bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impacts of sand and dust storms on food production
Authors: Middleton Nick 
Published: July 2024

Abstract
Sand and dust storms (SDS) are common in the world’s drylands, regions that are also critically important for global food production. Agriculture is the most prevalent land use resulting in anthropogenic SDS sources, resulting in impacts on cropland and rangeland, but food production is also affected by impacts from natural SDS sources. This review assesses our knowledge of SDS impacts on all the major types of food production in terrestrial and oceanic environments, impacts that occur in all three phases of the wind erosion system: during particle entrainment, during transport, and on deposition. These effects are short term and long term, direct and indirect. Wind erosion is a major cause of land degradation and there is good evidence to indicate that the deleterious effects of SDS can reduce food production via substantially diminished yields of crops, pastures and livestock. However, it is also clear that soil dust plays an important role in major biogeochemical cycles—especially phosphorus, nitrogen and iron—with implications for the valuable environmental services provided by numerous ecosystems, both terrestrial and marine. Ultimately, these nutrients have particular significance for soil formation, ecosystem productivity and food webs on land and at sea, and hence the provision of food for human societies. Efforts to mitigate the negative impacts of SDS on the sustainability of agriculture should be balanced with an appreciation of the significance of soil dust to the Earth system.
HyperGen: compact and efficient genome sketching using hyperdimensional vectors
Authors: Xu Weihong , Hsu Po-Kai , Moshiri Niema , Yu Shimeng , Rosing Tajana 
Published: July 2024

Abstract

Motivation
Genomic distance estimation is a critical workload since exact computation for whole-genome similarity metrics such as Average Nucleotide Identity (ANI) incurs prohibitive runtime overhead. Genome sketching is a fast and memory-efficient solution to estimate ANI similarity by distilling representative k-mers from the original sequences. In this work, we present HyperGen that improves accuracy, runtime performance, and memory efficiency for large-scale ANI estimation. Unlike existing genome sketching algorithms that convert large genome files into discrete k-mer hashes, HyperGen leverages the emerging hyperdimensional computing (HDC) to encode genomes into quasi-orthogonal vectors (Hypervector, HV) in high-dimensional space. HV is compact and can preserve more information, allowing for accurate ANI estimation while reducing required sketch sizes. In particular, the HV sketch representation in HyperGen allows efficient ANI estimation using vector multiplication, which naturally benefits from highly optimized general matrix multiply (GEMM) routines. As a result, HyperGen enables the efficient sketching and ANI estimation for massive genome collections.

Results
We evaluate HyperGen’s sketching and database search performance using several genome datasets at various scales. HyperGen is able to achieve comparable or superior ANI estimation error and linearity compared to other sketch-based counterparts. The measurement results show that HyperGen is one of the fastest tools for both genome sketching and database search. Meanwhile, HyperGen produces memory-efficient sketch files while ensuring high ANI estimation accuracy.

Availability and implementation
A Rust implementation of HyperGen is freely available under the MIT license as an open-source software project at https://github.com/wh-xu/Hyper-Gen. The scripts to reproduce the experimental results can be accessed at https://github.com/wh-xu/experiment-hyper-gen.
Controlled noise: evidence of epigenetic regulation of single-cell expression variability
Authors: Zhong Yan , Cui Siwei , Yang Yongjian , Cai James J 
Published: July 2024

Abstract

Motivation
Understanding single-cell expression variability (scEV) or gene expression noise among cells of the same type and state is crucial for delineating population-level cellular function. While epigenetic mechanisms are widely implicated in gene expression regulation, a definitive link between chromatin accessibility and scEV remains elusive. Recent advances in single-cell techniques enable the study of single-cell multiomics data that include the simultaneous measurement of scATAC-seq and scRNA-seq within individual cells, presenting an unprecedented opportunity to address this gap.

Results
This article introduces an innovative testing pipeline to investigate the association between chromatin accessibility and scEV. With single-cell multiomics data of scATAC-seq and scRNA-seq, the pipeline hinges on comparing the prediction performance of scATAC-seq data on gene expression levels between highly variable genes (HVGs) and non-highly variable genes (non-HVGs). Applying this pipeline to paired scATAC-seq and scRNA-seq data from human hematopoietic stem and progenitor cells, we observed a significantly superior prediction performance of scATAC-seq data for HVGs compared to non-HVGs. Notably, there was a substantial overlap between well-predicted genes and HVGs. The gene pathways enriched from well-predicted genes are highly pertinent to cell type-specific functions. Our findings support the notion that scEV largely stems from cell-to-cell variability in chromatin accessibility, providing compelling evidence for the epigenetic regulation of scEV and offering promising avenues for investigating gene regulation mechanisms at the single-cell level.

Availability and implementation
The source code and data used in this article can be found at https://github.com/SiweiCui/EpigeneticControlOfSingle-CellExpressionVariability.
Brain inflammation co-localizes highly with tau in mild cognitive impairment due to early-onset Alzheimer’s disease
Authors: Appleton Johanna , Finn Quentin , Zanotti-Fregonara Paolo , Yu Meixiang , Faridar Alireza , Nakawah Mohammad O , Zarate Carlos , Carrillo Maria C , Dickerson Bradford C , Rabinovici Gil D , Apostolova Liana G , Masdeu Joseph C , Pascual Belen 
Published: July 2024

Abstract
Brain inflammation, with an increased density of microglia and macrophages, is an important component of Alzheimer’s disease and a potential therapeutic target. However, it is incompletely characterized, particularly in patients whose disease begins before the age of 65 years and, thus, have few co-pathologies. Inflammation has been usefully imaged with translocator protein (TSPO) PET, but most inflammation PET tracers cannot image subjects with a low-binder TSPO rs6971 genotype. In an important development, participants with any TSPO genotype can be imaged with a novel tracer, 11C-ER176, that has a high binding potential and a more favourable metabolite profile than other TSPO tracers currently available. We applied 11C-ER176 to detect brain inflammation in mild cognitive impairment (MCI) caused by early-onset Alzheimer’s disease. Furthermore, we sought to correlate the brain localization of inflammation, volume loss, elevated amyloid-β (Aβ)and tau.
We studied brain inflammation in 25 patients with early-onset amnestic MCI (average age 59 ± 4.5 years, 10 female) and 23 healthy controls (average age 65 ± 6.0 years, 12 female), both groups with a similar proportion of all three TSPO-binding affinities. 11C-ER176 total distribution volume (VT), obtained with an arterial input function, was compared across patients and controls using voxel-wise and region-wise analyses. In addition to inflammation PET, most MCI patients had Aβ (n = 23) and tau PET (n = 21). For Aβ and tau tracers, standard uptake value ratios were calculated using cerebellar grey matter as region of reference. Regional correlations among the three tracers were determined. Data were corrected for partial volume effect. Cognitive performance was studied with standard neuropsychological tools.
In MCI caused by early-onset Alzheimer’s disease, there was inflammation in the default network, reaching statistical significance in precuneus and lateral temporal and parietal association cortex bilaterally, and in the right amygdala. Topographically, inflammation co-localized most strongly with tau (r = 0.63 ± 0.24). This correlation was higher than the co-localization of Aβ with tau (r = 0.55 ± 0.25) and of inflammation with Aβ (0.43 ± 0.22). Inflammation co-localized least with atrophy (−0.29 ± 0.26). These regional correlations could be detected in participants with any of the three rs6971 TSPO polymorphisms. Inflammation in Alzheimer’s disease-related regions correlated with impaired cognitive scores.
Our data highlight the importance of inflammation, a potential therapeutic target, in the Alzheimer’s disease process. Furthermore, they support the notion that, as shown in experimental tissue and animal models, the propagation of tau in humans is associated with brain inflammation.
Get out of my head: social evaluative brain states carry over into post-feedback rest and influence remembering how others view us
Authors: Brietzke Sasha C , Barbarossa Klara , Meyer Meghan L 
Published: July 2024

Abstract
Learning how others perceive us helps us tune our behavior to form adaptive relationships. But which perceptions stick with us? And when in the learning process are they codified in memory? We leveraged a popular television series—The Office—to answer these questions. Prior to their functional magnetic resonance imaging (fMRI) session, viewers of The Office reported which characters they identified with, as well as which characters they perceived another person (i.e. counterpart) was similar to. During their fMRI scan, participants found out which characters other people thought they and the counterpart were like, and also completed rest scans. Participants remembered more feedback inconsistent with their self-views (vs. views of the counterpart). Although neural activity while encoding self-inconsistent feedback did not meaningfully predict memory, returning to the inconsistent self feedback during subsequent rest did. During rest, participants reinstated neural patterns engaged while receiving self-inconsistent feedback in the dorsomedial prefrontal cortex (DMPFC). DMPFC reinstatement also quadratically predicted self-inconsistent memory, with too few or too many reinstatements compromising memory performance. Processing social feedback during rest may impact how we remember and integrate the feedback, especially when it contradicts our self-views.
Carbon dots as reductants to fabricate three-dimensional Au mesoflowers as SERS substrates
Authors: Wang Chenxu , Lin Zhilong , Wang Wenqin 
Published: July 2024

Abstract
Reductive carbon dots (CDs) were obtained by a hydrothermal method using citric acid and diethylenetriamine as carbon sources. Three-dimensional Au mesoflowers (3D Au MFs) could be fabricated by directly mixing HAuCl4 and CD solution without using any extra reductant and morphology-directing reagent. The as-obtained 3D Au MFs exhibited high surface-enhanced Raman spectroscopy (SERS) activity in detection of methylene blue.
Exploring the Resurgence of a Neglected Disease: Lessons From the 2023–2024 Mpox Outbreak in Rio de Janeiro, Brazil
Authors: Silva Mayara Secco Torres , Coutinho Carolina , Torres Thiago Silva , Magalhães Monica Avelar , Yanavich Carolyn , Echeverría-Guevara Amanda , Bastos Matheus Oliveira , Martins Pedro Silva , Mesquita Maira Braga , Reges Paula Pereira de Souza , Meneguetti Maria Roberta , Santana Ana Paula Lovetro , Terra Marcela , Nunes Estevão Portela , Lessa Flavia Cristina Serrão , Moreira Ronaldo Ismério , Peixoto Eduardo Mesquita , Paulo Karolyne Wolch de Almeida , Sant’Ana Andryelle Cristina , Elias da Silva Edson , Cardoso Sandra Wagner , Veloso Valdilea Gonçalves , Grinsztejn Beatriz ,   for the Instituto Nacional de Infectologia Evandro Chagas (INI)–Fiocruz Mpox Study Group, Soares João Paulo Bortot , Hottz Giselle , Santos Cicero , Rendelli Bruna Fabris , Tuccori Luciana Patricia , Neto Jadir Rodrigues Fagundes , Freitas Lucilene , Wakimoto Mayumi , Azevedo Katia , Escada Rodrigo Otavio da Silva , Ribeiro Maria Pia Diniz , Tavares Isabel Cristina Ferreira , Santos Desirée Vieira , Camacho Luiz Ricardo Siqueira , Rosadas Leonardo , Fares Luisa , Amparo Pedro , Andrade Hugo Boechat , Coutinho José Ricardo Hildebrant , Barbosa Hugo Perazzo Pedroso , Nazer Sandro , Calvet Guilherme Amaral , Menezes Rodrigo Caldas , Pereira Sandro Antônio 
Published: July 2024

Abstract
Following the 2022 global mpox outbreak, diagnoses decreased worldwide, even in settings with limited vaccine access. In 2023–2024, a new outbreak emerged in Rio de Janeiro, Brazil, highlighting the importance of continuous surveillance, preventive measures such as vaccination in vulnerable populations, and treatment options, emphasizing equitable global health technology distribution.
ChatGPT vs Medical Professional: Analyzing Responses to Laboratory Medicine Questions on Social Media
Authors: Girton Mark R , Greene Dina N , Messerlian Geralyn , Keren David F , Yu Min 
Published: July 2024

Abstract

Background
The integration of ChatGPT, a large language model (LLM) developed by OpenAI, into healthcare has sparked significant interest due to its potential to enhance patient care and medical education. With the increasing trend of patients accessing laboratory results online, there is a pressing need to evaluate the effectiveness of ChatGPT in providing accurate laboratory medicine information. Our study evaluates ChatGPT's effectiveness in addressing patient questions in this area, comparing its performance with that of medical professionals on social media.

Methods
This study sourced patient questions and medical professional responses from Reddit and Quora, comparing them with responses generated by ChatGPT versions 3.5 and 4.0. Experienced laboratory medicine professionals evaluated the responses for quality and preference. Evaluation results were further analyzed using R software.

Results
The study analyzed 49 questions, with evaluators reviewing responses from both medical professionals and ChatGPT. ChatGPT's responses were preferred by 75.9% of evaluators and generally received higher ratings for quality. They were noted for their comprehensive and accurate information, whereas responses from medical professionals were valued for their conciseness. The interrater agreement was fair, indicating some subjectivity but a consistent preference for ChatGPT's detailed responses.

Conclusions
ChatGPT demonstrates potential as an effective tool for addressing queries in laboratory medicine, often surpassing medical professionals in response quality. These results support the need for further research to confirm ChatGPT's utility and explore its integration into healthcare settings.
Emerging opportunities to target inflammation: myocardial infarction and type 2 diabetes
Authors: Kufazvinei Tafadzwa T J , Chai Jason , Boden Katherine A , Channon Keith M , Choudhury Robin P 
Published: July 2024

Abstract
After myocardial infarction (MI), patients with type 2 diabetes have an increased rate of adverse outcomes, compared to patients without. Diabetes confers a 1.5–2-fold increase in early mortality and, importantly, this discrepancy has been consistent over recent decades, despite advances in treatment and overall survival. Certain assumptions have emerged to explain this increased risk, such as differences in infarct size or coronary artery disease severity. Here, we re-evaluate that evidence and show how contemporary analyses using state-of-the-art characterization tools suggest that the received wisdom tells an incomplete story. Simultaneously, epidemiological and mechanistic biological data suggest additional factors relating to processes of diabetes-related inflammation might play a prominent role. Inflammatory processes after MI mediate injury and repair and are thus a potential therapeutic target. Recent studies have shown how diabetes affects immune cell numbers and drives changes in the bone marrow, leading to pro-inflammatory gene expression and functional suppression of healing and repair. Here, we review and re-evaluate the evidence around adverse prognosis in patients with diabetes after MI, with emphasis on how targeting processes of inflammation presents unexplored, yet valuable opportunities to improve cardiovascular outcomes in this vulnerable patient group.
Friction versus frictionless mechanics during maxillary en-masse retraction in adult patients with Class I bimaxillary dentoalveolar protrusion: a randomized clinical trial
Authors: Magdi Sally , Abdelsayed Fatma A , Aboulfotouh Mai H , Fahim Fady H 
Published: July 2024

Abstract

Background
Extraction space closure is a challenging phase during orthodontic treatment that affects not only the total treatment duration but also the whole treatment outcome.

Objective
To compare the efficiency of friction and frictionless mechanics during en-masse retraction of maxillary anterior teeth in adult patients with bimaxillary dentoalveolar protrusion.

Trial design
Two-arm parallel group, single-center randomized clinical trial.

Materials and methods
Thirty-two adult patients with bimaxillary protrusion were recruited and randomly allocated to two different retraction mechanics. A friction group, using NiTi coil springs and a frictionless group using closing T-loops for en-masse retraction. Randomization in a 1:1 ratio was generated by Microsoft Excel. The randomization numbers were secured in opaque sealed envelopes for allocation concealment. Retraction started in all patients following first premolars extraction using miniscrews as a source of indirect anchorage. Activation was done on a monthly basis until complete retraction of anterior segment. The rate of retraction, amount of anchorage loss, the dental, and soft tissue changes were analyzed on digital models and lateral cephalograms taken before retraction and after space closure.

Blinding
The outcome assessor was blinded through data concealment during assessment.

Results
Two patients were lost to follow up, so 30 patients completed the trial. The rate of anterior segment retraction was 0.88 ± 0.66 mm/month in the frictionless group compared to 0.72 ± 0.36 mm/month in the friction group which was statistically significant. Anchorage loss of 1.18 ± 0.72 mm in the friction group compared to 1.29 ± 0.55 mm in the frictionless group with no significant difference. Comparable dental and soft tissue changes following en-masse retraction were reported in both groups, with no statistically significant difference.

Harm
one patient complained of soft tissue swelling following miniscrew insertion, but the swelling disappeared after one week of using mouth wash.

Limitation
The study focused only on the maxillary arch.

Conclusion
Both mechanics have successfully achieved the required treatment objectives in patients with bimaxillary dentoalveolar protrusion. Frictionless group showed a faster rate of retraction than the friction group, which was statistically but not clinically significant.

Trial registration
Clinicaltrials.gov with the identifier NCT03261024.
Substrate complexity buffers negative interactions in a synthetic community of leaf litter degraders
Authors: Abdoli Parmis , Vulin Clément , Lepiz Miriam , Chase Alexander B , Weihe Claudia , Rodríguez-Verdugo Alejandra 
Published: July 2024

Abstract
Leaf litter microbes collectively degrade plant polysaccharides, influencing land–atmosphere carbon exchange. An open question is how substrate complexity—defined as the structure of the saccharide and the amount of external processing by extracellular enzymes—influences species interactions. We tested the hypothesis that monosaccharides (i.e. xylose) promote negative interactions through resource competition, and polysaccharides (i.e. xylan) promote neutral or positive interactions through resource partitioning or synergism among extracellular enzymes. We assembled a three-species community of leaf litter-degrading bacteria isolated from a grassland site in Southern California. In the polysaccharide xylan, pairs of species stably coexisted and grew equally in coculture and in monoculture. Conversely, in the monosaccharide xylose, competitive exclusion and negative interactions prevailed. These pairwise dynamics remained consistent in a three-species community: all three species coexisted in xylan, while only two species coexisted in xylose, with one species capable of using peptone. A mathematical model showed that in xylose these dynamics could be explained by resource competition. Instead, the model could not predict the coexistence patterns in xylan, suggesting other interactions exist during biopolymer degradation. Overall, our study shows that substrate complexity influences species interactions and patterns of coexistence in a synthetic microbial community of leaf litter degraders.
Who participates in value-based care models? Physician characteristics and implications for value-based care
Authors: Winberg Debra R , Baker Matthew C , Hu Xiaochu , Horvath Keith A 
Published: July 2024

Abstract
Value-based care (VBC) payment models are becoming increasingly prevalent as alternatives to the traditional fee-for-service paradigm. This research quantifies the relationship between physician characteristics and participation in VBC payment models using the Association of American Medical Colleges’ 2022 National Sample Survey of Physicians. We specified logistic regressions using physician-level variables to assess associations with current and new participation in Accountable Care Organizations, Primary Care First model, capitation, and bundled payments. Our results indicate that most respondents engaged in at least 1 VBC. Participation varied based on several characteristics, and physician specialty was highly predictive of overall participation. Compared with primary care physicians (PCPs), hospital-based physicians (odds ratio [OR] = 0.6, P &lt; .001), medical specialists (OR = 0.5, P &lt; .001), psychiatrists (OR = 0.4, P &lt; .001), and surgeons (OR = 0.5, P &lt; .001) were less likely to participate in VBC models. Medical specialists and surgeons were less likely to participate in commercial capitation than PCPs, while medical specialists and obstetricians/gynecologists were more likely to participate in certain bundles than PCPs. We suggest several policies to close the cross-specialty participation gap by including specialists and appealing to providers and patients.
The role of news and rumour during the Peasants’ Revolt, 1381
Authors: Schoon Paul 
Published: July 2024

Abstract
This article uses an interdisciplinary approach to examine the role of news and rumour during the Peasants’ Revolt, an aspect of the rising that has not been the subject of a detailed study. It considers the circulation of news in written and oral form and its importance in driving the rebellion. Sources suggest that the news of the revolt traversed the country quickly, moving at up to sixty-five miles a day, and its transmission is shown through an isopleth map to radiate outwards across the country from its point of origin in south-east England. Rumour is considered by means of a thought experiment using three examples drawn from rebel activities in London in June 1381. It thrived in the absence of news, particularly in a highly stressed environment. It is possible that rumour was used as a tactic by rebel commanders, who were able to generate and manipulate rumours to their own advantage.