bluuebunny/crossref_metadata_2025_split huggingface dataset:
Potential for functional divergence in ectomycorrhizal fungal communities across a precipitation gradient
Authors: Pellitier Peter T , Van Nuland Michael , Salamov Asaf , Grigoriev Igor V , Peay Kabir G 
Published: March 2024

Abstract
Functional traits influence the assembly of microbial communities, but identifying these traits in the environment has remained challenging. We studied ectomycorrhizal fungal (EMF) communities inhabiting Populus trichocarpa roots distributed across a precipitation gradient in the Pacific Northwest, USA. We profiled these communities using taxonomic (meta-barcoding) and functional (metagenomic) approaches. We hypothesized that genes involved in fungal drought-stress tolerance and fungal mediated plant water uptake would be most abundant in drier soils. We were unable to detect support for this hypothesis; instead, the abundance of genes involved in melanin synthesis, hydrophobins, aquaporins, trehalose-synthases, and other gene families exhibited no significant shifts across the gradient. Finally, we studied variation in sequence homology for certain genes, finding that fungal communities in dry soils are composed of distinct aquaporin and hydrophobin gene sequences. Altogether, our results suggest that while EMF communities exhibit significant compositional shifts across this gradient, coupled functional turnover, at least as inferred using community metagenomics is limited. Accordingly, the consequences of these distinct EMF communities on plant water uptake remain critically unknown, and future studies targeting the expression of genes involved in drought stress tolerance are required.
Chromatin accessibility profiling reveals that human fibroblasts respond to mechanical stimulation in a cell-specific manner
Authors: Logan Niall J , Broda Krystyna L , Pantelireis Nikolaos , Williams Greg , Higgins Claire A 
Published: March 2024

AbstractFibroblasts in the skin are highly heterogeneous, both in vivo and in vitro. One difference between follicular (dermal papilla fibroblasts [DP]) and interfollicular fibroblasts (papillary fibroblasts [PFi]) in vitro is their ability to differentiate in response to osteogenic media (OM), or mechanical stimulation. Here, we asked whether differences in the ability of DP and PFi to respond to differentiation stimuli are due to differences in chromatin accessibility. We performed chromatin accessibility and transcriptional profiling of DP and PFi in human skin, which arise from a common progenitor during development, yet display distinct characteristics in adult tissue and in vitro. We found that cells cultured in growth media had unique chromatin accessibility profiles; however, these profiles control similar functional networks. Upon introduction of a chemical perturbation (OM) to promote differentiation, we observed a divergence not only in the accessible chromatin signatures but also in the functional networks controlled by these signatures. The biggest divergence between DP and PFi was observed when we applied 2 perturbations to cells: growth in OM and mechanical stimulation (a shock wave [OMSW]). DP readily differentiate into bone in OMSW conditions, while PFi lack differentiation capability in vitro. In the DP we found a number of uniquely accessible promoters that controlled osteogenic interaction networks associated with bone and differentiation functions. Using ATAC-seq and RNA-seq we found that the combination of 2 stimuli (OMSW) could result in significant changes in chromatin accessibility associated with osteogenic differentiation, but only within the DP (capable of osteogenic differentiation). De novo motif analysis identified enrichment of motifs bound by the TEA domain (TEAD) family of transcription factors, and inter-cell comparisons (UpSet analysis) displayed large groups of genes to be unique to single cell types and conditions. Our results suggest that these 2 stimuli (OMSW) elicit cell-specific responses by modifying chromatin accessibility of osteogenic-related gene promoters.
A homozygous SP7/OSX mutation causes osteogenesis and dentinogenesis imperfecta with craniofacial anomalies
Authors: Al-Mutairi Dalal A , Jarragh Ali A , Alsabah Basel H , Wein Marc N , Mohammed Wasif , Alkharafi Lateefa 
Published: March 2024

Abstract
Osteogenesis imperfecta (OI) is a heterogeneous spectrum of hereditary genetic disorders that cause bone fragility, through various quantitative and qualitative defects of type 1 collagen, a triple helix composed of two α1 and one α2 chains encoded by COL1A1 and COL1A2, respectively. The main extra–skeletal manifestations of OI include blue sclerae, opalescent teeth, and hearing impairment. Moreover, multiple genes involved in osteoblast maturation and type 1 collagen biosynthesis are now known to cause recessive forms of OI. In this study a multiplex consanguineous family of two affected males with OI was recruited for genetic screening. To determine the causative, pathogenic variant(s), genomic DNA from two affected family members were analyzed using whole exome sequencing, autozygosity mapping, and then validated with Sanger sequencing. The analysis led to the mapping of a homozygous variant previously reported in SP7/OSX, a gene encoding for Osterix, a transcription factor that activates a repertoire of genes involved in osteoblast and osteocyte differentiation and function. The identified variant (c.946C &gt; T; p.Arg316Cys) in exon 2 of SP7/OSX results in a pathogenic amino acid change in two affected male siblings and develops OI, dentinogenesis imperfecta, and craniofacial anomaly. On the basis of the findings of the present study, SP7/OSX:c. 946C &gt; T is a rare homozygous variant causing OI with extra–skeletal features in inbred Arab populations.
Automated CAD-to-BIM generation of restroom sanitary plumbing system
Authors: Shin Minso , Park Seonghun , Koo Bonsang , Kim Tae Wan 
Published: March 2024

Abstract
Mechanical, electrical, and plumbing (MEP) system experts often have difficulties in converting their designs, in computer-aided design (CAD), into building information models (BIMs) owing to excessive repetitive work, lack of BIM skilled workers, frequent BIM recreations, etc. Therefore, this study aimed to formalize the CAD-to-BIM process of MEP systems, focusing on sanitary plumbing system, including soil, drain system, hot water supply, and cold water supply system. Each system’s process is composed of a combination of the following five common modules: pipeline processing module, pipe connection module, initial level setting module, addition riser nipple module, and clash resolution module. Consequently, a prototype developed based on the formalized process produced a sanitary plumbing BIM model that is identical to the CAD drawings and has no clashes. This study contributes to the MEP BIM theory by identifying considerations for CAD-to-BIM conversion of sanitary plumbing system and formalizing the process reflecting them.
Fasting in Early Sufi Literature
Authors: Khalil Atif 
Published: March 2024

Abstract
This article offers an analysis of conceptions of fasting in early Islamic spirituality. By drawing on the literature of Sufism, with special attention to the writings of al-Sarrāj (d. 378/988), al-Makkī (d. 386/996), al-Kharkūshī (= Khargūshī; d. 407/1016), al-Hujwīrī (d. ca. 465/1071), al-Qushayrī (d. 465/1072) and al-Sīrjānī (d. 470/1077), it thematically outlines (1) the value placed on fasting in early tradition, (2) the dangers believed to lie in the practice, and finally, (3) the need to transcend, in the final scheme of things, any attachment one may form with it, through ‘detachment from detachment’. In the process, the article aims not only to decipher and make sense of the various aphorisms and stories that make up the early literature of taṣawwuf, but also to resolve their apparent contradictions.
A new Mexican endemic species of yellow-eared bat in the genus Vampyressa (Phyllostomidae, Stenodermatinae)
Authors: Garbino Guilherme S T , Hernández-Canchola Giovani , León-Paniagua Livia , Tavares Valéria da C 
Published: March 2024

Abstract
Bats from the genus Vampyressa Thomas, 1900 are known from a relatively small number of individuals in Mexico. Through recent collecting efforts in southwestern Mexico, we detected several previously unknown populations of Vampyressa, which appeared to represent a lineage independent from but closely related to V. thyone. Here, we describe this lineage as a new species of the genus Vampyressa from the Mexican states of Guerrero and Oaxaca. The new species is currently known from at least 8 collected specimens and 3 released individuals from 8 localities, and can be differentiated from V. pusilla and V. thyone based on pelage and skull characters, size, mitochondrial Cytochrome b, and nuclear Recombination-activating gene 2 sequence data. The new species has been captured mainly in the lowlands but occurs along a wide altitudinal range from 150 to 2,200 m above sea level. Most of the records of the new species are from west of the Isthmus of Tehuantepec, which evidences a new case of a phylogenetic break at this biogeographic barrier. The genus Vampyressa now includes 6 species, and Mexico expands its position as the country with the largest number of endemic bats in the Neotropics, totaling 20 endemics.
Enhancing access to digital justice: digital governance of dispute resolution and dispute prevention in online commercial activities
Authors: Zhao Yun , Chen Hui 
Published: March 2024

Abstract
This article examines relevant theories and practices concerning the strengthening of access to digital justice and explores pathways to expanding the application of online dispute resolution (ODR) to dispute prevention in online commercial activities. It focuses on how to enhance both efficiency and fairness in four stages of commercial activities, namely, deal-making (contract formation), contract performance, dispute resolution, and the enforcement of final results. At the deal-making stage, the application of e-signatures is analysed with respect to the prevention of compliance and security risks. The best practices of smart contracts and blockchain technology are also investigated to promote relevant innovative designs in the digital governance of online contract performance. In addition, top-down and bottom-up ODR platforms are compared in terms of their respective patterns for enhancing efficiency and fairness, as well as their differing potential for institutionalization. Finally, existing ODR self-enforcement models are explored, with emphasis on the ‘preauthorization’ model and the example of Taobao.
Delayed duodenal/gastric fistula resulting in persistent perihepatic abscesses as a late complication of laparoscopic cholecystectomy
Authors: Vu Phuong , Daneshvar Meelod , Chintanaboina Jayakrishna , Fathi Amir 
Published: March 2024

Abstract
Since the early 1990’s, laparoscopic cholecystectomy has become the gold standard for the treatment of symptomatic gallbladder disease. Although the incidence of postoperative complications is generally lower with this approach, gallbladder perforation represents a serious risk that is among the most common complications of laparoscopic cholecystectomy. The sequalae that can follow iatrogenic perforation have not been well documented and only a few case reports exist in the current literature. In this paper we discuss two case reports of delayed perihepatic abscesses following prior laparoscopic cholecystectomy, ultimately resulting in fistulous tracts. The course of the disease is discussed along with the diagnostic workup and eventual successful management of the aforementioned complications. Treating enteric fistulae requires a systematic approach and is carried out in phases. Enteric fistula formation following laparoscopic cholecystectomy is a rare complication of retained gallstones that can present months to years following the index operation. Significant care should be taken to avoid perforation and all efforts should be made to retrieve stones if spillage occurs.
Battle of the Bands: The Psalter vs. Demonic Noise
Authors: Abbott Philip 
Published: March 2024

Abstract
When scholars discuss the use of the Psalms in early Christianity, they typically underscore how the Psalter functioned as an instrument to harmonize the self with the divine. In other words, the Psalms transformed Christian readers, allowing them to internalize the Gospel and exorcize their inner demons. This article argues, however, that there is a more externalized aspect of apotropaism to the Psalter in the writings of Athanasius. According to the bishop of Alexandria, the Psalter had real prophylactic power against embodied evil forces. Conceptualizing the Book of Psalms as an aural incarnation of Jesus that anticipated his physical incarnation, Athanasius believed that the Psalter contained Christ’s presence and could be employed to drive demons out of their strongholds and Christianize the landscape. In his Life of Antony, Athanasius’ Antony uses the Psalter in this manner as he advances into demonic territory and threatens demonic hegemony. In response, demons launch sonic attacks of their own on the great ascetic, producing a terrible cacophony. More than mere distraction, this demonic noise signifies resistance to the shifting power dynamics in the unseen realm. Thus, Life of Antony recounts a holy battle of the bands, where Christ via the Psalter competes with the devil and his motley crew of noisy demons.
Root topological order drives variation of fine root vessel traits and hydraulic strategies in tropical trees
Authors: Zhang Guangqi , Fortunel Claire , Niu Shan , Zuo Juan , Maeght Jean-Luc , Yang Xiaodong , Xia Shangwen , Mao Zhun 
Published: March 2024

Abstract
Vessel traits contribute to plant water transport from roots to leaves and thereby influence how plants respond to soil water availability, but the sources of variation in fine root anatomical traits remain poorly understood. Here, we explore the variations of fine root vessel traits along topological orders within and across tropical tree species. Anatomical traits were measured along five root topological orders in 80 individual trees of 20 species from a tropical forest in southwestern China. We found large variations for most root anatomical traits across topological orders, and strong co-variations between vessel traits. Within species, theoretical specific xylem hydraulic conductivity (Kth) increased with topological order due to increased mean vessel diameter, size heterogeneity, and decreased vessel density. Across species, Kth was associated with vessel fraction in low-order roots and correlated with mean vessel diameter and vessel density in high-order roots, suggesting a shift in relative anatomical contributors to Kth from the second- to fifth-order roots. We found no clear relationship between Kth and stele: root diameter ratios. Our study shows strong variations in root vessel traits across topological orders and species, and highlights shifts in the anatomical underpinnings by varying vessel-related anatomical structures for an optimized water supply.
Imposters among us: globular cluster kinematics and the halo mass of ultra-diffuse galaxies in clusters
Authors: Doppel Jessica E , Sales Laura V , Benavides José A , Toloba Elisa , Peng Eric W , Nelson Dylan , Navarro Julio F 
Published: March 2024

ABSTRACT
The velocity dispersion of globular clusters (GCs) around ultra-diffuse galaxies (UDGs) in the Virgo cluster spans a wide range, including cases where GC kinematics suggest haloes as massive as (or even more massive than) that of the Milky Way around these faint dwarfs. We analyse the catalogues of GCs derived in post-processing from the TNG50 cosmological simulation to study the GC system kinematics and abundance of simulated UDGs in galaxy groups and clusters. UDGs in this simulation reside exclusively in dwarf-mass haloes with M200 ≲ 1011.2 M⊙. When considering only GCs gravitationally bound to simulated UDGs, we find GCs properties that overlap well with several observational measurements for UDGs. In particular, no bias towards overly massive haloes is inferred from the study of bound GCs, confirming that GCs are good tracers of UDG halo mass. However, we find that contamination by intracluster GCs may, in some cases, substantially increase velocity dispersion estimates when performing projected mock observations of our sample. We caution that targets with less than 10 GC tracers are particularly prone to severe uncertainties. Measuring the stellar kinematics of the host galaxy should help confirm the unusually massive haloes suggested by GC kinematics around some UDGs.
Bioorthogonal labeling and profiling of N6-isopentenyladenosine (i6A) modified RNA
Authors: Li Yuanyuan , Zhou Hongling , Chen Shasha , Li Yinan , Guo Yuyang , Chen Xiaoqian , Wang Sheng , Wang Li , Gan Youfang , Zhang Shusheng , Zheng Ya Ying , Sheng Jia , Zhou Zhipeng , Wang Rui 
Published: March 2024

Abstract
Chemical modifications in RNAs play crucial roles in diversifying their structures and regulating numerous biochemical processes. Since the 1990s, several hydrophobic prenyl-modifications have been discovered in various RNAs. Prenyl groups serve as precursors for terpenes and many other biological molecules. The processes of prenylation in different macromolecules have been extensively studied. We introduce here a novel chemical biology toolkit that not only labels i6A, a prenyl-modified RNA residue, by leveraging the unique reactivity of the prenyl group, but also provides a general strategy to incorporate fluorescence functionalities into RNAs for molecular tracking purposes. Our findings revealed that iodine-mediated cyclization reactions of the prenyl group occur rapidly, transforming i6A from a hydrogen-bond acceptor to a donor. Based on this reactivity, we developed an Iodine-Mediated Cyclization and Reverse Transcription (IMCRT) tRNA-seq method, which can profile all nine endogenous tRNAs containing i6A residues in Saccharomyces cerevisiae with single-base resolution. Furthermore, under stress conditions, we observed a decline in i6A levels in budding yeast, accompanied by significant decrease of mutation rate at A37 position. Thus, the IMCRT tRNA-seq method not only permits semi-quantification of i6A levels in tRNAs but also holds potential for transcriptome-wide detection and analysis of various RNA species containing i6A modifications.
Proximal versus distal diuretics in congestive heart failure
Authors: Nardone Massimo , Sridhar Vikas S , Yau Kevin , Odutayo Ayodele , Cherney David Z I 
Published: March 2024

ABSTRACT
Volume overload represents a hallmark clinical feature linked to the development and progression of heart failure (HF). Alleviating signs and symptoms of volume overload represents a foundational HF treatment target that is achieved using loop diuretics in the acute and chronic setting. Recent work has provided evidence to support guideline-directed medical therapies, such as sodium glucose cotransporter 2 (SGLT2) inhibitors and mineralocorticoid receptor (MR) antagonists, as important adjunct diuretics that may act synergistically when used with background loop diuretics in people with chronic HF. Furthermore, there is growing interest in understanding the role of SGLT2 inhibitors, carbonic anhydrase inhibitors, thiazide diuretics, and MR antagonists in treating volume overload in patients hospitalized for acute HF, particularly in the setting of loop diuretic resistance. Thus, the current review demonstrates that: (i) SGLT2 inhibitors and MR antagonists confer long-term cardioprotection in chronic HF patients but it is unclear whether natriuresis or diuresis represents the primary mechanisms for this benefit, (ii) SGLT2 inhibitors, carbonic anhydrase inhibitors, and thiazide diuretics increase natriuresis in the acute HF setting, but implications on long-term outcomes remain unclear and warrants further investigation, and (iii) a multi-nephron segment approach, using agents that act on distinct segments of the nephron, potentiate diuresis to alleviate signs and symptoms of volume overload in acute HF.
Epidemiology, Timing, and Secondary Prophylaxis of Recurrent Nocardiosis
Authors: Yetmar Zachary A , Khodadadi Ryan B , Chesdachai Supavit , McHugh Jack W , Challener Douglas W , Wengenack Nancy L , Bosch Wendelyn , Seville Maria Teresa , Beam Elena 
Published: March 2024

Abstract

Background
Nocardia tends to cause infection in immunocompromised patients or those with chronic pulmonary disease. Nocardia is known to recur, prompting the practice of secondary prophylaxis in patients perceived at high risk. However, few data exist regarding the epidemiology of recurrent nocardiosis or the effectiveness of secondary prophylaxis.

Methods
We performed a multicenter, retrospective cohort study of adults diagnosed with nocardiosis from November 2011 to April 2022, including patients who completed primary treatment and had at least 30 days of posttreatment follow-up. Propensity score matching was used to analyze the effect of secondary prophylaxis on Nocardia recurrence.

Results
Fifteen of 303 (5.0%) patients developed recurrent nocardiosis after primary treatment. Most recurrences were diagnosed either within 60 days (N = 6/15, 40.0%) or between 2 to 3 years (N = 4/15, 26.7%). Patients with primary disseminated infection tended to recur within 1 year, whereas later recurrences were often nondisseminated pulmonary infection. Seventy-eight (25.7%) patients were prescribed secondary prophylaxis, mostly trimethoprim-sulfamethoxazole (N = 67/78). After propensity-matching, secondary prophylaxis was not associated with reduced risk of recurrence (hazard ratio, 0.96; 95% confidence interval, .24–3.83), including in multiple subgroups. Eight (53.3%) patients with recurrent nocardiosis required hospitalization and no patients died from recurrent infection.

Conclusions
Recurrent nocardiosis tends to occur either within months because of the same Nocardia species or after several years with a new species. Although we did not find evidence for the effectiveness of secondary prophylaxis, the confidence intervals were wide. However, outcomes of recurrent nocardiosis are generally favorable and may not justify long-term antibiotic prophylaxis for this indication alone.
SULTR2;1 Adjusts the Bolting Timing by Transporting Sulfate from Rosette Leaves to the Primary Stem
Authors: Soudthedlath Khamsalath , Nakamura Toshiki , Ushiwatari Tsukasa , Fukazawa Jutarou , Osakabe Keishi , Osakabe Yuriko , Maruyama-Nakashita Akiko 
Published: March 2024

Abstract
Sulfur (S) is an essential macronutrient for plant growth and metabolism. SULTR2;1 is a low-affinity sulfate transporter facilitating the long-distance transport of sulfate in Arabidopsis. The physiological function of SULTR2;1 in the plant life cycle still needs to be determined. Therefore, we analyzed the sulfate transport, S-containing metabolite accumulation and plant growth using Arabidopsis SULTR2;1 disruption lines, sultr2;1–1 and sultr2;1–2, from seedling to mature growth stages to clarify the metabolic and physiological roles of SULTR2;1. We observed that sulfate distribution to the stems was affected in sultr2;1 mutants, resulting in decreased levels of sulfate, cysteine, glutathione (GSH) and total S in the stems, flowers and siliques; however, the GSH levels increased in the rosette leaves. This suggested the essential role of SULTR2;1 in sulfate transport from rosette leaves to the primary stem. In addition, sultr2;1 mutants unexpectedly bolted earlier than the wild-type without affecting the plant biomass. Correlation between GSH levels in rosette leaves and the bolting timing suggested that the rosette leaf GSH levels or limited sulfate transport to the early stem can trigger bolting. Overall, this study demonstrated the critical roles of SULTR2;1 in maintaining the S metabolite levels in the aerial part and transitioning from the vegetative to the reproductive growth phase.