bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Sahara and the South
Authors: Baum Robert M 
Published: July 2024

Abstract
This chapter focuses on Sub Saharan Africa before the founding of Islam. It analyzes the growing importance of blacksmith shrines, both as guild shrines and their relationship to rain rituals. As Bantu-speaking communities moved south and east, they developed symbiotic relationships with older communities, “owners of the land,” including Batwa and Khoisan who embodied client status and ritual prestige. As trans-Saharan trade increased in importance, urbanization increased in West Africa’s Sahel region, culminating in the founding of Ghana (Wagadu) toward the end of this period. Changing concepts of the supreme being and the increasing importance of territorial and ancestral cults are central to this chapter.
Investigating alignment-free machine learning methods for HIV-1 subtype classification
Authors: Wade Kaitlyn E , Chen Lianghong , Deng Chutong , Zhou Gen , Hu Pingzhao 
Published: July 2024

Abstract

Motivation
Many viruses are organized into taxonomies of subtypes based on their genetic similarities. For human immunodeficiency virus 1 (HIV-1), subtype classification plays a crucial role in infection management. Sequence alignment-based methods for subtype classification are impractical for large datasets because they are costly and time-consuming. Alignment-free methods involve creating numerical representations for genetic sequences and applying statistical or machine learning methods. Despite their high overall accuracy, existing models perform poorly on less common subtypes. Furthermore, there is limited work investigating the impact of sequence vectorization methods, in particular natural language-inspired embedding methods, on HIV-1 subtype classification.

Results
We present a comprehensive analysis of sequence vectorization methods across machine learning methods. We report a k-mer-based XGBoost model with a balanced accuracy of 0.84, indicating that it has good overall performance for both common and uncommon HIV-1 subtypes. We also report a Word2Vec-based support vector machine that achieves promising results on precision and balanced accuracy. Our study sheds light on the effect of sequence vectorization methods on HIV-1 subtype classification and suggests that natural language-inspired encoding methods show promise. Our results could help to develop improved HIV-1 subtype classification methods, leading to improved individual patient outcomes, and the development of subtype-specific treatments.

Availability and implementation
Source code is available at https://www.github.com/kwade4/HIV_Subtypes
DeepCRISTL: deep transfer learning to predict CRISPR/Cas9 on-target editing efficiency in specific cellular contexts
Authors: Elkayam Shai , Tziony Ido , Orenstein Yaron 
Published: July 2024

Abstract

Motivation
CRISPR/Cas9 technology has been revolutionizing the field of gene editing. Guide RNAs (gRNAs) enable Cas9 proteins to target specific genomic loci for editing. However, editing efficiency varies between gRNAs and so computational methods were developed to predict editing efficiency for any gRNA of interest. High-throughput datasets of Cas9 editing efficiencies were produced to train machine-learning models to predict editing efficiency. However, these high-throughput datasets have a low correlation with functional and endogenous datasets, which are too small to train accurate machine-learning models on.

Results
We developed DeepCRISTL, a deep-learning model to predict the editing efficiency in a specific cellular context. DeepCRISTL takes advantage of high-throughput datasets to learn general patterns of gRNA editing efficiency and then fine-tunes the model on functional or endogenous data to fit a specific cellular context. We tested two state-of-the-art models trained on high-throughput datasets for editing efficiency prediction, our newly improved DeepHF and CRISPRon, combined with various transfer-learning approaches. The combination of CRISPRon and fine-tuning all model weights was the overall best performer. DeepCRISTL outperformed state-of-the-art methods in predicting editing efficiency in a specific cellular context on functional and endogenous datasets. Using saliency maps, we identified and compared the important features learned by DeepCRISTL across cellular contexts. We believe DeepCRISTL will improve prediction performance in many other CRISPR/Cas9 editing contexts by leveraging transfer learning to utilize both high-throughput datasets and smaller and more biologically relevant datasets.

Availability and implementation
DeepCRISTL is available via https://github.com/OrensteinLab/DeepCRISTL.
Acceptance and results of cryoablation for the treatment of early breast cancer in non-surgical patients
Authors: Graña-López Lucía L , Abelairas-López Laura L , Fernández-Sobrado Ignacio I , Verea-Varela Sabela S , Villares-Armas Ángeles A 
Published: July 2024

Abstract

Objectives
Evaluate acceptance of percutaneous cryoablation (PCA) treatment by patients with early breast cancer (BC) who choose not to have surgery and present our experience in the use of PCA for the local control of BC in this group of patients.

Methods
All biopsy-proven early BC diagnosed in our institution as non-surgical patients between January 2020 and December 2023 were retrospectively reviewed. We recorded if PCA was offered and if it was accepted by the patient. PCA was performed under ultrasound (US) guidance, using a liquid nitrogen-based system. Mammography and US or contrast-enhanced mammography follow-up was scheduled every 6 months for 5 years. Patient’s tolerance to the procedure, adverse effects, and results regarding local control of the disease were assessed.

Results
A total of 66 early BC were diagnosed in 63 patients who decided not to have surgery. Median age was 88 years (range 60-99 years). Forty-three (95.6%) of the 45 patients offered PCA accepted. Thirty-nine malignant tumours (median size 24 mm) underwent PCA. All cases were previously reviewed in a multidisciplinary tumour board. Complete tumour necrosis was achieved in 81.3% of the cases followed for ≥ 6 months. After a median follow-up of 16 months, the complete ablation rate in Luminal BC ≤ 25 mm was 100%. No major complications were seen.

Conclusions
Non-surgical patients with early BC accepted PCA when the treatment was offered. PCA is safe, effective, and well-tolerated outpatient procedure. The study outcomes suggest that PCA could be an alternative to surgery for the management of BC in this group of patients.

Advances in knowledge
Patients with early BC who choose not to have surgery accept PCA. This percutaneous approach probably allows local control of early BC, mainly in ≤25 mm Luminal tumours.
Identification of neurotransmitter imbalances in the cingulate cortex of NMOSD patients using magnetic resonance spectroscopy
Authors: Zhao Min , Li Xiao , Li Fuyan , Hu Xin , Wang Jing , Liu Yuxi , Zhang Chuanchen , Bai Jie , Edden Richard A E , Gao Fei , Su Meixia , Ren Fuxin 
Published: July 2024

Abstract
Cognitive impairment affects 29–67% of patients with neuromyelitis optica spectrum disorder. Previous studies have reported glutamate homeostasis disruptions in astrocytes, leading to imbalances in gamma-aminobutyric acid levels. However, the association between these neurotransmitter changes and cognitive deficits remains inadequately elucidated. Point RESolved Spectroscopy and Hadamard Encoding and Reconstruction of MEGA-Edited Spectroscopy techniques were utilized to evaluate gamma-aminobutyric acid, glutamate, glutathione levels, and excitation/inhibition balance in the anterior cingulate cortex, posterior cingulate cortex, and occipital cortex of 39 neuromyelitis optica spectrum disorder patients and 41 healthy controls. Cognitive function was assessed using neurocognitive scales. Results showed decreased gamma-aminobutyric acid levels alongside increased glutamate, glutathione, and excitation/inhibition ratio in the anterior cingulate cortex and posterior cingulate cortex of neuromyelitis optica spectrum disorder patients. Specifically, within the posterior cingulate cortex of neuromyelitis optica spectrum disorder patients, decreased gamma-aminobutyric acid levels and increased excitation/inhibition ratio correlated significantly with anxiety scores, whereas glutathione levels predicted diminished executive function. The results suggest that neuromyelitis optica spectrum disorder patients exhibit dysregulation in the GABAergic and glutamatergic systems in their brains, where the excitation/inhibition imbalance potentially acts as a neuronal metabolic factor contributing to emotional disorders. Additionally, glutathione levels in the posterior cingulate cortex region may serve as predictors of cognitive decline, highlighting the potential benefits of reducing oxidative stress to safeguard cognitive function in neuromyelitis optica spectrum disorder patients.
Changes in functional connectivity and structural covariance between the fronto-parietal network and medial orbitofrontal cortex are associated with disinhibition in restrained eaters
Authors: Wang Shaorui , Han Jinfeng , Xiao Mingyue , Shi Pan , Chen Hong 
Published: July 2024

Abstract
Disinhibition, characterized by a loss of dietary control, is a significant risk factor for diet failure and the onset of eating disorders in restrained eaters. This study employs resting-state functional connectivity and structural covariance network analyses to explore the neural associations underlying this behavior. By analyzing functional MRI data from 63 female college students, we found that increased disinhibition correlates with enhanced functional connectivity between the medial orbitofrontal cortex and key components of the inhibition system, particularly within the fronto-parietal network. Moreover, we observed a relationship between the structural covariance of the medial orbitofrontal cortex and the inferior parietal lobule and the severity of disinhibition. Importantly, the functional connectivity between the medial orbitofrontal cortex and the inferior parietal lobule predicts the severity of binge eating symptoms in these individuals. These findings indicate that imbalances in the interaction between the brain’s reward and inhibition systems can lead to dietary failures and eating disorders, emphasizing the need for targeted interventions.
Saline suppression testing-induced hypocalcemia and implications for clinical interpretations
Authors: Parksook Wasita W , Brown Jenifer M , Milks Julia , Tsai Laura C , Chan Justin , Moore Anna , Niebuhr Yvonne , Honzel Brooke , Newman Andrew J , Vaidya Anand 
Published: July 2024

Abstract

Background
Extracellular calcium critically regulates physiologic aldosterone production. Moreover, abnormal calcium flux and signaling are involved in the pathogenesis of the majority of primary aldosteronism cases.

Methods
We investigated the influence of the saline suppression test (SST) on calcium homeostasis in prospectively recruited participants (n = 86).

Results
During SST, 100% of participants had decreases in serum calcium, with 48% developing frank hypocalcemia. Serum calcium declined from 2.30 ± 0.08 mmol/L to 2.13 ± 0.08 mmol/L (P &lt; .001) with parallel increases in parathyroid hormone from 6.06 ± 2.39 pmol/L to 8.13 ± 2.42 pmol/L (P &lt; .001). In contrast, serum potassium and bicarbonate did not change, whereas eGFR increased and serum glucose decreased (P &lt; .001). Lower body surface area (translating to greater effective circulating volume expansion during SST) was associated with greater reductions in (β = .33, P = .001), and absolutely lower, serum calcium levels (β = .25, P = .001). When evaluating clinically-relevant diagnostic thresholds, participants with post-SST aldosterone levels &lt;138 pmol/L had lower post-SST calcium and 25-hydroxyvitamin D levels (P &lt; .05), and higher post-SST parathyroid hormone levels (P &lt; .05) compared with those with post-SST aldosterone levels &gt;277 pmol/L.

Conclusion
SST uniformly decreases serum calcium, which is likely to be due to the combination of variable dilution, increased renal clearance, and vitamin D status. These acute reductions in bioavailable calcium are associated with lower post-SST aldosterone. Given the critical role of extracellular calcium in regulating aldosterone production, these findings warrant renewed inquiry into the validity of SST interpretations for excluding primary aldosteronism.
Legal-Conflict Constellations. A Political Approach to the ‘Labour Rights-Human Rights’ Debate
Authors: Lobato Julieta 
Published: July 2024

Abstract
The shift towards human rights is a cornerstone of contemporary labour law scholarship. However, the debate primarily follows a naturalistic approach, heavily reliant on an orthodox account of human rights as universal moral claims for all individuals. This article challenges this approach, arguing that it frames the debate in an antagonistic and compartmentalized manner, where the two legal domains are seen as distinct and homogeneous. By adopting a political approach, the article proposes framing the interactions between these legal realms through the notion of legal-conflict constellations, wherein labour-capital conflicts manifest as specific social problems that may be addressed, wholly or partially, through rights discourse. These legal-conflict constellations are built around three interconnected processes: politicization, recentring class and the formation of productive resistance alliances. The article makes the following contributions. First, it situates the debate within the broader context of the reshaping of labour law under neoliberalism. Second, it sheds light on the prevailing naturalistic approach and its shortcomings. Third, it proposes a political approach to the debate, advancing a framework to explore the intricate links between these legal fields.
Energy Security, Climate Change, and Routines as Maladaptive Politics
Authors: Heinrichs Pauline Sophie 
Published: July 2024

Abstract
Energy transitions suffer from a central political challenge. Future costs of the energy transition are directly linked to investments in mitigation and adaptation measures today, yet governments continue to underinvest in decarbonization policies and are far from meeting legally binding targets. While interdisciplinary explanations trace multiple motives behind inaction, I argue that climate inaction must be embedded in political mechanisms that sustain it. Routines are one such mechanism. Building on literatures of temporality, normative change in international politics, critical energy security studies, and routines, I argue that moments of crises have so far not been transformative in the context of climate and energy security because of how actors construct the politics of crises temporally. The temporal construction of crisis engenders a selective reading of the timescales that are perceived to matter, which in turn gives way to reproducing dominant routines that have historically been thought to secure against crises. Such routines, however, no longer secure outcomes against crises; they reproduce the very cause of climate change, namely the dependence on fossil fuels. I illustrate the explanatory mechanism between crises and routines through a case study of Germany’s energy security response to the Russian invasion of Ukraine.
Cell motility empowers bacterial contact weapons
Authors: Booth Sean C , Meacock Oliver J , Foster Kevin R 
Published: July 2024

Abstract
Many bacteria kill competitors using short-range weapons, such as the Type VI secretion system and contact dependent inhibition (CDI). Although these weapons can deliver powerful toxins, they rely on direct contact between attacker and target cells. We hypothesized that movement enables attackers to contact more targets and thus greatly empower their weapons. To explore this, we developed individual-based and continuum models of contact-dependent combat which show that motility greatly improves toxin delivery through two underlying processes. First, genotypic mixing increases the inter-strain contact probability of attacker and sensitive cells. Second, target switching ensures attackers constantly attack new cells, instead of repeatedly hitting the same cell. We test our predictions with the pathogen Pseudomonas aeruginosa, using genetically engineered strains to study the interaction between CDI and twitching motility. As predicted, we find that motility works synergistically with CDI, in some cases increasing weapon efficacy up to 10,000-fold compared with non-motile scenarios. Moreover, we demonstrate that both mixing processes occur using timelapse single-cell microscopy and quantify their relative importance by combining experimental data with our model. Our work shows how bacteria can combine cell movement with contact-based weapons to launch powerful attacks on their competitors.
Unpacking Legitimacy Perceptions of Investment Dispute Settlement: Effects of Outcome and Procedure
Authors: Dotzauer Marius 
Published: July 2024

AbstractHow do citizens perceive different avenues for resolving investor–state disputes in case of an unfavorable decision? In this article, I argue that the interplay between procedure- and outcome-related considerations influences citizens’ legitimacy beliefs toward investor-state dispute settlement (ISDS) systems. First, an unfavorable ISDS ruling should decrease public legitimacy beliefs in the country that got sued. Second, the type of dispute settlement mechanism should influence legitimacy beliefs, leading to different assessments of the legal proceedings. I fielded a survey experiment in France, Germany, and the United States to test these theoretical expectations. The findings confirm that an unfavorable ISDS ruling has a strong negative effect on public perceptions of the legal proceeding, but further show that appropriate design choices can boost public legitimacy beliefs. These results have important implications for the debate about ISDS reform and the scholarship on legitimacy in global governance. The impact of unfavorable decisions on public legitimacy beliefs has been widely overlooked.
Designing (restorative) remedies for abuses of dominance by online platforms
Authors: Mandrescu Daniel 
Published: July 2024

Abstract
The debate surrounding the application of European Union competition law to online platforms so far has predominantly focused on identifying anti-competitive practices. The design of corresponding remedies has been far less explored, although it is of equal importance to practice. In the absence of effective remedies, the mere identification of anti-competitive practices can do little to protect competition. Given the difficulties associated with identifying competition law infringements by online platforms, there is no reason to assume that the design of remedies intended to tackle the effects of such infringements will be straightforward. Therefore, this article aims to show the intricacies of designing effective remedies for Article 102 TFEU infringements by online platforms based on the case study of tying and bundling practices. In this process, the article clarifies the importance of incorporating restorative measures in competition law remedies that may require opting for structural interventions, which are difficult to impose under the scope of Regulation 1/2003. The article offers three potential options to overcome such difficulties within the ambit of this regulation, namely through the strategic use of interim measures, the introduction of flexible remedies, and the incorporation of the regulatory restraints of the Digital Markets Act.
Bhakti, Equality, and Power: Temple Potters and Sacred Food (Mahaprasada) in Orissa
Authors: Chakrabarti Upal 
Published: July 2024

Abstract
This article analyses the relationship between Bhakti, power, and equality in South Asia, by studying the meanings of Mahaprasada, or the sacred food of the Jagannatha temple in Orissa, as represented in nineteenth-century European and Indian texts. The article further juxtaposes these textual meanings with the social practices of the low-caste potters of the temple who make the vessels where the sacred food is prepared. Despite missionary condemnations of the idolatry of the Jagannatha cult and administrative attacks on the cult’s rituals and practices, Mahaprasada was paradoxically celebrated by these same texts as embodying the potential of destroying caste hierarchies. The article critically examines such colonial framings of Mahaprasada, by bringing them into conversation with the community cosmologies, economic practices, and political strategies of the temple potters. The article argues that the potters’ entanglements with the temple revealed complex contingencies in the ways in which Mahaprasada determined relations of caste and market. As a low-caste, yet ritually significant, group instrumental in the making of Mahaprasada, the temple potters participated in a market of the sacred food, where ritual and economic values merged, and were shaped by other power relations of the temple. In matters of caste, the potters both upheld and challenged caste distinctions by both their ritual roles and heterogeneous sectarian inheritances. Put together, I examine how paradoxical subtleties of colonial constructions of Bhakti were defied by the economically complex and religiously multiple worlds of marginal communities.
A High-Quality Genome Assembly for Aureobasidium pullulans CG163, the Active Ingredient in Aureo Gold, a Bio-Bactericide Registered for Control of Bacterial Canker of Kiwifruit Caused by Pseudomonas syringae pv. actinidiae Biovar 3
Authors: de Jong Huub , Arshed Saadiah , Yu Janet , Cornish Deirdre , Vanneste Joel L. , Reglinski Tony , Elmer Philip A. G. , Templeton Matthew D. 
Published: July 2024

Aureobasidium pullulans (de Bary) Arnaud (isolate CG163) is a recently commercialized biocontrol agent for the control of Pseudomonas syringae pv. actinidiae (Psa) on kiwifruit ( Actinidia spp.). A long-read nanopore assembly, polished with Illumina short reads, resulted in a telomere-to-telomere assembly of CG163. The completed genome has 12 chromosomes ranging from 0.9 to 4.6 Mb and a circular mitogenome of 37.5 kb. A second A. pullulans isolate, which did not inhibit Psa on Actinidia chinensis ‘Hayward’ potted plants (isolate HRY276), was also assembled from long reads for this study. Comparative genomic studies were performed between CG163 and HRY276 (both isolated in New Zealand) and the complete sequence of Aureobasidium pullulans isolate NBB 7.2.1 from Switzerland. There was extensive synteny between the respective chromosomes of all three isolates. The exception was chromosome 12 from CG163, which was not present in the other isolates and may be a dispensable mini chromosome. Mining of the genome of CG163 identified a variety of potential antimicrobial hydrolytic enzymes and secondary metabolite biosynthesis genes that may contribute to the ability of this isolate to suppress Psa on kiwifruit tissues. A complete highly accurate chromosome-scale assembly of CG163’s reference genome will be a valuable resource for future studies investigating the basic underlying molecular genetic mechanisms involved in the biocontrol of Psa, or other plant pathogens, by different isolates of A. pullulans. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .