer network security through deep learning and cloud technologies, focusing on combating insider DDoS attacks in cloud computing. By employing the IRBM architecture and a trust-oriented secure cloud framework, the work utilizes parameter tuning in RBM through the Gradient-Based Optimization (GBO) algorithm resulting in the proposed IRBM-GBO model. This model significantly outperforms SVM, SC-CNSP-ML, and RBM in terms of latency and Packet Delivery Ratio (PDR), showing 21.67%, 14.55%, and 9.62% improvements in latency, and 10.23%, 5.43%, and 12.79% in PDR, respectively. The research highlights the potential of combining soft computing with deep learning and cloud technologies to identify cyberattacks by emphasising improvements in latency, Quality of Service (QoS), throughput, and PDR across various cybersecurity datasets.
Interpreting and Using Basil Bernstein’s Sociology of Education
Authors: Kwok Henry , Singh Parlo
Published: April 2024

For four decades, Basil Bernstein developed a distinct and original contribution to the sociology of education. Despite his death in 2000, Bernstein’s theories still attract attention, not just in the United Kingdom, but all over the world, beyond Anglophone academic circuits. Yet, his work is sometimes regarded as too theoretical with minor significance to current educational issues and problems. Is Bernstein’s sociological theory relevant to the challenges of the 21st century? How should his work and research approach be understood and better utilized? While not claiming an orthodox interpretation, we do suggest that three crucial principles should underpin any engagement with t Bernstein’s theory for educational research. First, the researcher’s encounter with a specific problem in empirical reality is pivotal. Concepts which carry sociological sensibilities should be assembled around the problem. Second, while Bernstein has developed a bewildering array of concepts, it is better to use them lightly, for the sake of a more accurate description of complex, open, dynamic social systems such as education and schooling. Third, the gaze of Bernstein’s sociological theory is relational not only towards the object of inquiry but also to other theoretical frameworks. This relational gaze means that the theory can be used to dialogue with other theories as well as open dynamic social systems. Such relational capacities enable the theory to grow through the refinement and extension of existing concepts and the introduction of additional concepts. Three examples of research drawing upon these principles are provided as an illustration.
Skepticism and Education
Authors: Takeda Yuya , Manoff Itamar
Published: April 2024

Skepticism is a stance that is both called for and warned against in the public discourse in general, and in education in particular. Although the size of the educational literature dedicated to this topic is limited, the importance of cultivating skepticism has been discussed by a number of critically oriented researchers. When skepticism is discussed as a desirable trait for education to cultivate, this recommendation nonetheless comes with cautionary adjectives like “healthy,” “constructive,” and “hopeful.” These adjectives suggest that the desirability of skepticism is a matter of degree: Pushed to the extreme, skepticism becomes unhealthy, naïve, destructive, and dismissive. This makes intuitive sense, but with a spirit of skepticism, the following question is posed—when is it necessary to judge whether a particular enactment of skepticism is healthy or not? It is important to explore different vocabularies to enliven educational conversations on skepticism.

At different historical junctures, skepticism manifests with different emphasis and orientations: from the ancient attitude associated with the figure of Pyrrho, in which skepticism is a means to achieve the goal of ataraxia, to the epistemological project initiated by Descartes, and taken to its logical endpoint by Hume, that raises a generalized, global doubt of our ability to attain knowledge. More recently, there have been two anti-foundationalist responses to skepticism: one by Richard Rorty and another by Stanley Cavell. Although their diagnoses of philosophical skepticism do not differ substantially, Rorty and Cavell diverge significantly in their response to it: While Rorty turns it into a futile project, Cavell takes it as an inevitable crisis for finite linguistic beings. A juxtaposition of their widely different responses provides a useful set of vocabulary for nuanced treatment of skepticism in education.
Reimagining Arabic in Islamic Schools
Authors: Selim Nadia
Published: April 2024

Islamic schools have become a noticeable feature of the educational landscapes of multicultural, English-dominant, Muslim-minority contexts like Australia and the United Kingdom. The number of Islamic schools has progressively increased since the 1980s, and the growing nongovernmental Islamic schooling sector caters to several thousands of diverse Muslim learners. Islamic schools are key providers of K–12 Arabic learning with great potential for promoting Arabic language learning innovation and research. While Arabic provisions in Islamic schools are not fully understood due to research paucity, some emergent findings with adolescent research participants suggest that dissonance arises between learners’ goals and interests and the nature of their programs. The contemporary realities of Muslim learners of Arabic and Arabic programs at Islamic schools can result in dissonance, and using a whole-school approach that promotes an Arabic-integrated ethos could help in bridging the gaps between students and their Arabic language education.
Critical Perspectives on Positive Youth Development and Environmental Education
Authors: Krasny Marianne E. , Schusler Tania M. , Delia Jesse , Armstrong Anne Katherine , Briggs Lilly
Published: April 2024

Positive youth development (PYD) assumes that, when given appropriate support, all youth have the capacity to develop the assets that enable them to succeed in life. Such assets include competence, confidence, connection, character, caring, and contribution to community, otherwise known as the six Cs of PYD. Environmental education (EE) programs that focus on youth action and empowerment offer the support needed for youth to develop these assets.

Youth after-school, summer, and residential programs, often serving low-income and minoritized youth, increasingly are using environmental action and learning as a means to achieve PYD outcomes. Yet both PYD and EE have been criticized for not addressing the root causes of poverty and environmental degradation. In response, critical traditions in PYD and EE have emerged, in which youth reflect and act on structural barriers to human and environmental well-being in their communities. As youth and their mentors seek to address systemic inequities impacting themselves and their environment, they develop additional “Critical Positive Youth Development/Environmental Education” assets including critical reflection, efficacy, the ability to take collective action, and community-level empowerment.
Partition and the Reorganization of Commercial Networks
Authors: Mirza Rinchan Ali
Published: April 2024

The Partition of British India represents one of the largest episodes of involuntary mass migration in recorded history—an estimated 17 million people were displaced because of the event. Among the many changes that resulted from the Partition was the substantive untangling of the business architecture that had developed under the colonial regime. A central feature of the untangling was the separation of the extensive commodity trade network that had developed in areas that went to Pakistan from its agro-processing base that was inherited by areas that became part of post-independence India. The implications of such a restructuring of the business architecture were particularly relevant for Pakistan, which started off with a severe imbalance between its commodity trade and industrial sectors, the former of which was at a much more advanced stage than the latter. The rudimentary industrial base from which Pakistan started off in turn fostered a greater reliance of the state on the private capital of a small business elite when it came to promoting industrial growth. It is the changing dynamics of just such a relationship between the state and a small close knit business elite that has characterized the post-Partition business history of the country.
The History of Anthropometry and Fingerprinting in Colonial South Asia
Authors: Waits Mira Rai
Published: April 2024

In the late 19th century, an obsession with identifying and classifying people emerged in the West. Efforts to develop lines of inquiry to support this obsession were common; visual technologies were harnessed and invented to further the acquisition of knowledge about human identity and classification. Anthropometry, the measurement of the human individual to understand physical variation, was used as the foundation for Bertillonage, a system designed to identify recidivists through a standardized collection of images and data sets about the human body. Consequently, anthropometry came to be associated with broader efforts to manage crime in the late 19th and early 20th centuries, as law enforcement touted the potential of visual technologies and their related archival systems as mechanisms for improving criminal identification.

This interest in visual technologies and criminal identification coupled with the colonial exploration of South Asia in the 19th century led to anthropometric studies of South Asian peoples. Some of these studies were tied to institutions of colonial law enforcement, such as the police or prison system, but others, including the late 19th-century study of the people of the Andaman Islands, demonstrate how the broader obsession with human identification and classification was tied to efforts to study race as a measurable subject. Colonial civil servants also turned to visual technologies for assistance with the management of colonial subjects. In 1858, Sir William James Herschel, the chief administrator of the Hooghly district of Bengal, after observing a native practice where fingermarks were used as marks of authenticity for the illiterate, began to experiment with taking handprints and fingerprints as identifying images. Scottish doctor Henry Faulds had contemporaneously expressed a similar interest in studying fingerprints after observing sample prints on ancient pottery while serving as a medical missionary in Japan. Herschel shared his findings with Sir Francis Galton, the founder of eugenics, who, after reviewing Herschel’s findings, posited that fingerprints were permanent visual markers of identity. Following this observation, Sir Edward Richard Henry, inspector-general of police of Bengal, along with police sub-inspectors Chandra Bose and Azizul Haque, developed a classification system for using fingerprints to identify recidivist criminals. This system was exported from colonial India to Britain and then on to police organizations globally.
Art and Peacebuilding
Authors: de Guevara Berit Bliesemann , Cole Lydia C.
Published: April 2024

While the arts can be observed to play a role in both violence and peacemaking, they are often assumed to make positive contributions to postwar peacebuilding processes and have increasingly become attached to ideas of “positive peace” in different key (sub-)disciplines that contribute to the field of “art and peacebuilding” scholarship. Art forms that have been linked with peacebuilding include animation, curating and exhibiting, dance, drawing and painting, filmmaking, music, photography, poetry and fiction, sculpture, sound art, storytelling, street art, textile-making, and theater and performance, among others. The most common uses and potentials of art in and for peacebuilding concern artistic forms as peacebuilding tools; the power of peace aesthetics in changing sociopolitical imaginaries; and the community-building potentials of the arts. Research increasingly suggests that the particular value of the arts with regard to peacebuilding may lie in their capacity to bear and hold within them tensions, struggles, and differences, and thereby to contribute not to an idealized “harmonious” but a more real-type agonistic peace. There are, however, also important limits and challenges of art in and for peacebuilding, such as the risk of political and epistemic closure when arts are instrumentalized for predefined ends, questions of hierarchies regarding different artistic forms, and ethical questions arising from relationships involving large power differentials. These limits and challenges need to be addressed for the arts’ positive contribution to peacebuilding processes to unfold.
Theoretical Perspectives in Peruvian Archaeology
Authors: Tantaleán Henry
Published: April 2024

This article explains the development of theoretical perspectives in Peruvian archaeology from the end of the 19th century to the first decades of the 21st century. These perspectives have been characterized by having been influenced, mainly from Western Europe and United States of America, in various ways due to the nature of the Peruvian archaeological remains and their sociopolitical context. Likewise, in Peru, there is an important diversity in the use of hegemonic archaeological theories and the particular use of theories by Peruvian and even foreign archaeologists. Therefore, in this entry, we will refer to the most relevant archaeological theoretical perspectives recognized in Peru and which are evolutionary, culture-historical, Marxist, processualist, and postprocessualist. However, no one archaeologist is a “pure example” of each theory. In fact, many archaeologists have used different theories in archaeological explanations. Because a significant number of archaeologists have focused on the study of the Andes, mainly from the pre-Hispanic era, in this article a series of significant periods and themes of Peruvian archeology have been selected in which a significant number of studies have been carried out. In this way, archaeological perspectives have developed in the concrete practice of such archaeologists. Thus, in this article, we will see how archaeological theoretical perspectives in Peruvian archaeology have been developed in relation to the following areas, social phenomena, and periods: the Norte Chico area and the Late Preceramic Period (3000–1800 bc), Chavín de Huántar and the Early Horizon (1000–200 bc), the North Coast and Moche Society (200–800 ad), Huari and the Andean Imperial Phenomenon (600–1000 ad), and Cusco and the Inca Empire (1300–1532 ad).
Natural Parks: Political, Economic, and Socioecological Relations
Authors: Paradiso Cecilia
Published: April 2024

Protected areas occupy a high-profile position in the politics of environmental conservation, largely due to their history and their contemporary distribution. Although these institutions’ stated goals appear as largely unequivocal (e.g., the preservation of one or more environmental elements), numerous studies in the social sciences have revealed the complex and diverse realities that hide behind their designations and models. By observing the political, economic, and socioecological relationships in which natural parks (and especially national parks) participate, we can sketch an overview of this complexity, along with the plurality of critical approaches to these topics found within the panorama of contemporary anthropology. First, the history of national parks and its intertwinement with the emergence of environmental concerns on the global political stage demonstrates the political impact of this topic, located at the center of shifting geopolitical contexts. Next, a thematic review of anthropological studies on environmental conservation, which also touches upon the interdisciplinary dialogues that characterize the field, helps us to grasp connections between different stakes (epistemological, economic, political, symbolic) and to evaluate the frictions between broad dynamics and localized scenarios. In this sense, ethnographic evidence from the national park of the Maddalena archipelago (Sardinia) enables us to deepen our understanding of the directions considered more or less innovative for conservation, such as sustainable development and its corollaries or cap-and-trade systems for emissions. This approach is founded on a situated context, nourished by an interdisciplinary dialogue, and develops an attentiveness to the interrelations between living species, climactic elements, and inorganic elements. As such, this work invites us to move beyond the conceptual vagueness of notions that cut across the field of environmental conservation and to note the political dimension of individual and collective engagements.
Theology in Translation: Latin American and Iranian Efforts
Authors: Molina Ángel Horacio , Vittor Luis Alberto
Published: April 2024

“Turkish” migrants , in fact Ottoman Arab who entered the American continent with identity documents issued by the Ottoman authorities and traveled with their languages or dialects, arrived at the end of the 19th century and in the first decades of the 20th century. However, the migratory wave extended almost until the middle of the 20th century after going through a complex political, social, and cultural process that substantially modified various aspects of the migrants’ lives. Their religious lives were progressively hampered in terms of ritual practice because their faith of origin was in the minority with no adequate spaces for collective prayer. They encountered the increasingly pressing need to translate their Islamic sources, on the one hand because of the gradual loss of the Arabic language in some communities and on the other because of the need to maintain it—not only through translation but also by teaching the language in mosques and community centers. The arrival of Iranian migrants to different destinations in Latin America starting in the 1980s enriched this process of translation and dissemination of Islamic texts (Arabic and Persian) in Latin America.

The Muslim diaspora was the first group who, for various reasons, left their homeland while maintaining a close relationship with their language and culture of origin, and later, Muslim converts devoted themselves to the task of translating (inversely, directly, and indirectly) the Islamic theological texts from Arabic to Spanish or Portuguese. The very possibility of translation is a type of migration—a transfer that modifies a source language into a target language. One’s own language is poured into a foreign language. Translating is the disposition of language from the “I” that leads the reader to meet the “you” of otherness. This migratory process is also the inner journey made by the Latin American convert to the Islamic faith: their effort to first learn a language that is not their own in order to translate it into their own in the act of translating. Translation is a form of migration that has become an essential tool for mediation, conversion, knowledge, and dissemination. Both Muslim Arabs and converts devoted themselves to this task: for Muslim Arabs because of the progressive loss in the use of the language of their ancestors, and for converts, out of a pious duty to learn Arabic, the language in which the Qur’an was revealed in the Scripture that guides their new faith and to benefit those who do not know the language.
Islamic Bioethics: Circumcision
Authors: El Bernoussi Zaynab , Dupret Baudouin
Published: April 2024

In both cases of male circumcision (khitan) and female circumcision (khifad), the laws and regulations in different Muslim-majority countries inform the rules of sexual morality in these societies. Moreover, the religious rationale behind circumcision is bodily purification for worship, while many medical professionals also argue for male circumcision as a way of maintaining bodily hygiene.
South-Eastern Gallo-Romance: Francoprovençal
Authors: Kristol Andres M.
Published: April 2024

Francoprovençal is on UNESCO’s red list of the world’s most endangered languages. It is in danger of disappearing within one to two generations. Historically spoken in a large region of south-eastern France, northern Italy and French-speaking Switzerland, and lacking political unity, it is not ‘a’ language, but a set of dialects with common characteristics. Lacking any standardisation, its dialects show many of the evolutionary possibilities of Western Romance languages. Long regarded as a late separation from the Oïl area, it was traditionally described as a conservative Gallo-Romance language, rejecting Oïl innovations from about the eighth century onwards. More recent research has shown that its earliest linguistic features date back to the very beginning of the linguistic fragmentation of Galloromania (6th century at the latest); it is therefore just as ‘old’ as the other Gallo-romance languages. It thus has its own characteristic mixture of conservative and innovative phenomena among the Gallo-romance languages.
Jebb, Eglantyne
Authors: Payne Malcolm
Published: April 2024

Eglantyne Jebb (1876–1928) was a passionate campaigner against oppression and poverty in the early 20th century, founder of the Save the Children organization, and an early thinker about international social work. She authored the first (Geneva) Declaration of Children’s Rights, adopted by the League of Nations—the forerunner of the United Nations Convention on the Rights of the Child. An early settlement and Charity Organization Society worker, she was an inspiration to activist women of a younger generation, using writing and influencing skills, and author of a survey of local social services that was a model to later researchers.
Spira, Marcia
Authors: Grossman Susan F. , Northcut Terry B. , Dentato Michael P. , Mason Christie , Morhardt Darby J. , Golden Robyn L. , Kenemore Thomas K. , Spira Lauren
Published: April 2024

Marcia Kornfeld Spira, PhD, LCSW, BCD (1950–2022) was a pioneering social work clinician, scholar, teacher, and leader in the fields of social work with older adults and social work in health settings. Her work with older adults extended the understanding of clinical practice with an aging population and intergenerational work with families. Her focus on health care examined health and aging, challenged myths about that process, and guided practice around end-of-life care. She also considered the impact of health concerns on family relationships. She loved teaching and clinical practice and continued to do both after her retirement from Loyola University Chicago in 2020.
Achieving Durable Forehead Line Outcomes With DaxibotulinumtoxinA: Early Experience in Real-World Clinical Practice
Authors: Lafkas Michael
Published: April 2024

Background

Irrespective of botulinum toxin type A (BoNT-A) product used, differences in duration between the frontalis and glabella can be a challenge. Since the approval of daxibotulinumtoxinA for injection (DAXI, DAXXIFY; Revance, Nashville, TN), injectors have been eager not only to reproduce the durable results observed in the glabella but also to achieve an extended duration in the frontalis.

Objectives

To describe how the author has successfully modified their injection technique to achieve extended DAXI duration in the frontalis.

Methods

In this study, the author presents an approach to obtaining longevity in the forehead with DAXI based on clinical experience performing more than 400 treatments on more than 250 patients with DAXI since product approval.

Results

DAXI has a limited diffusion profile. If patients are not injected in the mid-to-low frontalis directly, compensatory motion of the lower frontalis leads to premature return of movement, which can result in suboptimal DAXI injection and shortened patient-reported duration. With previous generations of BoNT-A products, some degree of migration from the upper frontalis injection sites and/or the glabella injection sites into the mid and low frontalis is sufficient to prevent this effect, but the precision of DAXI demands that these fibers be more deliberately addressed with a larger number of individual injections.

Conclusions

Through the use of more injection points, a wider area of treatment, and customization to fit patient needs, duration similar to that observed in clinical studies (20.9 weeks) can be achieved using between 20% and 33% fewer units of DAXI.

Level of Evidence: 4
Understanding YTHDF2-mediated mRNA degradation by m6A-BERT-Deg
Authors: Zhang Ting-He , Jo Sumin , Zhang Michelle , Wang Kai , Gao Shou-Jiang , Huang Yufei
Published: April 2024

N6-methyladenosine (m6A) is the most abundant mRNA modification within mammalian cells, holding pivotal significance in the regulation of mRNA stability, translation and splicing. Furthermore, it plays a critical role in the regulation of RNA degradation by primarily recruiting the YTHDF2 reader protein. However, the selective regulation of mRNA decay of the m6A-methylated mRNA through YTHDF2 binding is poorly understood. To improve our understanding, we developed m6A-BERT-Deg, a BERT model adapted for predicting YTHDF2-mediated degradation of m6A-methylated mRNAs. We meticulously assembled a high-quality training dataset by integrating multiple data sources for the HeLa cell line. To overcome the limitation of small training samples, we employed a pre-training-fine-tuning strategy by first performing a self-supervised pre-training of the model on 427 760 unlabeled m6A site sequences. The test results demonstrated the importance of this pre-training strategy in enabling m6A-BERT-Deg to outperform other benchmark models. We further conducted a comprehensive model interpretation and revealed a surprising finding that the presence of co-factors in proximity to m6A sites may disrupt YTHDF2-mediated mRNA degradation, subsequently enhancing mRNA stability. We also extended our analyses to the HEK293 cell line, shedding light on the context-dependent YTHDF2-mediated mRNA degradation.
Surgery for advanced neuroendocrine tumours of the small bowel: recommendations based on a consensus meeting of the European Society of Endocrine Surgeons (ESES)
Authors: Van Den Heede Klaas , van Beek Dirk-Jan , Van Slycke Sam , Borel Rinkes Inne , Norlén Olov , Stålberg Peter , Nordenström Erik
Published: April 2024

Background

Small bowel neuroendocrine tumours often present with locally advanced or metastatic disease. The aim of this paper is to provide evidence-based recommendations regarding (controversial) topics in the surgical management of advanced small bowel neuroendocrine tumours.

Methods

A working group of experts was formed by the European Society of Endocrine Surgeons. The group addressed 11 clinically relevant questions regarding surgery for advanced disease, including the benefit of primary tumour resection, the role of cytoreduction, the extent of lymph node clearance, and the management of an unknown primary tumour. A systematic literature search was performed in MEDLINE to identify papers addressing the research questions. Final recommendations were presented and voted upon by European Society of Endocrine Surgeons members at the European Society of Endocrine Surgeons Conference in Mainz in 2023.

Results

The literature review yielded 1223 papers, of which 84 were included. There were no randomized controlled trials to address any of the research questions and therefore conclusions were based on the available case series, cohort studies, and systematic reviews/meta-analyses of the available non-randomized studies. The proposed recommendations were scored by 38–51 members and rated ‘strongly agree’ or ‘agree’ by 64–96% of participants.

Conclusion

This paper provides recommendations based on the best available evidence and expert opinion on the surgical management of locally advanced and metastatic small bowel neuroendocrine tumours.
Testing of putative antiseizure medications in a preclinical Dravet syndrome zebrafish model
Authors: Whyte-Fagundes Paige A , Vance Anjelica , Carroll Aloe , Figueroa Francisco , Manukyan Catherine , Baraban Scott C
Published: April 2024

Dravet syndrome is a severe genetic epilepsy primarily caused by de novo mutations in a voltage-activated sodium channel gene (SCN1A). Patients face life-threatening seizures that are largely resistant to available anti-seizure medications. Preclinical Dravet syndrome animal models are a valuable tool to identify candidate anti-seizure medications for these patients. Among these, scn1lab mutant zebrafish, exhibiting spontaneous seizure-like activity, are particularly amenable to large-scale drug screening. Thus far, we have screened more than 3000 drug candidates in scn1lab zebrafish mutants, identifying valproate, stiripentol, and fenfluramine e.g. Food and Drug Administration-approved drugs, with clinical application in the Dravet syndrome population. Successful phenotypic screening in scn1lab mutant zebrafish is rigorous and consists of two stages: (i) a locomotion-based assay measuring high-velocity convulsive swim behaviour and (ii) an electrophysiology-based assay, using in vivo local field potential recordings, to quantify electrographic seizure-like events. Historically, nearly 90% of drug candidates fail during translation from preclinical models to the clinic. With such a high failure rate, it becomes necessary to address issues of replication and false positive identification. Leveraging our scn1lab zebrafish assays is one approach to address these problems. Here, we curated a list of nine anti-seizure drug candidates recently identified by other groups using preclinical Dravet syndrome models: 1-Ethyl-2-benzimidazolinone, AA43279, chlorzoxazone, donepezil, lisuride, mifepristone, pargyline, soticlestat and vorinostat. First-stage locomotion-based assays in scn1lab mutant zebrafish identified only 1-Ethyl-2-benzimidazolinone, chlorzoxazone and lisuride. However, second-stage local field potential recording assays did not show significant suppression of spontaneous electrographic seizure activity for any of the nine anti-seizure drug candidates. Surprisingly, soticlestat induced frank electrographic seizure-like discharges in wild-type control zebrafish. Taken together, our results failed to replicate clear anti-seizure efficacy for these drug candidates highlighting a necessity for strict scientific standards in preclinical identification of anti-seizure medications.
Artificial Wombs: Could They Deliver an Answer to the Problem of Frozen Embryos?
Authors: Gross Christopher
Published: April 2024

Catholic thinkers generally agree that artificial womb technology (AWT) would be permissible in cases of partial ectogenesis to assist severely premature infants, but there is substantially more debate concerning whether AWT could be used to save frozen embryos, which are the result of in vitro fertilization (IVF). In many cases, these embryos have been abandoned and left in a permanently cryogenic state, which is an affront to their human dignity. While AWT would allow people to adopt these embryos and give them an opportunity to develop, it gives rise to serious concerns over the possibility of scandal and the potential for cooperation in evil. Therefore, the author argues that even though AWT may one day represent a solution to this tragedy, it is currently not a morally licit answer, given the widespread use and approval of IVF in our culture.
What is a B chromosome? Early definitions revisited
Authors: Ferree Patrick M , Blagojević Jelena , Houben Andreas , Martins Cesar , Trifonov Vladimir A , Vujošević Mladen
Published: April 2024

Since the discovery of B chromosomes, multiple different definitions of these selfish genetic elements have been put forth. We reconsidered early definitions in light of recently published studies. While there are many characteristics that vary among different B chromosomes, such as their evolutionary origins, size, segregation behaviors, gene content, and function, there is one defining trait of all B chromosomes: they are nonessential for the organism. The points raised here may be useful for framing future B chromosome studies and help guide the categorization of new chromosomal elements that are uncovered in genomic studies.
An effective strategy for assembling the sex-limited chromosome
Authors: Wang Xiao-Bo , Lu Hong-Wei , Liu Qing-You , Li A-Lun , Zhou Hong-Ling , Zhang Yong , Zhu Tian-Qi , Ruan Jue
Published: April 2024

Background

Most currently available reference genomes lack the sequence map of sex-limited (such as Y and W) chromosomes, which results in incomplete assemblies that hinder further research on sex chromosomes. Recent advancements in long-read sequencing and population sequencing have provided the opportunity to assemble sex-limited chromosomes without the traditional complicated experimental efforts.

Findings

We introduce the first computational method, Sorting long Reads of Y or other sex-limited chromosome (SRY), which achieves improved assembly results compared to flow sorting. Specifically, SRY outperforms in the heterochromatic region and demonstrates comparable performance in other regions. Furthermore, SRY enhances the capabilities of the hybrid assembly software, resulting in improved continuity and accuracy.

Conclusions

Our method enables true complete genome assembly and facilitates downstream research of sex-limited chromosomes.
Enhanced bovine genome annotation through integration of transcriptomics and epi-transcriptomics datasets facilitates genomic biology
Authors: Beiki Hamid , Murdoch Brenda M , Park Carissa A , Kern Chandlar , Kontechy Denise , Becker Gabrielle , Rincon Gonzalo , Jiang Honglin , Zhou Huaijun , Thorne Jacob , Koltes James E , Michal Jennifer J , Davenport Kimberly , Rijnkels Monique , Ross Pablo J , Hu Rui , Corum Sarah , McKay Stephanie , Smith Timothy P L , Liu Wansheng , Ma Wenzhi , Zhang Xiaohui , Xu Xiaoqing , Han Xuelei , Jiang Zhihua , Hu Zhi-Liang , Reecy James M
Published: April 2024

Background

The accurate identification of the functional elements in the bovine genome is a fundamental requirement for high-quality analysis of data informing both genome biology and genomic selection. Functional annotation of the bovine genome was performed to identify a more complete catalog of transcript isoforms across bovine tissues.

Results

A total of 160,820 unique transcripts (50% protein coding) representing 34,882 unique genes (60% protein coding) were identified across tissues. Among them, 118,563 transcripts (73% of the total) were structurally validated by independent datasets (PacBio isoform sequencing data, Oxford Nanopore Technologies sequencing data, de novo assembled transcripts from RNA sequencing data) and comparison with Ensembl and NCBI gene sets. In addition, all transcripts were supported by extensive data from different technologies such as whole transcriptome termini site sequencing, RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression, chromatin immunoprecipitation sequencing, and assay for transposase-accessible chromatin using sequencing. A large proportion of identified transcripts (69%) were unannotated, of which 86% were produced by annotated genes and 14% by unannotated genes. A median of two 5′ untranslated regions were expressed per gene. Around 50% of protein-coding genes in each tissue were bifunctional and transcribed both coding and noncoding isoforms. Furthermore, we identified 3,744 genes that functioned as noncoding genes in fetal tissues but as protein-coding genes in adult tissues. Our new bovine genome annotation extended more than 11,000 annotated gene borders compared to Ensembl or NCBI annotations. The resulting bovine transcriptome was integrated with publicly available quantitative trait loci data to study tissue–tissue interconnection involved in different traits and construct the first bovine trait similarity network.

Conclusions

These validated results show significant improvement over current bovine genome annotations.
Inhibition of RhoA Prevents Cryptococcus neoformans Capsule Glucuronoxylomannan-Stimulated Brain Endothelial Barrier Disruption
Authors: Munzen Melissa E , Mathew Cristian , Enriquez Vanessa , Minhas Amanjeet , Charles-Niño Claudia L , Saytoo Durvinand , Reguera-Gomez Marta , Dores Michael R , Martinez Luis R
Published: April 2024

Cryptococcus neoformans (Cn) is an opportunistic fungus that causes severe central nervous system (CNS) disease in immunocompromised individuals. Brain parenchyma invasion requires fungal traversal of the blood-brain barrier. In this study, we describe that Cn alters the brain endothelium by activating small GTPase RhoA, causing reorganization of the actin cytoskeleton and tight junction modulation to regulate endothelial barrier permeability. We confirm that the main fungal capsule polysaccharide glucuronoxylomannan is responsible for these alterations. We reveal a therapeutic benefit of RhoA inhibition by CCG-1423 in vivo. RhoA inhibition prolonged survival and reduced fungal burden in a murine model of disseminated cryptococcosis, supporting the therapeutic potential of targeting RhoA in the context of cryptococcal infection. We examine the complex virulence of Cn in establishing CNS disease, describing cellular components of the brain endothelium that may serve as molecular targets for future antifungal therapies to alleviate the burden of life-threatening cryptococcal CNS infection.
Abstract Spaces for Intervention in Libya and Nigeria
Authors: Malito Debora V , Dan Suleiman Muhammad
Published: April 2024

How is the space for contemporary interventions constructed? This article deepens our understanding of counterterrorism as a dialectical form of intervention by highlighting the importance of unifying rationalities in the creation of “ungoverned spaces” as abstract spaces for intervention purposes. We combine dialectical and decolonial thinking to track how unifying rationalities in Nigeria and Libya are deployed across cognitive, normative, and operational constructs. The article examines how interventions are cognitively tied to coloniality of knowing, being, and power, which exploit identity, religion, or societal divisions to justify ungovernance and normalize state and foreign violence. The simultaneous and reciprocal globalization of local security concerns and localization of global security predicaments facilitates the formation of abstract spaces for counterterrorism purposes. Empirically, our analysis shows how portraying Libya and Nigeria as ungoverned creates a void of meaning, putting external actors in charge of restoring governance and protecting human security, modernity, and civility. Interveners in Libya contributed to normalizing a broader spectrum of violence, frequently internalized by competing actors through their normative tropes. In Nigeria, state and foreign interventionism and counterinsurgency have been responsible for the widespread use of violence against entire communities.
Yeast communities of a North American hybrid wine grape differ between organic and conventional vineyards
Authors: Bunbury-Blanchette Adele L , Fan Lihua , Kernaghan Gavin
Published: April 2024

Aims

To compare the species diversity and composition of indigenous yeast communities of hybrid grapes from conventionally and organically cultivated vineyards of an emerging cool-climate wine producing region.

Methods and Results

Illumina MiSeq sequences from L'Acadie blanc grape musts were processed and filtered to characterize indigenous yeast communities in organic and conventional vineyards of the Annapolis Valley wine region in Nova Scotia, Canada. While cultivation practice was not associated with yeast diversity or species richness, there was a strong effect on yeast community composition, with conventional vineyards characterized by higher proportions of Sporidiobolales and Filobasidium magnum, and organic vineyards supporting Filobasidium species other than F. magnum and higher proportions of Symmetrospora. There was also variation in yeast community composition among individual vineyards, and from year to year.

Conclusions

This is the first comprehensive assessment of yeasts associated with hybrid grapes grown using different cultivation practices in a North American cool climate wine region. Communities were dominated by basidiomycete yeasts and species composition of these yeasts differed significantly between vineyards employing organic and conventional cultivation practices. The role of basidiomycete yeasts in winemaking is not well understood, but some species may influence wine characteristics.