bluuebunny/crossref_metadata_2025_split huggingface dataset:
Construction and analysis of telomere-to-telomere genomes for 2 sweet oranges: Longhuihong and Newhall (Citrus sinensis)
Authors: Hong Lin , Xu Xin-Dong , Yang Lei , Wang Min , Li Shuang , Yang Haijian , Ye Si-Ying , Chen Ling-Ling , Song Jia-Ming 
Published: November 2024

AbstractBackgroundSweet orange (Citrus sinensis Osbeck) is a fruit crop of high nutritional value that is widely consumed around the world. However, its susceptibility to low-temperature stress limits its cultivation and production in regions prone to frost damage, severely impacting the sustainable development of the sweet orange industry. Therefore, developing cold-resistant sweet orange varieties is of great necessity. Traditional hybrid breeding methods are not feasible due to the polyembryonic phenomenon in sweet oranges, necessitating the enhancement of its germplasm through molecular breeding. High-quality reference genomes are valuable for studying crop resistance to biotic and abiotic stresses. However, the lack of genomic resources for cold-resistant sweet orange varieties has hindered the progress in developing such varieties and researching their molecular mechanisms of cold resistance.FindingsThis study integrated PacBio HiFi, ONT, Hi-C, and Illumina sequencing data to assemble telomere-to-telomere (T2T) reference genomes for the cold-resistant sweet orange mutant “Longhuihong” (Citrus sinensis [L.] Osb. cv. LHH) and its wild-type counterpart “Newhall” (C. sinensis [L.] Osb. cv. Newhall). Comprehensive evaluations based on multiple criteria revealed that both genomes exhibit high continuity, completeness, and accuracy. The genome sizes were 340.28 Mb and 346.33 Mb, with contig N50 of 39.31 Mb and 36.77 Mb, respectively. In total, 31,456 and 30,021 gene models were annotated in the respective genomes. Leveraging these assembled genomes, comparative genomics analyses were performed, elucidating the evolutionary history of the sweet orange genome. Moreover, the study identified 2,886 structural variants between the 2 genomes, with several SVs located in the upstream, downstream, or intronic regions of homologous genes known to be associated with cold resistance.ConclusionsThe study de novo assembled 2 T2T reference genomes of sweet orange varieties exhibiting different levels of cold tolerance. These genomes serve as valuable foundational resources for genomic research and molecular breeding aimed at enhancing cold tolerance in sweet oranges. Additionally, they expand the existing repository of reference genomes and sequencing data resources for C. sinensis. Moreover, these genomes provide a critical data foundation for comparative genomics analyses across different plant species.
Japanese Gold Standard for Added Matter and Its Similarity with G2/21 (Plausibility)
Authors: Morishima Masaki 
Published: November 2024

Abstract
In common with many jurisdictions worldwide, in Japan a patent application or a patent may not be amended in such a way that it contains subject matter that extends beyond the content of the specification as originally filed, i.e., added subject matter (or new matter). However, the method of determining the boundary between allowable and unallowable amendments is unique in Japan, and the Japanese approach is arguably one of the most generous among all major jurisdictions. If a scale is drawn ranging from a ‘photographic’ level at one end (where literal support for an amendment must always be found in the original application) to an ‘impressionistic’ level at the other (where literal support for an amendment does not play any role at all), the Japanese standard is perhaps closer to the latter. This article firstly aims to serve as a practical guide into this unique practice for international users.
As the author believes that the rationale behind the Japanese standard regarding the allowability of amendments shares many things in common with the standard given in G2/21 (i.e., the EPO’s Enlarged Board of Appeal decision regarding a reliance on a purported technical effect for inventive step), the rest of this article then strives to provide a unique approach to interpret the G2/21’s standard, while comparing it with the Japanese added matter standard.
Diversity, occurrence, and conservation status of large branchiopods (Crustacea: Anostraca, Notostraca, Laevicaudata and Spinicaudata) in Northern Cape province, South Africa
Authors: Dabrowski Jackie , Meyer-Milne Elizabeth , Mantshi Hlumelo T , Majingo Zamabhisi , Bills Daksha , Mlambo Musa C 
Published: November 2024

Abstract
We combined historical records from the literature (1950–2022) with recent field surveys and mesocosm-hatching assays conducted in 2018–2023 and found a total of thirty-two species of large branchiopods in Northern Cape province of South Africa, the largest absolute species richness reported in any area in southern Africa. This highlights this province as an important hotspot for large branchiopods, with six endemic species. Five new species (two anostracans and three spinicaudatans) described in the past six years from southern Africa were from the province. Moreover, our study identified four new species awaiting formal description, which not only enrich the overall diversity but also contribute significantly to the conservation value and functional roles within ephemeral waterbodies. Two new South Africa and province records, namely Leptestheria calcarata (Wolf in Daday, 1923) and a potentially undescribed species of PhallocryptusBirabén, 1951 were recorded. Based on the IUCN conservation assessment, three species are classified as critically endangered (CR), 14 as least concern (LC), and seven as data deficient (DD). It is now an opportune time to update the assessment given that the previous assessment of large branchiopods in southern Africa was conducted in the early 90s. This large-scale, province-wide study, taken together with historical records aims to contribute to our understanding of large branchiopods in the Northern Cape province of South Africa.
Characterization of the exopolysaccharides produced by the industrial yeast Komagataella phaffii
Authors: Fischer Amanda , Castagna Vanessa , Omer Shafraz , Marmorstein Micah , Wu Junqi , Ceballos Shannon , Skoog Emma , Lebrilla Carlito B , Suarez Chris , Schnitzler Aletta 
Published: November 2024

Abstract

The yeast Komagataella phaffii has become a popular host strain among biotechnology start-up companies for producing recombinant proteins for food and adult nutrition applications. Komagataella phaffii is a host of choice due to its long history of safe use, open access to protocols and strains, a secretome free of host proteins and proteases, and contract manufacturing organizations with deep knowledge in bioprocess scale-up. However, a recent publication highlighted the abundance of an unknown polysaccharide that accumulates in the supernatant during fermentation. This poses a significant challenge in using K. phaffii as a production host. This polysaccharide leads to difficulties in achieving high purity products and requires specialized and costly downstream processing steps for removal. In this study, we describe the use of the common K. phaffii host strain YB-4290 for production of the bioactive milk protein lactoferrin. Upon purification of lactoferrin using membrane-based separation methods, significant amounts of carbohydrate were copurified with the protein. It was determined that the carbohydrate is mostly composed of mannose residues with minor amounts of glucose and glucosamine. The polysaccharide fraction has an average molecular weight of 50 kDa and consists mainly of mannan, galactomannan, and amylose. In addition, a large fraction of the carbohydrate has an unknown structure likely composed of oligosaccharides. Additional strains were tested in fermentation to further understand the source of the carbohydrates. The commonly used industrial hosts, BG10 and YB-4290, produce a basal level of exopolysaccharide; YB-4290 producing slightly more than BG10. Overexpression of recombinant protein stimulates exopolysaccharide production well above levels produced by the host strains alone. Overall, this study aims to provide a foundation for developing methods to improve the economics of recombinant protein production using K. phaffii as a production host.

One-Sentence Summary
Overexpression of recombinant protein stimulates the hyperproduction of high-molecular-weight, mannose-based, exopolysaccharides by the industrial yeast Komagataella phaffii.
Structure and functions of soil microbial communities and tree composition are more closely associated with keystone microbes than rare microbes in a subtropical forest
Authors: Wu Xian , Deane David C , Xing Hua , Yang Jiarong , Chen Junfang , Liu Xiaolin , Dong Shu , He Fangliang , Liu Yu 
Published: November 2024

Abstract
The significance of microbes for ecosystem functioning is well known; however, within a single system, the relative contributions of keystone and rare taxa to soil microbial functions are less well quantified, as are their shared or unique responses to abiotic conditions. Furthermore, their associations with tree community composition in natural forest ecosystems are not well understood. In this study, a total of 1,287 soil samples were collected from a 20-ha subtropical forest plot and analyzed using high-throughput sequencing. Based on co-occurrence network analyses, we conducted a comparison of the associations between keystone and rare taxa with the structure, functions, and stability of soil microbial communities. Additionally, we examined their associations with tree community composition. Results showed that keystone taxa made a significantly greater contribution than rare taxa in all comparisons of microbial functions and stability. Keystone taxa had direct effects on microbial community structure and also mediated indirect effects of abiotic conditions. Neither effect was evident for rare taxa. The importance of keystone taxa also extended to aboveground composition, where tree community composition was more closely associated with keystone taxa than with rare taxa. While it may still be premature to establish causality, our study represents one of the initial attempts to compare the relative importance of keystone and rare microbial taxa in forest soils. These findings offer the potential to improve natural forest ecosystem functioning and tree diversity through the manipulation of a small number of keystone soil microbial taxa, as has been demonstrated in agroecosystems.
Psychosocial correlates of alcohol and substance use in college youth with type 1 diabetes
Authors: Tsevat Rebecca K , Weitzman Elissa R , Wisk Lauren E 
Published: November 2024

Abstract

Objective
Adolescents and young adults with chronic diseases face unique challenges during the college years and may consume alcohol and other substances to cope with stressors. This study aimed to assess the patterns of substance use and to determine psychosocial correlates of these behaviors among college youth with type 1 diabetes (T1D).

Methods
College youth with T1D were recruited via social media and direct outreach into a web-based study. Participants answered validated questions about substance use, and they completed validated screeners of depressive and anxiety symptoms (PHQ-2 and GAD-2), illness acceptance (ICQ), interpersonal support (ISEL), and grit (Grit scale). Descriptive statistics, bivariate analyses, and multivariable regression evaluated substance use behaviors as a function of psychosocial factors while adjusting for age and sex.

Results
Alcohol (84.06%) and marijuana (41.30%) were the most common substances reported. In bivariate analyses, depressive symptoms were positively associated (p = .01) and illness acceptance was inversely associated (p = .02) with marijuana use. Higher grit scores were inversely associated with marijuana use (p &lt; .001) and prescription drug misuse (p = .04). The significant associations between marijuana use and depressive symptoms (adjusted odds ratio [AOR] 1.31, 95% confidence interval [CI] 1.04–1.66), illness acceptance (AOR 0.96, 95% CI 0.91–0.99), and grit (AOR 0.32, 95% CI 0.17–0.60) persisted after adjustment for age and sex.

Conclusions
Substance use is prevalent among college youth with T1D. While psychosocial factors such as depressive symptoms may confer an increased risk, illness acceptance and grit may be protective—especially against marijuana use. Providers should address both positive and negative psychosocial factors to mitigate substance use in this population.
Perforated anterior tenia coli-type appendicitis in a case of vermiform appendix duplex in a toddler: a case report
Authors: Zvizdic Zlatan , Bukvic Melika , Ibisevic Nermina , Firdus Alena , Jonuzi Asmir , Vranic Semir 
Published: November 2024

Abstract
Duplication of the vermiform appendix is a rare anomaly observed in patients undergoing appendectomy. A 27-month-old male toddler presented with a 9-day history of abdominal pain, vomiting, and diarrhea, progressing to an acute abdomen with signs of severe peritonitis. Intraoperative findings revealed a periappendicular infiltrate from a perforated vermiform appendix of the tenia coli type. A second, inflamed appendix was incidentally discovered in its typical location during the procedure. Vermiform appendix duplication presents a clinical challenge due to its rarity and potential for complications. According to the Cave–Wallbridge classification, this case represents Type B2, or the tenia coli variant, characterized by a perforated appendix originating at the tenia coli convergence and a smaller, secondary appendix in a retrocecal position. This case emphasizes the importance of thorough distal and proximal exploration during initial appendectomy when this anomaly is suspected, particularly in cases of Type B2.
Serotonin signaling to regulate energy metabolism: a gut microbiota perspective
Authors: Li Guoli , Dong Sijing , Liu Chunhao , Yang Jing , Rensen Patrick C N , Wang Yanan 
Published: November 2024

Abstract
Serotonin is one of the most potent gastrointestinal, peripheral, and neuronal signaling molecules and plays a key role in regulating energy metabolism. Accumulating evidence has shown the complex interplay between gut microbiota and host energy metabolism. In this review, we summarize recent findings on the role of gut microbiota in serotonin metabolism and discuss the complicated mechanisms by which serotonin, working in conjunction with the gut microbiota, affects total body energy metabolism in the host. Gut microbiota affects serotonin synthesis, storage, release, transport, and catabolism. In addition, serotonin plays an indispensable role in regulating host energy homeostasis through organ crosstalk and microbe–host communication, particularly with a wide array of serotonergic effects mediated by diverse serotonin receptors with unique tissue specificity. This fresh perspective will help broaden the understanding of serotonergic signaling in modulating energy metabolism, thus shedding light on the design of innovative serotonin-targeting strategies to treat metabolic diseases.
Three-dimensional Stacking of Phase Plates for Advanced Electron Beam Shaping
Authors: Ruffato Gianluca , Beleggia Marco , Tavabi Amir Hossein , Rotunno Enzo , Viani Lorenzo , Rosi Paolo , Kavkani Payam Habibzadeh , Chiari Caterina , Frabboni Stefano , Gazzadi Gian Carlo , Pozzi Giulio , Bertoni Giovanni , Tiemeijer Peter , Dunin-Borkowski Rafal Edward , Grillo Vincenzo 
Published: November 2024

Abstract
Tuneable phase plates for free electrons are a highly active area of research. However, their widespread implementation, similar to that of spatial light modulators in light optics, has been hindered by both conceptual and technical challenges. A specific technical challenge involves the need to minimize obstruction of the electron beam by supporting films and electrodes. Here, we describe numerical and analytical mathematical frameworks for three-dimensional stacks of phase plates that can be used to provide near-arbitrary electron beam shaping with minimal obstruction.
Dosimetry as a Lagging Indicator of Occupational Exposure to Nitrous Oxide in Pediatric Sedation: A Collaborative Process Improvement Project With Industrial Hygiene
Authors: Kicker Jennifer S , Timbie Cynthia Y , Kline Susan L 
Published: November 2024

ABSTRACT

Introduction
Nitrous oxide (N2O) is commonly used in pediatric procedural sedation. It is an attractive option to facilitate intravenous line placement, as it does not extend sedation recovery from subsequently administered agents. Although debate exists regarding health consequences of occupational exposure now that scavenging of exhaled gases is common, cooperation of pediatric patients to maximize engineering controls is not guaranteed and can contribute to repeated exposure over the course of a clinician’s career. There is no global consensus on personal exposure limits, but the National Institute for Occupational Safety and Health published U.S. guidelines. A dosimetry survey of our sedation team during a short N2O procedure for intravenous line placement exceeded the National Institute for Occupational Safety and Health Recommended Exposure Limit (REL) of 25 parts per million. We designed a process improvement initiative to reduce occupational exposure below the Recommended Exposure Limit on serial surveys.

Materials and Methods
A continuous flow, titratable, full-face mask N2O delivery system with scavenging by a central vacuum connection was used. A retrospective chart review of N2O procedures performed before the initial dosimetry survey revealed practice trends in provider behavior during N2O administration. Initiation of N2O gas flow and maintenance of face mask seal on an uncooperative patient were identified as two sources of variability. Two-handed face-masking technique, initiation of N2O gas flow only after masking, and continued masking for 2 min of exhaled scavenging were standardized and socialized as best practices. Subsequent dosimetry surveys of the sedation team were coordinated by Industrial Hygiene.

Results
Pre- and post-intervention phases were 17 months each and included 92 and 201 N2O patients, respectively. Six dosimetry surveys occurred in the post phase. Intravenous line placement was the typical procedure surveyed. Dosimetry results for all team members during surveys 1-4 were below the REL, with 14 of 16 samples falling below the level of quantitation. Elevated dosimetry results in survey 5 prompted reevaluation of work practices and equipment. A loose component on the delivery system was discovered, corrected, and incorporated as a pre-procedure check. With no further changes to work practices, dosimetry results were below the REL for survey 6.

Conclusion
We layered work practice changes atop engineering controls to reduce occupational exposure levels for medical team members. We utilized dosimetry as a lagging indicator, prompting frequent reassessments of our equipment and processes that we might not otherwise have performed. Pediatric sedation programs are encouraged to consider whether Industrial Hygiene resources might provide synergy to process improvement efforts with inhalational sedation agents.
Navigating the Leadership Tightrope: A Case Study in the Art of Following and Supporting
Authors: Pflipsen Matthew C 
Published: November 2024

ABSTRACT
Military physicians serve as staff officers where both leading and following are important competencies. Navigating between the two roles is a necessary skill to avoid undermining one’s boss and to support the mission. This case describes a deployed junior officer reconciling his role as the lead medical expert while supporting a Commander’s decision, highlighting the challenges of followership in situations of disagreement.
The temporal and spatial variations of lithium abundance in the Galactic disc
Authors: Sun Tiancheng , Bi Shaolan , Chen Xunzhou , Lu Yuxi (Lucy) , Chen Yuqin , Ding Ming-Yi , Shi Jianrong , Yan Hongliang , Ge Zhishuai 
Published: November 2024

ABSTRACT
This study investigates the temporal and spatial variations in lithium abundance within the Milky Way using a sample of 22 034 main-sequence turn-off (MSTO) stars and subgiants, characterized by precise stellar ages, 3D non-local thermodynamic equilibrium lithium abundances, and birth radii. Our results reveal a complex variation in lithium abundance with stellar age: a gradual increase from 14 to 6 Gyr, followed by a decline between 6 and 4.5 Gyr, and a rapid increase thereafter. We find that young Li-rich stars (ages $\lt $ 4 Gyr, A(Li) $\gt $ 2.7 dex) predominantly originate from the outer disc. By binning the sample according to guiding centre radius and z$_{\rm max}$, we observe that these young Li-rich stars migrate radially to the local and inner discs. In addition, the stars originating from the inner disc experienced a rapid Li enrichment process between 8 and 6 Gyr. Our analysis suggests that the age range of Li-dip stars is 4–5 Gyr, encompassing evolution stages from MSTO stars to subgiants. The Galactic radial profile of A(Li) (with respect to birth radius), as a function of age, reveals three distinct periods: 14–6 Gyr ago, 6–4 Gyr ago, and 4–1 Gyr ago. Initially, the lithium abundance gradient is positive, indicating increasing Li abundance with birth radius. During the second period, it transitions to a negative and broken gradient, mainly affected by Li-dip stars. In the final period, the gradient reverts to a positive trend.
Portraits of Galeommatoidea
Authors: Bouchet Philippe , Strong E E 
Published: November 2024

ABSTRACT
Galeommatoidea are bivalves with small (usually 1–15 mm), fragile, sometimes vestigial, shells, occurring free-living or in association with other benthic invertebrates from the intertidal to depths in excess of 7,000 m. They are the most diverse but least studied and most underrepresented group of bivalves in biodiversity surveys and museum collections. The majority of commensal species of Galeommatoidea have dull, frequently uncoloured, unsculptured shells, but free-living species have papillate, sometimes coloured, mantles; they can be gregarious, and superficially resemble crawling gastropods. Many species of Galeommatoidea remain to be discovered, and we argue that future descriptions of free-living new species should ideally include photos of living animals, while many of the historically known species described based on their shells will probably be best treated as nomina dubia.
Metals in the gut: microbial strategies to overcome nutritional immunity in the intestinal tract
Authors: Egan Marisa S , de Macedo Raquel , Zackular Joseph P 
Published: November 2024

Abstract
Trace metals are indispensable nutritional factors for all living organisms. During host-pathogen interactions, they serve as crucial resources that dictate infection outcomes. Accordingly, the host uses a defense strategy known as nutritional immunity, which relies on coordinated metal chelation to mitigate bacterial advances. In response, pathogens employ complex strategies to secure these resources at sites of infection. In the gastrointestinal (GI) tract, the microbiota must also acquire metals for survival, making metals a central line of competition in this complex ecosystem. In this minireview, we outline how bacteria secure iron, zinc, and manganese from the host with a focus on the GI tract. We also reflect on how host dietary changes impact disease outcomes and discuss therapeutic opportunities to target bacterial metal uptake systems. Ultimately, we find that recent discoveries on the dynamics of transition metals at the host-pathogen-microbiota interface have reshaped our understanding of enteric infections and provided insights into virulence strategies, microbial cooperation, and antibacterial strategies.