bluuebunny/crossref_metadata_2025_split huggingface dataset:
Economic and environmental performance of controlled-environment supply chains for leaf lettuce
Authors: Nicholson Charles F , Eaton Michael , Gómez Miguel I , Mattson Neil S 
Published: June 2023

Abstract
We assess landed costs and selected environmental metrics for field-based and controlled-environment agriculture greenhouse (GH) supply chains for leaf lettuce delivered to New York City. Landed costs for a GH are 46 to 174 per cent higher than field production, with the lower value for an automated GH located in the peri-urban area. Energy use and global warming potential per kg lettuce delivered were larger for the GH, particularly if located in a peri-urban area. Water use was much higher for the field-based supply chain. Controlled-environment GH technologies will require further development to meet goals for lower costs and environmental impact.
Real-world utilization of the pill-in-the-pocket method for terminating episodes of atrial fibrillation: data from the multinational Antiarrhythmic Interventions for Managing Atrial Fibrillation (AIM-AF) survey
Authors: Reiffel James A , Blomström-Lundqvist Carina , Boriani Giuseppe , Goette Andreas , Kowey Peter R , Merino Jose L , Piccini Jonathan P , Saksena Sanjeev , Camm A John 
Published: June 2023

Abstract

Aims
Atrial fibrillation (AF) is the most common sustained arrhythmia encountered in clinical practice. Episodes may stop spontaneously (paroxysmal AF); may terminate only via intervention (persistent AF); or may persist indefinitely (permanent AF) (see European and American guidelines, referenced below, for more precise definitions). Recently, there has been renewed interest in an approach to terminate AF acutely referred to as ‘pill-in-the-pocket’ (PITP). The PITP is recognized in both the US and European guidelines as an effective option using an oral antiarrhythmic drug for acute conversion of acute/recent-onset AF. However, how PITP is currently used has not been systematically evaluated.

Methods and results
The recently published Antiarrhythmic Interventions for Managing Atrial Fibrillation (AIM-AF) survey included questions regarding current PITP usage, stratified by US vs. European countries surveyed, by representative countries within Europe, and by cardiologists vs. electrophysiologists. This manuscript presents the data from this planned sub-study. Our survey revealed that clinicians in both the USA and Europe consider PITP in about a quarter of their patients, mostly for recent-onset AF with minimal or no structural heart disease (guideline appropriate). However, significant deviations exist. See the Graphical abstract for a summary of the data.

Conclusion
Our findings highlight the frequent use of PITP and the need for further physician education about appropriate and optimal use of this strategy.
Dynamic heterogeneity of colorectal cancer during progression revealed clinical risk-associated cell types and regulations in single-cell resolution and spatial context
Authors: Ke Haoxian , Li Zhihao , Li Peisi , Ye Shubiao , Huang Junfeng , Hu Tuo , Zhang Chi , Yuan Ming , Chen Yuan , Wu Xianrui , Lan Ping 
Published: June 2023

Abstract

Background
Tumor heterogeneity is contributed by tumor cells and the microenvironment. Dynamics of tumor heterogeneity during colorectal cancer (CRC) progression have not been elucidated.

Methods
Eight single-cell RNA sequencing (scRNA-seq) data sets of CRC were included. Milo was utilized to reveal the differential abundance of cell clusters during progression. The differentiation trajectory was imputed by using the Palantir algorithm and metabolic states were assessed by using scMetabolism. Three spatial transcription sequencing (ST-seq) data sets of CRC were used to validate cell-type abundances and colocalization. Cancer-associated regulatory hubs were defined as communication networks affecting tumor biological behaviors. Finally, quantitative reverse transcription polymerase chain reaction and immunohistochemistry staining were performed for validation.

Results
TM4SF1+, SOX4+, and MKI67+ tumor cells; CXCL12+ cancer-associated fibroblasts; CD4+ resident memory T cells; Treg; IgA+ plasma cells; and several myeloid subsets were enriched in stage IV CRC, most of which were associated with overall survival of patients. Trajectory analysis indicated that tumor cells from patients with advanced-stage CRC were less differentiated, when metabolic heterogeneity showed a highest metabolic signature in terminal states of stromal cells, T cells, and myeloid cells. Moreover, ST-seq validated cell-type abundance in a spatial context and also revealed the correlation of immune infiltration between tertiary lymphoid structures and tumors followed by validation in our cohort. Importantly, analysis of cancer-associated regulatory hubs revealed a cascade of activated pathways including leukocyte apoptotic process, MAPK pathway, myeloid leukocyte differentiation, and angiogenesis during CRC progression.

Conclusions
Tumor heterogeneity was dynamic during progression, with the enrichment of immunosuppressive Treg, myeloid cells, and fibrotic cells. The differential state of tumor cells was associated with cancer staging. Assessment of cancer-associated regulatory hubs suggested impaired antitumor immunity and increased metastatic ability during CRC progression.
Impacts of Sex Ratio Meiotic Drive on Genome Structure and Function in a Stalk-Eyed Fly
Authors: Reinhardt Josephine A , Baker Richard H , Zimin Aleksey V , Ladias Chloe , Paczolt Kimberly A , Werren John H , Hayashi Cheryl Y , Wilkinson Gerald S 
Published: June 2023

Abstract
Stalk-eyed flies in the genus Teleopsis carry selfish genetic elements that induce sex ratio (SR) meiotic drive and impact the fitness of male and female carriers. Here, we assemble and describe a chromosome-level genome assembly of the stalk-eyed fly, Teleopsis dalmanni, to elucidate patterns of divergence associated with SR. The genome contains tens of thousands of transposable element (TE) insertions and hundreds of transcriptionally and insertionally active TE families. By resequencing pools of SR and ST males using short and long reads, we find widespread differentiation and divergence between XSR and XST associated with multiple nested inversions involving most of the SR haplotype. Examination of genomic coverage and gene expression data revealed seven X-linked genes with elevated expression and coverage in SR males. The most extreme and likely drive candidate involves an XSR-specific expansion of an array of partial copies of JASPer, a gene necessary for maintenance of euchromatin and associated with regulation of TE expression. In addition, we find evidence for rapid protein evolution between XSR and XST for testis expressed and novel genes, that is, either recent duplicates or lacking a Dipteran ortholog, including an X-linked duplicate of maelstrom, which is also involved in TE silencing. Overall, the evidence suggests that this ancient XSR polymorphism has had a variety of impacts on repetitive DNA and its regulation in this species.
Social Isolation/Loneliness and Tooth Loss in Community-Dwelling Older Adults: The Sukagawa Study
Authors: Takahashi Sei , Naganuma Toru , Kurita Noriaki , Omae Kenji , Ohnishi Tsuyoshi , Yoshioka Takashi , Ito Fumihito , Takeshima Taro , Fukuma Shingo , Hamaguchi Sugihiro , Fukuhara Shunichi ,   Sukagawa Study Group, Hasegawa Takeshi , Yajima Nobuyuki , Niihata Kakuya , Iida Hidekazu , Kobayashi Susumu , Sasaki Sho , Nishiwaki Hiroki , Tominaga Ryoji 
Published: June 2023

Abstract

Background and Objectives
The relationship between social isolation/loneliness and oral health is unclear. This study investigated the association between social isolation/loneliness and tooth loss in older Japanese adults.

Research Design and Methods
This was a cross-sectional study of a population-based cohort (the Sukagawa Study); 5,490 cohort study participants aged ≥75 years and who were independent answered a self-administered questionnaire in 2018. Social isolation was defined based on the 6-item Japanese version of the Lubben Social Network Scale. Loneliness was measured by the 3-item Japanese version of the University of California, Los Angeles (UCLA) Loneliness Scale version 3. The primary outcome was tooth loss, defined as having fewer than 20 teeth. The secondary outcomes were decreased toothbrushing frequency and diminished ability to chew food. Prevalence ratios (PRs) were estimated using a modified Poisson regression analysis in 2 models—Model 1, which adjusted for age, gender, smoking status, alcohol consumption, low annual income, and short education period, and Model 2, which added history of depression, history of diabetes mellitus, history of stroke, and cognitive impairment to Model 1.

Results
The primary analysis included 5,490 participants. Adjusted PRs of social isolation and loneliness for tooth loss (Model 1) were 0.97 (95% confidence interval [CI] 0.93–1.01) and 1.07 (95% CI 1.02–1.12), respectively; those for decreased toothbrushing frequency were 1.17 (95% CI 0.98– 1.39) and 1.59 (95% CI 1.30–1.93), respectively; and those for chewing difficulty were 1.65 (95% CI 1.12–2.43) and 3.01 (95% CI 2.02–4.51), respectively. The adjusted PRs in Model 2 demonstrated results similar to that of Model 1.

Discussion and Implications
Loneliness is associated with tooth loss among older adults, whereas social isolation is not. Our findings can inform plans for policymakers, professionals, and organizations to identify lonely older adults and provide social prescriptions to improve their access to oral health care services.
Learning to Move in a Changing Body in a Changing World
Authors: Cole Whitney G , Adolph Karen E 
Published: June 2023

Synopsis
Infants of all species learn to move in the midst of tremendous variability and rapid developmental change. Traditionally, researchers consider variability to be a problem for development and skill acquisition. Here, we argue for a reconsideration of variability in early life, taking a developmental, ecological, systems approach. Using the development of walking in human infants as an example, we argue that the rich, variable experiences of infancy form the foundation for flexible, adaptive behavior in adulthood. From their first steps, infants must cope with changes in their bodies, skills, and environments. Rapid growth spurts and a continually expanding environment of surfaces, elevations, and obstacles alter the biomechanical constraints on balance and locomotion from day to day and moment to moment. Moreover, infants spontaneously generate a variable practice regimen for learning to walk. Self-initiated locomotion during everyday activity consists of immense amounts of variable, time-distributed, error-filled practice. From infants’ first steps and continuing unabated over the next year, infants walk in short bursts of activity (not continual steps), follow curved (not straight) paths, and take steps in every direction (not only forward)—all the while, accompanied by frequent falls as infants push their limits (rather than a steady decrease in errors) and explore their environments. Thus, development ensures tremendous variability—some imposed by physical growth, caregivers, and a changing environment outside infants’ control, and some self-generated by infants’ spontaneous behavior. The end result of such massive variability is a perceptual-motor system adept at change. Thus, infants do not learn fixed facts about their bodies or environments or their level of walking skill. Instead, they learn how to learn—how to gauge possibilities for action, modify ongoing movements, and generate new movements on the fly from step to step. Simply put, variability in early development is a feature, not a bug. It provides a natural training regimen for successfully navigating complex, ever-changing environments throughout the lifespan. Moreover, observations of infants' natural behavior in natural, cluttered environments—rather than eliciting adult-like behaviors under artificial, controlled conditions—yield very different pictures of what infants of any species do and learn. Over-reliance on traditional tasks that artificially constrain variability therefore risks distorting researchers’ understanding of the origins of adaptive behavior.
Integrating habitat features into spatio-temporal biomass dynamics models for a better understanding of stock productivity: a case study of sea scallop in the Bay of Fundy
Authors: McDonald Raphaël R , Keith David M , Sameoto Jessica A , Mills Flemming Joanna 
Published: June 2023

Abstract
Recent efforts in ocean mapping of seafloor habitat have made data increasingly available. For bottom-dwelling and/or sessile species, there is often a strong relationship between population productivity and habitat, and stock assessment models are likely to be improved by the inclusion of habitat. Here, we extend a recently developed spatio-temporal biomass dynamics model to allow habitat to inform probabilities of non-zero tows and catchability. Simulation experiments demonstrate the ability of this new approach to reliably capture population trends over time and space, with the applicability of the method further demonstrated using data from the Canadian Maritimes Inshore Sea Scallop Fishery in the Bay of Fundy. This habitat-informed spatio-temporal biomass dynamics model better captures underlying processes, reduces uncertainty, thereby improving our understanding of stock status from which fisheries management decisions can be based.
Effect of preterm birth on growth and blood pressure in adulthood in the Pelotas 1993 cohort
Authors: Lapidaire Winok , Proaño Alvaro , Blumenberg Cauane , Loret de Mola Christian , Delgado Carlos A , del Castillo Darwin , Wehrmeister Fernando C , Gonçalves Helen , Gilman Robert H , Oberhelman Richard A , Lewandowski Adam J , Wells Jonathan C K , Miranda J Jaime 
Published: June 2023

Abstract

Background
Preterm birth has been associated with increased risk of hypertension and cardiovascular disease later in adulthood, attributed to cardiovascular and metabolic alterations in early life. However, there is paucity of evidence from low- and middle-income countries (LMICs).

Methods
We investigated the differences between preterm (&lt;37 weeks gestational age) and term-born individuals in birth length and weight as well as adult (18 and 20 years) height, weight and blood pressure in the Brazilian 1993 Pelotas birth cohort using linear regressions. Analyses were adjusted for the maternal weight at the beginning of pregnancy and maternal education and family income at childbirth. Additional models were adjusted for body mass index (BMI) and birthweight. Separate analyses were run for males and females. The complete sample was analysed with an interaction term for sex.

Results
Of the 3585 babies included at birth, 3010 were followed up in adulthood at 22 years. Preterm participants had lower length and weight at birth. This difference remained for male participants in adulthood, but female participants were no shorter than their term counterparts by 18 years of age. At 22 years, females born preterm had lower blood pressures (systolic blood pressure −1.00 mmHg, 95%CI −2.7, 0.7 mmHg; diastolic blood pressure −1.1 mmHg, 95%CI −2.4, 0.3 mmHg) than females born at term. These differences were not found in male participants.

Conclusions
In this Brazilian cohort we found contrasting results regarding the association of preterm birth with blood pressure in young adulthood, which may be unique to an LMIC.
Civilian Protection Payment and the Escalation of Violence against Civilians in Northwestern Nigeria
Authors: Buba Imrana 
Published: June 2023

AbstractHow do civilian protection payments to militias affect the dynamics of communal conflict? Building on the literature on communal conflict, civilian agency, rebel taxation, and criminal extortion, I argue that civilian protection payment is not a sustainable self-protection strategy. Civilian protection payment refers to an arrangement whereby communities pay levies to militias for protection against attacks, often buying temporary safety. Drawing on fieldwork in Nigeria’s conflict-ridden northwest region, I inductively build a theory that identifies two pathways that explain how protection payments transform into extortion and contribute to the escalation of militia violence: acquiescence or resistance. The acquiescence pathway shows how militias increase predation by demanding ever higher payments. The resistance pathway theorizes militias’ violent retaliation to punish communities that refuse to pay, instilling fear in communities that may be considering resisting and justifying their protection role for those communities that pay. The article improves our understanding of the unintended negative consequences of civilian self-protection and changing dynamics of conflict in northwestern Nigeria.
Patterns of gender identity data within electronic health record databases can be used as a tool for identifying and estimating the prevalence of gender-expansive people
Authors: Hines Nicole G , Greene Dina N , Imborek Katherine L , Krasowski Matthew D 
Published: June 2023

Abstract

Objective
Electronic health records (EHRs) within the United States increasingly include sexual orientation and gender identity (SOGI) fields. We assess how well SOGI fields, along with International Statistical Classification of Diseases and Related Health Problems, 10th Revision (ICD-10) codes and medication records, identify gender-expansive patients.

Materials and Methods
The study used a data set of all patients that had in-person inpatient or outpatient encounters at an academic medical center in a rural state between December 1, 2018 and February 17, 2022. Chart review was performed for all patients meeting at least one of the following criteria: differences between legal sex, sex assigned at birth, and gender identity (excluding blank fields) in the EHR SOGI fields; ICD-10 codes related to gender dysphoria or unspecified endocrine disorder; prescription for estradiol or testosterone suggesting use of gender-affirming hormones.

Results
Out of 123 441 total unique patients with in-person encounters, we identified a total of 2236 patients identifying as gender-expansive, with 1506 taking gender-affirming hormones. SOGI field differences or ICD-10 codes related to gender dysphoria or both were found in 2219 of 2236 (99.2%) patients who identify as gender-expansive, and 1500 of 1506 (99.6%) taking gender-affirming hormones. For the gender-expansive population, assigned female at birth was more common in the 12–29 year age range, while assigned male at birth was more common for those 40 years and older.

Conclusions
SOGI fields and ICD-10 codes identify a high percentage of gender-expansive patients at an academic medical center.
Voyage optimization using dynamic programming with initial quadtree based route
Authors: Choi Gwang-Hyeok , Lee Wonhee , Kim Tae-wan 
Published: June 2023

Abstract
This research proposes an integrated voyage optimization algorithm that combines quadtree graph generation, visibility graph simplification, Dijkstra’s algorithm, and a 3D dynamic programming (3DDP) method. This approach enables the determination of a minimum distance initial reference route and the creation of a 2D navigational graph for efficient route optimization. We effectively store and process complex terrain information by transforming the GEBCO uniform grid into a quadtree structure. By utilizing a nearest neighbour search algorithm, edges are connected between adjacent ocean nodes, facilitating the generation of a quadtree graph. Applying Dijkstra’s algorithm to the quadtree graph, we derive the shortest initial route and construct a visibility graph based on the waypoints. This results in a simplified reference route with reduced search distance, allowing for more efficient navigation. For each waypoint along the reference route, a boundary is defined angled at 90 degrees to the left and right, based on the waypoint’s reference bearing. A line segment formed by the waypoint and both boundaries is defined as a navigational stage. A navigational graph is defined by connecting adjacent stages. Employing a 3DDP method on the navigational graph, and incorporating weather forecasting data, including wind, wave, and currents, we search for a route that minimizes fuel oil consumption with estimated time of arrival restrictions. Our approach is tested on several shipping routes, demonstrating a fuel consumption reduction compared to other voyage optimization routes. This integrated algorithm offers a potential solution for tackling complex voyage optimization problems in marine environments while considering various weather factors.
Towards Tree Species Preservation: Protecting Ash Amidst the Emerald Ash Borer Invasion in the Northeast
Authors: D’Amato Anthony W , Orwig David A , Siegert Nathan W , Mahaffey Amanda , Benedict Les , Everett Tyler , Daigle John , Johnson Logan , Catanzaro Paul , Cusack Caitlin 
Published: June 2023

Abstract
The introduced emerald ash borer (EAB) represents the costliest invasive forest insect in US history, causing significant mortality of ash species across much of eastern North America as well as in Colorado and Oregon. Few surviving overstory ash trees exist in areas first invaded by EAB, such as the Lake States region; however, forests with healthy, mature ash remain in recently invaded regions, such as the northeastern United States. Given the importance of ash to cultural lifeways of Indigenous peoples and the ecology and economies of working forest lands, there is growing interest in applying protection measures to maintain ash in forested settings. We further develop our call for species preservation by presenting Indigenous and Western science case studies of ongoing efforts to mitigate the impacts of EAB, illustrating specific applications of these strategies for meeting different preservation goals in lowland and northern hardwood forests in northeastern North America.
Study Implications: The introduced emerald ash borer (EAB) threatens to functionally eliminate ash species from large portions of the United States. Although the impacts of EAB are now widespread in many areas, portions of the United States, such as the Northeast, still contain forests with healthy, mature ash. This presents a unique opportunity to apply the integrated pest management strategies and knowledge gained from other invaded regions to preserve the cultural and ecological values provided by ash in the forest. Multistakeholder partnerships built around preserving the cultural and ecological values of ash have provided a powerful approach for sustaining ash into the future.