bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating the potential of (epi)genotype-by-low pass nanopore sequencing in dairy cattle: a study on direct genomic value and methylation analysis
Authors: González-Recio Oscar , López-Catalina Adrián , Peiró-Pastor Ramón , Nieto-Valle Alicia , Castro Monica , Fernández Almudena 
Published: July 2023

Abstract
Background
Genotype-by-sequencing has been proposed as an alternative to SNP genotyping arrays in genomic selection to obtain a high density of markers along the genome. It requires a low sequencing depth to be cost effective, which may increase the error at the genotype assigment. Third generation nanopore sequencing technology offers low cost sequencing and the possibility to detect genome methylation, which provides added value to genotype-by-sequencing. The aim of this study was to evaluate the performance of genotype-by-low pass nanopore sequencing for estimating the direct genomic value in dairy cattle, and the possibility to obtain methylation marks simultaneously.

Results
Latest nanopore chemistry (LSK14 and Q20) achieved a modal base calling accuracy of 99.55%, whereas previous kit (LSK109) achieved slightly lower accuracy (99.1%). The direct genomic value accuracy from genotype-by-low pass sequencing ranged between 0.79 and 0.99, depending on the trait (milk, fat or protein yield), with a sequencing depth as low as 2 × and using the latest chemistry (LSK114). Lower sequencing depth led to biased estimates, yet with high rank correlations. The LSK109 and Q20 achieved lower accuracies (0.57–0.93). More than one million high reliable methylated sites were obtained, even at low sequencing depth, located mainly in distal intergenic (87%) and promoter (5%) regions.

Conclusions
This study showed that the latest nanopore technology in useful in a LowPass sequencing framework to estimate direct genomic values with high reliability. It may provide advantages in populations with no available SNP chip, or when a large density of markers with a wide range of allele frequencies is needed. In addition, low pass sequencing provided nucleotide methylation status of > 1 million nucleotides at ≥ 10 × , which is an added value for epigenetic studies.
Determinants and consequences of employer-provided training program resilience post-Covid-19
Authors: Caves Katherine M. , McDonald Patrick 
Published: July 2023

AbstractEconomic shocks provide both risks and opportunities for workplace training programs—the risk of program cancellation or interruption to skills development, and the opportunity to be at the vanguard of economic recovery. This paper analyzes the impact of Covid-19 and the resulting economic shock on training programs in the US using a survey amongst employers participating in training support networks, run from April-June 2021. We anticipate that programs expressly motivated by returns to investment and those that are higher quality and leading to stronger credentials will be most likely to survive the shock and have minimal disruption to skills acquisition. Results suggest that expressed motivations to train are generally not linked to training disruption or skills loss, while there is some evidence of paid programs and those offering better credentials being more likely to survive. Internships and programs that are more demographically diverse show a greater likelihood of disruption and skills loss.
Mathematical modeling of modified atmosphere package/LDPE film combination and its application to design breathing cylinders for extending the shelf life of green asparagus
Authors: Lu Wen-Chien , Cheng Yu-Tsung , Lai Chien-Jung , Chiang Been-Huang , Huang Ping-Hsiu , Li Po-Hsien 
Published: July 2023

Abstract
Background
The O2 levels in food packaging systems play an essential role in the deterioration of food quality and shelf life. Modified atmosphere packaging (MAP) supports the storage of fresh and processed foods by inhibiting chemical and physical changes while reducing the deterioration caused by microorganisms.

Materials and methods
This study established and validated the equations for the relationship between MAP formulation reagents, asparagus respiration, permeability of packaging film, and rates of O2 and CO2 mass transfer in which different interactions occur and affect each other.

Results
The resulting atmosphere of packaging was determined to be the key to achieving the MAP benefits. The active MAP formulations developed in this study were combined with very-low-density polyethylene films to store green asparagus spears. During storage, the combined films effectively maintained the firmness of green asparagus spears, fiber, and vitamin C content, and outperformed the passive MAP and control groups. The above results confirm all the equations in the passive and active MAP systems established in this study.

Conclusions
Hence, maintaining the asparagus quality with an active MAP treatment will reduce economic loss and possibly provide new insights into applying active MAP retail packages to preserve fruits and vegetables in post-harvest shelf life.

Graphical Abstract
Gun violence and the voices of youth on community safety in the time of COVID-19 in East Harlem, NY: a youth participatory action research cross-sectional study
Authors: Wallace Jacqueline G. , Chernet Rachel , Formica Margaret K. , Adeonigbagbe Olusola , Flores Roseanne L. , Marchesani Robert , Goldberg Danielle , Wridt Pamela , Laraque-Arena Danielle 
Published: July 2023

Abstract
Background
The USA has failed to codify the protection of children from gun violence (GV) as a human right. This study employs a youth participatory action research methodology, within the framework of the United Nations Convention on the Rights of the Child (UNCRC), to investigate the relationships between GV exposure, self-identified gender and perceptions of children’s rights and safety.

Methods
An anonymous survey based on UNICEF USA’s Child Friendly Cities Initiative interactive survey tool targeting adolescents was modified by East Harlem, New York high school student co-researchers in collaboration with near-peer graduate students. The 61-question survey was administered at an East Harlem high school. Analysis consisted of univariate, bivariate and logistic regression using SPSS®.

Results
A total of 153 students completed the survey: 48.4% self-identified as male and 45.8% as female. Thirty-five percent reported witnessing GV. Most (79.1%) were aware of child rights regardless of gender or GV exposure but there were differences in perceptions of safety. Fifteen percent of females reported never feeling safe at school compared to 3% of males (p = 0.01). Females were 2.2 times as likely as males to report transportation waiting areas as never safe (p = 0.008). Almost a third of females reported never feeling safe from sexual harassment in public, compared to 10% of males (p = 0.004). In multivariable logistic regression adjusted for gender, race/ethnicity and grade level, students who witnessed GV were 4.6 times more likely to report never feeling safe from violence (95% CI 1.7–12.4). Thirty percent of students who witnessed GV reported not attending school because of safety concerns. Students who witnessed GV had 2.2 times the odds of carrying a weapon to school (95% CI 1.1–4.5). These patterns continued for other perceptions of safety.

Conclusions
The students in this study affirmed their rights to participate and express their views on matters that may affect them, as articulated in the UNCRC. The study revealed differences in perceptions of safety by self-identified gender and identified gun violence as a major contributor of youth’s perception of lack of safety. The study evinces the efficacy of employing YPAR methodology to identify and answer youth concerns of community safety and prioritize honoring child rights.
Prediction and detection of virtual reality induced cybersickness: a spiking neural network approach using spatiotemporal EEG brain data and heart rate variability
Authors: Yang Alexander Hui Xiang , Kasabov Nikola Kirilov , Cakmak Yusuf Ozgur 
Published: July 2023

AbstractVirtual Reality (VR) allows users to interact with 3D immersive environments and has the potential to be a key technology across many domain applications, including access to a future metaverse. Yet, consumer adoption of VR technology is limited by cybersickness (CS)—a debilitating sensation accompanied by a cluster of symptoms, including nausea, oculomotor issues and dizziness. A leading problem is the lack of automated objective tools to predict or detect CS in individuals, which can then be used for resistance training, timely warning systems or clinical intervention. This paper explores the spatiotemporal brain dynamics and heart rate variability involved in cybersickness and uses this information to both predict and detect CS episodes. The present study applies deep learning of EEG in a spiking neural network (SNN) architecture to predict CS prior to using VR (85.9%, F7) and detect it (76.6%, FP1, Cz). ECG-derived sympathetic heart rate variability (HRV) parameters can be used for both prediction (74.2%) and detection (72.6%) but at a lower accuracy than EEG. Multimodal data fusion of EEG and sympathetic HRV does not change this accuracy compared to ECG alone. The study found that Cz (premotor and supplementary motor cortex) and O2 (primary visual cortex) are key hubs in functionally connected networks associated with both CS events and susceptibility to CS. F7 is also suggested as a key area involved in integrating information and implementing responses to incongruent environments that induce cybersickness. Consequently, Cz, O2 and F7 are presented here as promising targets for intervention.
How forest management changed the course of the Washburn fire and the fate of Yosemite’s giant sequoias (Sequoiadendron giganteum)
Authors: Hankin Lacey E. , Anderson Chad T. , Dickman Garrett J. , Bevington Parker , Stephens Scott L. 
Published: July 2023

Abstract
Background
The Washburn fire started on July 7, 2022 in the lower Mariposa Grove in Yosemite National Park, posing immediate threats to the iconic giant sequoias (Sequoiadendron giganteum), critical Pacific fisher (Pekania pennanti) habitat, and the community of Wawona. The wildfire quickly gained national attention and the public followed Yosemite’s firefighting efforts closely. In the aftermath of the Washburn fire, we evaluate how decades of fire management and recent roadside thinning in the Park shaped the tactics and outcomes of this wildfire. Fuels reduction and prescribed fire have been at the core of Yosemite’s fire management program since the 1970s and much of this activity has been concentrated in the two areas where firefighting operations were most successful in protecting key resources. We use long-term fire effects monitoring data, airborne light detection and ranging data, and operational perspectives to link together science, management, and fire operations.

Results
Successful initial attack and suppression efforts kept fire out of the Mariposa Grove and the community, where topography and the distribution of heavy fuels largely drove fire behavior throughout the course of the fire. We demonstrate the cumulative effects of decades of fuels treatments in reducing two major drivers of fire behavior – tree density and fuel load – and highlight substantially lower ladder fuels and fire severity in treatment units compared to untreated areas within the Washburn fire footprint.

Conclusions
We show how repeated prescribed fire and fuels treatments can promote forest structure indicative of frequent-fire regimes, moderate extreme fire behavior, improve the ability to protect key resources of concern, and increase human safety in the face of unplanned wildfire. Strategically placed prescribed fire and fuels treatments surrounding the Washburn fire were key considerations in wildfire suppression tactics and were instrumental in protecting the Mariposa Grove.
Evaluation and Comparison of Real-World Databases for Conducting Research in Patients With Colorectal Cancer
Authors: Wang Ching-Yu , Shao Changxia , McDonald Alicia C. , Amonkar Mayur M. , Zhou Wei , Bortnichak Edward A. , Liu Xinyue 
Published: July 2023

PURPOSE Evaluating whether patient populations in clinico-genomic oncology databases are comparable with whom in other databases without genomic component is important. METHODS Four databases were compared for colorectal cancer (CRC) cases and stage IV CRC cases: American Association for Cancer Research Project Genomics Evidence Neoplasia Information Exchange Biopharma Collaborative (GENIE-BPC), The Cancer Genome Atlas (TCGA), SEER-Medicare, and MarketScan Commercial and Medicare Supplemental claims databases. These databases were also compared with the SEER registry database which serves as national benchmarks. Demographics, clinical characteristics, and overall survival were compared in patients with newly diagnosed CRC and patients with stage IV CRC across databases. Treatment patterns were further compared in patients with stage IV CRC. RESULTS A total of 65,976 patients with CRC and 13,985 patients with stage IV CRC were identified. GENIE-BPC had the youngest patient population (mean age [years]: CRC, 54.1; stage IV CRC, 52.7). SEER-Medicare had the oldest patient population (CRC, 77.7; stage IV CRC, 77.3). Most patients were male and of White race across databases. GENIE-BPC had the highest proportion of patients with stage IV CRC (48.4% v other databases 13.8%-25.4%) and patients receiving treatments (95.7% v 37.6%-59.1%). Infusional fluorouracil, leucovorin, and oxaliplatin with or without bevacizumab was the most common regimen across databases accounting for 47.3%-78.5% of patients receiving first line of therapy. The median survival from diagnosis was 36, 94, 44 months (CRC) and 23, 36, 15 months (stage IV CRC) for patients in GENIE-BPC after left truncation, TCGA, and SEER-Medicare databases, respectively. CONCLUSION Compared with other databases, GENIE-BPC had the youngest patients with CRC with the most advanced disease and the largest proportion of patients receiving treatment. Investigators should consider adjustments when extrapolating results from clinico-genomic databases to the general CRC population.
Complexity of networks: A structural heterogeneity approach
Authors: Liu Gang , Tian Tian , Huang Chengfu , Mou Biao 
Published: July 2023

Abstract
The complexity measurement of networks is one of the hot topics in complex networks. How to accurately describe the complexity difference between networks is helpful to the study of network structure. This paper proposes a method for measuring the network complexity considering the local and global structural heterogeneity. This method introduces the k-order neighbors to examine the local structural heterogeneity. Besides, the standard deviation is used to evaluate the global structural heterogeneity. Based on this, the complexity measurement model is established. In order to testify the efficiency of the method, the ER random networks, BA scale-free networks and real networks (including four social networks and two infrastructure networks) are used for experiments. The results show that the proposed method is sensitive and can effectively describe the subtle difference of structure complexity between networks.
Parent Perspectives on Complex Needs in Patients With MCT8 Deficiency: An International, Prospective, Registry Study
Authors: van Geest Ferdy S , Groeneweg Stefan , Popa Veronica M , Stals Milou A M , Visser W Edward 
Published: July 2023

Abstract

Context
Monocarboxylate transporter 8 (MCT8) deficiency is a rare neurodevelopmental and metabolic disorder, with daily care posing a heavy burden on caregivers. A comprehensive overview of these complex needs and daily care challenges is lacking.

Design
We established an international prospective registry to systemically capture data from parents and physicians caring for patients with MCT8 deficiency. Parent-reported data on complex needs and daily care challenges were extracted.

Results
Between July 17, 2018, and May 16, 2022, 51 patients were registered. Difficulties in daily life care were mostly related to feeding and nutritional status (17/33 patients), limited motor skills (12/33 patients), and sleeping (11/33 patients). Dietary advice was provided for 11/36 patients. Two of 32 patients were under care of a cardiologist. Common difficulties in the diagnostic trajectory included late diagnosis (20/35 patients) and visiting a multitude of specialists (15/35 patients). Median diagnostic delay was significantly shorter in patients born in or after 2017 vs before 2017 (8 vs 19 months, P &lt; .0001).

Conclusions
Feeding and sleeping problems and limited motor skills mostly contribute to difficulties in daily care. The majority of patients did not receive professional dietary advice, although being underweight is a key disease feature, strongly linked with poor survival. Despite sudden death being a prominent cause of death, potentially related to the cardiovascular abnormalities frequently observed, patients were hardly seen by cardiologists. These findings can directly improve patient-centered multidisciplinary care and define patient-centered outcome measures for intervention studies in patients with MCT8 deficiency.
The Impact of Gender-Affirming Hormone Therapy on Physical Performance
Authors: Cheung Ada S , Zwickl Sav , Miller Kirsti , Nolan Brendan J , Wong Alex Fang Qi , Jones Patrice , Eynon Nir 
Published: July 2023

Abstract

Context
The inclusion of transgender people in elite sport has been a topic of debate. This narrative review examines the impact of gender-affirming hormone therapy (GAHT) on physical performance, muscle strength, and markers of endurance.

Evidence Acquisition
MEDLINE and Embase were searched using terms to define the population (transgender), intervention (GAHT), and physical performance outcomes.

Evidence Synthesis
Existing literature comprises cross-sectional or small uncontrolled longitudinal studies of short duration. In nonathletic trans men starting testosterone therapy, within 1 year, muscle mass and strength increased and, by 3 years, physical performance (push-ups, sit-ups, run time) improved to the level of cisgender men. In nonathletic trans women, feminizing hormone therapy increased fat mass by approximately 30% and decreased muscle mass by approximately 5% after 12 months, and steadily declined beyond 3 years. While absolute lean mass remains higher in trans women, relative percentage lean mass and fat mass (and muscle strength corrected for lean mass), hemoglobin, and VO2 peak corrected for weight was no different to cisgender women. After 2 years of GAHT, no advantage was observed for physical performance measured by running time or in trans women. By 4 years, there was no advantage in sit-ups. While push-up performance declined in trans women, a statistical advantage remained relative to cisgender women.

Conclusion
Limited evidence suggests that physical performance of nonathletic trans people who have undergone GAHT for at least 2 years approaches that of cisgender controls. Further controlled longitudinal research is needed in trans athletes and nonathletes.
Significant High Lipid Profile in a Woman With Obstructive Jaundice
Authors: Albargawi Mashael , Abdulaal Ibtihal 
Published: July 2023

Abstract
Gallbladder disease is one of the most common gastrointestinal tract diseases. In obstructive jaundice, there is a reduction in bile flow out of the liver secondary to the blocked bile or pancreatic duct, which leads to excess bile and its products accumulating in the blood. One of these products is lipoprotein X (LpX); its presence is associated with a lipoprotein pattern characterized by an increased concentration of low-density lipoprotein (LDL) cholesterol. Few published articles have reported the association between obstructive jaundice and hyperlipidemia. This report describes a unique case of a Saudi female patient diagnosed with obstructive jaundice, presenting with extreme hypercholesterolemia, which was reduced significantly 1 week after endoscopic retrograde cholangiopancreatography (ERCP). Correct recognition and investigation of the lipid profile are important for differentiating LpX-mediated hypercholesterolemia caused by obstructive jaundice from other causes of elevated LDL concentrations. Differentiation may affect the patient's therapeutic management.
A Generational Shift: Race and the Declining Lifetime Risk of Imprisonment
Authors: Robey Jason P. , Massoglia Michael , Light Michael T. 
Published: July 2023

Abstract
Mass incarceration fundamentally altered the life course for a generation of American men, but sustained declines in imprisonment in recent years raise questions about how incarceration is shaping current generations. This study makes three primary contributions to a fuller understanding of the contemporary landscape of incarceration in the United States. First, we assess the scope of decarceration. Between 1999 and 2019, the Black male incarceration rate dropped by 44%, and notable declines in Black male imprisonment were evident in all 50 states. Second, our life table analysis demonstrates marked declines in the lifetime risks of incarceration. For Black men, the lifetime risk of incarceration declined by nearly half from 1999 to 2019. We estimate that less than 1 in 5 Black men born in 2001 will be imprisoned, compared with 1 in 3 for the 1981 birth cohort. Third, decarceration has shifted the institutional experiences of young adulthood. In 2009, young Black men were much more likely to experience imprisonment than college graduation. Ten years later, this trend had reversed, with Black men more likely to graduate college than go to prison. Our results suggest that prison has played a smaller role in the institutional landscape for the most recent generation compared with the generation exposed to the peak of mass incarceration.
DELLA proteins positively regulate seed size inArabidopsis
Authors: Gomez Maria Dolores , Cored Isabel , Barro-Trastoy Daniela , Sanchez-Matilla Joaquin , Tornero Pablo , Perez-Amador Miguel A. 
Published: July 2023

ABSTRACTHuman and animal nutrition is mainly based on seeds. Seed size is a key factor affecting seed yield and has thus been one of the primary objectives of plant breeders since the domestication of crop plants. Seed size is coordinately regulated by signals of maternal and zygotic tissues that control the growth of the seed coat, endosperm and embryo. Here, we provide previously unreported evidence for the role of DELLA proteins, key repressors of gibberellin responses, in the maternal control of seed size. The gain-of-function della mutant gai-1 produces larger seeds as a result of an increase in the cell number in ovule integuments. This leads to an increase in ovule size and, in turn, to an increase in seed size. Moreover, DELLA activity promotes increased seed size by inducing the transcriptional activation of AINTEGUMENTA, a genetic factor that controls cell proliferation and organ growth, in the ovule integuments of gai-1. Overall, our results indicate that DELLA proteins are involved in the control of seed size and suggest that modulation of the DELLA-dependent pathway could be used to improve crop yield.