bluuebunny/crossref_metadata_2025_split huggingface dataset:
Making forest landscape restoration work for livelihoods and well-being of local communities
Authors: Djoudi Houria , Djenontin Ida N S , Pierce Colfer Carol J 
Published: September 2024

Abstract
This chapter advocates for increased consideration of local level needs in the planning, execution, and monitoring of Forest Landscape Restoration (FLR). The predominant emphasis on environmental and ecological outcomes limits FLR’s potential to equitably and inclusively support a wide range of ecosystem services for local people and their landscapes, underscoring the persistent challenges and trade-offs in balancing local needs and global objectives. This chapter anticipates the significant consequences of disregarding local well-being in FLR initiatives by exploring three key questions: (1) What is the potential of FLR to enhance local livelihoods and well-being? (2) What are the existing challenges and trade-offs in connecting restoration efforts with local livelihoods and well-being? (3) What are some approaches to enhance the socio-ecological benefits and co-benefits of FLR initiatives? Addressing these questions leads to recommendations for giving greater attention to local needs and aspirations within FLR processes and outcomes.
An economic view on the costs and benefits of forest restoration
Authors: Pacheco Pablo , Beatty Craig , Patel Jwalin 
Published: September 2024

Abstract
This chapter focuses on assessing the costs and benefits of forest restoration. It provides key findings and knowledge gaps drawing on a review of available studies and data, assessing the costs and benefits of forest restoration across six different restoration options. It looks at both financial analysis of the costs incurred and benefits accrued by private actors or enterprises and wider economic analysis of the returns of forest restoration to society at large. It shows that while financial costs and benefits vary widely across and within forest restoration options, almost all forest restoration options are financially attractive. Natural regeneration options are the least costly options, followed by tree plantations. Agroforestry systems are most costly, requiring higher upfront investments, yet may yield higher economic and ecological benefits depending on the agroforestry system. There are several trade-offs associated with forest restoration, mainly regarding the financial, socioeconomic, and environmental benefits of restoration.
Sustainable and fair forest and land restoration
Authors: de Jong Wil , Katila Pia , Winkel Georg , Pacheco Pablo , Galloway Glenn , Pierce Colfer Carol J 
Published: September 2024

Abstract
The chapter synthesizes the findings of the 11 chapters of this book and situates them in current debates on forest restoration and related literature. It explores forest restoration histories and trends; summarizes projections of what can be expected of future forest restoration; discusses the goals, costs, and actual and potential social, economic, and environmental benefits of forest restoration; and estimates how likely it is that benefits will be achieved in practice. The chapter deliberates on international, national, and local restoration governance, including how international restoration governance takes shape, how it relates to other international processes, and how it links to national and subnational forest restoration governance. The chapter, furthermore, discusses fairness and justice of local level governance. It ends by summarizing the major challenges of forest restoration and suggests how they might be overcome, reflecting on the best ways to translate the global restoration project into feasible pathways of doing restoration in a just and sustainable manner.
Coda
Authors: Kishi Madoka 
Published: September 2024

Abstract
This book closes with the Coda, “Hindsight 20/20, or Asiatic Im-personality,” which revisits Edward Ross’s initial inspiration for the discourse of race suicide: Asian immigration. By overlaying the rhetoric of Asian exclusion at the turn of the century onto scenes of anti-Asian violence during the COVID-19 pandemic, the Coda inquires into the association between Asians and death in the American imaginary. In particular, the Coda traces how fears of fungible Asian bodies infecting the US social body—epitomized by “coolies”—gave rise to the discourse of race suicide. In this rhetoric, the figure of submissive, efficient, and impersonal Asian immigrants emerged as the antipode of the liberal subject, and yet tailor-made for the coming age of standardization and automation. The Coda terms this model of subjectivity “Asiatic im-personality” and reads it in relation to a number of Madame Butterfly texts.
Cervical cytology abnormalities and associated genotype patterns of High-Risk HPV Infection in Women of Tripura, North-East India: A Hospital-Based Study
Authors: Bhattacharya Amrapali , Chakraborty Kanak , Saha Partha , Saha Susmita , Roychaudhuri Parichita , Baidya Jahar Lal , Ghosh Arabinda , Chakraborty Debaprasad , Sengupta Sharmila , Sil Samir Kumar 
Published: September 2024

Abstract
The current study explored HPV prevalence and age variation in cervical samples of different cytological categories and HPV types from women seeking gynecological care in Tripura, northeast India. Pap smears, cervical tissues, and HPV/DNA specimens were collected from gynecological outpatient departments (OPD) or in-house patients and were screened for HPV16, HPV18, and other HPV types by PCR. Finally, logistic regression was performed to find the association between epidemiologic factors and HPV infection in women of different cytological grades. About 90% of HPV-screened women were found to be HPV positive. HPV16 was most common in HPV-positive women (53.27%), followed by HPV16/18 co-infection (26.17%). HPV16 or HPV18 was most frequent (86.45%) compared to others (13.55%). Among the confirmed cytological tests 68.83% showed normal cytology and 37.17% showed atypical abrasions. Among the abnormal cytology participants, 94.37% were HPV-positive, and 42.25% had cervical cancer. The prevalence of HPV increased with cytological abnormalities (p &lt; 0.01). Abnormal cytological lesions increased with age (p trend = 0.017). Among all epidemiologic factors studied, parity was strongly associated with overall HPV infection, regardless of cytological status. Observed very high frequency of HPV infection in the current study, warrants further investigations.
Designing interpretable deep learning applications for functional genomics: a quantitative analysis
Authors: van Hilten Arno , Katz Sonja , Saccenti Edoardo , Niessen Wiro J , Roshchupkin Gennady V 
Published: September 2024

Abstract
Deep learning applications have had a profound impact on many scientific fields, including functional genomics. Deep learning models can learn complex interactions between and within omics data; however, interpreting and explaining these models can be challenging. Interpretability is essential not only to help progress our understanding of the biological mechanisms underlying traits and diseases but also for establishing trust in these model’s efficacy for healthcare applications. Recognizing this importance, recent years have seen the development of numerous diverse interpretability strategies, making it increasingly difficult to navigate the field. In this review, we present a quantitative analysis of the challenges arising when designing interpretable deep learning solutions in functional genomics. We explore design choices related to the characteristics of genomics data, the neural network architectures applied, and strategies for interpretation. By quantifying the current state of the field with a predefined set of criteria, we find the most frequent solutions, highlight exceptional examples, and identify unexplored opportunities for developing interpretable deep learning models in genomics.
Investigation of protein family relationships with deep learning
Authors: Ponamareva Irina , Andreeva Antonina , Bileschi Maxwell L , Colwell Lucy , Bateman Alex 
Published: September 2024

Abstract

Motivation
In this article, we propose a method for finding similarities between Pfam families based on the pre-trained neural network ProtENN2. We use the model ProtENN2 per-residue embeddings to produce new high-dimensional per-family embeddings and develop an approach for calculating inter-family similarity scores based on these embeddings, and evaluate its predictions using structure comparison.

Results
We apply our method to Pfam annotation by refining clan membership for Pfam families, suggesting both new members of existing clans and potential new clans for future Pfam releases. We investigate some of the failure modes of our approach, which suggests directions for future improvements. Our method is relatively simple with few parameters and could be applied to other protein family classification models. Overall, our work suggests potential benefits of employing deep learning for improving our understanding of protein family relationships and functions of previously uncharacterized families.

Availability and implementation
github.com/iponamareva/ProtCNNSim, 10.5281/zenodo.10091909.
Hydrographic basins dictate the genetic structure of the paradoxical frog Pseudis bolbodactyla (Anura: Hylidae) in the rivers of Central Brazil
Authors: Santana Diego J , Myers Edward A , Fonseca Emanuel M , Gehara Marcelo , Oliveira Eliana F , Bonatto Sandro L , Burbrink Frank T , Garda Adrian A 
Published: September 2024

Abstract
Rivers are prominent landscape features, acting as key promoters of diversification among freshwater organisms. Albeit generally considered potential barriers to species movement, they may also facilitate gene flow and structure populations of semiaquatic species (Riverine Thruway Hypothesis, RTH). We evaluated the role of rivers on the processes responsible for current genetic variation in the semiaquatic frog Pseudis bolbodactyla, testing whether each hydrographic basin harbours distinct genetic lineages. We sequenced three markers on 166 samples from 13 localities along the Paraná (PR), Araguaia–Tocantins (AT), and São Francisco (SF) River basins in Brazil. We recovered three populations geographically matching each hydrographic basin. Our results indicate migration among basins, with the best model selected using approximate Bayesian computation, including migration between AT and SF and ancient gene flow from PR to the AT–SF ancestor. Our findings are likely related to the orogenic events in Central Brazil dating to the Late Miocene (5 Mya), when hydrographic basins and the geomorphological features of the Brazilian Shield were formed. This suggests that P. bolbodactyla probably represents a species complex, with each lineage occurring in a distinct hydrographic basin, matching the predictions of the RTH.
Economic impact of limb-salvage strategies in chronic limb-threatening ischaemia: modelling and budget impact study based on national registry data
Authors: Saratzis Athanasios , Zayed Hany , Buylova Anna , Rawlinson William , Veliu Giota , Siebert Markus 
Published: September 2024

Abstract

Background
Missed opportunities to reduce numbers of primary major lower-limb amputation and increase limb-salvage procedures when treating chronic limb-threatening ischaemia have previously been identified in the literature. However, the potential economic savings for healthcare providers when salvaging a chronic limb-threatening ischaemia-affected limb have not been well documented.

Methods
A model using National Health Service healthcare usage and cost data for 1.6 million individuals and averaged numbers of primary surgical procedures for chronic limb-threatening ischaemia from England and Wales in 2019–2021 was created to perform a budget impact analysis. Two scenarios were tested: the averaged national rates of major lower-limb amputation (above the ankle joint), angioplasty, open bypass surgery or arterial endarterectomy in the National Vascular Registry (current scenario); and revascularization rates adjusted based on the lowest amputation rate reported by the National Vascular Registry at the time of the study (hypothetical scenario). The primary outcome was the net impact on costs to the National Health Service over 12 months after the index procedure.

Results
In the current scenario, the proportions of different index procedures were 10% for lower-limb major amputation, 55% for angioplasty, 25% for open bypass surgery and 10% for arterial endarterectomy. In the hypothetical scenario, the procedure rates were 3% for major lower-limb amputation, 59% for angioplasty, 27% for open bypass surgery and 11% for arterial endarterectomy. For 16 025 index chronic limb-threatening ischaemia procedures, the total care cost in the current scenario was €243 924 927. In the hypothetical scenario, costs would be reduced for index procedures (−€10 013 814), community care (−€633 943) and major cardiovascular events (−€383 407), and increased for primary care (€59 827), outpatient appointments (€120 050) and subsequent chronic limb-threatening ischaemia-related surgery (€1 179 107). The net saving to the National Health Service would be €9 645 259.

Conclusion
A shift away from primary major lower-limb amputation towards revascularization could lead to substantial savings for the National Health Service without major cost increases later in the care pathway, indicating that care decisions taken in hospitals have wider benefits.
Subjective cognitive and olfactory impairments predict different prospective dementia outcomes
Authors: Cedres Nira , Olofsson Jonas K 
Published: September 2024

Abstract
Self-reported measures emerge as potential indicators for early detection of dementia and mortality. We investigated the predictive value of different self-reported measures, including subjective cognitive decline (SCD), subjective olfactory impairment (SOI), subjective taste impairment (STI), and self-reported poor health (SPH), in order to determine the risk of progressing to Alzheimer’s disease (AD) dementia, Parkinson’s disease (PD) dementia, or any-other-cause dementia. A total of 6,028 cognitively unimpaired individuals from the 8th wave of the English Longitudinal Study of Ageing (ELSA) were included as the baseline sample and 5,297 individuals from the 9th wave were included as 2-year follow-up sample. Self-rated measures were assessed using questions from the ELSA structured interview. Three logistic regression models were fitted to predict different the dementia outcomes. SCD based on memory complaints (OR = 11.145; P &lt; 0.001), and older age (OR = 1.108, P &lt; 0.001) significantly predicted the progression to AD dementia at follow-up. SOI (OR = 7.440; P &lt; 0.001) and older age (OR = 1.065, P = 0.035) significantly predicted the progression to PD dementia at follow-up. Furthermore, SCD based on memory complaints (OR = 4.448; P &lt; 0.001) jointly with complaints in other (non-memory) mental abilities (OR = 6.662; P &lt; 0.001), and older age (OR = 1.147, P &lt; 0.001) significantly predicted the progression to dementia of any other cause. Different types of complaints are specifically associated with different dementia outcomes. Our study demonstrates that self-reported measures are a useful and accessible tool when screening for individuals at risk of dementia in the general population.
Coalition Building and Sino–US Competition in the Digital Era
Authors: Liu Xinghua 
Published: September 2024

Abstract
Digital coalitions are the primary tool of the USA to compete with China in the digital age and differ markedly from traditional alliances and military coalitions. It is necessary to go beyond the vision of pure great power rivalry and probe Sino–US digital competition through the lens of coalitions and the relationship between the dominant state and coalition members. A digital coalition is a state consortium with an organisational nature, confrontational targets, common goals, and the capability to take collective action, formed to deal with the digital strategy, norms, standards, industry, and products. The two main determinants of the building and maintenance of the digital coalition are the security dependency of allies on the USA and the technological stranglehold in the digital relationship. Security dependency determines the likelihood of coalition construction; the higher the dependency, the more willing allies will be to respond to the dominant state’s digital security narrative and mobilisation. There is potential for the construction of simple digital coalitions centred on conceptions and governance initiatives. However, building and maintaining a complex digital coalition depends on the presence of a technological stranglehold as well as security dependencies. A technological stranglehold involves controlling the supply of key technologies critical to the survival of the industry, and compels allies to sacrifice market interests and participate in a digital coalition to ensure the integrity of their industries. The Chip 4 Alliance and Trade and Technology Council are typical examples of US-led digital coalitions.
Patient-Reported Racial and Ethnic Disparities in Patients With Ulcerative Colitis: Results From the National Health and Wellness Survey
Authors: Burbage Sabree C , Krupsky Kathryn L , Cambron-Mellott M Janelle , Way Nate , Patel Aarti A , Liu Julia J 
Published: September 2024

Abstract

Background
Ulcerative colitis (UC) is an inflammatory condition characterized by chronic, disabling gastrointestinal symptoms that can have detrimental effects on psychological, social, and professional quality of life. Few studies have examined patient-reported outcomes (PROs) and economic outcomes among individuals with varying UC severity and across different racial/ethnic groups.

Methods
This cross-sectional study assessed sociodemographic data, PROs, and economic outcomes for participants from the National Health and Wellness Survey (2018, 2019, and 2020) with UC. Multivariable analyses were used to assess the association of self-reported UC severity and race/ethnicity with health-related quality of life (HRQoL), work productivity and activity impairment (WPAI), healthcare resource utilization (HCRU), and medical costs.

Results
This study included 1500 participants with UC (1150 non-Hispanic White, 99 non-Hispanic Black, and 251 Hispanic). Moderate/severe disease was associated with significantly worse HRQoL and WPAI, greater HCRU, and higher direct medical costs than mild UC. Compared with non-Hispanic White participants, non-Hispanic Black participants reported better HRQoL, whereas Hispanic participants reported more HCRU and higher medical costs. Race/ethnicity significantly interacted with UC severity level in predicting labor force participation.

Conclusions
Participants with moderate/severe disease had worse outcomes than those with mild UC. Additionally, racial/ethnic differences were found in HRQoL, employment, WPAI, HCRU, and direct medical costs. Notably, Hispanic participants showed distinct patterns, particularly in how disease severity influenced employment outcomes. Further research is needed to better understand the differential burden among patients across racial/ethnic groups.
An uncommon cause of a common disease: a case report of a rare cause of hypertension
Authors: Rao Sarita , Rao Roshan , Kumar Achukatla , Benjamin Nitika , Pandey Akshat 
Published: September 2024

Abstract

Background
Severe hypertension in young patients presents a significant diagnostic dilemma, and treatment can often be codified. Therefore, it is crucial to diagnose these cases for probable secondary hypertension. Common causes of secondary hypertension include large vessel vasculitis, renal artery stenosis, coarctation of the aorta, and endocrine disorders.

Case summary
A 23-year-old Asian male, who was previously in good health, presented with symptoms of chest pain, shortness of breath on exertion grade II, and generalized weakness. On examination, his blood pressure was markedly elevated at 200/110 mmHg. Diagnostic investigations revealed significant vascular involvement, including bilateral renal artery stenosis accompanied by aneurysm formation, celiac trunk disease, and osteal stenosis of the superior mesenteric artery. The patient underwent successful interventional procedure, including renal angioplasty, stenting, and aneurysm coiling. This was followed by tailoring of medical management along with anti-inflammatory and disease-modifying drugs.

Discussion
The diagnosis of Takayasu arteritis (TAK) in this case is supported by the patients’ age, presentation, and imaging according to the new TAK classification criteria by the American College of Rheumatology/European League Against Rheumatism (EULAR) and emphasizes the potential benefits of a pharmaco-invasive approach for optimal outcomes.
Interacting phenotypic plasticities: do male and female responses to the sociosexual environment interact to determine fitness?
Authors: Simmons Leigh W , Lovegrove Maxine 
Published: September 2024

Abstract
Socially induced plasticity in reproductive effort is a widely documented phenomenon. However, few empirical studies have examined how male and female plastic responses to the social environment might interact in determining fitness outcomes. In field crickets, Teleogryllus oceanicus, males respond to rival songs by increasing expenditure on seminal fluid proteins that enhance competitive fertilization success at the cost of reduced embryo survival. It remains unknown whether plastic responses in females could moderate the effects of male competitiveness on offspring performance. Here, we used a fully factorial design to explore the interacting effects on fitness of male and female plasticity to the sociosexual environment. We found that female crickets exposed to male songs increased the number of eggs produced during early life reproduction, which came at the cost of reduced offspring size. There was evidence, albeit weak, that interacting effects of male and female sociosexual environments contributed to variation in the hatching success of eggs laid by females. Lifetime offspring production was unaffected by the sociosexual environments to which upstream male and female plastic responses were made. Our data offer a rare test of the theoretical expectation that male and female plasticities should interact in their effects on female fitness.
Genome sequence of the sugarcane aphid, Melanaphis sacchari (Hemiptera: Aphididae)
Authors: Zhao Jinshuai , Xie Liqiang , Zhao Xinrui , Li Luhua , Cui Jianghui , Chen Jinfeng 
Published: September 2024

Abstract
The sugarcane aphid, Melanaphis sacchari, is an agricultural pest that causes damage to plants in the Poaceae (the grasses) family, such as sorghum and sugarcane. In this study, we used nanopore long reads and a high-throughput chromosome conformation capture chromatin interaction maps to generate a chromosome-level assembly with a total length of 356.1 Mb, of which 85.5% (304.6 Mb) is contained within the 3 autosomes and the X chromosome. Repetitive sequences accounted for 16.29% of the chromosomes, and a total of 12,530 protein-coding genes were annotated, achieving 95.8% Benchmarking Universal Single-Copy Ortholog gene completeness. This offered a substantial improvement compared with previous low-quality genomic resources. A phylogenomic analysis by comparing M. sacchari with 24 published aphid genomes representing 3 aphid tribes revealed that M. sacchari belonged to the tribe Aphidini and maintained a conserved chromosome structure with other Aphidini species. The high-quality genomic resources reported in this study are useful for understanding the evolution of aphid genomes and studying pest management of M. sacchari.