bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epigenetic investigation into circulating microRNA 197-3p in sera from patients affected by malignant pleural mesothelioma and workers ex-exposed to asbestos
Authors: Di Mauro Giulia , Frontini Francesca , Torreggiani Elena , Iaquinta Maria Rosa , Caselli Andrea , Mazziotta Chiara , Esposito Valentina , Mazzoni Elisa , Libener Roberta , Grosso Federica , Maconi Antonio , Martini Fernanda , Bononi Ilaria , Tognon Mauro 
Published: April 2023

AbstractThe epigenetic role of microRNAs is established at both physiological and pathological levels. Dysregulated miRNAs and their targets appear to be a promising approach for innovative anticancer therapies. In our previous study, circulating miR-197-3p tested dysregulated in workers ex-exposed to asbestos (WEA). Herein, an epigenetic investigation on this circulating miRNA was carried out in sera from malignant pleural mesothelioma (MPM) patients. MiR-197-3p was quantified in MPM (n = 75) sera and comparatively analyzed to WEA (n = 75) and healthy subject (n = 75) sera, using ddPCR and RT-qPCR techniques. Clinicopathological characteristics, occupational, non-occupational information and overall survival (OS) were evaluated in correlation studies. MiR-197-3p levels, analyzed by ddPCR, were significantly higher in MPM than in WEA cohort, with a mean copies/µl of 981.7 and 525.01, respectively. Consistently, RT-qPCR showed higher miR-197-3p levels in sera from MPM with a mean copies/µl of 603.7, compared to WEA with 336.1 copies/µl. OS data were significantly associated with histologic subtype and pleurectomy. Circulating miR-197-3p is proposed as a new potential biomarker for an early diagnosis of the MPM onset. Indeed, miR-197-3p epigenetic investigations along with chest X-ray, computed tomography scan and spirometry could provide relevant information useful to reach an early and effective diagnosis for MPM.
Comparison of SARS-CoV-2 whole genome sequencing using tiled amplicon enrichment and bait hybridization
Authors: Koskela von Sydow Anita , Lindqvist Carl Mårten , Asghar Naveed , Johansson Magnus , Sundqvist Martin , Mölling Paula , Stenmark Bianca 
Published: April 2023

AbstractThe severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) pandemic has led to extensive virological monitoring by whole genome sequencing (WGS). Investigating the advantages and limitations of different protocols is key when conducting population-level WGS. SARS-CoV-2 positive samples with Ct values of 14–30 were run using three different protocols: the Twist Bioscience SARS‑CoV‑2 protocol with bait hybridization enrichment sequenced with Illumina, and two tiled amplicon enrichment protocols, ARTIC V3 and Midnight, sequenced with Illumina and Oxford Nanopore Technologies, respectively. Twist resulted in better coverage uniformity and coverage of the entire genome, but has several drawbacks: high human contamination, laborious workflow, high cost, and variation between batches. The ARTIC and Midnight protocol produced an even coverage across samples, and almost all reads were mapped to the SARS-CoV-2 reference. ARTIC and Midnight represent robust, cost-effective, and highly scalable methods that are appropriate in a clinical environment. Lineage designations were uniform across methods, representing the dominant lineages in Sweden during the period of collection. This study provides insights into methodological differences in SARS‑CoV‑2 sequencing and guidance in selecting suitable methods for various purposes.
Concurrent dilution and amplification effects in an intraguild predation eco-epidemiological model
Authors: Gómez-Hernández Enith A. , Moreno-Gómez Felipe N. , Bravo-Gaete Moisés , Córdova-Lepe Fernando 
Published: April 2023

AbstractThe dilution and amplification effects are important concepts in the field of zoonotic diseases. While the dilution effect predicts that pathogen prevalence is negatively correlated with increased species diversity, the opposite trend is observed when the amplification effect occurs. Understanding how interspecific interactions such as predation and competition within a community influence disease transmission is highly relevant. We explore the conditions under which the dilution and amplification effects arise, using compartmental models that integrate ecological and epidemiological interactions. We formulate an intraguild predation model where each species is divided into two compartments: susceptible and infected individuals. We obtained that increasing predation increases the disease transmission potential of the predator and the density of infected individuals, but decreases the disease transmission potential of the prey, as well as their density. Also, we found that interspecific competition always helps to decrease the number of infected individuals in the population of the two species. Therefore, dilution and amplification effects can be observed simultaneously but depending on different types of cological interactions.
Evaluation of infliximab/tocilizumab versus tocilizumab among COVID-19 patients with cytokine storm syndrome
Authors: Sarhan Neven Mohamed , Warda Ahmed Essam Abou , Ibrahim Haytham Soliman Ghareeb , Schaalan Mona Farag , Fathy Shaimaa Mohamed 
Published: April 2023

AbstractCoronavirus Disease 2019 (COVID-19) continues to spread rapidly. Monoclonal antibodies as well as anti-tumor necrosis factor are considered promising treatments for COVID-19. A prospective cohort study in which patients are divided into three groups. Group 1: moderate and severe COVID-19 patients received standard treatment; Group 2: moderate and severe COVID-19 patients received tocilizumab; Group 3: moderate and severe COVID-19 patients received treatment with infliximab and tocilizumab. 153 patients were recruited in the study. 40 received standard treatment alone, 70 received tocilizumab with standard treatment, and 43 received tocilizumab/infliximab with standard treatment. There was a significant difference in length of hospital stay (10.3, 8.9, and 7.6 days respectively P = 0.03), need for a non-invasive mechanical ventilator (4, 5, and one patient; P = 1.2E−8), intensive care admission (32, 45, and 16 patients; P = 2.5E−5), the occurrence of sepsis (18, 12, and 10 patients; P = 0.005) and in death (42.5%, 14.2%, and 7%; P = 0.0008) which were significantly lower in tocilizumab/infliximab group compared to tocilizumab and standard of care groups. Our study showed that tocilizumab/ infliximab in addition to standard of care was considered a promising treatment for moderate and severe COVID-19 patients.Trial registration number: ClinicalTrials.gov NCT04734678; date of registration: 02/02/2021.
Estimation and sensitivity analysis of a COVID-19 model considering the use of face mask and vaccination
Authors: Bai Zhongtian , Ma Zhihui , Jing Libaihe , Li Yonghong , Wang Shufan , Wang Bin-Guo , Wu Yan , Han Xiaotao 
Published: April 2023

AbstractTo model the COVID-19 infection and develop effective control measures, this paper proposes an SEIR-type epidemic model considering the impact of face-mask wearing and vaccination. Firstly, the effective reproduction number and the threshold conditions are obtained. Secondly, based on the data of South Korea from January 20, 2022 to March 21, 2022, the model parameters are estimated. Finally, a sensitivity analysis and the numerical study are conducted. The results show that the face-mask wearing is associated with $$83\%$$

83
%

and $$90\%$$

90
%

reductions in the numbers of cumulative cases and newly confirmed cases, respectively, after a period of 60 days, when the face mask wearing rate increases by $$15\%$$

15
%

. Furthermore, the vaccination rate is associated with $$75\%$$

75
%

and $$80\%$$

80
%

reductions in the numbers of cumulative cases and the newly confirmed cases, respectively, after the same period of 60 days when the vaccination rate is increased by $$15\%$$

15
%

. A combined measure involving face-mask wearing and vaccination may be more effective and reasonable in preventing and controlling this infection. It is also suggested that disease control departments should strongly recommended the wearing of face masks s as well as vaccination to prevent the unvaccinated people from becoming infected.
Measurement properties of 72 movement biomarkers aiming to discriminate non‑specific chronic low back pain patients from an asymptomatic population
Authors: Moissenet Florent , Armand Stéphane , Genevay Stéphane 
Published: April 2023

AbstractThe identification of relevant and valid biomarkers to distinguish patients with non-specific chronic low back pain (NSCLBP) from an asymptomatic population in terms of musculoskeletal factors could contribute to patient follow-up and to evaluate therapeutic strategies. Several parameters related to movement impairments have been proposed in the literature in that respect. However, most of them were assessed in only one study, and only 8% were evaluated in terms of reliability, validity and interpretability. The aim of this study was to consolidate the current knowledge about movement biomarkers to discriminate NSCLBP patients from an asymptomatic population. For that, an experimental protocol was established to assess the reliability, validity and interpretability of a set of 72 movement biomarkers on 30 asymptomatic participants and 30 NSCLBP patients. Correlations between the biomarkers and common patient reported outcome measures were also analysed. Four biomarkers reached at least a good level in reliability (ICC ≥ 0.75) and validity (significant difference between asymptomatic participants and NSCLBP patients, p ≤ 0.01) domains and could thus be possibly considered as valuable biomarkers: maximal lumbar sagittal angle, lumbar sagittal angle range of motion, mean lumbar sagittal angular velocity, and maximal upper lumbar sagittal angle during trunk sagittal bending. These four biomarkers demonstrated typically larger values in asymptomatic participants than in NSCLBP patients. They are in general weakly correlated with patient reported outcome measures, arguing for a potential interest in including related musculoskeletal factors in the establishment of a valuable diagnosis and in guiding treatment response.
Effect of green and roasted coffee storage conditions on selected characteristic quality parameters
Authors: Błaszkiewicz Justyna , Nowakowska-Bogdan Ewa , Barabosz Krzysztof , Kulesza Renata , Dresler Ewa , Woszczyński Piotr , Biłos Łukasz , Matuszek Dominika Barbara , Szkutnik Krzysztof 
Published: April 2023

AbstractThe paper attempts to determine the best storage conditions for green and roasted coffee beans. Coffee beans were processed in various ways—some of them were washed or left in their natural state after harvesting, then they were stored in two types of packaging with different permeability, i.e. jute bag and GrainPro polymer bag, ensuring stable conditions in three temperature chambers, i.e. − 10, 10 and 20 °C. The grains treated in this way were evaluated after 3, 6, 9, and 12 months. The selection of the analyzed parameters (in roasted coffee—cupping and 3 selected volatile organic compounds; in green coffee—average water activity, content of volatile fatty acids, 6 selected volatile organic compounds) was to monitor the ongoing processes, and thus the qualitative changes taking place in grains. The research shows that grain stored at 20 °C ages the fastest. Grains stored in − 10 °C and 10 °C chambers perform similarly well. The evaluation of the parameters shows that among the grains stored in these two chambers, the method of grain processing (Natural/Washed) had a greater impact on the results, while the type of packaging did not differentiate the grains to such a significant extent.
Micro-computed tomography for the identification and characterization of archaeological lime bark
Authors: Stelzner Jörg , Million Sebastian , Stelzner Ingrid , Nelle Oliver , Banck-Burgess Johanna 
Published: April 2023

AbstractIn the Neolithic pile-dwelling settlements of southwestern Germany, bark played a prominent role in the production of technical textiles. So far, the inner bark (phloem) of the lime tree (genus Tilia) could be detected most frequently. Microscopic examination of anatomical features can determine the taxon, requiring manipulation of samples and archaeological objects. In this study, micro-computed tomography (µCT) was reviewed as a method for determining the woody taxon and obtaining additional information from the inner bark. To this end, modern bark samples from different tree organs of lime were first analysed using both µCT and transmitted light microscopy. Both methods were able to detect all characteristic anatomical features in the phloem and identify the genus. With analysis based on µCT data, further anatomical information can be obtained. For example, the shape of the phloem rays in the bast strips can provide information on the position within the bark and on the original organ diameter. These results obtained on modern material were verified on four samples from archaeological objects. Based on µCT, all samples could be clearly identified as lime and in two cases conclusions could also be drawn about the raw material. This approach could lead to new results and interpretations in archaeological sciences.
Pipe vibration attenuation through internal damping and optimal design of vibro-impact systems
Authors: Aloschi Fabrizio , Andreotti Roberto , Bursi Oreste Salvatore 
Published: April 2023

AbstractPipelines periodically supported by rack structures (PPRs) are common in chemical and petrochemical plants, among others, and conventional tools such as dampers and hysteretic absorbers are commonly used to mitigate large vibrations in these systems. In this study, we explore two alternative strategies: (i) enhancing the attenuation rate of PPR vibrations through structural internal damping, and (ii) using nonlinear vibro-impact systems (VIS) to reduce seismic vibrations in a PPR. To shed light on the first strategy, we develop analytical dispersion relations for a PPR and show how damping can improve the mitigation capabilities of the periodic system. As for the second strategy, we consider a 9-node beam, i.e., a single span (SS) of a PPR equipped with a VIS, and combine the central composite design (CCD) and Kriging metamodelling to maximize dissipation energy and minimize the number of impacts. This multi-objective optimization problem aims to find the most effective design solution for the VIS in terms of gap and coefficient of restitution (COR). Additionally, we consider the stochastic nature of seismic input and the possible chaotic behavior of the VIS. To account for the sensitive variability of the number of impacts in seismic records, we perform incremental dynamic analyses and calculate fragility functions for various engineering demand parameters, including the number of impacts. We define a 3D surface for selecting the optimal gap-COR pair. When impacts occur, transient results can be chaotic, and we compute the largest Lyapunov exponents of a few representative trajectories.
Serum lipid mediator profiles in COVID-19 patients and lung disease severity: a pilot study
Authors: Irún Pilar , Gracia Rafael , Piazuelo Elena , Pardo Julián , Morte Elena , Paño José Ramon , Boza Julio , Carrera-Lasfuentes Patricia , Higuera Gustavo A. , Lanas Angel 
Published: April 2023

AbstractCoronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 infection is highly heterogeneous, ranging from asymptomatic to severe and fatal cases. COVID-19 has been characterized by an increase of serum pro-inflammatory cytokine levels which seems to be associated with fatal cases. By contrast, the role of pro-resolving lipid mediators (SPMs), involved in the attenuation of inflammatory responses, has been scarcely investigated, so further studies are needed to understand SPMs metabolism in COVID-19 and other infectious diseases. Our aim was to analyse the lipid mediator metabolome, quantifying pro- and anti-inflammatory serum bioactive lipids by LC–MS/MS in 7 non-infected subjects and 24 COVID-19 patients divided into mild, moderate, and severe groups according to the pulmonary involvement, to better understand the disease outcome and the severity of the pulmonary manifestations. Statistical analysis was performed with the R programming language (R Foundation for Statistical Computing, Vienna, Austria). All COVID-19 patients had increased levels of Prostaglandin E2. Severe patients showed a significant increase versus controls, mild- and moderate-affected patients, expressed as median (interquartile range), in resolvin E1 [112.6 (502.7) vs 0.0 (0.0) pg/ml in the other groups], as well as in maresin 2 [14.5 (7.0) vs 8.1 (4.2), 5.5 (4.3), and 3.0 (4.0) pg/ml, respectively]. Moreover, 14-hydroxy docosahexaenoic acid (14-HDHA) levels were also increased in severe vs control and mild-affected patients [24.7 (38.2) vs 2.4 (2.2) and 3.7 (6.4) ng/mL, respectively]. Resolvin D5 was also significantly elevated in both moderate [15.0 (22.4) pg/ml] and severe patients [24.0 (24.1) pg/ml] versus controls [0.0 (0.0) pg/ml]. These results were confirmed by sparse partial least squares discriminant analysis which highlighted the contribution of these mediators to the separation between each of the groups. In conclusion, the potent inflammatory response to SARS-CoV-2 infection involves not only pro- but also anti-inflammatory lipid mediators that can be quantified in easily accessible serum samples, suggesting the need to perform future research on their generation pathways that will help us to discover new therapeutic targets.
Early stoma closure after low anterior resection is not recommended due to postoperative complications and asymptomatic anastomotic leakage
Authors: Fukudome Ian , Maeda Hiromichi , Okamoto Ken , Yamaguchi Sachi , Fujisawa Kazune , Shiga Mai , Dabanaka Ken , Kobayashi Michiya , Namikawa Tsutomu , Hanazaki Kazuhiro 
Published: April 2023

AbstractThe safety of early stoma closure after lower anterior resection (LAR) for rectal cancer remains controversial. In this study, patients scheduled to undergo LAR and stoma creation for rectal cancer were recruited. In absence of anastomotic leakage on radiological examination, closure of the diverting ileostomy was performed within 2 weeks. The primary endpoint was incidence of the colorectal anastomosis leakage after early stoma closure. Because of the slow accrual rate, the study was closed before recruitment reached the planned number of patients (n = 20). Among the 13 patients enrolled between April 2019 and March 2021, early stoma closure was performed in seven patients (53.8%). Non-clinical anastomotic leakage, leakage identified only on radiological examination, occurred in five cases, resulting in rescheduling of stoma closure. One patient did not undergo early stoma closure due to ileus. After stoma closure, colorectal anastomotic leakage manifested in one case; its incidence rate was 14.2%. Surgical site infection occurred in 42.8% of patients. This study revealed that asymptomatic anastomotic leakage occurred frequently. Considering the low rate of successful cases and the high rate of complications, early stoma closure within 2 weeks after LAR should not be performed routinely. Trial registration: (UMIN000036382 registered on 03/04/2019).
White blood cell count profiles in anti-aquaporin-4 antibody seropositive neuromyelitis optica spectrum disorder and anti-myelin oligodendrocyte glycoprotein antibody-associated disease
Authors: Akaishi Tetsuya , Misu Tatsuro , Fujihara Kazuo , Nakaya Kumi , Nakaya Naoki , Nakamura Tomohiro , Kogure Mana , Hatanaka Rieko , Itabashi Fumi , Kanno Ikumi , Kaneko Kimihiko , Takahashi Toshiyuki , Fujimori Juichi , Takai Yoshiki , Nishiyama Shuhei , Ishii Tadashi , Aoki Masashi , Nakashima Ichiro , Hozawa Atsushi 
Published: April 2023

AbstractWhite blood cell (WBC) count profiles in anti-aquaporin-4 antibody-positive neuromyelitis optica spectrum disorder (AQP4-NMOSD) and anti-myelin oligodendrocyte glycoprotein antibody-associated disease (MOGAD) are still unknown. This study evaluated the total WBC count, differential WBC counts, monocyte-to-lymphocyte ratio (MLR), and neutrophil-to-lymphocyte ratio (NLR) in patients with these diseases within three months from an attack before acute treatment or relapse prevention and compared the profiles with those in matched volunteers or in multiple sclerosis (MS) patients. AQP4-NMOSD patients (n = 13) had a higher neutrophil count (p = 0.0247), monocyte count (p = 0.0359), MLR (p = 0.0004), and NLR (p = 0.0037) and lower eosinophil (p = 0.0111) and basophil (p = 0.0283) counts than those of AQP4-NMOSD-matched volunteers (n = 65). Moreover, patients with MOGAD (n = 26) had a higher overall WBC count (p = 0.0001), neutrophil count (p < 0.0001), monocyte count (p = 0.0191), MLR (p = 0.0320), and NLR (p = 0.0002) than those of MOGAD-matched volunteers (n = 130). The three demyelinating diseases showed similar levels of the total and differential WBC counts; however, MOGAD and MS showed different structures in the hierarchical clustering and distributions on a two-dimensional canonical plot using differential WBC counts from the other three groups. WBC count profiles were similar in patients with MOGAD and MS but differed from profiles in matched volunteers or patients with AQP4-NMOSD.
Topologically associating domain boundaries are required for normal genome function
Authors: Rajderkar Sudha , Barozzi Iros , Zhu Yiwen , Hu Rong , Zhang Yanxiao , Li Bin , Alcaina Caro Ana , Fukuda-Yuzawa Yoko , Kelman Guy , Akeza Adyam , Blow Matthew J. , Pham Quan , Harrington Anne N. , Godoy Janeth , Meky Eman M. , von Maydell Kianna , Hunter Riana D. , Akiyama Jennifer A. , Novak Catherine S. , Plajzer-Frick Ingrid , Afzal Veena , Tran Stella , Lopez-Rios Javier , Talkowski Michael E. , Lloyd K. C. Kent , Ren Bing , Dickel Diane E. , Visel Axel , Pennacchio Len A. 
Published: April 2023

AbstractTopologically associating domain (TAD) boundaries partition the genome into distinct regulatory territories. Anecdotal evidence suggests that their disruption may interfere with normal gene expression and cause disease phenotypes1–3, but the overall extent to which this occurs remains unknown. Here we demonstrate that targeted deletions of TAD boundaries cause a range of disruptions to normal in vivo genome function and organismal development. We used CRISPR genome editing in mice to individually delete eight TAD boundaries (11–80 kb in size) from the genome. All deletions examined resulted in detectable molecular or organismal phenotypes, which included altered chromatin interactions or gene expression, reduced viability, and anatomical phenotypes. We observed changes in local 3D chromatin architecture in 7 of 8 (88%) cases, including the merging of TADs and altered contact frequencies within TADs adjacent to the deleted boundary. For 5 of 8 (63%) loci examined, boundary deletions were associated with increased embryonic lethality or other developmental phenotypes. For example, a TAD boundary deletion near Smad3/Smad6 caused complete embryonic lethality, while a deletion near Tbx5/Lhx5 resulted in a severe lung malformation. Our findings demonstrate the importance of TAD boundary sequences for in vivo genome function and reinforce the critical need to carefully consider the potential pathogenicity of noncoding deletions affecting TAD boundaries in clinical genetics screening.