bluuebunny/crossref_metadata_2025_split huggingface dataset:
Botswana
Authors: Schneider Marius , Ho Tu Nam Nora 
Published: May 2024

Abstract
This chapter talks about Botswana, which is located in Southern Africa. Botswana is a member of the World Trade Organization and a party to the Banjul Protocol on marks in the framework of the African Regional Intellectual Property Organization (ARIPO). GIs are protected in Botswana via a sui generis system under the Industrial Property Act No 8 of 2010 (IPA), which came into force on 31 August 2012. It is further possible under the IPA to register a collective mark, although some GIs may be excluded from registration due to restrictions under the IPA. This chapter looks at the registrability of names, the procedure and requirements for registration of GIs and collective marks, the term of protection, the rights of the owner against infringers and customs enforcement. The chapter ends by looking at whether Botswana is party to any bilateral agreements touching on GIs.
Kenya
Authors: Schneider Marius , Ho Tu Nam Nora 
Published: May 2024

Abstract
This chapter focuses on Kenya, which is found in East Africa. Kenya has been a party to the Madrid Agreement Concerning International Registration of Marks, and the Protocol relating to that Agreement since 1998. Kenya is a member of the World Trade Organization (WTO). Although there has been various attempts to introduce geographical indications (GIs) in Kenyan law, there is no specific legislation regarding GIs currently in force in Kenya. Collective and certification marks are however available to both foreign and domestic applicants. This chapter discusses the registration of certification and collective marks, the registrability of names, the procedure and requirements for registration, the term of protection , the rights of the owner against infringers, enforcement by the Anti-Counterfeit Authority (ACA) and customs enforcement. The chapter ends by looking at whether there are any bilateral agreements regarding GIs to which Kenya is a party.
Mauritius
Authors: Schneider Marius , Ho Tu Nam Nora 
Published: May 2024

Abstract
This chapter discusses the island nation of Mauritius, found in the Indian Ocean. Mauritius is a member of the World Trade Organization (WTO), and must implement the WTO Agreement on Trade-Related Aspects of Intellectual Property Rights (TRIPS). The chapter explains how geographical indications (GIs) can be registered and enforced in Mauritius either through a sui generis system or as collective marks or certification marks. The sui generis registration of GIs is possible since 31 January 2022 after the coming into force of the Industrial Property Act. The chapter outlines the registration of GIs, certification and collective marks, the registrability of names, the procedure and requirements for registration, the term of protection, the rights of the owner against infringers and customs enforcement. The chapter ends by looking at whether there are any bilateral agreements regarding GIs to which Mauritius is a party.
Informed by Microbes
Authors: Armstrong Rachel 
Published: May 2024

Abstract
This chapter explores an alternative framework for human settlement by harnessing the environmental knowledge of microbes and advanced biotechnologies. It discusses the principles and practices underlying this platform’s development, with radical implications for design practice and its pedagogies by focusing on microbial cities, or biofilms, to address the environmental challenges of the Anthropocene era. Biofilms, formed by diverse communities of microbes, have played a crucial role in shaping the biosphere for billions of years, whose complex organisational principles resemble human settlements and engage in cooperative behaviours to enhance collective resilience. By studying and collaborating with microbes, humans can establish new forms of infrastructure and cohabitation that promote ecological collaboration and sustainability. Central to actualising this microbial framework is the bio-digital platform, where electroactive bacteria and artificial intelligence interface, exchanging electrons produced from metabolising organic waste. This convergence of organism, information, and machine offers transformative possibilities for cities.
Contestation: Challenges to the Absolute Prohibition of Torture
Authors: Oette Lutz 
Published: May 2024

Abstract
Chapter 1 sets out the genesis of and rationale for the absolute prohibition of torture before examining challenges to it in their wider historical, colonial, and imperial context. It analyses how the portrayal of torture as a ‘barbaric’ practice and the rationale for its prohibition in international law informed subsequent challenges. Focusing on France (Algeria), the United Kingdom (Northern Ireland), Israel (Palestinians), and the United States of America (counter-terrorism) as key case studies, it shows how states employed legal stratagems to narrow the prohibition’s application and necessity arguments, which were discursively underpinned by the ticking bomb scenario, to justify the use of torture while portraying themselves as ‘civilized’, ‘rational’, and ‘humane’. The discussion surrounding the case of Gäfgen v Germany where the police threatened a suspected kidnapper with torture in their attempt to rescue a kidnapped child illustrates doctrinal challenges to the absolute prohibition in exceptional circumstances beyond the counter-terrorism context. The chapter concludes by highlighting the ambivalent consequences of the ‘war on terror’ for the prohibition, resulting in both problematic legal grey areas and multiple initiatives, including a focus on effective interviewing as a means to reduce recourse to coercive interrogation techniques.
Diversity: Discriminatory Torture and Other Ill-treatment
Authors: Oette Lutz 
Published: May 2024

Abstract
The chapter examines the relationship between discrimination and torture and other ill-treatment. It focuses particularly on the interpretation of discriminatory torture, a notion that had long been neglected in international human rights law. A review of developments in four key areas in the field of non-discrimination, namely gender, including gender identity and sexual orientation, ‘race’, disability, and age (children) provides evidence of an increasingly rich yet fragmented and partial jurisprudence and treaty body practice. It also shows the ambivalent role of international law in legitimizing problematic practices. Based on this review, the chapter sets out its interpretation of the elements of discriminatory torture, which focuses on all grounds of discrimination, including intersectional discrimination and neglected characteristics such as poverty, and identifies indicators that demonstrate discriminatory purpose. It makes a case for discriminatory torture and other ill-treatment to become an integral part of the contextual interpretation of the prohibition that is embedded in a broader transformative agenda which, by seeking to bring about equality, addresses the structural causes underpinning persistent torture practices.
Expansion: Widespread and Systemic Suffering and the Future of the Prohibition
Authors: Oette Lutz 
Published: May 2024

Abstract
The chapter explores the future evolution of the prohibition. It examines the conceptual and doctrinal challenges posed by newly emerging methods of torture, namely less-lethal and autonomous weapons and digital torture as well as structural conditions, focusing on health, poverty, and environmental damage. Powerful and sophisticated weapons foster arsenals of repression, aggravate the impact of measures taken in the crowd-control context, and proliferate, in the absence of effective regulation, with the result of increasingly militarized law enforcement. Digital torture denotes a space for and mode of various forms of ill-treatment, which has distinctive features in terms of how its nature, impact, perpetrators, and setting inform the interpretation of the prohibition and states’ obligations. Structural conditions have traditionally not been viewed through the lens of the prohibition. As the chapter demonstrates, however, the prohibition can play a vital role in linking widespread, systemic human suffering to state indifference and highlighting how states contribute to such suffering through systemic policy failures. The application of the prohibition in fields that typically fall within the purview of economic, social and cultural rights or other rights provides a critical complementary dimension, with its focus on what action states must take to protect human dignity in such contexts.
Dancing to the Goldberg Variations
Authors: Knyt Erinn E 
Published: May 2024

Abstract
Since William Dollar’s Air and Variations in 1937, there have been at least nineteen additional choreographed versions of Bach’s Goldberg Variations, including an iconic classic by Jerome Robbins (1971). With dance styles ranging from tap dance, to modern dance, to classical ballet, Bach’s work, which was inspired by dance, has become a regularly choreographed work. Although many choreographers have shown reverence toward the Goldberg Variations and have viewed the dance movements as visual representations of Bach’s musical architecture, since the late 1990s, there has been more openness to the deconstruction and reorganization of the piece according to the conception of the choreographer and interpreter, through narrative and conceptual interpolations, through musical deconstruction and fragmentation, and through physical movements that go against the rhythms and themes in Bach’s composition. These trends coincide with the more open approach to the work concept described in the previous chapters.
Coda
Authors: Knyt Erinn E 
Published: May 2024

Abstract
The Coda summarizes main points from the book and also examines the continued dissemination of the Goldberg Variations in the twenty-first century, including during the COVID-19 pandemic. It documents the use of the piece in relation to postmodern media, such as video games and TikTok. It also documents literary, architectural, and artistic adaptations of the piece. Finally, it ties the topic to broader discourse about Bach reception, the work concept, and performance practice in general through a comparison to adaptations of Bach’s Concerto after the Italian Taste, BWV 971, and his passions. Once viewed as an object, Bach’s works are now becoming fluid ephemera that span generations and centuries. Bach and his music are made anew in the image of the present, in which the past lives on, transformed.
Isolated court determinations on the admissibility of arbitration: a case study of the German Federal Court of Justice’s recent decision on intra-EU ICSID proceedings
Authors: Steinbrück Ben , Krahé Justin Friedrich 
Published: May 2024

Abstract
The German Federal Court of Justice recently confirmed that German courts can issue declarations—with binding effect for the German legal order—finding intra-EU ICSID arbitration inadmissible. While this further step in the post-Achmea dismantling of the EU investment protection system is an important, if unsurprising, development for investment protection lawyers, the procedural mechanism used, section 1032(2) of the German Civil Procedural Code (Zivilprozessordnung—ZPO), is relevant to all forms of arbitration and is available as soon as one party is seated or even just has assets in Germany. This article provides an overview of the German mechanism for isolated determination of the admissibility of arbitration. It uses the recent Federal Court of Justice decision as a model example where such an early determination allows for significant costs savings, explores the functioning of the relevant statutory provision, and highlights situations in which this may be an appropriate means of determining the admissibility of arbitration while limiting costs exposure.
Relative telencephalon size does not affect collective motion in the guppy (Poecilia reticulata)
Authors: Boussard Annika , Ahlkvist Mikaela , Corral-López Alberto , Fong Stephanie , Fitzpatrick John , Kolm Niclas 
Published: May 2024

Abstract
Collective motion is common across all animal taxa, from swarming insects to schools of fish. The collective motion requires intricate behavioral integration among individuals, yet little is known about how evolutionary changes in brain morphology influence the ability for individuals to coordinate behavior in groups. In this study, we utilized guppies that were selectively bred for relative telencephalon size, an aspect of brain morphology that is normally associated with advanced cognitive functions, to examine its role in collective motion using an open-field assay. We analyzed high-resolution tracking data of same-sex shoals consisting of 8 individuals to assess different aspects of collective motion, such as alignment, attraction to nearby shoal members, and swimming speed. Our findings indicate that variation in collective motion in guppy shoals might not be strongly affected by variation in relative telencephalon size. Our study suggests that group dynamics in collectively moving animals are likely not driven by advanced cognitive functions but rather by fundamental cognitive processes stemming from relatively simple rules among neighboring individuals.
Deep learning in structural bioinformatics: current applications and future perspectives
Authors: Kumar Niranjan , Srivastava Rakesh 
Published: May 2024

AbstractIn this review article, we explore the transformative impact of deep learning (DL) on structural bioinformatics, emphasizing its pivotal role in a scientific revolution driven by extensive data, accessible toolkits and robust computing resources. As big data continue to advance, DL is poised to become an integral component in healthcare and biology, revolutionizing analytical processes. Our comprehensive review provides detailed insights into DL, featuring specific demonstrations of its notable applications in bioinformatics. We address challenges tailored for DL, spotlight recent successes in structural bioinformatics and present a clear exposition of DL—from basic shallow neural networks to advanced models such as convolution, recurrent, artificial and transformer neural networks. This paper discusses the emerging use of DL for understanding biomolecular structures, anticipating ongoing developments and applications in the realm of structural bioinformatics.
SpatialCells: automated profiling of tumor microenvironments with spatially resolved multiplexed single-cell data
Authors: Wan Guihong , Maliga Zoltan , Yan Boshen , Vallius Tuulia , Shi Yingxiao , Khattab Sara , Chang Crystal , Nirmal Ajit J , Yu Kun-Hsing , Liu David , Lian Christine G , DeSimone Mia S , Sorger Peter K , Semenov Yevgeniy R 
Published: May 2024

Abstract
Cancer is a complex cellular ecosystem where malignant cells coexist and interact with immune, stromal and other cells within the tumor microenvironment (TME). Recent technological advancements in spatially resolved multiplexed imaging at single-cell resolution have led to the generation of large-scale and high-dimensional datasets from biological specimens. This underscores the necessity for automated methodologies that can effectively characterize molecular, cellular and spatial properties of TMEs for various malignancies. This study introduces SpatialCells, an open-source software package designed for region-based exploratory analysis and comprehensive characterization of TMEs using multiplexed single-cell data. The source code and tutorials are available at https://semenovlab.github.io/SpatialCells. SpatialCells efficiently streamlines the automated extraction of features from multiplexed single-cell data and can process samples containing millions of cells. Thus, SpatialCells facilitates subsequent association analyses and machine learning predictions, making it an essential tool in advancing our understanding of tumor growth, invasion and metastasis.
Genotypic–phenotypic landscape computation based on first principle and deep learning
Authors: Liu Yuexing , Luo Yao , Lu Xin , Gao Hao , He Ruikun , Zhang Xin , Zhang Xuguang , Li Yixue 
Published: May 2024

Abstract
The relationship between genotype and fitness is fundamental to evolution, but quantitatively mapping genotypes to fitness has remained challenging. We propose the Phenotypic-Embedding theorem (P-E theorem) that bridges genotype–phenotype through an encoder–decoder deep learning framework. Inspired by this, we proposed a more general first principle for correlating genotype–phenotype, and the P-E theorem provides a computable basis for the application of first principle. As an application example of the P-E theorem, we developed the Co-attention based Transformer model to bridge Genotype and Fitness model, a Transformer-based pre-train foundation model with downstream supervised fine-tuning that can accurately simulate the neutral evolution of viruses and predict immune escape mutations. Accordingly, following the calculation path of the P-E theorem, we accurately obtained the basic reproduction number (${R}_0$) of SARS-CoV-2 from first principles, quantitatively linked immune escape to viral fitness and plotted the genotype-fitness landscape. The theoretical system we established provides a general and interpretable method to construct genotype–phenotype landscapes, providing a new paradigm for studying theoretical and computational biology.
TransAC4C—a novel interpretable architecture for multi-species identification of N4-acetylcytidine sites in RNA with single-base resolution
Authors: Liu Ruijie , Zhang Yuanpeng , Wang Qi , Zhang Xiaoping 
Published: May 2024

Abstract
N4-acetylcytidine (ac4C) is a modification found in ribonucleic acid (RNA) related to diseases. Expensive and labor-intensive methods hindered the exploration of ac4C mechanisms and the development of specific anti-ac4C drugs. Therefore, an advanced prediction model for ac4C in RNA is urgently needed. Despite the construction of various prediction models, several limitations exist: (1) insufficient resolution at base level for ac4C sites; (2) lack of information on species other than Homo sapiens; (3) lack of information on RNA other than mRNA; and (4) lack of interpretation for each prediction. In light of these limitations, we have reconstructed the previous benchmark dataset and introduced a new dataset including balanced RNA sequences from multiple species and RNA types, while also providing base-level resolution for ac4C sites. Additionally, we have proposed a novel transformer-based architecture and pipeline for predicting ac4C sites, allowing for highly accurate predictions, visually interpretable results and no restrictions on the length of input RNA sequences. Statistically, our work has improved the accuracy of predicting specific ac4C sites in multiple species from less than 40% to around 85%, achieving a high AUC &gt; 0.9. These results significantly surpass the performance of all existing models.
scEWE: high-order element-wise weighted ensemble clustering for heterogeneity analysis of single-cell RNA-sequencing data
Authors: Huang Yixiang , Jiang Hao , Ching Wai-Ki 
Published: May 2024

Abstract
With the emergence of large amount of single-cell RNA sequencing (scRNA-seq) data, the exploration of computational methods has become critical in revealing biological mechanisms. Clustering is a representative for deciphering cellular heterogeneity embedded in scRNA-seq data. However, due to the diversity of datasets, none of the existing single-cell clustering methods shows overwhelming performance on all datasets. Weighted ensemble methods are proposed to integrate multiple results to improve heterogeneity analysis performance. These methods are usually weighted by considering the reliability of the base clustering results, ignoring the performance difference of the same base clustering on different cells. In this paper, we propose a high-order element-wise weighting strategy based self-representative ensemble learning framework: scEWE. By assigning different base clustering weights to individual cells, we construct and optimize the consensus matrix in a careful and exquisite way. In addition, we extracted the high-order information between cells, which enhanced the ability to represent the similarity relationship between cells. scEWE is experimentally shown to significantly outperform the state-of-the-art methods, which strongly demonstrates the effectiveness of the method and supports the potential applications in complex single-cell data analytical problems.
mbDecoda: a debiased approach to compositional data analysis for microbiome surveys
Authors: Zong Yuxuan , Zhao Hongyu , Wang Tao 
Published: May 2024

Abstract
Potentially pathogenic or probiotic microbes can be identified by comparing their abundance levels between healthy and diseased populations, or more broadly, by linking microbiome composition with clinical phenotypes or environmental factors. However, in microbiome studies, feature tables provide relative rather than absolute abundance of each feature in each sample, as the microbial loads of the samples and the ratios of sequencing depth to microbial load are both unknown and subject to considerable variation. Moreover, microbiome abundance data are count-valued, often over-dispersed and contain a substantial proportion of zeros. To carry out differential abundance analysis while addressing these challenges, we introduce mbDecoda, a model-based approach for debiased analysis of sparse compositions of microbiomes. mbDecoda employs a zero-inflated negative binomial model, linking mean abundance to the variable of interest through a log link function, and it accommodates the adjustment for confounding factors. To efficiently obtain maximum likelihood estimates of model parameters, an Expectation Maximization algorithm is developed. A minimum coverage interval approach is then proposed to rectify compositional bias, enabling accurate and reliable absolute abundance analysis. Through extensive simulation studies and analysis of real-world microbiome datasets, we demonstrate that mbDecoda compares favorably with state-of-the-art methods in terms of effectiveness, robustness and reproducibility.
Colloidal titration: from the perspective of stability constants between oppositely charged polyelectrolytes
Authors: Hattori Toshiaki 
Published: May 2024

Abstract
Colloidal titration is a unique method to measure the concentration of charged groups based on the association between cationic and anionic colloids. Titrimetry must involve a unidirectional reaction with a large formation constant. However, the underlying polyelectrolyte complex (PEC) for colloidal titration lacks sufficient data regarding the stability constants (KI). To date, the stoichiometry of colloidal titration has not been discussed in relation to KI. Thus, in this paper, we reviewed PEC studies by focusing on KI and discuss colloidal titration comprehensively. The topics include the history of its establishment, the method to calculate KI, and the special characteristics of PEC compared with ion association reactions, the practical use of colloid titration, and the condition by which the stability constant can be increased. In terms of analytical reagents, polyelectrolytes are similar to (but positioned as a subspecies of) ion association reagents. Ionic strength strongly affects KIs values. Excluding coaggregation effects, the maximum values of log10 KI obtained from reliable data were found to decrease linearly as ionic strength increases logarithmically. The critical line connected with the maximum KI value at each ionic strength can be used as an empirical reference value and facilitate the analytical design of colloidal titration.