bluuebunny/crossref_metadata_2025_split huggingface dataset:
Subarctic sugar kelp (Saccharina latissima, Phaeophyceae) summer productivity and contribution to carbon budgets
Authors: Roy Stéphanie , Nozais Christian , Johnson Ladd E. , Noisette Fanny 
Published: November 2024

AbstractKelp forests are known to be very productive ecosystems and constitute a central component of the marine carbon cycle in coastal areas. Nevertheless, crucial carbon‐related data are missing to be able to include them properly in carbon budgets. A thorough understanding of the kelp contribution to the carbon cycle is especially important in regions prone to experiencing strong seasonal fluctuations in environmental conditions, such as subarctic regions. This study aimed to quantify primary productivity through growth rates and oxygen fluxes of a dominant kelp species in subarctic regions, Saccharina latissima, and to link oxygen fluxes to environmental parameters. Our results showed that strong primary productivity oxygen fluxes coincided with high light levels in July and most of August, while growth rates stayed similar all summer. An overall decline in all primary productivity proxies happened from late August, suggesting a seasonal slowing down of S. latissima metabolism. The estimated quantity of carbon stored in tissue during growth represented from 6% to 28% of the gross primary productivity. Further research is needed to explore how and how much carbon transits through living kelp tissue in different seasons, to better understand the contribution of subarctic kelp to coastal carbon budgets.
Demographic Change and Social Cohesion In Post‐Islamic State Iraq
Authors: Ali Omran Omer , Mohammed Nazar Ameen , Broeckerhoff Aurélie 
Published: November 2024

AbstractBetween 2014 and 2017, the Islamic State (ISIS) brutally ruled over a population of eight million in Iraq and Syria. The group systematically persecuted and murdered tens of thousands of people of minoritized ethnicities and destroyed their houses and heritage, schools and hospitals, resulting in the displacement of an estimated three to five million people. In this article, we analyze the ongoing impact of the ISIS occupation on social cohesion in Iraq. Our report is based on interviews conducted with community representatives in the Nineveh Plains of the country's northwest. We focus on the dynamics of displacement and return in historically Christian, Assyrian‐majority areas during and since the occupation. Our findings show that people's everyday experiences and senses of community in Nineveh are intertwined with adjusting to the recent population changes, which have redrawn ethnic minority/majority relations. The research illustrates that demographic change—which we define as shifts in ethnic composition—is a relevant consideration for policies that seek to foster social cohesion in post‐ISIS Iraq. More broadly, the article highlights how post‐conflict policy making benefits from research conducted directly with conflict‐affected populations, as it reflects communities’ experiences.
High school athletes' practical knowledge on where to find and order third‐party tested nutritional supplements increases after education when compared to a control group
Authors: Dow Emily , Schott Kinta D. , Morton Lindsay , Lybbert Hannah , Nam Kahyun , Shumate Colin , Kulinna Pamela , Wardenaar Floris C. 
Published: November 2024

AbstractTo promote safe supplement use, athletes are advised to choose third‐party tested (TPT) supplements to minimise doping risk. This study evaluated changes in knowledge on supplements in US high school athletes from a 2‐week online supplement education programme. One group of sophomores (ED, n = 48) completed a Canvas course on safe supplement use, based on the Theory of Planned Behaviour, while the other group of freshmen (NOED, n = 38) did not. Participants completed questionnaires pre‐ and post‐intervention to assess practical knowledge of finding and ordering TPT supplements, familiarity with World Anti‐Doping Agency (WADA) banned substances and decision‐making in supplement purchasing. Chi‐Square and McNemar tests were applied with significance set at p ≤ 0.05. Pre‐intervention no differences were found between groups (ages 14–17 years, 39.5% female) for any knowledge questions (p = 0.18). Post‐intervention, ED participants were more likely to know where to find (58.3% vs. 39.5%, p = 0.041), and order (62.5% vs. 28.9%, p = 0.001) TPT supplements, and more athletes in ED (72.9%) than NOED (40.0%) reported deciding to purchase supplements themselves (p = 0.015). Parents were less influential in ED (75.0% vs. 92.1%, p = 0.019). Importantly, positive changes over time were larger for ED versus NOED in knowing where to find (28% vs. 13%, p = 0.04) and order (28% vs. 7%, p < 0.001) TPT supplements and WADA familiarity (19% vs. 5%, p = 0.01). Within‐group changes showed ED improved on all practical knowledge questions (p = <0.001–0.008), whereas NOED only increased in knowing where to find TPT supplements (p = 0.003). These findings suggest an online educational programme may enhance practical knowledge of safe supplement use among high school athletes.
Patterns of presence–absence variation of NLRs across populations of Solanum chilense are clade‐dependent and mainly shaped by past demographic history
Authors: Silva‐Arias Gustavo A. , Gagnon Edeline , Hembrom Surya , Fastner Alexander , Khan Muhammad Ramzan , Stam Remco , Tellier Aurélien 
Published: November 2024

Summary

Understanding the evolution of pathogen resistance genes (nucleotide‐binding site‐leucine‐rich repeats, NLRs) within a species requires a comprehensive examination of factors that affect gene loss and gain.

We present a new reference genome of Solanum chilense, which leads to an increased number and more accurate annotation of NLRs. Using a target capture approach, we quantify the presence–absence variation (PAV) of NLR loci across 20 populations from different habitats. We build a rigorous pipeline to validate the identification of PAV of NLRs and then show that PAV is larger within populations than between populations, suggesting that maintenance of NLR diversity is linked to population dynamics.

The amount of PAV appears not to be correlated with the NLR presence in gene clusters in the genome, but rather with the past demographic history of the species, with loss of NLRs in diverging (smaller) populations at the distribution edges. Finally, using a redundancy analysis, we find limited evidence of PAV being linked to environmental gradients.

Our results suggest that random processes (genetic drift and demography) and weak positive selection for local adaptation shape the evolution of NLRs at the single nucleotide polymorphism and PAV levels in an outcrossing plant with high nucleotide diversity.
Three‐Dimensional Printed Prosthesis Reconstructs Bilateral Type III Pelvic Defect After Malignant Tumors Resection
Authors: He Xuanhong , Luo Yi , Zou Chang , Lu Minxun , Zhang Yuqi , Li Zhuangzhuang , Kenmegne Guy Romeo , Zhou Yong , Min Li , Tu Chongqi 
Published: November 2024

ABSTRACTObjectiveType III hemipelvectomy and reconstruction are challenging. Several reconstruction options, including autologous soft tissue, prosthesis patch, autologous, or allograft, were reported, but a variety of shortcomings limited their application. Three‐dimensional (3D)‐printed prosthesis was designed to reconstruct the unilateral Type III pelvic defect and had favorable clinical outcomes. However, the reconstruction method for bilateral Type III pelvic defect was few reported. This study aims to design a bilateral pubis prosthesis and evaluate the early clinical outcomes and complications.MethodsWe retrospectively collected patients receiving 3D‐printed bilateral pubis prosthesis reconstruction after malignant tumor resection between 2017 and 2021. Demographics, anatomic data, operation time, blood loss, and clinical outcomes of patients were analyzed. The Musculoskeletal Tumor Society‐93 (MSTS‐93) score was performed to evaluate the function and complications were recorded.ResultsFour patients, including three for females and one for males, were enrolled in this study. Prosthesis was designed according to the pelvic anatomical data. The mean operation time and blood loss were 308.8 min (range, 240–400 min) and 655 mL (range, 400–1100 mL), respectively. The average follow‐up was 15.5 months (range, 12–16 months). The mean MSTS was 28.5 (28–29). One patient had incision necrosis postoperatively. No hernia, prosthesis displacement, or implant failure occurred during follow‐up. Four patients with 15 interfaces showed good osteointegration.Conclusions3D‐printed bilateral pubis prosthesis could restore the integrity and stability of pelvic ring and improve limb function. Meanwhile, this reconstruction option provided a rigid bony‐soft support to prevent the development of hernia. In all, 3D‐printed bilateral pubis prosthesis is recommended to be a favorable selection for Type III pelvic defect reconstruction.
The SUMO‐conjugating enzyme OsSCE1a from wild rice regulates the functional stay‐green trait in rice
Authors: Yuan Xuzhao , Luan Yanfang , Liu Dong , Wang Jian , Peng Jianxiang , Zhao Jinlei , Li Lupeng , Su Jingjing , Xiao Yang , Li Yuanjie , Ma Xin , Zhu Xiaoyang , Tan Lubin , Liu Fengxia , Sun Hongying , Gu Ping , Xu Ran , Zhang Peijiang , Zhu Zuofeng , Sun Chuanqing , Fu Yongcai , Zhang Kun 
Published: November 2024

SummaryThe functional stay‐green trait is a major goal of rice breeding. Here, we cloned OsSCE1a encoding SUMO‐conjugating enzyme from Yuanjiang common wild rice, which simultaneously regulates the functional stay‐green trait and growth duration. Low expression or knocking out OsSCE1a corresponded to increased chlorophyll content, photosynthetic competence, N use efficiency and a shortened growth period without affecting yield. A natural MITE‐transposon insertion/deletion in the OsSCE1a promoter is the functional variation that regulates these traits. OsSCE1a was selected during evolution and shows significant variation between indica and japonica rice. OsNAC2 interacts with the MITE to enhance OsSCE1a expression. Genetic manipulation of OsSCE1a revealed its potential for rice improvement. OsSCE1a‐mediated SUMOylation of OsGS2 suppresses GS (involved in N assimilation) enzyme activity. OsSCE1a also regulates growth duration by SUMOylating the transcription factor such as OsGBP1, which regulates the expression of the key heading gene Ghd7. Our findings shed light on the role of SUMOylation in crops and provide a strategy for increasing agricultural productivity.
Deciphering Evolutionary Patterns and Multifaceted Drivers of Tibetan Buddhist Monasteries in Amdo's Tibetan Inhabited Area, China
Authors: Yang Yao , Zhao Yaolong , Fang Subin , Liu Xinxin , Li Xueting , Chen Danying 
Published: November 2024

ABSTRACTTibetan Buddhism, which has been nurtured and developed within the unique geographical environment of the Qinghai‐Tibet Plateau, represents a religious and cultural phenomenon that exhibits distinct regional and ethnic characteristics. Investigating the spatiotemporal evolution of Tibetan Buddhism is essential for a comprehensive understanding of this religious practice. Traditional research has largely concentrated on qualitative descriptions derived from historical data compilation, neglecting the quantitative analysis of its spatiotemporal evolution and underlying mechanisms. This study seeks to quantitatively explore evolutionary patterns and various factors influencing the historical development of Tibetan Buddhist culture within Amdo Tibetan cultural heartland in China. Utilizing Tibetan Buddhist monasteries as cultural carriers, the research employed spatiotemporal data mining and machine learning methods to uncover these dynamics. The results show that: (1) The quantity of Tibetan Buddhist monasteries in the Amdo region has substantially grown over time, exhibiting increasingly noticeable spatial clustering characteristics; (2) Factors such as the concentration of population and economic activities, accessibility to water resources, climate and agricultural production conditions, and convenience of transportation significantly impact the spatiotemporal evolution of Tibetan Buddhism; (3) Under the combined influence of macro‐geographical environment factors and micro‐level religious heritage history, the Amdo Tibetan inhabited area has gradually developed a spatial pattern characterized by clusters of monasteries centered in the Hehuang Valley, with widespread distribution throughout the eastern region. The quantitative research framework proposed in this paper offers an academic reference for exploring the spatiotemporal evolution of complex religious and cultural phenomena across long historical periods.
GhTBL3 is required for fiber secondary cell wall (SCW) formation via maintaining acetylation of xylan in cotton
Authors: Wang Yao , Zou Dan , Cheng Chang‐Hao , Zhang Jie , Zhang Jing‐Bo , Zheng Yong , Li Yang , Li Xue‐Bao 
Published: November 2024

SUMMARYTBL family proteins containing the domain of unknown function mainly act as xylan O‐acetyltransferases, but the specific molecular mechanism of their functions remains unclear in plants (especially in cotton) so far. In this study, we characterized the TBL family proteins containing the conserved GDS and DxxH motifs in cotton (Gossypium hirsutum). Among them, GhTBL3 is highly expressed in fibers at the stage of secondary cell wall (SCW) formation and mainly functions as O‐acetyltransferase to maintain acetylation of xylan in fiber SCW development. Overexpression of GhTBL3 in cotton promoted fiber SCW formation, resulting in increased fiber cell wall thickness. In contrast, suppression of GhTBL3 expression in cotton impaired fiber SCW synthesis, leading to the decreased fiber cell wall thickness, compared with wild type (WT). Furthermore, two fiber SCW‐related transcription factors GhMYBL1 and GhKNL1 were found to directly bind to the promoter of GhTBL3 in cotton. GhMYBL1 enhanced the transcription activity of GhTBL3, whereas GhKNL1 inhibited the expression of GhTBL3 in fibers. The acetylation level of xylan was remarkably decreased in fibers of GhMYBL1 RNAi transgenic cotton, but the acetylation level of xylan was significantly increased in fibers of GhKNL1 RNAi cotton, relative to WT. Given together, the above results suggested that GhTBL3 may be under the dual control of GhMYBL1 and GhKNL1 to maintain the suitable acetylation level of xylan required for fiber SCW formation in cotton. Thus, our data provide an effective clue for potentially improving fiber quality by genetic manipulation of GhTBL3 in cotton breeding.
Detection of quantitative trait loci for rice root systems grown in paddies based on nondestructive phenotyping using X‐ray computed tomography
Authors: Teramoto Shota , Uga Yusaku 
Published: November 2024

SUMMARYPlant roots are essential for water and nutrient uptake, as well as resistance to abiotic stresses. While measuring root systems under field conditions is labor‐intensive, most quantitative trait loci (QTLs) related to root traits have been detected under artificial conditions. However, QTLs identified under artificial conditions may not always manifest the expected effects that are observed under field conditions. To address this issue, we developed RSApaddy3D, a rapid phenotyping method for rice root systems, using X‐ray computed tomography (CT) volumes of soil blocks collected from paddies. RSApaddy3D employs 2‐dimensional kernel filters tailored to extract disk‐shaped fragments from the CT volumes. Tubular root fragments are expected to exhibit disk‐shaped cross‐sections along the x‐, y‐, or z‐axes. By applying these filters along all three axes and integrating the results, 3‐dimensional root fragments can be accurately extracted. Furthermore, vectorizing the root system enables geometrical removal of the roots of neighboring individuals. We conducted a genome‐wide association study (GWAS) of root diameter, number, and growth angle in 133 Japanese rice varieties and detected three QTLs (qNCR1, qNCR2, and qRGA1) that were associated with each trait. This process was completed within 10 person‐days from soil monolith collection in the paddy to the GWAS. Without RSApaddy3D, roots would need to be washed from the soil monolith and measured, which is estimated to require >500 person‐days. Therefore, RSApaddy3D was approximately 50× more labor‐saving. In summary, we have demonstrated that RSApaddy3D is an efficient method for phenotyping rice root systems under field conditions.
Finite subgroups of the profinite completion of good groups
Authors: Boggi Marco , Zalesskii Pavel 
Published: November 2024

AbstractLet be a residually finite, good group of finite virtual cohomological dimension. We prove that the natural monomorphism induces a bijective correspondence between conjugacy classes of finite ‐subgroups of and those of its profinite completion . Moreover, we prove that the centralizers and normalizers in of finite ‐subgroups of are the closures of the respective centralizers and normalizers in . With somewhat more restrictive hypotheses, we prove the same results for finite solvable subgroups of . In the last section, we give a few applications of this theorem to hyperelliptic mapping class groups and virtually compact special toral relatively hyperbolic groups (these include fundamental groups of 3‐orbifolds and of uniform standard arithmetic hyperbolic orbifolds).
Systematic analysis of the glucose-PTS in
Streptococcus sanguinis
highlighted its importance in central metabolism and bacterial fitness
Authors: Taylor Zachary A. , Pham Danniel N. , Zeng Lin 
Published: November 2024

ABSTRACT

Previous work reported that deletion of the Enzyme IIAB subunits (EIIAB
Man
and
manL
) of the glucose phosphotransferase system (PTS) (glucose-PTS,
manLMNO
) in
Streptococcus sanguinis
impacted carbon catabolite repression and bacterial fitness. Here, a single-nucleotide polymorphism in ManN, ManNA91E, produced the unusual phenotype of increased excretion of organic acids and H
2
O
2
yet elevated PTS activities. To characterize the contributions of each component of the glucose-PTS to bacterial fitness, we performed genetic analyses by deleting from
S. sanguinis
SK36 the entire operon and each EII
Man
subunit individually; and genes encoding the catabolite control protein A (Δ
ccpA
) and the redox regulator Rex (Δ
rex
) for comparison. Deletion of each subunit incurred a growth defect on glucose partly due to elevated excretion of H
2
O
2
; when supplemented with catalase, this defect was rescued, instead resulting in a significantly higher yield than the parent. All glucose-PTS deletion mutants presented an increased antagonism against the oral pathobiont
Streptococcus mutans
, a phenotype absent in Δ
ccpA
despite increased H
2
O
2
output. A shift in the pyruvate node toward mixed acid fermentation and increased arginine deiminase activity enhanced pH homeostasis in glucose-PTS mutants but not Δ
ccpA
. Despite the purported ability of Rex to regulate central carbon metabolism, deletion of
rex
had no significant impact on most of the phenotypes discussed here. These findings place glucose-PTS in the pivotal position of controlling central carbon flux in streptococci, with critical outcomes impacting acidogenicity, aciduricity, pH homeostasis, and antagonism, highlighting its potential as a therapeutic target for treating diseases with a dysbiotic microbiome.

IMPORTANCE

Management of carbohydrate metabolism and environmental stress is key to the survival of oral commensal species such as
S. sanguinis
. Antagonism of oral pathobionts and modulation of the environmental pH and oxidative potential by commensals are crucial to the maintenance of microbial homeostasis and prevention of oral diseases including dental caries. It is therefore vital to understand how these species regulate sugar fermentation, production of acids and ammonia, and stress management in an environment known for a feast-and-famine cycle of carbohydrates and similar fluctuations in pH and oxygen tension. Here, we detail that genetic alterations of the glucose-PTS transporter in
S. sanguinis
can significantly affect the regulation of factors required for bacterial fitness and homeostatic ability independent of known catabolic regulators. It is then discussed how these changes may impact the survival of streptococcal species and affect caries onset.
Emergence of terbinafine-resistant
Trichophyton indotineae
in Ontario, Canada, 2014–2023
Authors: McTaggart Lisa R. , Cronin Kirby , Ruscica Sonja , Patel Samir N. , Kus Julianne V. 
Published: November 2024

ABSTRACT

Trichophyton indotineae
is an emerging fungal pathogen capable of causing extensive recalcitrant dermatophytosis exacerbated by frequently retained terbinafine resistance. Cases of dermatophytosis due to
T. indotineae
have increased dramatically in India in recent years. Other countries have reported imported infection cases, causing public health concerns over the potential global spread of this drug-resistant pathogen. We describe
T. indotineae
from 47 clinical cases in Ontario, Canada, from 2014 to 2023, based on 50 isolates received by the provincial public health laboratory. Although detected in Ontario as early as 2014, cases increased sharply in 2022–2023. The majority of cases were found in 20 to 64-year-olds (83.0%). Cases from 2022 to 2023 were noted in only 8 of 34 public health units, clustering in large urban centers. Based on genomic epidemiology, Ontario isolates were genetically similar to isolates from other countries. Neither temporal nor geographic clustering based on country or public health unit was observed, suggesting Ontario cases represented recent introductions from endemic regions, although limited local transmission cannot be ruled out. Genome diversity (4.4 × 10
−6
) was extremely low, consistent with the hypothesized recent emergence and clonal population structure of
T. indotineae
. Most (71.4%) cases were terbinafine-resistant, with isolates exhibiting either the L393F/L393S (
n
= 3) or F397L (
n
= 27) squalene epoxidase substitution. Decreased susceptibility to itraconazole or voriconazole was found among 23.7% of isolates and was frequently associated with
CYP51B
gene duplication. Terbinafine-resistant
T. indotineae
infections are escalating in Ontario, meriting enhanced laboratory detection methods and public health efforts to increase the awareness of recalcitrant dermatophytoses in order to promptly initiate appropriate treatment and control transmission.

IMPORTANCE

Cases of dermatophytosis caused by emerging pathogen
Trichophyton indotineae
are increasing worldwide. Many are resistant to first-line treatment option terbinafine, resulting in difficult-to-treat cases. We describe the emergence of cases of
T. indotineae
infections in Ontario, Canada. The incidence in primarily urban centers increased dramatically in 2022–2023, with a large percentage of isolates resistant to terbinafine. Decreased susceptibility to azoles was also observed for some isolates, raising concern over the potential evolution of multi-drug resistance. Ontario
T. indotineae
isolates were genetically similar to those from disparate locales worldwide, signifying the global nature of this public health concern. Together with other reports, this study serves to raise public health awareness to promote better laboratory detection procedures, prompt appropriate treatment of recalcitrant dermatophytoses, and inform infection prevention and control measures.