bluuebunny/crossref_metadata_2025_split huggingface dataset:
Community Assembly Processes of Deadwood Mycobiome in a Tropical Forest Revealed by Long-Read Third-Generation Sequencing
Authors: Purahong Witoon , Ji Li , Wu Yu-Ting 
Published: May 2024

AbstractDespite the importance of wood-inhabiting fungi on nutrient cycling and ecosystem functions, their ecology, especially related to their community assembly, is still highly unexplored. In this study, we analyzed the wood-inhabiting fungal richness, community composition, and phylogenetics using PacBio sequencing. Opposite to what has been expected that deterministic processes especially environmental filtering through wood-physicochemical properties controls the community assembly of wood-inhabiting fungal communities, here we showed that both deterministic and stochastic processes can highly contribute to the community assembly processes of wood-inhabiting fungi in this tropical forest. We demonstrated that the dynamics of stochastic and deterministic processes varied with wood decomposition stages. The initial stage was mainly governed by a deterministic process (homogenous selection), whereas the early and later decomposition stages were governed by the stochastic processes (ecological drift). Deterministic processes were highly contributed by wood physicochemical properties (especially macronutrients and hemicellulose) rather than soil physicochemical factors. We elucidated that fine-scale fungal-fungal interactions, especially the network topology, modularity, and keystone taxa of wood-inhabiting fungal communities, strongly differed in an initial and decomposing deadwood. This current study contributes to a better understanding of the ecological processes of wood-inhabiting fungi in tropical regions where the knowledge of wood-inhabiting fungi is highly limited.
Heat stress-induced NO enhanced perylenequinone biosynthesis of Shiraia sp. via calcium signaling pathway
Authors: Bao Zhuanying , Chen Yunni , Zhang Zhibin , Yang Huilin , Yan Riming , Zhu Du 
Published: May 2024

Abstract
Perylenequinones (PQs) are natural photosensitizing compounds used as photodynamic therapy, and heat stress (HS) is the main limiting factor of mycelial growth and secondary metabolism of fungi. This study aimed to unravel the impact of HS-induced Ca2+ and the calcium signaling pathway on PQ biosynthesis of Shiraia sp. Slf14(w). Meanwhile, the intricate interplay between HS-induced NO and Ca2+ and the calcium signaling pathway was investigated. The outcomes disclosed that Ca2+ and the calcium signaling pathway activated by HS could effectively enhance the production of PQs in Shiraia sp. Slf14(w). Further investigations elucidated the specific mechanism through which NO signaling molecules induced by HS act upon the Ca2+/CaM (calmodulin) signaling pathway, thus propelling PQ biosynthesis in Shiraia sp. Slf14(w). This was substantiated by decoding the downstream positioning of the CaM/CaN (calcineurin) pathway in relation to NO through comprehensive analyses encompassing transcript levels, enzyme assays, and the introduction of chemical agents. Concurrently, the engagement of Ca2+ and the calcium signaling pathway in heat shock signaling was also evidenced. The implications of our study underscore the pivotal role of HS-induced Ca2+ and the calcium signaling pathway, which not only participate in heat shock signal transduction but also play an instrumental role in promoting PQ biosynthesis. Consequently, our study not only enriches our comprehension of the mechanisms driving HS signaling transduction in fungi but also offers novel insights into the PQ synthesis paradigm within Shiraia sp. Slf14(w).

Key points
• The calcium signaling pathway was proposed to participate in PQ biosynthesis under HS.
• HS-induced NO was revealed to act upon the calcium signaling pathway for the first time.
Dental plaque microbiota sequence counts for microbial profiling and resistance genes detection
Authors: Veschetti Laura , Paiella Salvatore , Carelli Maria , Zotti Francesca , Secchettin Erica , Malleo Giuseppe , Signoretto Caterina , Zulianello Giorgia , Nocini Riccardo , Crovetto Anna , Salvia Roberto , Bassi Claudio , Malerba Giovanni 
Published: May 2024

Abstract
Shotgun metagenomics sequencing experiments are finding a wide range of applications. Nonetheless, there are still limited guidelines regarding the number of sequences needed to acquire meaningful information for taxonomic profiling and antimicrobial resistance gene (ARG) identification. In this study, we explored this issue in the context of oral microbiota by sequencing with a very high number of sequences (~ 100 million), four human plaque samples, and one microbial community standard and by evaluating the performance of microbial identification and ARGs detection through a downsampling procedure. When investigating the impact of a decreasing number of sequences on quantitative taxonomic profiling in the microbial community standard datasets, we found some discrepancies in the identified microbial species and their abundances when compared to the expected ones. Such differences were consistent throughout downsampling, suggesting their link to taxonomic profiling methods limitations. Overall, results showed that the number of sequences has a great impact on metagenomic samples at the qualitative (i.e., presence/absence) level in terms of loss of information, especially in experiments having less than 40 million reads, whereas abundance estimation was minimally affected, with only slight variations observed in low-abundance species. The presence of ARGs was also assessed: a total of 133 ARGs were identified. Notably, 23% of them inconsistently resulted as present or absent across downsampling datasets of the same sample. Moreover, over half of ARGs were lost in datasets having less than 20 million reads. This study highlights the importance of carefully considering sequencing aspects and suggests some guidelines for designing shotgun metagenomics experiments with the final goal of maximizing oral microbiome analyses. Our findings suggest varying optimized sequence numbers according to different study aims: 40 million for microbiota profiling, 50 million for low-abundance species detection, and 20 million for ARG identification.

Key points
• Forty million sequences are a cost-efficient solution for microbiota profiling
• Fifty million sequences allow low-abundance species detection
• Twenty million sequences are recommended for ARG identification

Graphical Abstract
Bone morphology and physical characteristics of the pro-cyclist hip joint
Authors: Akiho Shunsuke , Hashida Ryuki , Tagawa Yoshihiko , Maeyama Akira , Kinoshita Koichi , Kanazawa Kazuki , Matsuse Hiroo , Hara Masafumi , Yamamoto Takuaki 
Published: May 2024

Abstract
Purpose
This study aimed to investigate the radiographic findings for the hip joint and hip range of motion in professional cyclists, and to determine their bone morphology and physical characteristics. The effects of physical characteristics on athletic performance were examined in terms of metabolic efficiency using simulation analysis.

Methods
We performed a case–control research study on 22 hips in 11 male professional cyclists (average age 28.5, height 1.73 m, weight 77.6 kg). Thirty hips in 15 healthy male volunteers were selected as controls. As radiographic evaluations, acetabular dysplasia was assessed on standardized radiographs. During physical evaluations, the hip range of motion was examined. We used simulation analysis to investigate the metabolic efficiency in the different cycling forms.

Results
The radiographic evaluations showed a significant difference in the incidence of acetabular dysplasia (p = 0.01): 59% (13/22 hips) in the pro-cyclist group versus 10% (3/30 hips) in the control group. The physical evaluations revealed significant differences in the hip internal rotation angle (p = 0.01), with greater ranges of internal rotation in the pro-cyclist group versus the control group. The simulation analyses showed that metabolism was reduced in the cycling form with hip internal rotation, especially in the lower extremities.

Conclusions
Pro-cyclists showed a high frequency of acetabular dysplasia and superior hip internal rotation. According to the cycling model analyses, hip internal rotation allowed pedaling with reduced metabolic power.
Predicting clinically significant prostate cancer following suspicious mpMRI: analyses from a high-volume center
Authors: Jahnen Matthias , Hausler Tanja , Meissner Valentin H. , Ankerst Donna P. , Kattan Michael W. , Sauter Andreas , Gschwend Juergen E. , Herkommer Kathleen 
Published: May 2024

Abstract
Purpose
mpMRI is routinely used to stratify the risk of clinically significant prostate cancer (csPCa) in men with elevated PSA values before biopsy. This study aimed to calculate a multivariable risk model incorporating standard risk factors and mpMRI findings for predicting csPCa on subsequent prostate biopsy.

Methods
Data from 677 patients undergoing mpMRI ultrasound fusion biopsy of the prostate at the TUM University Hospital tertiary urological center between 2019 and 2023 were analyzed. Patient age at biopsy (67 (median); 33–88 (range) (years)), PSA (7.2; 0.3–439 (ng/ml)), prostate volume (45; 10–300 (ml)), PSA density (0.15; 0.01–8.4), PI-RADS (V.2.0 protocol) score of index lesion (92.2% ≥3), prior negative biopsy (12.9%), suspicious digital rectal examination (31.2%), biopsy cores taken (12; 2–22), and pathological biopsy outcome were analyzed with multivariable logistic regression for independent associations with the detection of csPCa defined as ISUP ≥ 3 (n = 212 (35.2%)) and ISUP ≥ 2 (n = 459 (67.8%) performed on 603 patients with complete information.

Results
Older age (OR: 1.64 for a 10-year increase; p < 0.001), higher PSA density (OR: 1.60 for a doubling; p < 0.001), higher PI-RADS score of the index lesion (OR: 2.35 for an increase of 1; p < 0.001), and a prior negative biopsy (OR: 0.43; p = 0.01) were associated with csPCa.

Conclusion
mpMRI findings are the dominant predictor for csPCa on follow-up prostate biopsy. However, PSA density, age, and prior negative biopsy history are independent predictors. They must be considered when discussing the individual risk for csPCa following suspicious mpMRI and may help facilitate the further diagnostical approach.
Value of perilesional biopsies in multiparametric magnetic resonance imaging-targeted biopsy and systematic biopsy in detection of prostate cancer: results of a prospective, non-randomized, surgeon-blinded study
Authors: Duwe Gregor , Schmitteckert Melanie , Haack Maximilian , Sparwasser Peter , Dotzauer Robert , Thomas Anita , Tsaur Igor , Brandt Maximilian Peter , Kurosch Martin , Mager Rene , Haferkamp Axel , Boehm Katharina , Höfner Thomas 
Published: May 2024

Abstract
Purpose
The goal of this study is to address if detection rates of clinically significant prostate cancer (csPCa) can be increased by additional perilesional biopsies (PB) in magnetic resonance (MR)/ultrasound fusion prostate biopsy in biopsy-naïve men.

Methods
This prospective, non-randomized, surgeon-blinded study was conducted between February 2020 and July 2022. Patients were included with PSA levels < 20 ng/ml and ≥ one PI-RADS lesion (grades 3–5) per prostate lobe. Prostate biopsy was performed by two urologists. The first performed the MR-fusion biopsy with 3–5 targeted biopsies (TB) and 6 PB in a standardized pattern. The second performed the systematic (12-fold) biopsy (SB) without knowledge of the MR images. Primary outcome of this study is absence or presence of csPCa (≥ ISUP grade 2) comparing TB, PB and SB, using McNemar test.

Results
Analyses were performed for each PI-RADS lesion (n = 218). There was a statistically significant difference in csPC detection rate of TB + SB between PI-RADS 3, 4 and 5 lesions (18.0% vs. 42.5% vs. 82.6%, p < 0.001) and TB + PB (19.7% vs. 29.1% vs. 78.3%). Comparing only maximum ISUP grade per lesion, even SB plus TB plus PB did not detect more csPCa compared to SB plus TB (41.3% vs. 39.9%, p > 0.05).

Conclusion
We present prospective study data investigating the role of perilesional biopsy in detection of prostate cancer. We detected no statistically significant difference in the detection of csPCa by the addition of PB. Therefore, we recommend continuing 12-fold bilateral SB in addition to TB.
Downscaling the ocean response to the Madden–Julian Oscillation in the Northwest Atlantic and adjacent shelf seas
Authors: Renkl Christoph , Oliver Eric C. J. , Thompson Keith R. 
Published: May 2024

AbstractSubseasonal-to-seasonal (S2S) prediction is a global effort to forecast the state of the atmosphere and ocean with lead times between two weeks and a season. This study explores the feasibility of S2S prediction of the ocean using a variety of tools including statistical analysis, a statistical-dynamical mixed layer model, and a regional, high-resolution ocean circulation model based on physical principles. Ocean predictability on S2S timescales is analyzed by compositing winter sea surface temperature (SST) anomalies in the North Atlantic with respect to the state of the Madden–Julian Oscillation (MJO). It is found that statistically significant, large-scale SST changes, particularly along the eastern seaboard of North America, can be related to the MJO. This signal is shown to be driven by anomalous air–sea heat fluxes caused by atmospheric perturbations in response to the MJO. The high-resolution model of the Gulf of Maine and Scotian Shelf is used to downscale the mean ocean response to the MJO. The model is able to capture the observed relationship between the MJO and SST in the northwest Atlantic. It is also shown that the anomalous atmospheric circulation in response to the MJO leads to anomalous upwelling on the Scotian Shelf. Overall, this study demonstrates that it is feasible, and of value, to use regional ocean models for S2S prediction.
Total hysterectomy versus radical hysterectomy in neuroendocrine cervical cancer: a SEER-database analysis
Authors: Zeng Feitianzhi , Guo Peng , Xia Meng , He Mian 
Published: May 2024

Abstract
Purpose
We conducted this study to evaluate the efficacy of total hysterectomy versus radical hysterectomy in the treatment of neuroendocrine cervical cancer (NECC).

Methods
Eligible NECC patients were identified from the Surveillance, Epidemiology and End Results (SEER) database. Demographic characteristics, clinical treatment and survival of the patients were collected. The overall survival (OS) and cancer-specific survival (CSS) were estimated by Kaplan–Meier analysis with log-rank test.

Results
A total of 286 patients were included, with 104 patients undergoing total hysterectomy and 182 patients undergoing radical hysterectomy. The 5-year OS were 50.8% in the total hysterectomy group and 47.5% in the radical hysterectomy group (p = 0.450); and the corresponding 5-year CSS were 51.6% and 49.1% (p = 0.494), respectively. Along with surgery, radiotherapy was given to 49.0% of patients in the total hysterectomy group and 50.5% in the radical hysterectomy group; and chemotherapy was administered to 77.9% of patients in the total hysterectomy group and 85.7% in the radical hysterectomy group. Unexpectedly, in patients who received adjuvant radiotherapy with or without chemotherapy, the OS was superior in the total hysterectomy group compared with the radical hysterectomy group (p = 0.034). While in patients who received chemotherapy alone and those who received neither radiotherapy nor chemotherapy, the OS still remained comparable between the total hysterectomy and radical hysterectomy group.

Conclusion
Compared with radical hysterectomy, total hysterectomy was not associated with compromised survival prognosis in patients with NECC. Total hysterectomy has the potential to be a surgical alternative in the multimodal management of NECC.
A thermodynamically consistent phase transformation model for multiphase alloys: application to Ti$$_6$$Al$$_4$$V in laser powder bed fusion processes
Authors: Noll Isabelle , Bartel Thorsten , Menzel Andreas 
Published: May 2024

AbstractTitan aluminium alloys belong to the group of $$\alpha $$
α
–$$\beta $$
β
-alloys, which are used for many applications in industry due to their advantageous mechanical properties, e.g. for laser powder bed fusion (PBF-LB) processes. However, the composition of the crystal structure and the respective magnitude of the solid fraction highly influences the material properties of titan aluminium alloys. Specifically, the thermal history, i.e. the cooling rate, determines the phase composition and microstructure for example during heat treatment and PBF-LB processes. For that reason, the present work introduces a phase transformation framework based, amongst others, on energy densities and thermodynamically consistent evolution equations, which is able to capture the different material compositions resulting from cooling and heating rates. The evolution of the underlying phases is governed by a specifically designed dissipation function, the coefficients of which are determined by a parameter identification process based on available continuous cooling temperature (CCT) diagrams. In order to calibrate the model and its preparation for further applications such as the simulation of additive manufacturing processes, these CCT diagrams are computationally reconstructed. In contrast to empirical formulations, the developed thermodynamically consistent and physically sound model can straightforwardly be extended to further phase fractions and different materials. With this formulation, it is possible to predict not only the microstructure evolution during processes with high temperature gradients, as occurring in e.g. PBF-LB processes, but also the evolving strains during and at the end of the process.
Evaluation of optical coherence tomography angiography metrics in children and adolescents with type 1 diabetes: 4-year longitudinal study
Authors: Qin Xinran , Xiao Ying , Cui Lipu , Chen Shuli , An Qingyu , Yuan Tianyi , Wu Yiwei , Lin Qiurong , Yang Chenhao , Zou Haidong 
Published: May 2024

Abstract
Purpose
To evaluate longitudinal changes in optical coherence tomography angiography (OCTA) metrics in children and adolescents with type 1 diabetes (T1D).

Methods
This prospective observational cohort study included thirty-two eyes from thirty T1D children with no history of diabetic retinopathy (DR) who were followed up for 4 years. Participants underwent OCTA examinations at baseline and during follow-up. Quantitative OCTA metrics were measured using a customized MATLAB algorithm. Generalized mixed-effect models were used to determine their relationship with DR development. Systemic parameters and OCTA metrics were screened using least absolute shrinkage and selection operator to identify predictors for visual function.

Results
Over the 4-year period, seven of the included eyes developed DR, and most OCTA metrics decreased with diabetes duration. Higher peripapillary and parafoveal nasal quadrant vessel area density (VAD) in the superficial capillary plexus (SCP) and vessel skeleton density (VSD) in both the SCP and the deep capillary plexus (DCP) were associated with a lower risk of DR in T1D. Parafoveal DCP VSD and VAD in the temporal and inferior quadrants were anticorrelated with changes in best corrected visual acuity.

Conclusions
OCTA metrics dynamically change over the duration of diabetes and can be used as biomarkers to improve the risk evaluation of DR development and visual function in T1D children and adolescents.
Investigation of the fungiform papillae number in children with tooth number anomalies
Authors: Alp Belgin , Kalaoglu Elif Ece , Mentes Ali 
Published: May 2024

Abstract
Objective
This cross-sectional study investigated the association between fungiform papillae (FP) numbers and tooth number anomalies in children, considering variables related to hypodontia and hyperdontia. The aim was to explore this association while adjusting for age and sex differences.

Materials and methods
A total of 144 children (aged 8–10) were categorized into hypodontia (n = 48), hyperdontia (n = 48), and control groups (n = 48). Clinical and radiographic diagnoses were used to classify tooth number anomalies. Hypodontia was categorized by number and location, while hyperdontia was categorized by number, shape, and location. FP were assessed using the Denver Papillae Protocol. Data analyses were performed using NCSS software, with p < 0.05 considered statistically significant.

Results
The hypodontia group (22.5 ± 8.4) exhibited significantly lower FP than the control group (30.4 ± 9.2) and the hyperdontia group (27.9 ± 7.8) (p < 0.0005, p = 0.003, respectively). No significant difference existed between the hyperdontia and control groups. FP numbers in hypodontia subgroups showed no significant differences based on teeth agenesis numbers or locations. Similarly, hyperdontia subgroup analyses revealed no significant differences in FP numbers based on supernumerary teeth shapes (supplemental, conical, tuberculoid, paramolar) or the numbers of supernumerary teeth.

Conclusions
The lower FP numbers in children with hypodontia suggested an association between teeth and FP number. However, the non-significant difference in FP numbers with hyperdontia underscored the complexity of tooth development, warranting further investigations.

Clinical relevance
Children with hypodontia may exhibit distinct FP numbers compared to those without tooth number anomalies.
Transforming labour around food? the experience of community supported agriculture in Italy
Authors: Rossi Adanella , Piccoli Alessandra , Feola Giuseppe 
Published: May 2024

AbstractThis study examines the strategies developed by Italian Community Supported Agriculture (CSA) initiatives to de-commodify, de-instrumentalise and de-monetise labour in their attempt to prefigure alternatives to dominant capitalist agri-food systems. To do so we answer the following research questions: What type of strategies do these CSA initiatives employ to that end? What insights can be gained as regards the potential and barriers to fuller and more accomplished post-capitalist labour management within CSA initiatives? Data were collected through a participatory action research project involving 16 Italian CSAs, participant observation in meetings of CSA initiatives and the Italian CSA Network, and official documents collection. Across the three crucial moments considered in this study, we observe substantial difficulties in realising post-capitalist labour management as the initiatives are constrained by external requirements (e.g., legislation) and also internally by members’ weakness in implementing the CSA model due to their remaining integrated in the capitalist system. These findings point to the importance for CSA initiatives of deepening the collective process of deliberate deconstruction of valuation logics and predefined roles, as well as legal frameworks to find ways to enable the realisation of post-capitalist labour management. In this regard, we also suggest that the Italian CSA Network could play a more active role in addressing some of the internal and external factors hindering the consolidation of CSA initiatives and the manifestation of their transformative role.