bluuebunny/crossref_metadata_2025_split huggingface dataset:
How well does the implementation of corporate zero-deforestation commitments in Indonesia align with aims to halt deforestation and include smallholders?
Authors: Chandra Adelina , Garrett Rachael D , Carlson Kimberly M , Heilmayr Robert , Stigler Matthieu , Benedict Jason J , Grabs Janina 
Published: March 2024

Abstract
In response to growing scrutiny surrounding commodity-driven deforestation, companies have introduced zero-deforestation commitments (ZDCs) with ambitious environmental and social targets. However, such initiatives may not effectively reduce deforestation if they are not aligned with the spatial extent of remaining forests at risk. They may also fail to avert socio-economic risks if ZDCs do not consider smallholder farmers’ needs. We assess the spatial and functional fit of ZDCs by mapping commodity-driven deforestation and socio-economic risks, and comparing them to the spatial coverage and implementation of ZDCs in the Indonesian palm oil sector. Our study finds that companies’ ZDCs often underperform in four areas: traceability, compliance support for high-risk palm oil mills, transparency, and smallholder inclusion. In 2020, only one-third of companies sourcing from their own mills, and just 6% of those sourcing from external suppliers, achieved full traceability to plantations. Comparing the reach of ZDCs adopted by downstream buyers with those adopted by mill owners located further upstream, we find that high-quality ZDCs from buyers covered 62% of forests at risk, while mill owners’ ZDCs only covered 23% of forests at risk within the mill supply base. In Kalimantan and Papua, the current and future deforestation frontiers, the forests most at risk of conversion were predominantly covered by weak ZDCs lacking in policy comprehensiveness and implementation. Additionally, we find that only 46% of independent smallholder oil palm plots are in mill supply sheds whose owners offer programs and support for independent smallholders, indicating that smallholder inclusion is a significant challenge for ZDC companies. These results highlight the lack of spatial and functional alignment between supply chain policies and their local context as a significant gap in ZDC implementation and a challenge that the EU Deforestation Regulation will face.
Evaluating the impact of peat soils and snow schemes on simulated active layer thickness at pan-Arctic permafrost sites
Authors: Tao Jing , Riley William J , Zhu Qing 
Published: March 2024

Abstract
Permafrost stability is significantly influenced by the thermal buffering effects of snow and active-layer peat soils. In the warm season, peat soils act as a barrier to downward heat transfer mainly due to their low thermal conductivity. In the cold season, the snowpack serves as a thermal insulator, retarding the release of heat from the soil to the atmosphere. Currently, many global land models overestimate permafrost soil temperature and active layer thickness (ALT), partially due to inaccurate representations of soil organic matter (SOM) density profiles and snow thermal insulation. In this study, we evaluated the impacts of SOM and snow schemes on ALT simulations at pan-Arctic permafrost sites using the Energy Exascale Earth System Model (E3SM) land model (ELM). We conducted simulations at the Circumpolar Active Layer Monitoring (CALM) sites across the pan-Arctic domain. We improved ELM-simulated site-level ALT using a knowledge-based hierarchical optimization procedure and examined the effects of precipitation-phase partitioning methods (PPMs), snow compaction schemes, and snow thermal conductivity schemes on simulated snow depth, soil temperature, ALT, and CO2 fluxes. Results showed that the optimized ELM significantly improved agreement with observed ALT (e.g. RMSE decreased from 0.83 m to 0.15 m). Our sensitivity analysis revealed that snow-related schemes significantly impact simulated snow thermal insulation levels, soil temperature, and ALT. For example, one of the commonly used snow thermal conductivity schemes (quadratic Sturm or SturmQua) generally produced warmer soil temperatures and larger ALT compared to the other two tested schemes. The SturmQua scheme also amplified the model’s sensitivity to PPMs and predicted deeper ALTs than the other two snow schemes under both current and future climates. The study highlights the importance of accurately representing snow-related processes and peat soils in land models to enhance permafrost dynamics simulations.
The initial diversification of Greek dialects
Authors: Ringe Don 
Published: March 2024

Abstract
This chapter addresses the diversification of Greek into the attested groups of dialects. It demonstrates that a strict cladistic diversification cannot be proved—not surprisingly, as the Greek dialects remained in contact for centuries. But it also establishes that an Aiolic group and a South Greek group, both probably defined by changes spreading through a dialect continuum, are historically significant dialect groups. It is argued that West Greek and Arkado-Cyprian, by contrast, are conservative relic areas within Greek and South Greek respectively. Phonological and morphological evidence for each of these proposed groups is discussed. In addition, other widely shared phonological and morphological innovations are treated, especially the development of labiovelars and syllabic liquids. Finally, the relatively late creation of a preposition meaning ‘into’ is discussed.
Syntax
Authors: Ringe Don 
Published: March 2024

Abstract
This chapter discusses syntactic change in the prehistory and history of Ancient Greek. The most important change is a gradual shift in underlying constituent order spanning the whole attestation of Ancient Greek, which is outlined in some detail. Prohibitions are discussed in some detail because their structure might reveal something about the inherited verb system. Also discussed are the use of the moods, clitics, prepositions, univerbation of compound verbs, and the expression of reflexives.
Function and induction of the root barrier to radial O2 loss. A commentary on ‘Exogenous abscisic acid induces the formation of a suberized barrier to radial oxygen loss in adventitious roots of barley (Hordeum vulgare)’
Authors: Pedersen Ole , de la Cruz Jiménez Juan 
Published: March 2024

This article comments on:
Katsuhiro Shiono and Haruka Matsuura, Exogenous abscisic acid induces the formation of a suberized barrier to radial oxygen loss in adventitious roots of barley (Hordeum vulgare), Annals of Botany, Volume 133, Issue 7, 6 June 2024, Pages 931–940 https://doi.org/10.1093/aob/mcae010
Review and meta-analysis of the genetic Minimal Cut Set approach for gene essentiality prediction in cancer metabolism
Authors: Olaverri-Mendizabal Danel , Valcárcel Luis V , Barrena Naroa , Rodríguez Carlos J , Planes Francisco J 
Published: March 2024

Abstract
Cancer metabolism is a marvellously complex topic, in part, due to the reprogramming of its pathways to self-sustain the malignant phenotype in the disease, to the detriment of its healthy counterpart. Understanding these adjustments can provide novel targeted therapies that could disrupt and impair proliferation of cancerous cells. For this very purpose, genome-scale metabolic models (GEMs) have been developed, with Human1 being the most recent reconstruction of the human metabolism. Based on GEMs, we introduced the genetic Minimal Cut Set (gMCS) approach, an uncontextualized methodology that exploits the concepts of synthetic lethality to predict metabolic vulnerabilities in cancer. gMCSs define a set of genes whose knockout would render the cell unviable by disrupting an essential metabolic task in GEMs, thus, making cellular proliferation impossible. Here, we summarize the gMCS approach and review the current state of the methodology by performing a systematic meta-analysis based on two datasets of gene essentiality in cancer. First, we assess several thresholds and distinct methodologies for discerning highly and lowly expressed genes. Then, we address the premise that gMCSs of distinct length should have the same predictive power. Finally, we question the importance of a gene partaking in multiple gMCSs and analyze the importance of all the essential metabolic tasks defined in Human1. Our meta-analysis resulted in parameter evaluation to increase the predictive power for the gMCS approach, as well as a significant reduction of computation times by only selecting the crucial gMCS lengths, proposing the pertinency of particular parameters for the peak processing of gMCS.
MIKE: an ultrafast, assembly-, and alignment-free approach for phylogenetic tree construction
Authors: Wang Fang , Wang Yibin , Zeng Xiaofei , Zhang Shengcheng , Yu Jiaxin , Li Dongxi , Zhang Xingtan 
Published: March 2024

Abstract

Motivation
Constructing a phylogenetic tree requires calculating the evolutionary distance between samples or species via large-scale resequencing data, a process that is both time-consuming and computationally demanding. Striking the right balance between accuracy and efficiency is a significant challenge.

Results
To address this, we introduce a new algorithm, MIKE (MinHash-based k-mer algorithm). This algorithm is designed for the swift calculation of the Jaccard coefficient directly from raw sequencing reads and enables the construction of phylogenetic trees based on the resultant Jaccard coefficient. Simulation results highlight the superior speed of MIKE compared to existing state-of-the-art methods. We used MIKE to reconstruct a phylogenetic tree, incorporating 238 yeast, 303 Zea, 141 Ficus, 67 Oryza, and 43 Saccharum spontaneum samples. MIKE demonstrated accurate performance across varying evolutionary scales, reproductive modes, and ploidy levels, proving itself as a powerful tool for phylogenetic tree construction.

Availability and implementation
MIKE is publicly available on Github at https://github.com/Argonum-Clever2/mike.git.
Characterizing barriers and facilitators of metabolic bariatric surgery tourism: a systematic review
Authors: Zuberi Sharukh , Egiz Abdullah , Iqbal Hasan , Jambulingam Periyathambi , Whitelaw Douglas , Adil Tanveer , Jain Vigyan , Al-Taan Omar , Munasinghe Aruna , Askari Alan , Aly Mohamed K , Iqbal Fahad M 
Published: March 2024

Abstract

Background
Metabolic bariatric surgery tourism continues to rise and has become a growing concern for bariatric surgeons globally. With varying degrees of regulation, counselling and success, those that develop complications may have to deal with a multitude of challenges often distant from their country of operation. The aim of this study was to characterize the barriers and facilitators influencing individuals to undergo metabolic bariatric surgery tourism, in order to better understand the implications to the National Health Service and other healthcare systems.

Methods
A systematic literature search, restricted to the English language, was performed to identify relevant studies. All studies were included until December 2022, the last search date. Study quality was assessed with the validated mixed-methods appraisal tool. A Braun and Clarke thematic analysis was undertaken to identify themes and subthemes.

Results
A total of five studies met the inclusion criteria. Identified themes included: availability, accessibility, cost, eligibility, reputation, and stigma; the available evidence was of varying quality.

Conclusion
This work identifies a series of subthemes influencing the decision to undertake metabolic bariatric surgery tourism. The results highlight the limited literature available in understanding the complex motivational insights; the scale of the problem in the current healthcare system; cost and long-term outcomes. A National Emergency Bariatric Surgery audit would allow generation of more robust data to explore further the issues of clinical relationships and networks and to guide policy making.
Adherence to general national dietary guidelines and risk of psoriasis: results from a general population study of 105 332 individuals
Authors: Näslund-Koch Charlotte , Kjeldsen Emilie W , Vedel-Krogh Signe , Bojesen Stig E , Skov Lone 
Published: March 2024

Abstract

Background
It is unknown if an unhealthy diet can affect the risk of developing psoriasis.

Objectives
To test the hypothesis that individuals with an unhealthy diet have an increased risk of prevalent and incident psoriasis.

Methods
We included 105 332 adults from the Copenhagen General Population Study, who were invited to participate between 2003 and 2015. The response rate was 43%. An unhealthy vs. healthy diet was defined according to adherence to general national dietary guidelines. The participants were grouped into three groups: low, intermediate and high adherence to general national dietary guidelines; this was based on information from a food frequency questionnaire. Identification of psoriasis was made using International Classification of Diseases codes.

Results
Of the 105 332 individuals, 580 had a diagnosis of psoriasis at the time of enrolment and 640 received a diagnosis during the median follow-up of 9 years. Risk of prevalent psoriasis increased according to nonadherence to general national dietary guidelines in a stepwise manner with an age- and sex-adjusted odds ratio of 1.70 (95% confidence interval 1.26–2.30) in individuals with low vs. high adherence to dietary guidelines. Results were similar in a multivariable-adjusted model. Prospective analyses adjusted for age and sex showed a weak association between nonadherence to dietary guidelines and risk of incident psoriasis (P for trend 0.04). This association disappeared, when adjusting for multiple confounders (P for trend 0.50).

Conclusions
Although individuals with psoriasis have an unhealthier diet, diet alone does not appear to independently increase the risk of developing psoriasis.
Technical considerations and sizing of external annuloplasty in the Ross procedure
Authors: Myjavec Andrej , Gofus Jan , Zacek Pavel , Vobornik Martin , Shahin Youssef , Vojacek Jan 
Published: March 2024

Abstract
Pure aortic regurgitation and dilation of aortic annulus are the most significant risk factors for the failure of pulmonary autograft after the Ross procedure. Aortic annuloplasty has a positive effect on the durability of the autograft. Previously, we described a technique for external annuloplasty with dedicated CORONEO ring. In the present manuscript, we suggest the sizing of annuloplasty based on the diameter of pulmonary autograft annulus.
Imagining an anti-racist pronunciation pedagogy
Authors: Ramjattan Vijay A 
Published: March 2024

Abstract
This article is an initial imagining of what an anti-racist pronunciation pedagogy (APP) might look like in ELT contexts such as immigrant employment training and international students studying in North American higher-education institutions. Three possible foci of an APP are briefly explored. First, this pedagogy helps students refuse the idea of the phonological superiority of the white native speaker. Furthermore, it reinforces intelligibility as a joint goal of both speaker and listener, thereby acknowledging how race and racism inform listener perceptions of speakers. Finally, an APP is an activist pedagogy that seeks to address institutionalized racism with regard to speech accent.
Cereals can trap endophytic bacteria with potential beneficial traits when grown ex-situ in harsh soils
Authors: Amenta Maria Laura , Vaccaro Francesca , Varriale Stefano , Sangaré Jean Rodrigue , Defez Roberto , Mengoni Alessio , Bianco Carmen 
Published: March 2024

Abstract
Microbial communities associated with plants growing in harsh conditions, including salinity and water deficiency, have developed adaptive features which permit them to grow and survive under extreme environmental conditions. In the present study, an ex-situ plant trapping method has been applied to collect the culturable microbial diversity associated with the soil from harsh and remote areas. Oryza sativa cv. Baldo and Triticum durum Primadur plants were used as recruiters, while the soil surrounding the roots of Oryza glaberrima plants from remote regions of Mali (West Africa) was used as substrate for their growth. The endophytic communities recruited by the two plant species belonged to Proteobacteria and Firmicutes, and the dominant genera were Bacillus, Kosakonia, and Enterobacter. These endophytes were characterized by analyzing some of the most common plant growth promoting traits. Halotolerant, inorganic phosphate-solubilizing and N-fixing strains were found, and some of them simultaneously showing these three traits. We verified that ‘Baldo’ recruited mostly halotolerant and P-solubilizers endophytes, while the endophytes selected by ‘Primadur’ were mainly N-fixers. The applied ex-situ plant trapping method allowed to isolate endophytes with potential beneficial traits that could be applied for the improvement of rice and wheat growth under adverse environmental conditions.
Human genetics of face recognition: discovery of MCTP2 mutations in humans with face blindness (congenital prosopagnosia)
Authors: Sun Yun , Men Weiwei , Kennerknecht Ingo , Fang Wan , Zheng Hou-Feng , Zhang Wenxia , Rao Yi 
Published: March 2024

Abstract
Face recognition is important for both visual and social cognition. While prosopagnosia or face blindness has been known for seven decades and face-specific neurons for half a century, the molecular genetic mechanism is not clear. Here we report results after 17 years of research with classic genetics and modern genomics. From a large family with 18 congenital prosopagnosia (CP) members with obvious difficulties in face recognition in daily life, we uncovered a fully cosegregating private mutation in the MCTP2 gene which encodes a calcium binding transmembrane protein expressed in the brain. After screening through cohorts of 6589, we found more CPs and their families, allowing detection of more CP associated mutations in MCTP2. Face recognition differences were detected between 14 carriers with the frameshift mutation S80fs in MCTP2 and 19 noncarrying volunteers. Six families including one with 10 members showed the S80fs-CP correlation. Functional magnetic resonance imaging found association of impaired recognition of individual faces by MCTP2 mutant CPs with reduced repetition suppression to repeated facial identities in the right fusiform face area. Our results have revealed genetic predisposition of MCTP2 mutations in CP, 76 years after the initial report of prosopagnosia and 47 years after the report of the first CP. This is the first time a gene required for a higher form of visual social cognition was found in humans.
Simulation of the Mediterranean tsunami generated by the Mw 6.0 event offshore Bejaia (Algeria) on 18 March 2021
Authors: Heinrich P , Dupont A , Menager M , Trilla A , Gailler A , Delouis B , Hébert H 
Published: March 2024

SUMMARY
On 18 March 2021 an earthquake of magnitude Mw = 6.0 occurred offshore the Algerian coasts and generated a tsunami with offshore amplitudes smaller than a few millimetres crossing the western Mediterranean Sea. The objective of this study is threefold: first, to determine whether seismic sources calculated in the context of tsunami early warning are relevant; secondly, to determine whether tsunami simulations are able to reproduce tide-gauge observations and thirdly, to define the sensitivity of simulations to the grid resolutions and tsunami parameters. In the Mediterranean Sea, a very small number of available coastal tide gauges recorded the tsunami. Among them, a few French tide gauge stations recorded water waves with amplitudes smaller than a few centimetres and with periods ranging from 5 to 20 min associated to harbour or bay resonances. Numerical simulations of the tsunami are performed by the operational code Taitoko for seven different source fault models. Three of them allow for a rapid source detection and characterization in the framework of tsunami warning at CENALT (Centre National d'Alerte aux Tsunamis, France). The integrated code Taitoko uses a system of multiple nested grids. Standard Boussinesq equations are solved in the Mediterranean grid, whereas non-linear shallow water equations are solved in coastal and harbour grids with 25 and 5 m resolutions, respectively. Whatever the fault model, the observed time-series of water heights are reproduced satisfactorily both in phase and amplitude by the model at Nice and Monaco but poorly at Port Mahon (Minorca) and Toulon.
DAS for 2-D MASW imaging: a case study on the benefits of flexible subarray processing
Authors: Yust Michael B S , Cox Brady R , Vantassel Joseph P , Hubbard Peter G 
Published: March 2024

SUMMARY
Distributed acoustic sensing (DAS) is a relatively new technology for recording the propagation of seismic waves, with promising applications in both engineering and geophysics. DAS's ability to simultaneously collect high spatial resolution waveforms over long arrays suggests that it is well-suited for near-surface imaging applications such as 2-D multichannel analysis of surface waves (MASWs), which require, at a minimum, long, linear arrays of single-component receivers. The 2-D MASW method uses a large number of sensor subarrays deployed along a linear alignment to produce 1-D shear-wave velocity (VS) profiles beneath each subarray. The 1-D VS profiles are then combined to form a pseudo-2-D VS image beneath the entire linear alignment that can be used for the purpose of identifying and characterizing lateral variations in subsurface layering. Traditionally, 2-D MASW is conducted using arrays consisting of either 24 or 48 geophones. While additional receivers could easily be incorporated into the testing configuration, it is rare for researchers and practitioners to have access to greater numbers of seismographs and geophones. When a limited number of geophones are available for deployment, there is a need to pre-determine the geophone spacing and subarray length prior to field data acquisition. Studies examining how the choice of subarray geometry impacts the resulting pseudo-2-D VS cross-sections have been largely limited to synthetic data. In response, this study utilizes DAS data to examine the effects of using various subarray lengths by comparing pseudo-2-D VS cross-sections derived from active-source waveforms collected at a well-characterized field site. DAS is particularly useful for 2-D MASW applications because the subarray geometry does not need to be determined prior to field data acquisition. We organize the DAS waveforms into multiple sets of overlapping MASW subarrays of differing lengths, ranging from 11 to 47 m, along the same alignment, allowing for direct comparison of the derived pseudo-2-D VS results at the site. We show that the length of the individual MASW subarrays has a significant effect on the resulting VS cross-sections, including the resolved location of a strong impedance contrasts at our study site, and evaluate the results relative to ground truth from invasive testing. Our results suggest that the choice of subarray length is important and should be carefully chosen to meet project-specific goals. Furthermore, analysts may consider using multiple subarray geometries during the data processing stage, as is made possible by DAS, to properly evaluate the uncertainty of 2-D MASW results. This study demonstrates the potential of using DAS to collect data for 2-D MASW in a manner that is efficient and flexible, and can be easily scaled up for use with very long arrays.