bluuebunny/crossref_metadata_2025_split huggingface dataset:
House dust metagenome and pulmonary function in a US farming population
Authors: Lee Mikyeong , Kaul Abhishek , Ward James M. , Zhu Qiyun , Richards Marie , Wang Ziyue , González Antonio , Parks Christine G. , Beane Freeman Laura E. , Umbach David M. , Motsinger-Reif Alison A. , Knight Rob , London Stephanie J. 
Published: July 2024

Abstract
Background
Chronic exposure to microorganisms inside homes can impact respiratory health. Few studies have used advanced sequencing methods to examine adult respiratory outcomes, especially continuous measures. We aimed to identify metagenomic profiles in house dust related to the quantitative traits of pulmonary function and airway inflammation in adults. Microbial communities, 1264 species (389 genera), in vacuumed bedroom dust from 779 homes in a US cohort were characterized by whole metagenome shotgun sequencing. We examined two overall microbial diversity measures: richness (the number of individual microbial species) and Shannon index (reflecting both richness and relative abundance). To identify specific differentially abundant genera, we applied the Lasso estimator with high-dimensional inference methods, a novel framework for analyzing microbiome data in relation to continuous traits after accounting for all taxa examined together.

Results
Pulmonary function measures (forced expiratory volume in one second (FEV1), forced vital capacity (FVC), and FEV1/FVC ratio) were not associated with overall dust microbial diversity. However, many individual microbial genera were differentially abundant (p-value < 0.05 controlling for all other microbial taxa examined) in relation to FEV1, FVC, or FEV1/FVC. Similarly, fractional exhaled nitric oxide (FeNO), a marker of airway inflammation, was unrelated to overall microbial diversity but associated with differential abundance for many individual genera. Several genera, including Limosilactobacillus, were associated with a pulmonary function measure and FeNO, while others, including Moraxella to FEV1/FVC and Stenotrophomonas to FeNO, were associated with a single trait.

Conclusions
Using state-of-the-art metagenomic sequencing, we identified specific microorganisms in indoor dust related to pulmonary function and airway inflammation. Some were previously associated with respiratory conditions; others were novel, suggesting specific environmental microbial components contribute to various respiratory outcomes. The methods used are applicable to studying microbiome in relation to other continuous outcomes.
Gut virome-wide association analysis identifies cross-population viral signatures for inflammatory bowel disease
Authors: Tian Xiangge , Li Shenghui , Wang Chao , Zhang Yanyan , Feng Xiaoying , Yan Qiulong , Guo Ruochun , Wu Fan , Wu Chunxue , Wang Yan , Huo Xiaokui , Ma Xiaochi 
Published: July 2024

Abstract
Background
The gut virome has been implicated in inflammatory bowel disease (IBD), yet a full understanding of the gut virome in IBD patients, especially across diverse geographic populations, is lacking.

Results
In this study, we conducted a comprehensive gut virome-wide association study in a Chinese cohort of 71 IBD patients (15 with Crohn’s disease and 56 with ulcerative colitis) and 77 healthy controls via viral-like particle (VLP) and bulk virome sequencing of their feces. By utilizing an integrated gut virus catalog tailored to the IBD virome, we revealed fundamental alterations in the gut virome in IBD patients. These characterized 139 differentially abundant viral signatures, including elevated phages predicted to infect Escherichia, Klebsiella, Enterococcus_B, Streptococcus, and Veillonella species, as well as IBD-depleted phages targeting Prevotella, Ruminococcus_E, Bifidobacterium, and Blautia species. Remarkably, these viral signatures demonstrated high consistency across diverse populations such as those in Europe and the USA, emphasizing their significance and broad relevance in the disease context. Furthermore, fecal virome transplantation experiments verified that the colonization of these IBD-characterized viruses can modulate experimental colitis in mouse models.

Conclusions
Building upon these insights into the IBD gut virome, we identified potential biomarkers for prognosis and therapy in IBD patients, laying the foundation for further exploration of viromes in related conditions.
Carnivore space use behaviors reveal variation in responses to human land modification
Authors: Gorman Nicole T. , Eichholz Michael W. , Skinner Daniel J. , Schlichting Peter E. , Bastille-Rousseau Guillaume 
Published: July 2024

Abstract
Background
Spatial behavior, including home-ranging behaviors, habitat selection, and movement, can be extremely informative in estimating how animals respond to landscape heterogeneity. Responses in these spatial behaviors to features such as human land modification and resources can highlight a species’ spatial strategy to maximize fitness and minimize mortality. These strategies can vary on spatial, temporal, and individual scales, and the combination of behaviors on these scales can lead to very different strategies among species.

Methods
Harnessing the variation present at these scales, we characterized how species may respond to stimuli in their environments ranging from broad- to fine-scale spatial responses to human modification in their environment. Using 15 bobcat-years and 31 coyote-years of GPS data from individuals inhabiting a landscape encompassing a range of human land modification, we evaluated the complexity of both species’ responses to human modification on the landscape through their home range size, habitat selection, and functional response behaviors, accounting for annual, seasonal, and diel variation.

Results
Bobcats and coyotes used different strategies in response to human modification in their home ranges, with bobcats broadly expanding their home range with increases in human modification and displaying temporal consistency in functional response in habitat selection across both season and time of day. Meanwhile, coyotes did not expand their home ranges with increased human modification, but instead demonstrated fine-scale responses to human modification with habitat selection strategies that sometimes varied by time of day and season, paired with functional responses in selection behaviors.

Conclusions
These differences in response to habitat, resources, and human modification between the two species highlighted the variation in spatial behaviors animals can use to exist in anthropogenic environments. Categorizing animal spatial behavior based on these spatiotemporal responses and individual variation can help in predicting how a species will respond to future change based on their current spatial behavior.
Attending to STEM education in servingness at Hispanic-serving institutions: a systematic review of more than a decade of scholarship
Authors: Ro Hyun Kyoung , Aguilar-Smith Stephanie , Anderson Shirley Yang , Rodriguez Tricia , Ramon Elizabeth J. , Javier Damaris 
Published: July 2024

Abstract
Background, context, and purpose of the study
Enrolling over 60% of all Latinx undergraduate students, Hispanic-serving institutions (HSIs) are poised to play a critical role in diversifying and strengthening Science, Technology, Engineering, and Mathematics (STEM) education and the STEM workforce. However, how HSIs serve STEM students is not well understood. Accordingly, guided by Garcia et al. (Review of Educational Research 89:5–745, 2019) multidimensional servingness framework, we conducted a systematic review of the research on STEM education within the HSI context. By attending to STEM education in conversations around how HSIs may serve Latinx students and their campus communities, our ultimate aim is to improve STEM education particularly at HSIs and advance STEM servingness more broadly.

Results, main findings
Through our systematic review of STEM education research at HSIs, we identified (under)studied components of servingness and gaps within this literature base. Specifically, among the 128 qualifying articles, nearly two-thirds focused on student outcomes but overlooked institutions’ organizational context, raising questions about the effect(iveness) of the studied interventions. Additionally, we identified three thematic gaps in this literature: ghosting the HSI context (i.e., relying on HSIs as research sites without considering the unique HSI context); ghosting Latinx culture (i.e., decentering Latinx students and the Latinx community’s sociocultural aspects and assets), and ghosting people and places (i.e., under-examining certain student populations like Latino men in STEM and places like Hispanic-serving community colleges). Ultimately, our study extends the field’s understanding of servingness by attending to STEM education within the context of HSI institutions.

Conclusions, brief summary, and potential implications
By systematically reviewing studies on STEM education at HSIs, we identified (under)studied components of servingness and patterned gaps within this literature. In doing so, we highlight opportunities to advance STEM servingness at HSIs through future research, policy, and practice. Collectively, these avenues hold the promise of improving STEM education and diversifying the STEM workforce.
Ethnic integration in the “Lin-ge” migration epic: a grassroots perspective
Authors: Guo Wenzhi , Tan Biyou , Song Bruce Ming-Yeung 
Published: July 2024

AbstractThis study comprehensively analyzes China’s ethnic migration epic, “Lin-ge,” as a case study to explore the cultural and social phenomena it reveals about exchanges, communication and integration among ethnic groups. It reveals how this process has facilitated mutual understanding and integration among diverse ethnic communities from a grassroots level. Focusing on inter-ethnic religious syncretism, economic interactions, warfare exchanges, trade practices, and intermarriages depicted in “Lin-ge,” the research showcases the complexity and dynamism of ethnic integration. It emphasizes the pivotal role of regional community identity in bridging different ethnic groups and forming the foundational cultural logic behind the identity of the Chinese national community. Through textual analysis, this study finds that “Lin-ge” transcends the boundaries between official and folk, sacred and secular, and historical and contemporary narratives, presenting a more inclusive and diversified perspective of the Chinese national community. The research highlights that the syncretism of religious beliefs, cultural exchanges, and social practices are key mechanisms in shaping the identity of regional social communities and promoting harmonious coexistence among various ethnic groups. Moreover, by reviewing extensive literature and conducting case analyses, this study provides a thorough understanding of China’s ethnic policies, ethnic relations, and the formation and development of multi-ethnic communities. The findings are not only of significant academic relevance to the fields of ethnology and anthropology but also offer practical guidance for addressing ethnic issues and promoting ethnic unity and national integration in modern society.
Transcriptomic Profiling of Primary Prostate Cancers and Nonlocalized Disease on Prostate-Specific Membrane Antigen Positron Emission Tomography/Computed Tomography: A Multicenter Retrospective Study
Authors: Nikitas John , Subramanian Kritika , Gozal Nimrod Barashi , Ricaurte-Fajardo Andres , Li Eric , Proudfoot James A. , Davicioni Elai , Marciscano Ariel E. , Osborne Joseph R. , Barbieri Christopher E. , Armstrong Wesley R. , Smith Clayton P. , Valle Luca F. , Steinberg Michael L. , Boutros Paul C. , Nickols Nicholas G. , Rettig Matthew B. , Reiter Robert , Weiner Adam B. , Calais Jeremie , Czernin Johannes , Ross Ashley Evan , Kim Eric H. , Nagar Himanshu , Kishan Amar U. 
Published: July 2024

PURPOSE To characterize the relationship between Decipher genomic classifier scores and prostate-specific membrane antigen (PSMA) positron emission tomography/computed tomography (PET/CT)–based metastatic spread. MATERIALS AND METHODS We identified patients from four institutions who underwent PSMA PET/CT scans pretreatment for primary staging or postradical prostatectomy (RP) for suspected recurrence and had Decipher transcriptomic data available from biopsy or RP specimens. PSMA PET/CT-based patterns of spread were classified as localized (miT + N0M0) or nonlocalized (miN1M0 or miM1a-c). We calculated the association between Decipher scores and the risk of nonlocalized disease on PSMA PET/CT using multivariable logistic regression for pretreatment patients and multivariable Cox regression for post-RP patients. We also compared select transcriptomic signatures between patients with localized and nonlocalized diseases. RESULTS Five hundred eighty-six patients were included (pretreatment: n = 329; post-RP: n = 257). Higher Decipher scores were associated with nonlocalized disease on PSMA PET/CT both pretreatment (odds ratio, 1.18 [95% CI, 1.03 to 1.36] per 0.1 increase in Decipher score, P = .02) and post-RP (hazard ratio, 1.15 [95% CI, 1.05 to 1.27] per 0.1 increase in Decipher score, P = .003). In the pretreatment setting, nonlocalized disease was associated with higher rates of TP53 mutations and lower rates of PAM50 luminal A subtype compared with localized disease. In the post-RP setting, overexpression of signatures related to metabolism, DNA repair, and androgen receptor signaling were associated with higher rates of nonlocalized disease. CONCLUSION Higher Decipher scores were associated with nonlocalized disease identified on PSMA PET/CT both pretreatment and post-RP. There were several transcriptomic differences between localized and nonlocalized diseases in both settings.
Marooned
Authors: Otoya Natascha de Vasconcellos 
Published: July 2024

Abstract
Mr. João de Deus, an elderly Afro-Brazilian man, worked on the ground and contributed to the beginning of the modern Brazilian oil industry. His is a story of environmental hope and personal resilience with roots in the deep past and outcomes that reverberate to the present. João de Deus’s story reveals many layers of history beyond human activity, weaving together different temporalities and kinds of hope. This article layers different temporalities—geological, ecological, and human—to emphasize their interconnectedness. As a method, layering various chronological scales helps highlight how they collectively contribute to a complex and nuanced history of a particular individual, community, or place. It considers the simultaneous existence and impact of multiple historical layers, emphasizing the interplay of different historical timescales and historical actors. João de Deus, situated atop ancient geological layers potentially rich in oil, experienced life as a Black man in slavery-era Brazil. Amid the ecological presence of African oil palms and the emerging industrialization of the Maraú Peninsula, he found himself entangled in multiple concurrent histories of different chronological scales, all influencing his destiny.
Asbestos
Authors: Rose Arthur 
Published: July 2024

Abstract
Asbestos has long been a staple lesson for the precautionary principle. As a toxic material, it is often something people hope not to encounter. But before this, it often appeared as a substance of hope, carrying the promise of safety and economic rewards. This article uses these conflicting accounts of asbestos’s hope as a starting point for thinking about the conditions of hazardous hope. Turning to a vignette about an asbestos facility in Mike McCormack’s Solar Bones (2016), the article considers how stories of hazardous hope may produce a diminishment of hope. Rather than dismiss this as insufficiently hopeful, however, the article addresses the form of the novel as an exemplar of accessible experimentalism, suggesting it models new ways of communicating complex problems. If narrativizing hope demands an openness to multiple possible futures, then the form of such hope might need to defer resolution in much the same way as that adopted by modernist writing.
Beyond an Environmental “Hermeneutics of Suspicion”
Authors: Klaubert Hannah 
Published: July 2024

Abstract
This essay engages debates about hopeful critical scholarship in the environmental humanities via an analysis of the figure of the Babushka of Chornobyl in literature, film, and photography. The argument for hazardous hope unfolds in two steps. First, the article discusses how contaminated environments like the Chornobyl Exclusion Zone, where the Babushkas live, invite an interpretative move that models what Paul Ricoeur and, more recently, Rita Felski have problematized as the hermeneutics of suspicion. Such a move involves a mistrust of what is at the surface, calling for the exposure of hidden material agencies beyond what can be sensorily perceived. This suspicious disposition is also the critical stance of much environmental humanities scholarship, even when it attempts to be hopeful. Second, the article proposes that the cultural texts it examines not only model a suspicious gaze but can also easily be read suspiciously—as glossing over the harrowing realities of a precarious life in a sacrifice zone. Yet they also show us pockets of beauty, joy, and community and hint toward reformulations of environmental futurity that cannot easily be accounted for via such suspicious criticism. In that, they invite us to leave behind, if only temporarily, the hermeneutics of suspicion and to explore hazardous hope in a contaminated environment.
Changes on Cognition and Brain Network Temporal Variability After Pediatric Neurosurgery
Authors: Guan Xueyi , Hu Bohan , Zheng Wenjian , Chen Ning , Li Xiang , Hu Cuiling , Han Xu , Yan Zihan , Lu Zheng , Ou Yunwei , Gong Jian 
Published: July 2024

BACKGROUND AND OBJECTIVES:
Pediatric intracranial space–occupying lesions are common, with prognoses improving markedly in recent years, significantly extending survival. As such, there is an imperative to pay increased attention to the postoperative cognitive functions and brain network alterations in these children because these factors significantly influence their quality of life. Temporal variability (TV) analysis of brain networks captures the full extent of resting-state activities, reflecting cognitive functions and rehabilitation potential. However, previous research rarely uses TV analyses and most focus on adults or children after multidisciplinary treatments, not reflecting the combined effect caused by neurosurgery only and self-repair. This study gives our insights into this field from a holistic perspective.

METHODS:
We studied 35 children with intracranial space–occupying lesions, analyzing pre- and postsurgery MRI and cognitive tests. We used TV analysis to assess changes and correlated imaging indicators with cognitive performance.

RESULTS:
We observed a tendency for cognitive recovery after about 3 months postsurgery, primarily in the domains of social cognition and nonverbal reasoning. TV analysis of brain networks indicated increased nodal variability within systems such as the visual and sensorimotor networks, which are integral to external interactions. Correlative analysis showed that alterations in certain occipital regions were associated with changes in social cognition and nonverbal reasoning.

CONCLUSION:
These findings suggest significant intrinsic repair in cognitive functions and brain networks at around 3 months postneurosurgery in children. This study not only enriches our comprehension of postoperative cognitive and brain network self-repair processes in children but also furnishes potential therapeutic targets for rehabilitation interventions and establishes a theoretical foundation for proactive surgical interventions.
Body length determines flow refuging for rainbow trout (Oncorhynchus mykiss) behind wing dams
Authors: Dial Terry R. , Collins Laura A. , Liao James C. , Tobalske Bret W. 
Published: July 2024

ABSTRACT
Complex hydrodynamics abound in natural streams, yet the selective pressures these impose upon different size classes of fish are not well understood. Attached vortices are produced by relatively large objects that block freestream flow, which fish routinely utilize for flow refuging. To test how flow refuging and the potential harvesting of energy (as seen in Kármán gaiting) vary across size classes in rainbow trout (Oncorhynchus mykiss; fingerling, 8 cm; parr, 14 cm; adult, 22 cm; n=4 per size class), we used a water flume (4100 l; freestream flow at 65 cm s−1) and created vortices using 45 deg wing dams of varying size (small, 15 cm; medium, 31 cm; large, 48 cm). We monitored microhabitat selection and swimming kinematics of individual trout and measured the flow field in the wake of wing dams using time-resolved particle image velocimetry (PIV). Trout of each size class preferentially swam in vortices rather than the freestream, but the capacity to flow refuge varied according to the ratio of vortex width to fish length (WV:LF). Consistent refuging behavior was exhibited when WV:LF≥1.5. All size classes exhibited increased wavelength and Strouhal number and decreased tailbeat frequency within vortices compared with freestream, suggesting that swimming in vortices requires less power output. In 17% of the trials, fish preferentially swam in a manner that suggests energy harvesting from the shear layer. Our results can inform efforts toward riparian restoration and fishway design to improve salmonid conservation.
The effect of vitamin D on the development of Hashimoto's disease and the reduction of the inflammatory process in its course - review
Authors: Elias Jagoda , Woźniak Justyna , Womperski Karol , Szymonik Julia , Szopa Sebastian 
Published: July 2024

Introduction
Hashimoto's disease is an autoimmune chronic lymphocytic thyroiditis. It is a common condition, more frequent in women. Its diagnosis is based on the presence of specific antithyroid antibodies in the patient's blood which lead to the destruction of the thyroid gland. This can result in the development of hypothyroidism, requiring levothyroxine replacement therapy.
Aim of the review
A summary of the information gathered so far on the involvement of vitamin D in the development and course of Hashimoto's disease.
Results
The articles analyzed have mixed results. Most of them show a positive correlation between vitamin D and Hashimoto's disease, paying particular attention to the contribution of vitamin D in moderating the inflammatory process in HT. Other studies show significant differences in vitamin D levels between groups with different HT severity. Others show a negative correlation between vitamin D levels and the development of Hashimoto's disease.
Conclusions
Large well-controlled randomized double blind trials are needed in order to determine the exact role of vitamin D in Hashimoto’s disease.
The Vehicle Routing Problem with Access Restrictions
Authors: Şahin Munise Kübra , Yaman Hande 
Published: July 2024

To mitigate the negative effects of freight vehicles on urban areas, many cities have implemented road accessibility restrictions, including limited traffic zones, which restrict access to specific areas during certain times of the day. Implementing these zones creates a tradeoff between the delivery cost and time, even under the assumption of equal traversal time and travel cost. Consequently, the planners in charge of vehicle routing need to work with graphs containing information on all Pareto-optimal paths. Inspired by these changes in city logistics and the resulting computational challenges, we study the vehicle routing problem with access restrictions, where some streets are closed to traffic within a given time period. We formulate this problem using workday variables and propose two branch and price algorithms based on the underlying road network and multigraph. The results of our computational experiments demonstrate the effectiveness of the proposed algorithms, solving instances with up to 100 nodes and 33 customers, and underline the importance of considering alternative paths in reducing costs. Funding: This work was supported by KU Leuven [C14/22/026].