bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of k-mer-based de novo comparative metagenomic tools and approaches
Authors: Ponsero Alise Jany , Miller Matthew , Hurwitz Bonnie Louise 
Published: July 2023

Aim: Comparative metagenomic analysis requires measuring a pairwise similarity between metagenomes in the dataset. Reference-based methods that compute a beta-diversity distance between two metagenomes are highly dependent on the quality and completeness of the reference database, and their application on less studied microbiota can be challenging. On the other hand, de-novo comparative metagenomic methods only rely on the sequence composition of metagenomes to compare datasets. While each one of these approaches has its strengths and limitations, their comparison is currently limited.
Methods: We developed sets of simulated short-reads metagenomes to (1) compare k-mer-based and taxonomy-based distances and evaluate the impact of technical and biological variables on these metrics and (2) evaluate the effect of k-mer sketching and filtering. We used a real-world metagenomic dataset to provide an overview of the currently available tools for de novo metagenomic comparative analysis.
Results: Using simulated metagenomes of known composition and controlled error rate, we showed that k-mer-based distance metrics were well correlated to the taxonomic distance metric for quantitative Beta-diversity metrics, but the correlation was low for presence/absence distances. The community complexity in terms of taxa richness and the sequencing depth significantly affected the quality of the k-mer-based distances, while the impact of low amounts of sequence contamination and sequencing error was limited. Finally, we benchmarked currently available de-novo comparative metagenomic tools and compared their output on two datasets of fecal metagenomes and showed that most k-mer-based tools were able to recapitulate the data structure observed using taxonomic approaches.
Conclusion: This study expands our understanding of the strength and limitations of k-mer-based de novo comparative metagenomic approaches and aims to provide concrete guidelines for researchers interested in applying these approaches to their metagenomic datasets.
First-Principles investigation of the thermal properties of the XO (X = Be, Mg and Sr) nanosheet
Authors: Abdullah Botan Jawdat 
Published: July 2023

Abstract
The electronic structures and thermal characteristics of hexagonal XO nanosheets (where X = Be, Mg, and Sr) are investigated using the density functional theory. The electronic structures, including band structure and partial density of states are investigated, and it is found that BeO is an insulator, whereas MgO and SrO are semiconductors, according to the energy gap range of these three nanosheets. Thermal properties including as entropy, enthalpy, free energy, and heat capacity for XO nanosheets are identified and investigated in this study. Due to differences in the electronegativity and bonding nature of XO nanosheets, the thermodynamic parameters change dramatically with a similar trend as function of temperature. Enthalpy and entropy increase with temperature whereas free energy falls, owing to a change in the binary oxide internal energy of the system and the electron density distribution. Thermal energy is absorbed by lattices at low temperatures, and they grow until the point at which all of the lattices are enhanced and the system starts to produce lattice unharmonicity of the linear dependence. Varied ranges for the XO nanosheets’ parameters can be advantageous for thermoelectric nanodevices.
Fast catalytic degradation of organic dyes in aqueous media using copper sulfate deposited on biowaste-derived hydroxyapatite
Authors: Yarahmadi Hossein , Sheibani Reza 
Published: July 2023

Abstract
Conversion of biowastes into valuable products will assist sustainable development and waste management. Eggshell could be used as a bio-template for the synthesis of hydroxyapatite and widely applied in the field of catalytic processes. In this study, copper sulfate supported on hydroxyapatite (CuSO4@HAP) was rationally fabricated using biowaste eggshells (ES) by hydrothermal method and it was used for the fast catalytic degradation of organic pollutant dyes (OPDs) such as methylene blue (MB), 4-nitrophenol (4-NP) and 4-nitroaniline (4-NA) in the presence of sodium borohydride (NaBH4) in aqueous media. The physical and chemical properties of CuSO4@HAP were characterized via FTIR, XRD, BET, TEM, FE-SEM/EDS, and elemental mapping analyses. Results indicated that the synthesized catalyst was crystalline with great purity, homogeneous with fine particles, and mesoporous with a high specific surface area. Besides, the reaction progress was evaluated using a double-beam UV-vis spectrophotometer. The reaction conversion (%) under optimal conditions rapidly increased to an equilibrium state (99% for 4-NP, 96% for 4-NA, and 99.5% for MB) within a short time (t < 10 min). In addition, the catalytic rate constant of MB, 4-NP, and 4-NA in the presence of NaBH4 and CuSO4@HAP was calculated to be about 0.514, 0.492, and 0.317 min− 1, respectively. This study demonstrates the potential use of natural HAP-derived catalyst from biowaste eggshell with high efficiency and stability for degrading OPDs under mild reaction conditions. Additionally, CuSO4@HAP could be effectively separated and reused for four cycles with almost the same catalytic efficacy.
Effect of Bitter Orange Blossom Distillate on Anxiety and Sleep Disorder in Mothers with Infants Admitted to Neonatal Intensive Care unit: A Randomized Controlled Clinical Trial
Authors: Dehghan Zahra , amiri Seyedeh Roghaye Jafarian , Mozaffarpur Seyyed Ali , Shirafkan Hoda , Arzani Afsaneh 
Published: July 2023

Abstract
Background:Mothers of neonates admitted to the intensive care unit are prone to sleep disorders due to stress and anxiety. Some herbs have anti-anxiety and sedative properties.The aim of this study was to investigate the effect of bitter orange blossom distillate on anxiety and sleep disorder in mothers with infants admitted to neonatal intensive care unit.
Methods:This randomized controlled clinical trial was conducted in 2021on 60 mothers with NICU-admitted infants in one of the medical teaching centers affiliated to Babol University of Medical Sciences,Iran. Permuted block randomization was used to assign the mothers to the experimental (bitter orange blossom distillate syrup)and control groups(syrup prepared from water and sugar).Given the impossibility of blinding the participants, allocation concealment was used to prevent the researcher from predicting the future allocation of the samples to the groups. In addition, the statistical consultant received coded data pertaining to the type of intervention in each group.A demographic questionnaire,the Spielberger State and Trait Anxiety Inventory (STAI) and the General Sleep Disorder Scale were employed to collect data.We assessed the level of anxiety and sleep disorder (in both groups before the intervention and again after the last day of the intervention). Data were analyzed using SPSS V22 software. P value less than 0.05was considered significant.
Reasults: The mean and standard deviation of the sleep disorder score in the intervention group from (50.26±5.81) to (44.70±6.94) and in the control group from (50.46±6.95) to(48.53±8.62)changed. The covariance test showed that bitter orange blossom distillate syrup has a significant effect on the improvement of sleep disorders (P=0.01, Effect size=0.09), but there was no significant difference in the anxiety level of mothers(P> 0.05, Effect size < 0.06).
Conclusions:Due to the positive effect of bitter orange blossom distillate syrup on sleep disorders of mothers with hospitalized babies, this low-cost and low-risk intervention is recommended.
Trial registration: IRCTID: IRCT20201209049666N1. Registered 15-04-2021. Retrospectively registered. https://www.cochranelibrary.com/es/central/doi/10.1002/central/CN-02280085/full
https://trialsearch.who.int/Trial2.aspx?TrialID=IRCT20201209049666N1, 2021
Solitary waves management in α-helix protein chain with long-range interactions and asymmetric molecular vibrations
Authors: Fewu J. C. Mimshe , Belobo D. Belobo , Ondoua R.Y. 
Published: July 2023

Abstract
A three-stranded α-helix protein chain model with long-rangeinteractions, whose dynamic, in the continuum limit approximation isgoverned by three coupled nonlinear Schr\"{o}dinger equation typesis investigated. Applying the trial equation method, two- andfour-bright solitary wave solutions are constructed to explain theexciton dynamic through the protein chains. Intensive numericalsimulations allow to check the influence of key system parameters onthe dynamic of the solutions. It appears that nonlinear couplings,long-range interactions, asymmetric molecular vibrations, and thewave's velocity deeply alter the widths and amplitudes of oursolitary waves, two salient features which mean that the abovementioned parameters have a major impact on bioenergy transport inprotein chains. In the same vein, the number of solitary waves whichpropagate through the protein chain may be controlled by either thewave velocity, the asymmetric molecular vibrations strength or thelong-range interaction strength provided that values of the latterparameters are set below or above critical values identified.
Pre-hospital endotracheal intubation in traumatic brain injury – ventilation targets and mortality. A retrospective analysis of 308 patients
Authors: Knapp Jürgen , Doppmann Pascal , Huber Markus , Meuli Lorenz , Albrecht Roland , Sollid Stephen , Pietsch Urs 
Published: July 2023

Abstract
Background: Traumatic brain injury (TBI) remains one of the main causes of mortality and long-term disability worldwide. Maintaining physiology of brain tissue to the greatest extent possible through optimal management of blood pressure, airway, ventilation, and oxygenation, improves patient outcome. We studied the quality of prehospital care in TBI patients by analyzing adherence to recommended target ranges for ventilation and blood pressure, prehospital time expenditure, and their effect on mortality, as well as quality of prehospital ventilation assessed by arterial partial pressure of CO2 (paCO2) at hospital admission.
Methods: This is a retrospective cohort study of all TBI patients requiring tracheal intubation on scene who were transported to one of two major level 1 trauma centers in Switzerland between January 2014 and December 2019 by Swiss Air Rescue (Rega). We assessed systolic blood pressure (SBP), end-tidal partial pressure of CO2 (petCO2), and paCO2 at hospital admission as well as prehospital and on-scene time. Quality markers of prehospital care (petCO2, SBP, prehospital times) and prehospital ventilation (paCO2) are presented as descriptive analysis. Effect on mortality was calculated by multivariable regression analysis and a logistic general additive model.
Results: Of 557 patients after exclusions, 308 were analyzed. Adherence to blood pressure recommendations was 89%. According to petCO2 45% were normoventilated, and 29% had a SBP ≥90 mmHg and were normoventilated. Due to the poor correlation between paCO2 and petCO2, only 33% were normocapnic at hospital admission. Normocapnia at hospital admission was strongly associated with reduced probability of mortality. Prehospital and on-scene times had no impact on mortality.
Conclusions: paCO2 at hospital admission is strongly associated with mortality risk, but normocapnia is achieved only in a minority of patients. Therefore, the time required for placement of an arterial cannula and prehospital blood gas analysis may be warranted in TBI patients requiring on-scene tracheal intubation.
Nonlinear Indicial Functions for Modelling Aeroelastic Forces of Bluff Bodies
Authors: Gao Guangzhong , Zhu Ledong , Øiseth Ole Andre 
Published: July 2023

Abstract
This study introduces a novel time-domain model of nonlinear indicial functions to capture the amplitude dependency of self-excited forces in aeroelastic instabilities, including flutter, vortex-induced vibration (VIV), and unsteady galloping. The model aims to reproduce the nonlinear aerodynamic forces that arise from large amplitude oscillations causing variations in the transient wind angle of attack. The model assumes that the decay coefficients in the indicial functions can be taken as nonlinear functions of the transient angle of attack induced by the body motion, enabling the incorporation of both amplitude dependency and memory effect within a simple time domain model. The proposed model is experimentally validated considering an unsteady galloping test of an elastically supported rectangular 2:1 cylinder sectional model.
Modeling Mass Removal and Sediment Deposition in Stormwater Ponds Using Floating Treatment Islands: A Computational Approach
Authors: Xavier Manoel Lucas Machado , Janzen Johannes Gerson , Nepf Heidi 
Published: July 2023

Abstract
Floating Treatment Islands (FTIs) offers effective solutions for stormwater management, providing flood attenuation and pollutant removal capabilities. However, there remains a knowledge gap concerning their performance, specifically in terms of pollutant removal and sediment deposition. To address this gap, the present study employs Computational Fluid Dynamics (CFD) modeling to investigate the intricate interactions within FTI systems. Various FTI configurations are analyzed, considering mass removal through FTIs and sediment deposition. The findings demonstrate that FTIs have a significant influence on flow patterns and mass removal. Notably, FTIs enhance mass removal compared to the control case, with larger sediment particles exhibiting higher removal rates. The correlation between the short-circuit index and sedimentation in FTI ponds highlights the potential of FTIs as indicators of treatment efficiency. Furthermore, the study focuses on mass removal exclusively through the FTI root zones. The positioning of FTIs within the pond has a considerable impact, resulting in differences of up to 20% in mass removal. Moreover, the FTI configuration exerts a more pronounced influence on mass removal through FTIs than through sediment deposition alone. In cases where both processes occur simultaneously, the presence of FTIs lead to higher mass removal, primarily attributed to the FTIs themselves, particularly in the initial segment. Remarkably, certain FTI configurations enable mass removal exceeding 70% for large sediment particles, even with a pond length less than half of the original.
Clinical characteristics of a pediatric cohort of patients with combined pituitary insufficiency caused by mutations of the PROP1 gene
Authors: Zygmunt-Górska Agata , Wójcik Małgorzata , Gilis-Januszewska Aleksandra , Starmach Anna , Bik-Multanowski Mirosław , Starzyk Jerzy B. 
Published: July 2023

Abstract
The most commonly identified genetic cause of combined pituitary deficiency (CPHD) are PROP1 gene mutations.
The aim of the study was to compare selected clinical features of patients with CPHD caused by mutations of the PROP1 gene (CPHD-PROP1) and patients with inborn CPHD of other etiology (CPHD-nonPROP1).
Material and Methods: The retrospective analysis included childhood medical records of 74 patients (32 female) with CPHD, including 43 patients (23 female) with the mutation in the PROP1 gene.
Results: Patients with CPHD-PROP1 compared to the CPHD-nonPROP1 presented with: significantly higher mean birth weight (0.2 vs. -0.3 SDS, p=0.019), lower growth velocity within 3 years preceding growth hormone administration (-2.7 vs. -0.8 SDS, p<0.05), higher mean maximal blood concentration of growth hormone in the stimulation (1.2 vs. 1.08 ng/mL, p=0.0025), lower TSH (1.8 μIU/mL vs. 2.4 μIU/mL, p=0.0002) and prolactin (128 vs. 416.3 μIU/mL, p<0.001) concentrations, and less frequent typical signs of hypogonadism at birth in boys (n=6; 30% vs. n=12, 54%, p=0.0002). Secondary adrenal insufficiency was less frequent in CPHD-PROP1 (20 vs. 25 cases, p=0.006), and occurred at a later age (13.4 vs. 10.4 years). MRI of the pituitary gland in CPHD-PROP1 revealed: small pituitary gland (21 cases), pituitary gland enlargement (8 cases), 1 pituitary stalk interruption and posterior lobe ectopy, in 9 cases normal.
Conclusion: Patients with the PROP1mutations present a clinical picture significantly different from other forms of congenital hypopituitarism.
CD34+ cell transplantation alleviates fibrotic liver injury via innate immune modulation in non-alcoholic steatohepatitis mice
Authors: Masuda Atsutaka , Nakamura Toru , Iwamoto Hideki , Suzuki Hiroyuki , Sakaue Takahiko , Tanaka Toshimitsu , Imamura Yasuko , Mori Nobuyuki , Koga Hironori , Kawaguchi Takumi 
Published: July 2023

Abstract
Background/purpose of the study:
In drug-induced liver injury, vascular endothelial progenitor cells, specifically the CD34+ cell fractions, have been found to decrease liver fibrosis and promote regeneration. However, it is unclear whether CD34+ cell transplantation has anti-fibrogenic effects on NASH, which has been treated effectively with anti-angiogenic therapy. We investigated the efficacy of ex vivo-expanded CD34+ cells in treating NASH livers.
Methods
CD34+ cells were isolated from mice bone marrow and effectively expanded over 7 days. The mice were assigned to either a normal chow diet or a choline-deficient, L-amino acid-defined, high-fat diet, which was followed for 12 and 20 weeks to create a mild and severe fibrosis model, respectively.
Results
Expanded CD34+ cell transplantation ameliorated liver fibrosis, regardless of fibrosis degree, as indicated by the decrease in α-smooth muscle actin-positive cells, hydroxyproline concentration, and fibrogenic gene expression of Col1a1 and Timp1. Furthermore, engrafted CD34+ cells reduced alanine transaminase levels, the number of TUNEL+ hepatocytes, and 8-OHdG concentration. RNA-sequencing data showed that "defense response to virus" was the most down-regulated category in the Gene Ontology analysis and subsequent analysis revealed the suppression of RIG-I-like receptors/IRF7/STAT1/CXCL10 axis in expanded CD34+ cell-transplanted livers. Finally, the downregulation of CXCL10 expression inhibits the mobilization of inflammatory immune cells, macrophages, T cells, and natural killer cells to the NASH liver.
Conclusions
These findings suggest that transplanted expanded CD34+ cells alleviate fibrotic liver injury in NASH mouse models through possible modulation of the innate immune response, which is abnormally activated by hepatocyte lipotoxicity.
“I do not want an ambulance, I just need help” A Qualitative Study of Callers’ Experience of Calls to the Emergency Medical Communication Center
Authors: Spjeldnæs Trine Berglie , Nilsen Kristine A. Vik , Myrmel Lars , Sørnes Jan-Oddvar , Brattebø Guttorm 
Published: July 2023

Abstract
Background
The Emergency Medical Communications Center (EMCC) is essential in emergencies and often represents the public’s first encounter with the healthcare system. Previous research has mainly focused on the dispatcher’s perspective. Therefore, there is a lack of insight into the callers’ perspectives, the attainment of which may contribute significantly to improving the quality of this vital public service. Most calls are now made from mobile phones, opening up novel approaches for obtaining caller feedback using tools such as short-message services (SMS). Thus, this study aims to obtain a better understanding of callers’ actual experiences and how they perceived their interaction with the EMCC.
Methods
A combination of quantitative and qualitative study methods was used. An SMS survey was sent to the mobile phone numbers of everyone who had contacted 113 during the last months. This was followed by 31 in-depth interviews with people either satisfied or dissatisfied. Grounded theory and phenomenology inspired the interviews.
Results
We received 1680 (35%) responses to the SMS survey, sent to 4807 unique numbers. Most respondents (88%) were satisfied, evaluating their experience as 5 or 6 on a six-point scale, whereas 5% answered with 1 or 2. The interviews revealed that callers were in distress before calling 113. By actively listening and taking the caller seriously, and affirming that it was the right choice to call the emergency number, the EMCC make callers experience a feeling of help and satisfaction, regardless of whether an ambulance was dispatched to their location.
If callers did not feel taken seriously or listened to, they were less satisfied. A negative experience may lead to a higher distress threshold and an adjusted strategy before the caller makes contact 113 next time. Callers with positive experiences expressed more trust in the healthcare systems.
Conclusions
For the callers, the most important was being taken seriously and listened to. Additionally, they welcomed that dispatchers express empathy and affirm that callers made the right choice to call EMCC, as this positively affects communication with callers. The 113 calls aimed to cooperate in finding a solution to the caller’s problem.
Zika virus infection during pregnancy and vertical transmission: case reports and peptide-specific cellmediated immune responses.
Authors: Soudeyns Hugo , Hindle Stéphanie , Depatureaux Agnès , Fortin-Dion Samuel , Dieumegard Hinatea , Renaud Christian , Therrien Christian , Fallet-Bianco Catherine , Lamarre Valérie , Boucoiran Isabelle 
Published: July 2023

Abstract
Zika virus (ZIKV) infection in pregnant women is associated with birth defects which are more prevalent and severe the earlier in pregnancy the infection occurs. Pregnant women at risk of possible ZIKV exposure (n = 154) were screened using ELISA for ZIKV IgM and IgG. Plaque reduction neutralization tests (PRNT) confirmed ZIKV infection in 9 cases (5.84%). Two cases of vertical ZIKV transmission were confirmed by PCR. One infant showed no signs of birth defects and had a normal developmental profile despite first trimester maternal infection. In the second case, pregnancy was terminated. Production of interferon-γ (IFN-γ) by peripheral blood mononuclear cells obtained from pregnant women and umbilical cord blood was measured using enzyme-linked immunospot assay (ELISpot) following stimulation with panels of synthetic peptides derived from the sequence of ZIKV proteins. This analysis revealed that among all peptide pools tested, those derived from the ZIKV envelope protein generated the strongest IFN-γ response.
Therapeutic effect and transcriptome-methylome characteristics of METTL3 inhibition in liver hepatocellular carcinoma
Authors: Liu Qingbin , Qi Jingjing , Li Weiyang , Tian Xinchen , Zhang Jiaqi , Liu Fen , Lu Xiulian , Zang Hengchang , Liu Chenqiao , Ma Changlin , Yu Yong , Jiang Shulong 
Published: July 2023

Abstract
Methyltransferase-like 3 (METTL3) is the key subunit of methyltransferase complex responsible for catalyzing N6-methyladenosine (m6A) modification on mRNA, which is the most prevalent post-transcriptional modification in eukaryotes. In this study, we utilized online databases to analyze the association between METTL3 expression and various aspects of tumorigenesis, including gene methylation, immunity, and prognosis. Our investigation revealed that METTL3 serves as a prognostic marker and therapeutic target for liver hepatocellular carcinoma (LIHC). Through experimental studies, we observed frequent upregulation of METTL3 in LIHC tumor tissue and cells. Subsequent inhibition of METTL3 using a novel small molecule inhibitor, STM2457, significantly impeded tumor growth in LIHC cell lines, spheroids, and xenograft tumor model. Further, transcriptome and m6A sequencing of xenograft bodies unveiled that inhibition of METTL3-m6A altered genes enriched in SMAD and MAPK signaling pathways that are critical for tumorigenesis. These findings suggest that targeting METTL3 represents a promising therapeutic strategy for LIHC.