bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ash dieback assessments on intensive monitoring plots in Germany: influence of stand, site and time on disease progression
Authors: Fuchs Sebastian , Häuser Henriette , Peters Sandra , Knauf Luisa , Rentschler Felix , Kahlenberg Georgia , Kätzel Ralf , Evers Jan , Paar Uwe , Langer Gitta Jutta 
Published: March 2024

AbstractSince 2002, ash dieback caused by the invasive fungus Hymenoscyphus fraxineus has been observed in Germany. The pathogen and its associated symptoms have fatal consequences for the vitality and survival of European ash (Fraxinus excelsior L.), an economically and ecologically important tree species. This study analyses the ash monitoring results of eleven intensive monitoring plots of the FraxForFuture research network distributed across Germany and focuses on within-stand differences of symptoms in dependence of small-scale site and tree properties. A cohort of 1365 ash trees was surveyed six times over three years, testing and applying a summer and a winter version of a nationally standardised ash dieback assessment key. The main disease symptoms (crown dieback and basal lesions) were more pronounced in areas with higher ash density, in edaphically moist areas (hydromorphic soils), on younger/smaller ash trees, and generally increased over time. However, the trend over time differed between single plots. In case of considering only the surviving part of the ash populations, crown condition even improved in 6/11 plots, indicating a selection process. Large basal lesions at the beginning of the observation period were a very good predictor for deadfall probability, especially on trees with lower stem diameter. Generally, ash dieback related symptoms at stem and crown were highly correlated. Silvicultural management practice in the past that actively pushed ash towards the moister end of its water demand spectrum has to be questioned in the light of ash dieback. Cost-intensive ash re-cultivation in the future—possibly with less dieback-susceptible progenies—should avoid pure ash stands and hydromorphic soil conditions.
Simulation test on shaft deformation induced by mining subsidence under similar gravity field in deep soil strata
Authors: Han Xu , Qin Zhe , Han Ji-huan , Yang Wei-hao , Liu Yong-de , Zhang Jian 
Published: March 2024

AbstractMany shafts in China have experienced large deformations in the deep soil Strata, which has had a significant impact on mining safety. This study conducted a geotechnical model test called the seepage force model to address the deformation issues of shafts caused by mining solid mineral resources in regions with deep soil strata. This test simulated the impact of mining disturbance on shaft deformation within the soil section. The simulation utilized monitoring data from the model shaft, facilitating the determination of deflection displacements across different protection areas. The findings indicated a nearly linear relationship between the maximum horizontal displacement of the shaft and the mining coal seam thickness. The shaft protection areas within the soil section were reconfigured by modifying the movement angle from 45° to 37.6°. Consequently, the maximum horizontal displacements of the prototype shaft decreased to 73.8, 112.7, and 170.9 mm for mining coal thicknesses of 2.7, 5.3, and 8.0 m, respectively. These values represent 26%, 24.6%, and 26.7% reductions from the original design shaft displacements. When combined with the probability integral method, the simulation test results concerning the shaft protection rock pillars were exhaustively examined. This analysis paves the way for a more logical and reliable design approach for shaft protection rock pillars in areas characterized by deep soil and thin rock strata. The study findings hold immense significance in effectively mitigating and managing mining-induced subsidence disasters and ensuring the optimal design of shaft protection zones.
Automatic Liver Segmentation from Multiphase CT Using Modified SegNet and ASPP Module
Authors: Nayantara P. Vaidehi , Kamath Surekha , Kadavigere Rajagopal , Manjunath Kanabagatte Nanjundappa 
Published: March 2024

AbstractLiver cancer is one of the dominant causes of cancer death worldwide. Computed Tomography (CT) is the commonly used imaging modality for diagnosing it. Computer-based liver cancer diagnosis systems can assist radiologists in image interpretation and improve diagnosis speed and accuracy. Since liver segmentation is crucial to such systems, researchers are relentlessly pursuing various segmentation approaches. A clinically viable computer-aided system requires examining multiphase CT images. However, most of the research focuses only on the portal venous phase. In this work, we developed an automatic and efficient Deep Learning (DL) method using SegNet, atrous spatial pyramid pooling module and leaky ReLU layers for liver segmentation from quadriphasic abdominal CT volumes. The proposed method was validated on two datasets, an internal institutional dataset consisting of multiphase CT and a public dataset of portal venous phase CT volumes. The Dice Coefficients (DC) obtained were greater than 96% for the latter dataset and the portal venous phase of the former. For arterial, delayed and plain CT phases of the former dataset, the DC achieved were 94.61%, 95.01% and 93.23%, respectively. Experiments showed that our model performed better than the other state-of-the-art DL models. Ablation studies have revealed that the proposed model leverages the strengths of all the three components that make it up. The promising performance of the proposed method suggests that it is appropriate for incorporation in hepatic cancer diagnosis systems.
Conditioned Galton–Watson Trees: The Shape Functional, and More on the Sum of Powers of Subtree Sizes and Its Mean
Authors: Fill James Allen , Janson Svante , Wagner Stephan 
Published: March 2024

AbstractFor a complex number $$\alpha $$
α
, we consider the sum of the $$\alpha $$
α
th powers of subtree sizes in Galton–Watson trees conditioned to be of size n. Limiting distributions of this functional $$X_n(\alpha )$$

X
n

(
α
)

have been determined for $${\text {Re}}\alpha \ne 0$$

Re
α
≠
0

, revealing a transition between a complex normal limiting distribution for $${\text {Re}}\alpha < 0$$

Re
α
<
0

and a non-normal limiting distribution for $${\text {Re}}\alpha > 0$$

Re
α
>
0

. In this paper, we complete the picture by proving a normal limiting distribution, along with moment convergence, in the missing case $${\text {Re}}\alpha = 0$$

Re
α
=
0

. The same results are also established in the case of the so-called shape functional $$X_n'(0)$$

X
n
′

(
0
)

, which is the sum of the logarithms of all subtree sizes; these results were obtained earlier in special cases. In addition, we prove convergence of all moments in the case $${\text {Re}}\alpha < 0$$

Re
α
<
0

, where this result was previously missing, and establish new results about the asymptotic mean for real $$\alpha < 1/2$$

α
<
1
/
2

.A novel feature for $${\text {Re}}\alpha =0$$

Re
α
=
0

is that we find joint convergence for several $$\alpha $$
α
to independent limits, in contrast to the cases $${\text {Re}}\alpha \ne 0$$

Re
α
≠
0

, where the limit is known to be a continuous function of $$\alpha $$
α
. Another difference from the case $${\text {Re}}\alpha \ne 0$$

Re
α
≠
0

is that there is a logarithmic factor in the asymptotic variance when $${\text {Re}}\alpha =0$$

Re
α
=
0

; this holds also for the shape functional.The proofs are largely based on singularity analysis of generating functions.
Assessment of crushed rock aggregates addition to granular lateritic materials in sub-Saharan extensive urbanization context (Yaoundé Cameroon) for road construction purposes
Authors: Ndzié Mvindi Aloys Thierry , Lobe Bille Jean Francis , Ngo’o Ze Arnaud , Enock Embom Christophe , Tsoyi À Koung Emmanuel , Ngono Mbenti Emvana Michèle Stella , Onana Vincent Laurent 
Published: March 2024

AbstractGranular lateritic materials (GLM) suitability for road construction after the addition of crushed rock aggregates (CRA) in the sub-Saharan extensive urbanization context was evaluated. The urbanization rate was made by using Landsat7 and Landsat8 radar images. The studied materials were subject to petrographic description and geotechnical analysis. The urbanized surface in the Yaoundé area increased by 41.88% from 2004 to 2020. The studied rock are gneisses composed of quartz, garnet, biotite, pyroxene, and feldspars. The gneisses obtained CRA have fines content of less than 10%, maximum dry density value of more than 2.00 g/cm3, good bearing capacity (CBR = 88%), and excellent mechanical characteristics (Los Angeles < 40%). This recommend their use as base course for low to medium volume traffic pavements. Gneisses-derived GLM, less load-bearing (CBR = 39 to 42%) than CRA, have limited behaviour in road construction and can be used as sub-base for all volume traffics. Their use in base courses requires prior treatment. CRA addition to these GLM result in the plasticity index decrease and compaction parameters improvement. CBR values increase shows a perfect correlation (R2 > 0.90) with the addition of CRA. Litho-stabilised materials (CBR ≥ 60%) can be used as base course for low-volume trafficked pavements. The addition of a CRA percentage greater than or equal to 25% is efficient for the optimization of their use. By reducing the amount of quarry aggregates, the improved material could be an economical alternative for road projects. This reduces and controls the haulage of materials within crowded urban area.
Caffeine for apnea and prevention of neurodevelopmental impairment in preterm infants: systematic review and meta-analysis
Authors: Oliphant Elizabeth A. , Hanning Sara M. , McKinlay Christopher J. D. , Alsweiler Jane M. 
Published: March 2024

AbstractThis systematic review and meta-analysis evaluated the evidence for dose and effectiveness of caffeine in preterm infants. MEDLINE, EMBASE, CINHAL Plus, CENTRAL, and trial databases were searched to July 2022 for trials randomizing preterm infants to caffeine vs. placebo/no treatment, or low (≤10 mg·kg−1) vs. high dose (>10 mg·kg−1 caffeine citrate equivalent). Two researchers extracted data and assessed risk of bias using RoB; GRADE evaluation was completed by all authors. Meta-analysis of 15 studies (3530 infants) was performed in REVMAN across four epochs: neonatal/infant (birth-1 year), early childhood (1–5 years), middle childhood (6–11 years) and adolescence (12–19 years). Caffeine reduced apnea (RR 0.59; 95%CI 0.46,0.75; very low certainty) and bronchopulmonary dysplasia (0.77; 0.69,0.86; moderate certainty), with higher doses more effective. Caffeine had no effect on neurocognitive impairment in early childhood but possible benefit on motor function in middle childhood (0.72; 0.57,0.91; moderate certainty). The optimal dose remains unknown; further long-term studies, are needed.
A randomized controlled trial evaluating low-intensity shockwave therapy for treatment of persistent storage symptoms following transurethral surgery for benign prostatic obstruction
Authors: Hegazy Mohammed , Sheir Khaled Z. , Gaballah Mohamed A. , Elshal Ahmed M. 
Published: March 2024

Abstract
Background
Low-intensity shockwave therapy (Li-SWT) can improve bladder function through enhancement of angiogenesis and nerve regeneration and suppression of inflammation and overactivity. In this trial, we aimed to evaluate the efficacy of Li-SWT on persistent storage symptoms after transurethral surgery (TUS) for benign prostatic obstruction (BPO).

Methods
Between July 2020 and July 2022, 137 patients with persistent storage symptoms; urgency episodes/24 h ≥ 1 and daytime frequency ≥8, for at least three months after TUS for BPO were randomly allocated to Li-SWT versus sham versus solifenacin 10 mg/day in 3:1:1 ratio. The primary end point was the percent reduction from baseline in overactive bladder symptom score (OABSS) at 3-month follow-up. The changes in 3-day voiding diary parameters, quality of life (QoL) score, peak flow rate and residual urine at 3 and 6-month follow-up were compared. Treatment-related adverse effects were also evaluated.

Results
Baseline data were comparable between groups. The percent reduction from baseline in OABSS at 3-month follow-up was significantly higher in Li-SWT compared to sham (−55% versus −11%), and it was comparable between Li-SWT and solifenacin-10 (−55% versus −60%). Li-SWT achieved significant improvement like solifenacin-10 in 3-day voiding diary parameters and QoL score at 3-month follow-up. This improvement remained comparable between Li-SWT and solifenacin-10 at 6-month follow-up. No adverse effects related to Li-SWT were noted apart from tolerable pain during the procedure. Solifenacin-10 was associated with bothersome adverse effects in 73% of the patients with 11.5% discontinuation rate.

Conclusions
Li-SWT ameliorates persistent storage symptoms and promotes QoL after TUS for BPO, with comparable efficacy and better tolerance compared to solifenacin.
Microplastics dampen the self-renewal of hematopoietic stem cells by disrupting the gut microbiota-hypoxanthine-Wnt axis
Authors: Jiang Lingli , Ye Yishan , Han Yingli , Wang Qiwei , Lu Huan , Li Jinxin , Qian Wenchang , Zeng Xin , Zhang Zhaoru , Zhao Yanmin , Shi Jimin , Luo Yi , Qiu Yunfei , Sun Jun , Sheng Jinghao , Huang He , Qian Pengxu 
Published: March 2024

AbstractMicroplastics (MPs) are contaminants ubiquitously found in the global biosphere that enter the body through inhalation or ingestion, posing significant risks to human health. Recent studies emerge that MPs are present in the bone marrow and damage the hematopoietic system. However, it remains largely elusive about the specific mechanisms by which MPs affect hematopoietic stem cells (HSCs) and their clinical relevance in HSC transplantation (HSCT). Here, we established a long-term MPs intake mouse model and found that MPs caused severe damage to the hematopoietic system. Oral gavage administration of MPs or fecal transplantation of microbiota from MPs-treated mice markedly undermined the self-renewal and reconstitution capacities of HSCs. Mechanistically, MPs did not directly kill HSCs but disrupted gut structure and permeability, which eventually ameliorated the abundance of Rikenellaceae and hypoxanthine in the intestine and inactivated the HPRT-Wnt signaling in bone marrow HSCs. Furthermore, administration of Rikenellaceae or hypoxanthine in mice as well as treatment of WNT10A in the culture system substantially rescued the MPs-induced HSC defects. Finally, we validated in a cohort of human patients receiving allogenic HSCT from healthy donors, and revealed that the survival time of patients was negatively correlated with levels of MPs, while positively with the abundance of Rikenellaceae, and hypoxanthine in the HSC donors’ feces and blood. Overall, our study unleashes the detrimental roles and mechanisms of MPs in HSCs, which provides potential strategies to prevent hematopoietic damage from MPs and serves as a fundamental critique for selecting suitable donors for HSCT in clinical practice.
Hairpin trimer transition state of amyloid fibril
Authors: Sari Levent , Bali Sofia , Joachimiak Lukasz A. , Lin Milo M. 
Published: March 2024

AbstractProtein fibril self-assembly is a universal transition implicated in neurodegenerative diseases. Although fibril structure/growth are well characterized, fibril nucleation is poorly understood. Here, we use a computational-experimental approach to resolve fibril nucleation. We show that monomer hairpin content quantified from molecular dynamics simulations is predictive of experimental fibril formation kinetics across a tau motif mutant library. Hairpin trimers are predicted to be fibril transition states; one hairpin spontaneously converts into the cross-beta conformation, templating subsequent fibril growth. We designed a disulfide-linked dimer mimicking the transition state that catalyzes fibril formation, measured by ThT fluorescence and TEM, of wild-type motif - which does not normally fibrillize. A dimer compatible with extended conformations but not the transition-state fails to nucleate fibril at any concentration. Tau repeat domain simulations show how long-range interactions sequester this motif in a mutation-dependent manner. This work implies that different fibril morphologies could arise from disease-dependent hairpin seeding from different loci.
DELVE: feature selection for preserving biological trajectories in single-cell data
Authors: Ranek Jolene S. , Stallaert Wayne , Milner J. Justin , Redick Margaret , Wolff Samuel C. , Beltran Adriana S. , Stanley Natalie , Purvis Jeremy E. 
Published: March 2024

AbstractSingle-cell technologies can measure the expression of thousands of molecular features in individual cells undergoing dynamic biological processes. While examining cells along a computationally-ordered pseudotime trajectory can reveal how changes in gene or protein expression impact cell fate, identifying such dynamic features is challenging due to the inherent noise in single-cell data. Here, we present DELVE, an unsupervised feature selection method for identifying a representative subset of molecular features which robustly recapitulate cellular trajectories. In contrast to previous work, DELVE uses a bottom-up approach to mitigate the effects of confounding sources of variation, and instead models cell states from dynamic gene or protein modules based on core regulatory complexes. Using simulations, single-cell RNA sequencing, and iterative immunofluorescence imaging data in the context of cell cycle and cellular differentiation, we demonstrate how DELVE selects features that better define cell-types and cell-type transitions. DELVE is available as an open-source python package:https://github.com/jranek/delve.
Structure of alpha-synuclein fibrils derived from human Lewy body dementia tissue
Authors: Dhavale Dhruva D. , Barclay Alexander M. , Borcik Collin G. , Basore Katherine , Berthold Deborah A. , Gordon Isabelle R. , Liu Jialu , Milchberg Moses H. , O’Shea Jennifer Y. , Rau Michael J. , Smith Zachary , Sen Soumyo , Summers Brock , Smith John , Warmuth Owen A. , Perrin Richard J. , Perlmutter Joel S. , Chen Qian , Fitzpatrick James A. J. , Schwieters Charles D. , Tajkhorshid Emad , Rienstra Chad M. , Kotzbauer Paul T. 
Published: March 2024

AbstractThe defining feature of Parkinson disease (PD) and Lewy body dementia (LBD) is the accumulation of alpha-synuclein (Asyn) fibrils in Lewy bodies and Lewy neurites. Here we develop and validate a method to amplify Asyn fibrils extracted from LBD postmortem tissue samples and use solid state nuclear magnetic resonance (SSNMR) studies to determine atomic resolution structure. Amplified LBD Asyn fibrils comprise a mixture of single protofilament and two protofilament fibrils with very low twist. The protofilament fold is highly similar to the fold determined by a recent cryo-electron microscopy study for a minority population of twisted single protofilament fibrils extracted from LBD tissue. These results expand the structural characterization of LBD Asyn fibrils and approaches for studying disease mechanisms, imaging agents and therapeutics targeting Asyn.
The initial stages of cement hydration at the molecular level
Authors: Xu Xinhang , Qi Chongchong , Aretxabaleta Xabier M. , Ma Chundi , Spagnoli Dino , Manzano Hegoi 
Published: March 2024

AbstractCement hydration is crucial for the strength development of cement-based materials; however, the mechanism that underlies this complex reaction remains poorly understood at the molecular level. An in-depth understanding of cement hydration is required for the development of environmentally friendly cement and consequently the reduction of carbon emissions in the cement industry. Here, we use molecular dynamics simulations with a reactive force field to investigate the initial hydration processes of tricalcium silicate (C3S) and dicalcium silicate (C2S) up to 40 ns. Our simulations provide theoretical support for the rapid initial hydration of C3S compared to C2S at the molecular level. The dissolution pathways of calcium ions in C3S and C2S are revealed, showing that, two dissolution processes are required for the complete dissolution of calcium ions in C3S. Our findings promote the understanding of the calcium dissolution stage and serve as a valuable reference for the investigation of the initial cement hydration.
Identification of spatially-resolved markers of malignant transformation in Intraductal Papillary Mucinous Neoplasms
Authors: Agostini Antonio , Piro Geny , Inzani Frediano , Quero Giuseppe , Esposito Annachiara , Caggiano Alessia , Priori Lorenzo , Larghi Alberto , Alfieri Sergio , Casolino Raffaella , Scaglione Giulia , Tondolo Vincenzo , Cammarota Giovanni , Ianiro Gianluca , Corbo Vincenzo , Biankin Andrew V. , Tortora Giampaolo , Carbone Carmine 
Published: March 2024

AbstractThe existing Intraductal Papillary Mucinous Neoplasm (IPMN) risk stratification relies on clinical and histological factors, resulting in inaccuracies and leading to suboptimal treatment. This is due to the lack of appropriate molecular markers that can guide patients toward the best therapeutic options. Here, we assess and confirm subtype-specific markers for IPMN across two independent cohorts of patients using two Spatial Transcriptomics (ST) technologies. Specifically, we identify HOXB3 and ZNF117 as markers for Low-Grade Dysplasia, SPDEF and gastric neck cell markers in borderline cases, and NKX6-2 and gastric isthmus cell markers in High-Grade-Dysplasia Gastric IPMN, highlighting the role of TNFα and MYC activation in IPMN progression and the role of NKX6-2 in the specific Gastric IPMN progression. In conclusion, our work provides a step forward in understanding the gene expression landscapes of IPMN and the critical transcriptional networks related to PDAC progression.
Immunosenescence and vaccine efficacy revealed by immunometabolic analysis of SARS-CoV-2-specific cells in multiple sclerosis patients
Authors: De Biasi Sara , Lo Tartaro Domenico , Neroni Anita , Rau Moritz , Paschalidis Nikolaos , Borella Rebecca , Santacroce Elena , Paolini Annamaria , Gibellini Lara , Ciobanu Alin Liviu , Cuccorese Michela , Trenti Tommaso , Rubio Ignacio , Vitetta Francesca , Cardi Martina , Argüello Rafael José , Ferraro Diana , Cossarizza Andrea 
Published: March 2024

AbstractDisease-modifying therapies (DMT) administered to patients with multiple sclerosis (MS) can influence immune responses to SARS-CoV-2 and vaccine efficacy. However, data on the detailed phenotypic, functional and metabolic characteristics of antigen (Ag)-specific cells following the third dose of mRNA vaccine remain scarce. Here, using flow cytometry and 45-parameter mass cytometry, we broadly investigate the phenotype, function and the single-cell metabolic profile of SARS-CoV-2-specific T and B cells up to 8 months after the third dose of mRNA vaccine in a cohort of 94 patients with MS treated with different DMT, including cladribine, dimethyl fumarate, fingolimod, interferon, natalizumab, teriflunomide, rituximab or ocrelizumab. Almost all patients display functional immune response to SARS-CoV-2. Different metabolic profiles characterize antigen-specific-T and -B cell response in fingolimod- and natalizumab-treated patients, whose immune response differs from all the other MS treatments.