bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reference genome of California walnut,Juglans californica, and resemblance with other genomes in the order Fagales
Authors: Fitz-Gibbon Sorel , Mead Alayna , O’Donnell Scott , Li Zhi-Zhong , Escalona Merly , Beraut Eric , Sacco Samuel , Marimuthu Mohan P A , Nguyen Oanh , Sork Victoria L 
Published: June 2023

AbstractJuglans californica, California walnut, is a vulnerable small tree that is locally abundant but restricted to woodland and chaparral habitats of Southern California threatened by urbanization and land use change. This species is the dominant species in a unique woodland ecosystem in California. It is one of 2 endemic California walnut species (family Juglandaceae). The other species, Northern California black walnut (J. hindsii), has been suggested controversially to be a variety of J. californica. Here, we report a new, chromosome-level assembly of J. californica as part of the California Conservation Genomics Project (CCGP). Consistent with the CCGP common methodology across ~150 genomes, we used Pacific Biosciences HiFi long reads and Omni-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises 137 scaffolds spanning 551,065,703 bp, has a contig N50 of 30 Mb, a scaffold N50 of 37 Mb, and BUSCO complete score of 98.9%. Additionally, the mitochondrial genome has 701,569 bp. In addition, we compare this genome with other existing high-quality Juglans and Quercus genomes, which are in the same order (Fagales) and show relatively high synteny within the Juglans genomes. Future work will utilize the J. californica genome to determine its relationship with the Northern California walnut and assess the extent to which these 2 endemic trees might be at risk from fragmentation and/or climate warming.
Functional response of 3 green lacewing species (Neuroptera: Chrysopidae) toLeucoptera coffeella(Lepidoptera: Lyonetiidae)
Authors: Dami Bruno Gomes , Dos Santos Josy Aparecida , Barbosa Enes Pereira , Rodriguez-Saona Cesar , Vacari Alessandra M 
Published: June 2023

AbstractGreen lacewings (Neuroptera: Chrysopidae) are predators commonly found in coffee plantations in Brazil that can serve as important biological control agents against insect pests such as the coffee leaf miner, Leucoptera coffeella (Lepidoptera: Lyonetiidae). However, the efficacy of different lacewing species in controlling L. coffeella needs to be evaluated before they are used in augmentative biological control programs. Here, laboratory experiments were conducted to investigate the effects of the L. coffeella developmental stage on the functional response of 3 species of green lacewings: Chrysoperla externa, Ceraeochrysa cincta, and Ceraeochrysa cornuta. The attack rate, handling time, and the number of prey attacked during 24 h with different densities (1, 2, 4, 8, 16, 32, and 64 individuals) of either L. coffeella larvae or pupae were recorded for each of the 3 lacewing species. Based on logistic regression models, all 3 predators showed a Type II functional response when consuming both larvae and pupae of L. coffeella. All 3 species also had similar attack rates (0.0091 larva/h and 0.0095 pupa/h), handling times (3.5 and 3.7 h for larvae and pupae, respectively), and estimated number of prey attacked during the observation period (6.9 larvae and 6.6 pupae) for L. coffeella larvae and pupae. Therefore, our laboratory studies show that the 3 green lacewings Ch. externa, Ce. cincta, and Ce. cornuta have potential for the biological control of L. coffeella, although these results need to be confirmed under field conditions. These findings have implications for the selection of lacewings for augmentative L. coffeella biocontrol.
Strengths-Based Factors Related to Post-Traumatic Stress Problems in Black Youth with High Body Weights
Authors: Campbell Kaytryn D , Howell Kathryn H , Napier Taylor R , Maye Caitlyn , Thurston Idia B 
Published: June 2023

Abstract

Objective
Black youth with high body weights [BYHW; Body Mass Index (BMI)≥95th percentile] endure unique stressors (e.g., exposure to discrimination due to race and size) that may contribute to psychopathology. Factors that decrease mental health problems associated with these stressors have been underexamined in BYHW. The current study assessed how multisystemic resilience, weight-related quality of life (QOL), and discrimination were associated with post-traumatic stress problems in BYHW from the perspective of youth and their caregivers.

Methods
A total of 93 BYHW and one of their primary caregivers were recruited from a Midsouth children’s hospital. Youth ranged in age from 11 to 17 years (Mage=13.94, SD = 1.89), were mostly girls (61.3%), and had CDC-defined BMI scores above the 95th percentile. Nearly all caregivers were mothers (91.4%; Mage=41.73 years, SD = 8.08). Youth and their caregivers completed measures of resilience, discrimination, weight-related QOL, and post-traumatic stress problems.

Results
Utilizing linear regression modeling, the youth model was significant [F(3, 89)=31.63, p&lt;.001, Adj. R2=.50], with higher resilience (β=−.23; p=.01) and lower discrimination (β=.52; p&lt;.001) associated with fewer post-traumatic stress problems. The caregiver regression model was also significant [F(2, 90)=10.45, p&lt;.001, Adj. R2=.17], with higher weight-related QOL associated with lower post-traumatic stress problems (β=−.37; p&lt;.001).

Conclusions
Findings illustrate differences in youth and caregiver perceptions of factors related to post-traumatic stress problems in BYHW. Youth emphasized both internal and external contributors to stress, while caregivers focused on internal variables. Such knowledge could be harnessed to develop strengths-based interventions that address health and well-being among BYHW.
Small area estimation under a spatially correlated multivariate area-level model
Authors: Guha Saurav , Chandra Hukum 
Published: June 2023

Abstract
Spatial version of multivariate Fay–Herriot model is introduced and small area predictor under this model is proposed. The residual maximum likelihood is employed for estimating the parameters of the proposed model. Analytical and bootstrap approaches for estimating the mean squared error (MSE) of the proposed predictor are also developed. The performance of the proposed predictor and the MSE estimators are evaluated through various simulation studies. The results evidently show that the proposed predictor outperforms the existing predictors. An application of the proposed methodology has also been made using the 2011–12 Consumer Expenditure Survey data of India.
A case of cutaneous psoriasis vulgaris achieving complete remission post major breast reconstructive surgery
Authors: Ngiam Erica Hian Kim , Fok Denise , Sim Nadia , Wong Allen , Feng Jiajun , Pearlie Tan , Chua Hui Wen , Chan Grace , Kok Yee Onn 
Published: June 2023

Abstract
Psoriasis is a debilitating chronic inflammatory systemic condition largely affecting the skin. Major surgery is relatively contraindicated due to the propensity for triggering psoriatic flares and koebnerization of the surgical scars. We detail an interesting case of complete psoriasis remission following a right nipple-sparing mastectomy with sentinel lymph node biopsy with vascular augmented pedicled transverse rectus abdominal myocutaneous (TRAM) flap in a patient with systemic psoriasis vulgaris and arthropathy. Intra-operatively, majority of the psoriatic plaques were excised or de-epithelized and used as part of the ipsilateral TRAM flap. Post-operatively, koebnerization did not occur and her psoriasis was cured completely even after cancer chemotherapy. One of several hypotheses include excision with de-epithelization of most of the psoriatic plaques reduces disease and inflammatory burden leading to complete remission. Perhaps, surgery could one day play a supporting role to existing treatment options to achieve psoriasis remission.
Defining drivers of under-immunization and vaccine hesitancy in refugee and migrant populations
Authors: Deal Anna , Crawshaw Alison F , Carter Jessica , Knights Felicity , Iwami Michiyo , Darwish Mohammad , Hossain Rifat , Immordino Palmira , Kaojaroen Kanokporn , Severoni Santino , Hargreaves Sally 
Published: June 2023

Abstract

Background/objective
Some refugee and migrant populations globally showed lower uptake of COVID-19 vaccines and are also considered to be an under-immunized group for routine vaccinations. These communities may experience a range of barriers to vaccination systems, yet there is a need to better explore drivers of under-immunization and vaccine hesitancy in these mobile groups.

Methods
We did a global rapid review to explore drivers of under-immunization and vaccine hesitancy to define strategies to strengthen both COVID-19 and routine vaccination uptake, searching MEDLINE, Embase, Global Health PsycINFO and grey literature. Qualitative data were analysed thematically to identify drivers of under-immunization and vaccine hesitancy, and then categorized using the ‘Increasing Vaccination Model’.

Results
Sixty-three papers were included, reporting data on diverse population groups, including refugees, asylum seekers, labour migrants and undocumented migrants in 22 countries. Drivers of under-immunization and vaccine hesitancy pertaining to a wide range of vaccines were covered, including COVID-19 (n = 27), human papillomavirus (13), measles or Measles-mumps-rubella (MMR) (3), influenza (3), tetanus (1) and vaccination in general. We found a range of factors driving under-immunization and hesitancy in refugee and migrant groups, including unique awareness and access factors that need to be better considered in policy and service delivery. Acceptability of vaccination was often deeply rooted in social and historical context and influenced by personal risk perception.

Conclusions
These findings hold direct relevance to current efforts to ensure high levels of global coverage for a range of vaccines and to ensure that marginalized refugee and migrant populations are included in the national vaccination plans of low-, middle- and high-income countries. We found a stark lack of research from low- and middle-income and humanitarian contexts on vaccination in mobile groups. This needs to be urgently rectified if we are to design and deliver effective programmes that ensure high coverage for COVID-19 and routine vaccinations.
A Century and a Quarter of Hoyle
Authors: Levy David 
Published: June 2023

Abstract
Edmond Hoyle wrote the first instructional books on the strategy for card play in the 1740s. The copyright owners, the Proprietors, published them successfully as Hoyle’s Games for a generation. The 1774 decision in Donaldson v Beckett invalidated the copyright and the Proprietors faced legal competition for the first time. Competing booksellers published innovative gaming manuals, marketing them as improved versions of Hoyle, with clearer prose, treatment of additional games, and new formats.
Despite the loss of copyright protection and the resulting competition, an ever-changing group of Proprietors dominated the market for gaming literature until the 1860s. With a bibliographical examination of the books, supplemented by archival records of the book trade, this article documents the Proprietor’s success and the reasons for it. The study provides a nuanced perspective of the impact of the Donaldson decision on an unfamiliar genre of literature.
Five nucleotides found in RCTG motifs are essential for post-fertilization methylation imprinting of the H19 ICR in YAC transgenic mice
Authors: Matsuzaki Hitomi , Takahashi Takuya , Kuramochi Daichi , Hirakawa Katsuhiko , Tanimoto Keiji 
Published: June 2023

Abstract
Genomic imprinting at the mouse Igf2/H19 locus is controlled by the H19 ICR, within which paternal allele-specific DNA methylation originating in sperm is maintained throughout development in offspring. We previously found that a 2.9 kb transgenic H19 ICR fragment in mice can be methylated de novo after fertilization only when paternally inherited, despite its unmethylated state in sperm. When the 118 bp sequence responsible for this methylation in transgenic mice was deleted from the endogenous H19 ICR, the methylation level of its paternal allele was significantly reduced after fertilization, suggesting the activity involving this 118 bp sequence is required for methylation maintenance at the endogenous locus. Here, we determined protein binding to the 118 bp sequence using an in vitro binding assay and inferred the binding motif to be RCTG by using a series of mutant competitors. Furthermore, we generated H19 ICR transgenic mice with a 5-bp substitution mutation that disrupts the RCTG motifs within the 118 bp sequence, and observed loss of methylation from the paternally inherited transgene. These results indicate that imprinted methylation of the H19 ICR established de novo during the post-fertilization period involves binding of specific factors to distinct sequence motifs within the 118 bp sequence.
Mutation signature filtering enables high-fidelity RNA structure probing at all four nucleobases with DMS
Authors: Mitchell David , Cotter Jennifer , Saleem Irfana , Mustoe Anthony M 
Published: June 2023

Abstract
Chemical probing experiments have transformed RNA structure analysis, enabling high-throughput measurement of base-pairing in living cells. Dimethyl sulfate (DMS) is one of the most widely used structure probing reagents and has played a pivotal role in enabling next-generation single-molecule probing analyses. However, DMS has traditionally only been able to probe adenine and cytosine nucleobases. We previously showed that, using appropriate conditions, DMS can also be used to interrogate base-pairing of uracil and guanines in vitro at reduced accuracy. However, DMS remained unable to informatively probe guanines in cells. Here, we develop an improved DMS mutational profiling (MaP) strategy that leverages the unique mutational signature of N1-methylguanine DMS modifications to enable high-fidelity structure probing at all four nucleotides, including in cells. Using information theory, we show that four-base DMS reactivities convey greater structural information than current two-base DMS and SHAPE probing strategies. Four-base DMS experiments further enable improved direct base-pair detection by single-molecule PAIR analysis, and ultimately support RNA structure modeling at superior accuracy. Four-base DMS probing experiments are straightforward to perform and will broadly facilitate improved RNA structural analysis in living cells.
Structural and biochemical insights into the molecular mechanism of TRPT1 for nucleic acid ADP-ribosylation
Authors: Yang Xiaoyun , Wang Jiaxu , Li Simin , Li Xiaobing , Gong Jingjing , Yan Zhenzhen , Zhou Huan , Wu Chen , Liu Xiuhua 
Published: June 2023

Abstract
Nucleic acid ADP-ribosylation has been established as a novel modification found in a wide diversity of prokaryotic and eukaryotic organisms. tRNA 2′-phosphotransferase 1 (TRPT1/TPT1/KptA) possesses ADP-ribosyltransferase (ART) activity and is able to ADP-ribosylate nucleic acids. However, the underlying molecular mechanism remains elusive. Here, we determined crystal structures of TRPT1s in complex with NAD+ from Homo sapiens, Mus musculus and Saccharomyces cerevisiae. Our results revealed that the eukaryotic TRPT1s adopt common mechanisms for both NAD+ and nucleic acid substrate binding. The conserved SGR motif induces a significant conformational change in the donor loop upon NAD+ binding to facilitate the catalytic reaction of ART. Moreover, the nucleic acid-binding residue redundancy provides structural flexibility to accommodate different nucleic acid substrates. Mutational assays revealed that TRPT1s employ different catalytic and nucleic acid-binding residues to perform nucleic acid ADP-ribosylation and RNA 2′-phosphotransferase activities. Finally, cellular assays revealed that the mammalian TRPT1 is able to promote endocervical HeLa cell survival and proliferation. Together, our results provide structural and biochemical insights into the molecular mechanism of TRPT1 for nucleic acid ADP-ribosylation.
Pyrimidine catabolism is required to prevent the accumulation of 5-methyluridine in RNA
Authors: Gao Shangyu , Sun Yu , Chen Xiaoguang , Zhu Changhua , Liu Xiaoye , Wang Wenlei , Gan Lijun , Lu Yanwu , Schaarschmidt Frank , Herde Marco , Witte Claus-Peter , Chen Mingjia 
Published: June 2023

Abstract
5-Methylated cytosine is a frequent modification in eukaryotic RNA and DNA influencing mRNA stability and gene expression. Here we show that free 5-methylcytidine (5mC) and 5-methyl-2′-deoxycytidine are generated from nucleic acid turnover in Arabidopsis thaliana, and elucidate how these cytidines are degraded, which is unclear in eukaryotes. First CYTIDINE DEAMINASE produces 5-methyluridine (5mU) and thymidine which are subsequently hydrolyzed by NUCLEOSIDE HYDROLASE 1 (NSH1) to thymine and ribose or deoxyribose. Interestingly, far more thymine is generated from RNA than from DNA turnover, and most 5mU is directly released from RNA without a 5mC intermediate, since 5-methylated uridine (m5U) is an abundant RNA modification (m5U/U ∼1%) in Arabidopsis. We show that m5U is introduced mainly by tRNA-SPECIFIC METHYLTRANSFERASE 2A and 2B. Genetic disruption of 5mU degradation in the NSH1 mutant causes m5U to occur in mRNA and results in reduced seedling growth, which is aggravated by external 5mU supplementation, also leading to more m5U in all RNA species. Given the similarities between pyrimidine catabolism in plants, mammals and other eukaryotes, we hypothesize that the removal of 5mU is an important function of pyrimidine degradation in many organisms, which in plants serves to protect RNA from stochastic m5U modification.
Evaluating Survival After Hospitalization Due to Immune-Related Adverse Events From Checkpoint Inhibitors
Authors: Silverstein Jordyn , Wright Francis , Wang Michelle , Young Arabella , Kim Daniel , De Dios Kimberly , Brondfield Sam , Quandt Zoe 
Published: June 2023

Abstract

Background
As immune checkpoint inhibitors (CPI) are increasingly approved for cancer treatment, hospitalizations related to severe immune-related adverse events (irAE) will increase. Here, we identify patients hospitalized due to irAEs and describe survival outcomes across irAE, CPI, and cancer type.

Methods
We identified patients hospitalized at our institution from January 2012 to December 2020 due to irAEs. Survival was analyzed using Kaplan-Meier survival curves with log-rank tests.

Results
Of 3137 patients treated with CPIs, 114 (3.6%) were hospitalized for irAEs, resulting in 124 hospitalizations. Gastrointestinal (GI)/hepatic, endocrine, and pulmonary irAEs were the most common causes of irAE-related hospitalization. After CPI initiation, the average time to hospitalization was 141 days. Median survival from hospital admission was 980 days. Patients hospitalized due to GI/hepatic and endocrine irAEs had longer median survival than patients with pulmonary irAEs (795 and 949 days vs. 83 days [P &lt; .001]). Patients with melanoma and renal cell carcinoma had longer median survival than patients with lung cancer (2792 days and not reached vs. 159 days [P &lt; .001]). There was longer median survival in the combination group compared to the PD-(L)1 group (1471 vs. 529 days [P = .04]).

Conclusions
As CPI use increases, irAE-related hospitalizations will as well. These findings suggest that among patients hospitalized for irAEs, survival differs by irAE and cancer type, with worse survival for patients with irAE pneumonitis or lung cancer. This real-world data contributes to research pertaining to hospitalization due to severe irAEs, which may inform patient counseling and treatment decision-making.
Health Equity in Patients Receiving Durvalumab for Unresectable Stage III Non-Small Cell Lung Cancer in the US Veterans Health Administration
Authors: Moore Amanda M , Nooruddin Zohra , Reveles Kelly R , Koeller Jim M , Whitehead Jennifer M , Franklin Kathleen , Datta Paromita , Alkadimi Munaf , Brannman Lance , Cotarla Ion , Frankart Andrew J , Mulrooney Tiernan , Jones Xavier , Frei Christopher R 
Published: June 2023

Abstract

Background
Real-world evidence is limited regarding the relationship between race and use of durvalumab, an immunotherapy approved for use in adults with unresectable stage III non-small cell lung cancer (NSCLC) post-chemoradiotherapy (CRT). This study aimed to evaluate if durvalumab treatment patterns differed by race in patients with unresectable stage III NSCLC in a Veterans Health Administration (VHA) population.

Materials and Methods
This was a retrospective analysis of White and Black adults with unresectable stage III NSCLC treated with durvalumab presenting to any VHA facility in the US from January 1, 2017, to June 30, 2020. Data captured included baseline characteristics and durvalumab treatment patterns, including treatment initiation delay (TID), interruption (TI), and discontinuation (TD); defined as CRT completion to durvalumab initiation greater than 42 days, greater than 28 days between durvalumab infusions, and more than 28 days from the last durvalumab dose with no new durvalumab restarts, respectively. The number of doses, duration of therapy, and adverse events were also collected.

Results
A total of 924 patients were included in this study (White = 726; Black = 198). Race was not a significant factor in a multivariate logistic regression model for TID (OR, 1.39; 95% CI, 0.81-2.37), TI (OR, 1.58; 95% CI, 0.90-2.76), or TD (OR, 0.84; 95% CI, 0.50-1.38). There were also no significant differences in median (interquartile range [IQR]) number of doses (White: 15 [7-24], Black: 18 [7-25]; P = .25) or median (IQR) duration of therapy (White: 8.7 months [2.9-11.8], Black: 9.8 months [3.6-12.0]; P = .08), although Black patients were less likely to experience an immune-related adverse event (28% vs. 36%, P = .03) and less likely to experience pneumonitis (7% vs. 14%, P &lt; .01).

Conclusion
Race was not found to be linked with TID, TI, or TD in this real-world study of patients with unresectable stage III NSCLC treated with durvalumab at the VHA.
Arabidopsis lamin-like proteins CRWN1 and CRWN2 interact with SUPPRESSOR OF NPR1-1 INDUCIBLE 1 and RAD51D to prevent DNA damage
Authors: Yin Chunmei , Sun Aiqing , Guo Tongtong , Mao Xuegao , Fang Yuda 
Published: June 2023

Abstract
Plants cope with various recurring stress conditions that often induce DNA damage, ultimately affecting plant genome integrity, growth, and productivity. The CROWDED NUCLEI (CRWN) family comprises lamin-like proteins with multiple functions, such as regulating gene expression, genome organization, and DNA damage repair in Arabidopsis (Arabidopsis thaliana). However, the mechanisms and consequences of CRWNs in DNA damage repair are largely unknown. Here, we reveal that CRWNs maintain genome stability by forming repairing nuclear bodies at DNA double-strand breaks. We demonstrate that CRWN1 and CRWN2 physically associate with the DNA damage repair proteins RAD51D and SUPPRESSOR OF NPR1-1 Inducible 1 (SNI1) and act in the same genetic pathway to mediate this process. Moreover, CRWN1 and CRWN2 partially localize at γ-H2AX foci upon DNA damage. Notably, CRWN1 and CRWN2 undergo liquid–liquid phase separation to form highly dynamic droplet-like structures with RAD51D and SNI1 to promote the DNA damage response (DDR). Collectively, our data shed light on the function of plant lamin-like proteins in the DDR and maintenance of genome stability.