bluuebunny/crossref_metadata_2025 huggingface dataset:
Uncertainty quantification by direct propagation of shallow ensembles
Authors: Kellner Matthias , Ceriotti Michele
Published: June 2024

Statistical learning algorithms provide a generally-applicable framework to sidestep time-consuming experiments, or accurate physics-based modeling, but they introduce a further source of error on top of the intrinsic limitations of the experimental or theoretical setup. Uncertainty estimation is essential to quantify this error, and to make application of data-centric approaches more trustworthy. To ensure that uncertainty quantification is used widely, one should aim for algorithms that are accurate, but also easy to implement and apply. In particular, including uncertainty quantification on top of an existing architecture should be straightforward, and add minimal computational overhead. Furthermore, it should be easy to manipulate or combine multiple machine-learning predictions, propagating uncertainty over further modeling steps. We compare several well-established uncertainty quantification frameworks against these requirements, and propose a practical approach, which we dub direct propagation of shallow ensembles, that provides a good compromise between ease of use and accuracy. We present benchmarks for generic datasets, and an in-depth study of applications to the field of atomistic machine learning for chemistry and materials. These examples underscore the importance of using a formulation that allows propagating errors without making strong assumptions on the correlations between different predictions of the model.
Synthesis, physico-chemical characterization, DFT simulation, and field electron behaviour of 2D layered Ti3C2Tx MXene nanosheets
Authors: Sumbe Priyanka R , Chhote Ujjwala , Sanyal Gopal , Chakraborty Brahmananda , Sayeed Ahmed , More Mahendra A
Published: June 2024

Nanostructures of Ti3C2Tx, one of the members of the MXenes family, have been successfully prepared by chemical etching of Al from Ti3AlC2 (MAX phase) using Hydrofluoric Acid (HF) for various etching durations at room temperature. The phase, morphological, structural, and chemical analysis was performed using XRD, FESEM, TEM, Raman, and x-ray photoelectron spectroscopy. The surface morphology of as-synthesized Ti3C2Tx (MXene) phase is characterized by stacks of layered sheets like structures. Field electron emission (FEE) behaviour was investigated at the base pressure of 1 × 10−8 mbar. The pristine Ti3AlC2 (MAX) and Ti3C2Tx (MXene) nanosheets emitters showed values of turn-on field (defined at current density ∼ 1 μA cm−2) as 4.18 and 1.67 V μm−1, respectively. Furthermore, maximum emission current density of ∼ 825 μA cm−2 was extracted from the MXene nanosheets emitter at an applied field of 3.60 V μm−1, in contrast to ∼71 μA cm−2 drawn at 7.31 V μm−1 from the pristine MAX emitter. The MXene nanosheets emitter exhibited good emission current stabilities at pre-set values ∼ 10 and 100 μA over 3 h duration. Work function values of the MAX and MXene nanosheets emitters were measured using a retarding field analyzer, and found to be 4.4 and 3.6 eV, respectively. Extensive ab-initio simulations have been performed to provide structural and electronic properties, as well as for estimating the work function of Ti3C2 layered material. The estimated electronic density of states revealed its metallic character. The improved FEE performance exhibited by the 2D layered Ti3C2Tx (MXene) nanosheets emitter is attributed to its unique morphology characterized by high aspect ratio, metallic electronic properties and relatively lower work function.
Presentness
Authors: Torrengo Giuliano
Published: June 2024

The present is now, where we, the things we have experience of, and the things we act upon also are. The past and the future are somewhere else. In this chapter, the author argues that this fundamental ‘locational fact’ underpins the perceived prominence of presentness in our lives. The chapter elucidates a distinction between what the perceptual dimension of the present—which according to the author does not have any phenomenological distinctiveness, and the conceptual dimension of the present—which holds significant structural relevance within our narrative cognition. An error theoretic perspective on our linguistic and cognitive representations of the present is proposed and defended. The chapter asserts that our ordinary discourse and thought patterns concerning events and their presence are explicable by appealing to a narrative present.
Dignity Beyond Price: Kant and His Revolutionary British Contemporary
Authors: Ameriks Karl
Published: June 2024

This chapter provides a comparison of the philosophies of Richard Price and Immanuel Kant. They were almost exact contemporaries and equally important in their respective cultures but apparently did not know of each other. Price’s outstanding achievements have been underappreciated ever since he was unfairly criticized by Edmund Burke. In their general moral theory, common respect for dignity, positive orientation to rationalism, and enlightened involvement in public issues, Price and Kant have a lot in common that is still relevant to contemporary philosophy. But whereas Price hailed the Glorious Revolution, the Declaration of Independence, and French Revolution, Kant only mentioned the French. Like Thomas Jefferson, they both asserted the self-evidence of human equality, and yet they did not explain how a doctrine could be presented both as revolutionary and self-evident. The chapter concludes with a discussion of self-evidence in the context of writings by Danielle Allen and other contemporary scholars.
LGBTI and Indigenous Groups in Ecuadoran Media
Authors: Chavero Ramírez Palmira , Oller Alonso Martín
Published: June 2024

Public opinion is strongly influenced by the images that media present of the outside world and the frames of the main issues. In the case of Ecuador, this media content has been characterized by a strong presence of discriminatory and biased content. This kind of content contributes to the exclusion of some citizens, especially social minorities such as LGBTI; indigenous; and other identities people. As a consequence, the role of the state is more important to generate public policies in order to protect the minorities and to recognize others kinds of media.

In the last three decades, some of these groups have taken an important role in the social and political sphere, in addition to the academic one. The LGBTI collective has seen some of the historically denied rights recognized (such as equal marriage, approved in 2019), and progress has been made in the public debate on some women’s rights. For their part, indigenous people have taken a leading role in political action and have managed, at least for a time, to stop regressive public policies of rights, thereby becoming one of the main political actors today. The role played by the media in making these actors and their actions visible has also taken center stage.

The situation of these groups is currently in a drastic process of change, although they still feel discriminated against and judged by society and by current legislation. This situation is aggravated due to the image that the media show of them, based on stereotypes and the lack of knowledge of their diversity identity.

The main challenge continues to be for the mainstream media to move away from their economic and political nature to approach an inclusive communication, with a rights-based approach that recognizes and allows the development of equality in all citizens.
Sampling from Online Panels
Authors: Shi Luzi , Roche Sean Patrick
Published: June 2024

Since the 2010s, online surveys have become a popular method among criminologists. Often these surveys are conducted with the assistance of private survey research companies, which gather large groups of people (i.e., respondents) who have indicated a willingness to share their opinions on a variety of issues. These panels of potential respondents vary in size and quality. Researchers planning to collect survey data via these online panels must also consider probability versus non-probability sampling methods. Probability samples provide stronger assurances that sample statistics—particularly, univariate point estimates—are generalizable to broader populations (e.g., adult Americans). They are also often very expensive, although this is somewhat dependent on the size and complexity of the proposed project. Two popular providers of probability samples of the American public are the Ipsos Knowledge Panel and the AmeriSpeak Omnibus panel. In criminology and criminal justice, researchers have used online probability panels to study a variety of topics, including behaviors regarding firearms, attitudes toward policing, and experiences of violence.

Non-probability samples present a budget-friendly alternative but may be less generalizable to populations of interest. Since 2010, these samples have become especially popular in the criminological literature and are much more commonly used than online probability samples. Findings from non-probability online surveys often yield remarkably similar relational inferences (e.g., correlations) to those obtained from probability samples. However, non-probability samples are generally unsuitable for providing generalizable univariate point estimates. Some of the leading providers of non-probability samples from panels are YouGov, Qualtrics, and Lucid. As of 2024, YouGov uses a matched opt-in sample with a more sophisticated sampling design, while Qualtrics and Lucid provide quota samples. Researchers may also directly recruit non-probability samples of respondents via crowdsourcing platforms, such as Amazon Mechanical Turk, or services that incorporate those platforms into their own business model, such as CloudResearch. Research suggests that platforms with more sophisticated sampling procedures tend to yield more accurate results. Consequently, matched opt-in samples such as YouGov are approximately twice as expensive as Qualtrics samples and are many times more expensive than crowdsourcing platforms. Finally, it should be noted that the demographic composition of online samples, even those that have been simply crowdsourced, tend to be more diverse than typical in-person non-probability samples used in criminology and criminal justice research (e.g., college students).
The Treaty Port System in Japan, 1858–1899
Authors: Phipps Catherine
Published: June 2024

The treaty port system largely defined the legal and spatial parameters of Japan’s international trade and relationships during the second half of the 19th century. The treaty ports were designated port cities along Japan’s coast where foreign vessels anchored and foreigners came ashore to reside and conduct trade within circumscribed geographical limits. The system was based on a series of treaties that the Japanese negotiated with Western powers, especially the United States, Great Britain, and Russia, under the threat of force at a time when the Japanese shogunate did not wish to alter the country’s highly restricted level of foreign engagement. The treaties followed similar ones that had already been signed in China and they served as the instruments of informal imperialism’s advance into the region. The resulting infrastructure joined new patterns of transportation and trade with longer-standing domestic and East Asian regional networks, linking Japan’s treaty ports to those in China and to broader networks of global exchange that used common currencies, regulatory principles, institutions, and shipping lines.

The five port cities, to varying degrees, became cosmopolitan sites where Japanese, European, American, and Chinese merchants traded, tourists visited, sailors took shore leave, traffickers operated, and consular officials, diplomats, and judges endeavored to manage interactions in their own national interests. The treaty ports were the centers of a maritime infrastructure that also served Japan’s rapid modernization, the return of its full sovereignty, and its emergence as an imperial power in Asia, including through naming Special Trading Ports at home and establishing treaty ports in Korea and Taiwan. Overall, the treaty port system structured and informed Japan’s international relations within a competitive global environment dominated by imperialist expansion, capitalist accumulation, industrial and technological revolutions, resource extraction, and new patterns of global migration and labor, as well as shifting practices of access and exclusion throughout the Pacific world.
Sacred Cairns ( Ovoo ) in the Mongolian Cultural World
Authors: Dumont Aurore
Published: June 2024

The word ovoo means “heap” or “pile” in Mongolian. The ovoo are highly significant features of Inner Asia’s sacred landscape and are present in Mongolian-speaking areas (Mongolia, Inner Mongolia, Buryatia, Kalmykia), as well as in Turkic-speaking Tuva. Depending on the area and the immediate environment in which they are erected, the ovoo have various features, from simple round heaps of stones and branches to more elaborate structures, such as a circular mound of stones with a central pole topped with brushwood and decorated with prayer flags and/or colored ribbons. Built by local people for centuries, the ovoo serve as territorial markers and ritual altars. Ovoo found on ritually significant mountains are worshipped annually by a given social group (people from the same village [sum], a clan, an ethnic group, etc.) to propitiate the various divinities of the land, ensuring protection and prosperity. Like other ritual activities, ovoo worship was banned in Mongolia, China, and Russia as a result of communist antireligious polices. In the early 21st century, ovoo worship constitutes a revived religious practice in all three countries and has drawn the attention of politicians and scholars.
The Book of Hosea
Authors: Kelle Brad E.
Published: June 2024

The Hebrew Bible (Old Testament) book of Hosea presents the messages associated with Hosea the son of Beeri, a prophet active in the Northern Kingdom of Israel during the second half of the 8th century bce. Hosea is the first book in the Book of the Twelve (Minor Prophets) and is canonical for Jews and Christians. The book contains a vast diversity of metaphors that describe Yhwh and Israel in multiple, sometimes paradoxical, ways, and it features (often negative) imagery drawn from realms such as family, sexuality, nature, wildlife, and farming. The book is best known for the portrayal of the prophet’s marriage to a sexually promiscuous woman (Gomer) and their tumultuous family life as a metaphor for Yhwh’s relationship with Israel, especially its rulers (chs. 1–3). However, debate surrounds most issues related to the book’s origins, composition, setting, and relationship to history (and to any biographical information about Hosea and Gomer), as well the interpretation of its depictions of gender and violence and its portrayals of women. Often thought to be concerned solely with Israel’s religious life (perhaps especially the people’s abandonment of Yhwh for other gods), Hosea shows a broader interest in Israel’s political, social, and economic realities. Set against the backdrop of the growing imperialism of the Neo-Assyrian Empire across the ancient Near East in the mid-8th century bce, Hosea’s messages advocate a particular understanding of Israel’s identity as Yhwh’s people (and the political, socioeconomic, and religious practices that should accompany it). Israel should be exclusively devoted to Yhwh and resist seeking other gods, religious practices, economic systems, and political alliances for their provision and protection. Major theological themes include the people’s abandonment of Yhwh, judgment, repentance, and hope for restoration. The rhetoric and language with which these messages are presented call for the ongoing use of metaphor theory; gender analysis; feminist criticism; masculinity studies; trauma interpretation; and violence studies; alongside more traditional historical, literary, and theological inquiries.
Morphologization and the Boundary Between Morphology and Phonology in the Romance Languages
Authors: O'Neill Paul
Published: June 2024

This article analyses, from a Romance perspective, the concept of morphologization and seeks to answer the following question: At what point does a historically proven phonological cause-and-effect relationship, whereby phonological feature X causes and determines phonological feature Y, cease to hold and the dephonologized Y element stand as a marker of some morphological distinction? The question is relevant to cases in which the original phonological conditioning element is still present and where it has disappeared. I explain that the answer to this question depends entirely on one’s conception of morphology and phonology. I argue against theories that adhere to the principle of lexical minimization and have a static conception of morphology, which is restricted to the concatenation of idiosyncratic morphemes. These theories are forced by their theoretical underpinnings, which are often ideological and not supported by robust empirical evidence, to explain morphologized phenomena as being synchronically derived by phonology. This approach comes at a huge cost: the model of phonology is endowed with powerful tools to make the analysis fit the theory and which ultimately diminishes the empirical content and plausibility of the phonological hypotheses; such approaches also constitute serious problems for language acquisition and learning. I argue for more dynamic and abstractive models of morphology, which do not impose strict restrictions on lexical storage. I ultimately view morphologization as an instance of morphologically conditioned phonology and uphold that there is no strict boundary between the phonology and morphology but both systems overlap and interact.

I analyze data and phonological explanations of metaphony in nouns and verbs in Italo-Romance, plural formation in Spanish and Portuguese, the distribution of velar allomorphy in the Italian and Spanish verbs, and the distribution of verbal stress in Surmiran Romansh and Spanish. With reference to the latter, the contribution dedicates significant space exploring the extent to which the diphthong/monophthong alternation in Spanish, and different types of allomorphy in Surmiran Romansh, is a matter of phonologically conditioned allomorphy or morphologically conditioned phonology.
The Study of the Epidemiology of Pediatric Hypertension Registry (SUPERHERO): rationale and methods
Authors: South Andrew M , Giammattei Victoria C , Bagley Kiri W , Bakhoum Christine Y , Beasley William H , Bily Morgan B , Biswas Shupti , Bridges Aaron M , Byfield Rushelle L , Campbell Jessica Fallon , Chanchlani Rahul , Chen Ashton , D'Agostino McGowan Lucy , Downs Stephen M , Fergeson Gina M , Greenberg Jason H , Hill-Horowitz Taylor A , Jensen Elizabeth T , Kallash Mahmoud , Kamel Margret , Kiessling Stefan G , Kline David M , Laisure John R , Liu Gang , Londeree Jackson , Lucas Caroline B , Mannemuddhu Sai Sudha , Mao Kuo-Rei , Misurac Jason M , Murphy Margaret O , Nugent James T , Onugha Elizabeth A , Pudupakkam Ashna , Redmond Kathy M , Riar Sandeep , Sethna Christine B , Siddiqui Sahar , Thumann Ashley L , Uss Stephen R , Vincent Carol L , Viviano Irina V , Walsh Michael J , White Blanche D , Woroniecki Robert P , Wu Michael , Yamaguchi Ikuyo , Yun Emily , Weaver Donald J
Published: June 2024

Despite increasing prevalence of hypertension in youth and high adult cardiovascular mortality rates, the long-term consequences of youth-onset hypertension remain unknown. This is due to limitations of prior research, such as small sample sizes, reliance on manual record review, and limited analytic methods, that did not address major biases. The Study of the Epidemiology of Pediatric Hypertension (SUPERHERO) is a multisite, retrospective registry of youth evaluated by subspecialists for hypertension disorders. Sites obtain harmonized electronic health record data using standardized biomedical informatics scripts validated with randomized manual record review. Inclusion criteria are index visit for International Classification of Diseases, 10th Revision (ICD-10) code–defined hypertension disorder on or after January 1, 2015, and age < 19 years. We exclude patients with ICD-10 code–defined pregnancy, kidney failure on dialysis, or kidney transplantation. Data include demographics, anthropomorphics, US Census Bureau tract, histories, blood pressure, ICD-10 codes, medications, laboratory and imaging results, and ambulatory blood pressure. SUPERHERO leverages expertise in epidemiology, statistics, clinical care, and biomedical informatics to create the largest and most diverse registry of youth with newly diagnosed hypertension disorders. SUPERHERO’s goals are to reduce CVD burden across the life course and establish gold-standard biomedical informatics methods for youth with hypertension disorders.
Transformation of Applied Linguistics in the Global South Context of Bangladesh: Researcher Agency, Imagination, and North-South Cooperation
Authors: Hamid M Obaidul , Sultana Shaila , Roshid Mohammod Moninoor
Published: June 2024

This article examines the transformation of applied linguistics knowledge production in the Global South taking postcolonial Bangladesh as a case. In the 1990s, one could not locate even a dozen applied linguistics articles in international journals authored by Bangladeshi researchers. However, in about two decades, Bangladeshi researchers can claim hundreds of journal articles, book chapters, monographs, and edited volumes. Drawing on bibliometric data and autoethnography, this article seeks to document a new dawn in applied linguistics research in Bangladesh complemented by researchers’ engagement in Southern epistemological thinking in a decolonial spirit. While demonstrating the role of researcher agency and imagination in this transformation, we also highlight the role of North-South interaction and collaboration. We argue that despite the hegemony of Eurocentric views underpinning language, epistemology and geopolitics of knowledge, there may be hope for Southern applied linguists to decolonize their research imagination and bring disciplinary changes in line with Southern perspectives to make the world a better place for the global community.
A global initiative on addressing bioinformatics’ grand challenges
Authors: Khan Asif M , Işık Esra Büşra , Tan Tin Wee
Published: June 2024

The Bioinformatics Grand Challenges Consortium (BGCC) is a collaborative effort to address the most pressing challenges in bioinformatics. Initially focusing on education and training, the consortium successfully defined seven key grand challenges and is actively developing actionable solutions for these challenges. Building on this foundation, the BGCC plans to broaden its focus to include additional grand challenges in emerging areas.
SNP-slice resolves mixed infections: simultaneously unveiling strain haplotypes and linking them to hosts
Authors: Ju Nianqiao , Liu Jiawei , He Qixin
Published: June 2024

Motivation

Multi-strain infection is a common yet under-investigated phenomenon of many pathogens. Currently, biologists analyzing SNP information sometimes have to discard mixed infection samples as many downstream analyses require monogenomic inputs. Such a protocol impedes our understanding of the underlying genetic diversity, co-infection patterns, and genomic relatedness of pathogens. A scalable tool to learn and resolve the SNP-haplotypes from polygenomic data is an urgent need in molecular epidemiology.

Results

We develop a slice sampling Markov Chain Monte Carlo algorithm, named SNP-Slice, to learn not only the SNP-haplotypes of all strains in the populations but also which strains infect which hosts. Our method reconstructs SNP-haplotypes and individual heterozygosities accurately without reference panels and outperforms the state-of-the-art methods at estimating the multiplicity of infections and allele frequencies. Thus, SNP-Slice introduces a novel approach to address polygenomic data and opens a new avenue for resolving complex infection patterns in molecular surveillance. We illustrate the performance of SNP-Slice on empirical malaria and HIV datasets and provide recommendations for using our method on empirical datasets.

Availability and Implementation

The implementation of the SNP-Slice algorithm, as well as scripts to analyze SNP-Slice outputs, are available at https://github.com/nianqiaoju/snp-slice.
Acceleration of uterine 3D T2-weighted imaging by compressed SENSE—a multicentre study
Authors: Song Qingling , Ma Changjun , Tian Shifeng , Meng Xing , Chen Lihua , Wang Nan , Song Qingwei , Lu Shan , Liu Dengping , Gui Haiyan , Chen Honghao , Lin Liangjie , Xu Xiaofang , Wang Jiazheng , Liu Ailian
Published: June 2024

Objectives

To find the optimal acceleration factor (AF) of the compressed SENSE (CS) technique for uterine isotropic high-resolution 3D T2-weighted imaging (3D-ISO-T2WI).

Methods

A total of 91 female volunteers from the First Affiliated Hospital of Dalian Medical University, Chu Hsien-I Memorial Hospital and Tianjin Institute of Endocrinology, and The Fourth Hospital of Harbin were recruited. A total of 44 volunteers received uterus sagittal 3D-ISO-T2WI scans on 3.0T MRI device with different CS AFs (including SENSE3, CS3, CS4, CS5, CS6, and CS7), 51 received 3D-ISO-T2WI scans with different degrees of fat suppression (none, light, moderate, and severe), while 4 volunteers received both series of scans. Image quality was subjectively evaluated with a 3-point scoring system. Junction zone signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR), and myometrial SNR were also calculated. Intraclass correlation coefficients were used to analyse the consistency of the measurement results by 2 observers. Analysis of variance test or Friedman rank sum test was used to compare the differences in subjective scores, SNR, and CNR under different AFs/different degrees of fat suppression.

Results

Images by AFs of CS3, CS4, and CS5 had the highest SNR and CNR. Among them, CS5 had the shortest scan time. CS5 also had one of the highest subjective scores. There was no significant difference in SNR and CNR among images acquired with different degrees of fat suppression. Also, images with moderate fat suppression had the highest subjective scores.

Conclusion

The CS5 combined with moderate fat suppression is recommended for routine female pelvic 3D-ISO-T2WI scan.

Advances in knowledge

The CS5 has the highest image quality and has the shortest scan time, which is the best AF. Moderate fat suppression has the highest subjective scores. The CS5 and moderate fat suppression are the best combination for a female pelvic 3D-ISO-T2WI scan.
Early short-term hypoxia promotes epidermal cell migration by activating the CCL2-ERK1/2 pathway and epithelial–mesenchymal transition during wound healing
Authors: Jin Linbo , Zhou Shiqi , Zhao Shihan , Long Junhui , Huang Zhidan , Zhou Junli , Zhang Yiming
Published: June 2024

Background

Due to vasculature injury and increased oxygen consumption, the early wound microenvironment is typically in a hypoxic state. We observed enhanced cell migration ability under early short-term hypoxia. CCL2 belongs to the CC chemokine family and was found to be increased in early hypoxic wounds and enriched in the extracellular signal-regulated kinase (ERK)1/2 pathway in our previous study. However, the underlying mechanism through which the CCL2-ERK1/2 pathway regulates wound healing under early short-term hypoxia remains unclear. Activation of epithelial–mesenchymal transition (EMT) is a key process in cancer cell metastasis, during which epithelial cells acquire the characteristics of mesenchymal cells and enhance cell motility and migration ability. However, the relationship between epithelial cell migration and EMT under early short-term hypoxia has yet to be explored.

Methods

HaCaT cells were cultured to verify the effect of early short-term hypoxia on migration through cell scratch assays. Lentiviruses with silenced or overexpressed CCL2 were used to explore the relationship between CCL2 and migration under short-term hypoxia. An acute full-thickness cutaneous wound rat model was established with the application of an ERK inhibitor to reveal the hidden role of the ERK1/2 pathway in the early stage of wound healing. The EMT process was verified in all the above experiments through western blotting.

Results

In our study, we found that short-term hypoxia promoted cell migration. Mechanistically, hypoxia promoted cell migration through mediating CCL2. Overexpression of CCL2 via lentivirus promoted cell migration, while silencing CCL2 via lentivirus inhibited cell migration and the production of related downstream proteins. In addition, we found that CCL2 was enriched in the ERK1/2 pathway, and the application of an ERK inhibitor in vivo and in vitro verified the upstream and downstream relationships between the CCL2 pathway and ERK1/2. Western blot results both in vivo and in vitro demonstrated that early short-term hypoxia promotes epidermal cell migration by activating the CCL2-ERK1/2 pathway and EMT during wound healing.

Conclusions

Our work demonstrated that hypoxia in the early stage serves as a stimulus for triggering wound healing through activating the CCL2-ERK1/2 pathway and EMT, which promote epidermal cell migration and accelerate wound closure. These findings provide additional detailed insights into the mechanism of wound healing and new targets for clinical treatment.
A case of adult-onset Still disease with eyelid xanthogranuloma mimicking Erdheim–Chester disease
Authors: Hirafuku Keigo , Kanbe Masahiro , Dekio Itaru , Yoshida Ken , Kurosaka Daitaro , Honda Akira , Kurokawa Mineo , Asahina Akihiko
Published: June 2024

We report an exceptionally rare but interesting case of adult-onset Still disease (AOSD) accompanied by large xanthogranuloma of the eyelid in a patient who had symptoms reminiscent of Erdheim–Chester disease (ECD). The symptoms of AOSD and ECD overlap; therefore, we believe it is important to remind clinicians that when xanthogranuloma occurs in a patient with AOSD, the possibility of ECD should be considered.
Quantum Cluster Algebras and 3D Integrability: Tetrahedron and 3D Reflection Equations
Authors: Inoue Rei , Kuniba Atsuo , Terashima Yuji
Published: June 2024

We construct a new solution to the tetrahedron equation and the three-dimensional (3D) reflection equation by extending the quantum cluster algebra approach by Sun and Yagi concerning the former. We consider the Fock–Goncharov quivers associated with the longest elements of the Weyl groups of type $A$ and $C$, and investigate the cluster transformations corresponding to changing a reduced expression into a “most distant” one. By devising a new realization of the quantum $y$-variables in terms of $q$-Weyl algebra, the solutions are extracted as the operators whose adjoint actions yield the cluster transformations of the quantum $y$-variables. Explicit formulas of their matrix elements are also derived for some typical representations.
In Search of Effective Corporate Grievance Mechanisms: Can Mandatory Due Diligence Laws be a Progressive Force?
Authors: Harrison James , Wielga Mark , Parejo Margarita
Published: June 2024

Mandatory human rights due diligence (mHRDD) laws are currently being proposed and/or implemented in countries around the world. Increasingly, these laws place obligations on corporations to establish or participate in corporate grievance mechanisms (CGMs). CGMs have the potential to ensure that rightsholders are empowered to hold corporations accountable for their human rights performance. But our limited knowledge of how CGMs operate indicates that many are not producing results that are valuable for workers and communities. CGM provisions in mHRDD laws in Germany and Norway, and draft laws produced in the European Union and Brazil are rudimentary and unlikely to produce better-performing CGMs. Analysis of Norwegian mHRDD corporate reporting identifies that many corporations fail to understand the basic elements of an effective CGM. The article therefore argues that requirements for CGMs in mHRDD laws will only be a progressive move if such laws also demand disclosure of information that empowers national authorities, as well as civil society actors and researchers, to scrutinize CGMs to ensure they are effective. Disclosure requirements must speak to three issues: (1) how accessible CGMs are, (2) the way complaints are handled, and (3) the remedies provided to rightsholders. If, as a result of scrutiny of this data, mHRDD laws can produce well-functioning CGMs, this could lead to rightsholder concerns becoming more central to due diligence processes, potentially addressing cosmetic compliance with due diligence obligations.
Ground beetle movement is deterred by habitat edges: a mark-release-recapture study on the effectiveness of border crops in an agricultural landscape
Authors: Anderson Magdeline E , Harman Rachel R , Kim Tania N
Published: June 2024

Border crops can increase beneficial insect biodiversity within agricultural fields by supplementing insects with food and nesting resources. However, the effectiveness of border crops relies on insect movement between adjacent habitats and some insects might consider habitat boundaries as barriers. Therefore, understanding insect movement between habitats is needed to determine the effectiveness of border crops for ecosystem services such as pest control within agricultural habitats. Our objective was to compare ground beetle (Coleoptera: Carabidae) movement across soybean plots that were bordered by corn and grassland habitat to determine whether habitat boundaries were considered barriers of movement to predatory beetles. Using a grid of pitfall traps within these habitats, we conducted a mark, release, and recapture experiment to track and evaluate ground beetle movement patterns. We found that ground beetles stayed in the habitat of their release and that movement between habitats, despite the type of bordering habitat or type of edge, was uncommon. We also found that long-distance movement was rare as most beetles moved less than 5 m (regardless of release or recaptured habitat) and movement was perpendicular to habitat edges. These results suggest that any edge habitat, including agricultural–agricultural boundaries and natural–agricultural boundaries, are likely barriers to ground beetle movement. Therefore, in order for border crops to be effective in pest management by ground beetles, making habitat edges more permeable, especially using techniques such as edge softening, could promote cross-habitat movement and ultimately contribute to natural pest control in agricultural systems.
Wakefield’s Harm-Based Critique of the Biostatistical Theory
Authors: Boorse Christopher
Published: June 2024

Jerome Wakefield criticizes my biostatistical analysis of the pathological—as statistically subnormal biological part-functional ability relative to species, sex, and age—for its lack of a harm clause. He first charges me with ignoring two general distinctions: biological versus medical pathology, and disease of a part versus disease of a whole organism. He then offers 10 counterexamples that, he says, are harmless dysfunctions but not medical disorders. Wakefield ends by arguing that we need a harm clause to explain American psychiatry’s 1973 decision to declassify homosexuality. I reply, first, that his two distinctions are philosophic fantasies alien to medical usage, invented only to save his own harmful-dysfunction analysis (HDA) from a host of obvious counterexamples. In any case, they do not coincide with the harmless/harmful distinction. In reality, medicine admits countless chronic diseases that are, contrary to Wakefield, subclinical for most of their course, as well as many kinds of typically harmless skin pathology. As for his 10 counterexamples, no medical source he cites describes them as he does. I argue that none of his examples contradicts the biostatistical analysis: all either are not part-dysfunctions (situs inversus, incompetent sperm, normal-flora infection) or are indeed classified as medical disorders (donated kidney, Typhoid Mary’s carrier status, latent tuberculosis or HIV, cherry angiomas). And if Wakefield’s HDA fits psychiatry, the fact that it does not fit medicine casts doubt on psychiatry’s status as a medical specialty.
(016) SALVAGE VAGINOPLASTY WITH SINGLE-PORT ROBOT ASSISTED TUBULARIZED URACHUS PERITONEAL HINGE FLAP: TECHNIQUE HIGHLIGHTS, OUTCOMES, AND AN EVIDENCE-BASED PROPOSAL FOR HOW AND WHEN TO USE (AND NOT USE!) PERITONEUM WITH VAGINOPLASTY
Authors: Sandhu S , Smith S , Mallavarapu S , Stelmar J , Yuan N , Gupta A , Kim H , Garcia M
Published: June 2024

Introduction

Vaginoplasty is a commonly performed genital gender affirming surgery. Currently there are two published techniques that describe using peritoneal tissue to contribute to the necessary tissue to line the neovaginal canal: The modified Davydov technique, first described in 2019 by Zhao et al, and the Tubularized Urachus-Peritoneal Hinge Flap, described by Garcia et al in 2022. Today many providers use the Davydov technique at time of primary vaginoplasty, while other providers argue that use of peritoneum is not necessary at the time of primary vaginoplasty. We use the urachus flap only for salvage surgery.

Objective

Herein, we report our technical innovations related to the urachus hinge flap, and our clinical outcomes at 1.5 years post-op. We also review the literature to determine whether there is evidence to support using peritoneum at time of primary vaginoplasty.

Methods

We review our single-port robot assisted urachus hinge flap technique to augment neovaginal depth after primary vaginoplasty complicated by loss of vaginal depth. We also review technical innovations to maximize neovaginal depth with primary vaginoplasty using only penile and scrotal skin. We present our literature review, and posit a theory that explains why, regardless of PV technique, mean neovaginal depth is 11-13 cm in all series.

Results

Our mean neovaginal depth after our salvage urachus hinge flap technique is 12.5 cm (range 11-14.2) at 409 days post-op. This is comparable to the Davydov PV technique. With primary vaginoplasty using only penile and scrotal skin, our mean depth is 12.5 cm, which is > other series using only penile/scrotal skn, and comparable to series that also use peritoneum. We use video to show how, with the Davydov technique, rectum and bowel are pulled deep into the pelvis post-op, which increases risk of bowel injury at time of salvage surgery with intestine.

Conclusions

By the techniques described herein, in our hands, with primary vaginoplasty using only penile and scrotal skin we achieve vaginal depth comparable to techniques that augment with peritoneum. We suggest that peritoneum is rarely to never necessary at primary vaginoplasty, and should be reserved for use as a salvage surgery if and when it is needed. We also suggest that the urachus flap is a safer alternative to the Davydov technique if and when PV fails and salvage intestinal vaginoplasty must be undertaken.

Disclosure

No.
RAD18 directs DNA double-strand break repair by homologous recombination to post-replicative chromatin
Authors: Palek Matous , Palkova Natalie ,   consortium CZECANCA, Cerna Marta , Horackova Klara , Hovhannisyan Milena , Janatova Marketa , Jelinkova Sandra , Nehasil Petr , Soukupova Jana , Stastna Barbora , Zemankova Petra , Foretova Lenka , Machackova Eva , Krutilkova Vera , Tavandzis Spiros , Cerna Leona , Chvojka Stepan , Koudova Monika , Havranek Ondrej , Novotny Jan , Vesela Kamila , Vocka Michal , Hruskova Lucie , Michalovska Renata , Schwetzova Denisa , Vlckova Zdenka , Cerna Monika , Hejnalova Marketa , Jedlickova Nikol , Subrt Ivan , Zavoral Tomas , Kosarova Marcela , Vacinova Gabriela , Janikova Maria , Kratochvilova Romana , Curtisova Vaclava , Vrtel Radek , Scheinost Ondrej , Duskova Petra , Stranecky Viktor , Kleiblova Petra , Kleibl Zdenek , Macurek Libor
Published: June 2024

RAD18 is an E3 ubiquitin ligase that prevents replication fork collapse by promoting DNA translesion synthesis and template switching. Besides this classical role, RAD18 has been implicated in homologous recombination; however, this function is incompletely understood. Here, we show that RAD18 is recruited to DNA lesions by monoubiquitination of histone H2A at K15 and counteracts accumulation of 53BP1. Super-resolution microscopy revealed that RAD18 localizes to the proximity of DNA double strand breaks and limits the distribution of 53BP1 to the peripheral chromatin nanodomains. Whereas auto-ubiquitination of RAD18 mediated by RAD6 inhibits its recruitment to DNA breaks, interaction with SLF1 promotes RAD18 accumulation at DNA breaks in the post-replicative chromatin by recognition of histone H4K20me0. Surprisingly, suppression of 53BP1 function by RAD18 is not involved in homologous recombination and rather leads to reduction of non-homologous end joining. Instead, we provide evidence that RAD18 promotes HR repair by recruiting the SMC5/6 complex to DNA breaks. Finally, we identified several new loss-of-function mutations in RAD18 in cancer patients suggesting that RAD18 could be involved in cancer development.
ENL reads histone β-hydroxybutyrylation to modulate gene transcription
Authors: Chen Chen , Chen Cong , Wang Aiyuan , Jiang Zixin , Zhao Fei , Li Yanan , Han Yue , Niu Ziping , Tian Shanshan , Bai Xue , Zhang Kai , Zhai Guijin
Published: June 2024

Histone modifications are typically recognized by chromatin-binding protein modules (referred to as ‘readers’) to mediate fundamental processes such as transcription. Lysine β-hydroxybutyrylation (Kbhb) is a new type of histone mark that couples metabolism to gene expression. However, the readers that prefer histone Kbhb remain elusive. This knowledge gap should be filled in order to reveal the molecular mechanism of this epigenetic regulation. Herein, we developed a chemical proteomic approach, relying upon multivalent photoaffinity probes to capture binders of the mark, and identified ENL as a novel target of H3K9bhb. Biochemical studies and CUT&Tag analysis further suggested that ENL favorably binds to H3K9bhb, and co-localizes with it on promoter regions to modulate gene expression. Notably, disrupting the interaction between H3K9bhb and ENL via structure-based mutation led to the suppressed expression of genes such MYC that drive cell proliferation. Together, our work offered a chemoproteomics approach and identified ENL as a novel histone β-hydroxybutyrylation effector that regulates gene transcription, providing new insight into the regulation mechanism and function of histone Kbhb.
Enhancing insights into diseases through horizontal gene transfer event detection from gut microbiome
Authors: Wang Shuai , Jiang Yiqi , Che Lijia , Wang Ruo Han , Li Shuai Cheng
Published: June 2024

Horizontal gene transfer (HGT) phenomena pervade the gut microbiome and significantly impact human health. Yet, no current method can accurately identify complete HGT events, including the transferred sequence and the associated deletion and insertion breakpoints from shotgun metagenomic data. Here, we develop LocalHGT, which facilitates the reliable and swift detection of complete HGT events from shotgun metagenomic data, delivering an accuracy of 99.4%—verified by Nanopore data—across 200 gut microbiome samples, and achieving an average F1 score of 0.99 on 100 simulated data. LocalHGT enables a systematic characterization of HGT events within the human gut microbiome across 2098 samples, revealing that multiple recipient genome sites can become targets of a transferred sequence, microhomology is enriched in HGT breakpoint junctions (P-value = 3.3e-58), and HGTs can function as host-specific fingerprints indicated by the significantly higher HGT similarity of intra-personal temporal samples than inter-personal samples (P-value = 4.3e-303). Crucially, HGTs showed potential contributions to colorectal cancer (CRC) and acute diarrhoea, as evidenced by the enrichment of the butyrate metabolism pathway (P-value = 3.8e-17) and the shigellosis pathway (P-value = 5.9e-13) in the respective associated HGTs. Furthermore, differential HGTs demonstrated promise as biomarkers for predicting various diseases. Integrating HGTs into a CRC prediction model achieved an AUC of 0.87.
HIV Subtypes and Drug-resistance-associated Mutations in US Blood Donors, 2015–2020
Authors: Custer Brian , Altan Eda , Montalvo Leilani , Coyne Alison , Grebe Eduard , Deng Xutao , Stone Mars , Delwart Eric , Bakkour Sonia , Hailu Benyam , Reik Rita , Kessler Debra , Stramer Susan L , Busch Michael P ,   for the Transfusion Transmissible Infections Monitoring System (TTIMS) Program, Notari E , Stramer S , Dodd R , Conti G , Fayed R , Nelson D , Townsend R , Foster G , Haynes J , Crawford E , Huseynova E , Krysztof D , Burke D , Lanteri M , Green V , Cyrus S , Williamson P , Kessler D , Gorlin J , Milan-Benson L , DelValle C , Chien P , Brown T , Reik R , Shea C , Lopez M , Richards K , Foster T , Brodsky J , Barr M , Rains T , Custer B , Bruhn R , Grebe E , Busch M , Stone M , Di Germanio C , Hindes D , Kaidarova Z , Zurita K , Tadena A , Montalvo L , Dayana A , Hughes S , Townsend M , Bravo M , Vannoy J , Fallon S , Anderson S , Whitaker B , Yang H , Belov A , Eder A , Hailu B , Zou S , Berger J , Custer Brian , Stramer Susan , Kessler Debra , Reik Rita , Williamson Phillip , Anderson Steven A , Hailu Benyam
Published: June 2024

Background

Monitoring genotypes of HIV infections in blood donors may provide insights into infection trends in the general population.

Methods

HIV RNA was extracted from plasma samples of blood donors confirmed as HIV positive by blood screening nucleic acid and antibody tests. HIV genome target regions were amplified using nested real time-polymerase chain reaction followed by next-generation sequencing. Sequences were compared to those in the Los Alamos National Laboratory (LANL) database. Sequences were also assessed for drug resistance mutations (DRM) using the Stanford HIV DRM Database.

Results

From available HIV-positive donations collected between 1 September 2015 and 31 December 2020, 563 of 743 (75.8%) were successfully sequenced; 4 were subtype A, 543 subtype B, 5 subtype C, 1 subtype G, 5 circulating recombinant forms (CRF), and 2 were subtype B and D recombinants. Overall, no significant differences between blood donor and available LANL genotypes were found, and the genotypes of newly acquired versus prevalent HIV infections in donors were similar. The proportion of non-B subtypes and CRF remained a small fraction, with no other subtype or CRF representing more than 1% of the total. DRM were identified in 122 (21.6%) samples with protease inhibitor, nucleoside reverse transcriptase inhibitor and non-nucleoside reverse transcriptase inhibitor DRMs identified in 4.9%, 4.6% and 14.0% of samples, respectively.

Conclusions

HIV genetic diversity and DRM in blood donors appear representative of circulating HIV infections in the US general population and may provide more information on infection diversity than sequences reported to LANL, particularly for recently transmitted infections.
The Music of Urban Lăutari in Southern Romania
Authors: Rădulescu Speranţa , Beissinger Margaret Hiebert
Published: June 2024

In the last decades of the nineteenth century and the first decades of the twentieth, two types of oral traditional music created and performed by professional Romani musicians (lăutari) emerged in southern Romanian cities and towns. The first, an instrumental genre, was aimed mainly at the middle class and expressed aspirations of creating a national popular cultural symbol in both local and European terms: arii naţionale (national arias). This genre would endure as an aural emblem of the Romanian nation for a long time. The second, muzica lăutărească (lăutar music), song and dance genres that developed among in-group Romani musicians, became a representative emblem of race and occupation. Later on, people of all ethnicities in poor, outlying, urban neighborhoods adopted it under an alternative name: muzica de mahala (slum music). The discussion of these urban expressive forms includes considerations of historical, musical, textual, social, political, and racial perspectives.