bluuebunny/crossref_metadata_2025_split huggingface dataset:
Candidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut but differentially influences the resident microbiome
Authors: Huang Shi , Jiang Shuaiming , Huo Dongxue , Allaband Celeste , Estaki Mehrbod , Cantu Victor , Belda-Ferre Pedro , Vázquez-Baeza Yoshiki , Zhu Qiyun , Ma Chenchen , Li Congfa , Zarrinpar Amir , Liu Yang-Yu , Knight Rob , Zhang Jiachao 
Published: June 2021

Abstract
Background
Improving probiotic engraftment in the human gut requires a thorough understanding of the in vivo adaptive strategies of probiotics in diverse contexts. However, for most probiotic strains, these in vivo genetic processes are still poorly characterized. Here, we investigated the effects of gut selection pressures from human, mice, and zebrafish on the genetic stability of a candidate probiotic Lactiplantibacillus plantarum HNU082 (Lp082) as well as its ecological and evolutionary impacts on the indigenous gut microbiota using shotgun metagenomic sequencing in combination with isolate resequencing methods.

Results
We combined both metagenomics and isolate whole genome sequencing approaches to systematically study the gut-adaptive evolution of probiotic L. plantarum and the ecological and evolutionary changes of resident gut microbiomes in response to probiotic ingestion in multiple host species. Independent of host model, Lp082 colonized and adapted to the gut by acquiring highly consistent single-nucleotide mutations, which primarily modulated carbohydrate utilization and acid tolerance. We cultivated the probiotic mutants and validated that these gut-adapted mutations were genetically stable for at least 3 months and improved their fitness in vitro. In turn, resident gut microbial strains, especially competing strains with Lp082 (e.g., Bacteroides spp. and Bifidobacterium spp.), actively responded to Lp082 engraftment by accumulating 10–70 times more evolutionary changes than usual. Human gut microbiota exhibited a higher ecological and genetic stability than that of mice.

Conclusions
Collectively, our results suggest a highly convergent adaptation strategy of Lp082 across three different host environments. In contrast, the evolutionary changes within the resident gut microbes in response to Lp082 were more divergent and host-specific; however, these changes were not associated with any adverse outcomes. This work lays a theoretical foundation for leveraging animal models for ex vivo engineering of probiotics to improve engraftment outcomes in humans.
Non-acid reflux and sleep apnea: The importance of drug induced sleep endoscopy
Authors: O'Connor-Reina Carlos , Garcia Jose Maria Ignacio , Baptista Peter , Garcia-Iriarte Maria Teresa , Alba Carlos Casado , Perona Monica , Borrmann Paz Francisca , Alcala Laura Rodriguez , Plaza Guillermo 
Published: June 2021

Background We present the first case of a patient with obstructive sleep apnea syndrome (OSA), where drug induced sleep endoscopy was helpful to suspect a non-acid reflux disease and showed an improvement in a swollen epiglottis after treatment. Patient ameliorated significantly his disease only with medical therapy. Case presentation A 54-year-old man without significant anatomical findings with obstructive sleep apnea syndrome and non-acid gastroesophageal reflux disease (GERD) disease whose Apnea- hypopnea index (AHI) was significantly reduced with the intake of 500 mg of sodium alginate twice a day for 6 months. Conventional digestive tests such as esophagoscopy and simple- and double-channel 24-h pH-metry suggested mild GERD. Conventional proton-pump inhibitor treatment with pantoprazole (40 mg daily) was started without any improvement in his sleep. Multichannel intraluminal 24-h impedanciometry indicated the presence of severe pathological GER of gaseous origin. The patient's AHI decreased from 25.3 at baseline to 8 after treatment with sodium alginate. A drug-induced sleep endoscopy study showed the changes before and after this treatment and was helpful for the diagnosis. Conclusions Thus, medical treatment can be a therapeutic option in some patients with OSA. Multichannel 24-h impedanciometry should be performed when nonacid GERD is suspected.
Spatial progression and molecular heterogeneity of IDH-mutant glioblastoma determined by DNA methylation-based mapping
Authors: Lyon James F. , Vasudevaraja Varshini , Mirchia Kanish , Walker Jamie M. , Corona Robert J. , Chin Lawrence S. , Tran Ivy , Snuderl Matija , Richardson Timothy E. , Viapiano Mariano S. 
Published: June 2021

AbstractGlioblastoma (GBM) is the most common malignant primary central nervous system (CNS) neoplasm in adults, and has an almost universally poor prognosis. Recently, an emphasis on genetic and epigenetic profiling has revealed a number of molecular features useful in the diagnostic and prognostic classification of GBM, advancing our understanding of the underlying features that make these tumors so aggressive and providing the rationale for the creation of better targeted therapeutics. One such method, DNA methylation profiling, has recently emerged as an important technique for the classification of CNS tumors, with diagnostic accuracy in some cases surpassing traditional methods. However, how DNA methylation profiles change with the course of the disease remains less understood. Here, we present a case of a 30-year-old male with primary IDH-mutant GBM with widespread recurrence and death two years later. Using unsupervised hierarchical clustering of methylation probes, we created a phylogenetic map to trace the tumor path as it spread from the initial biopsy site throughout the right hemisphere, across the corpus callosum to the contralateral hemisphere, and into the brainstem. We identified molecular divergence between the right and left hemisphere GBM samples marked by distinct copy number profile alterations, alterations in specific methylation sites, and regional loss of MGMT promoter methylation, providing a potential mechanism for treatment resistance in this case. In summary, this case both highlights the molecular diversity in GBM, and illustrates a novel use for methylation profiling in establishing a phylogenetic profile to allow for spatial mapping of tumor progression.
Molecular diagnostics helps to identify distinct subgroups of spinal astrocytomas
Authors: Biczok Annamaria , Strübing Felix L. , Eder Julia M. , Egensperger Rupert , Schnell Oliver , Zausinger Stefan , Neumann Julia E. , Herms Jochen , Tonn Joerg-Christian , Dorostkar Mario M. 
Published: June 2021

AbstractPrimary spinal cord astrocytomas are rare, hence few data exist about the prognostic significance of molecular markers. Here we analyze a panel of molecular alterations in association with the clinical course. Histology and genome sequencing was performed in 26 spinal astrocytomas operated upon between 2000 and 2020. Next-generation DNA/RNA sequencing (NGS) and methylome analysis were performed to determine molecular alterations. Histology and NGS allowed the distinction of 5 tumor subgroups: glioblastoma IDH wildtype (GBM); diffuse midline glioma H3 K27M mutated (DMG-H3); high-grade astrocytoma with piloid features (HAP); diffuse astrocytoma IDH mutated (DA), diffuse leptomeningeal glioneural tumors (DGLN) and pilocytic astrocytoma (PA). Within all tumor entities GBM (median OS: 5.5 months), DMG-H3 (median OS: 13 months) and HAP (median OS: 8 months) showed a fatal prognosis. DMG-H3 tend to emerge in adolescence whereas GBM and HAP develop in the elderly. HAP are characterized by CDKN2A/B deletion and ATRX mutation. 50% of PA tumors carried a mutation in the PIK3CA gene which is seemingly associated with better outcome (median OS: PIK3CA mutated 107.5 vs 45.5 months in wildtype PA). This exploratory molecular profiling of spinal cord astrocytomas allows to identify distinct subgroups by combining molecular markers and histomorphology. DMG-H3 tend to develop in adolescence with a similar dismal prognosis like GBM and HAP in the elderly. We here describe spinal HAP with a distinct molecular profile for the first time.
Medication adherence among the elderly: applying grounded theory approach in a developing country
Authors: Bastani Peivand , Bikineh Parisa , Mehralian Gholamhossein , Sadeghkhani Omid , Rezaee Rita , Kavosi Zahra , Ravangard Ramin 
Published: June 2021

Abstract
Background
Medication adherence is an important concept particularly among the elderly that can, directly and indirectly, affect the health system’s costs and the elderly’s health, quality of life, and functional abilities. This study aimed to determine the model of medication adherence among the Iranian elderly using the grounded theory approach.

Methods
The concept of medication adherence and the determination of its process among the elderly is a multidisciplinary social issue that can be affected by many contextual factors. Grounded theory with the approach of Strauss and Corbin (2004) was applied to determine the customized model. Data triangulation occurred through semi-structured interviews, observation, field notes, and memoing. Open coding, selective coding, and axial coding were applied to analyze the data.

Results
Delinquency in the medication use among the elderly was caused by factors such as doubtfulness, fear of complications, not following the patients by the physicians, and negative others and medical staff’s impacts. During the process of medication adherence, the patient’s lack of knowledge, lack of sufficient education, inappropriate and restricted lifestyle, difficult living conditions, and social pressures imposed on individuals could exacerbate and worsen the delinquency in medication adherence. It should not be neglected that some other factors such as lack of an effective supervision system, lack of supportive organizations, stakeholders’ market-based behaviors, consumption inconvenience, consumption stress, hopelessness, and misunderstanding could also aggravate the delinquency.

Conclusions
Although the proposed theory and model were customized and context-based for the Iranian elderly, in general, making positive changes in the process of adherence to the medication use among the elderly requires scientific and basic management and planning of its factors. It should be noted that making these changes requires some interventions in and cooperation of all levels of the country's health system, from the Ministry of Health and Medical Education to the individual level of the elderly.
Effects of stand features and soil enzyme activity on spontaneous pedunculate oak regeneration in Scots pine dominated stands – implication for forest management
Authors: Dorota Dobrowolska , Przemysław Kurek , Grażyna Olszowska , Bolibok Leszek 
Published: June 2021

AbstractBackgroundA challenge in current forestry is adaptation of managed forests to climate change, which is likely to alter the main processes of forest dynamics, i.e. natural regeneration. Scots pine will probably lose some parts of its distribution area in Europe. However, two native oaks, pedunculate and sessile may maintain or expand the area of their occurrence in central Europe. The utilization of spontaneous (not initialized by foresters) oak regeneration in Scots pine stands for the creation of next generation stands is one of the adaptation methods to climate change. Many factors influencing pedunculate oak regeneration are well known, but there is a lack of knowledge on the relation between soil enzyme activity and the establishment and development of the species. The aim of the study was to identify the relationships among stand characteristics, herb species composition, soil enzyme activity and the establishment or recruitment of oak regeneration in Scots pine-dominated stands.ResultsThe one of the most influential factors shaping the oak seedling count was dehydrogenase activity in the humus horizon. We found that plots without litter and fern cover had higher seedling density. The raspberry ground cover and birch crown projection area had a positive influence on oak seedling number. The factor indicating good conditions for high density of oak saplings was phosphatase activity in the organic horizon. The same enzyme activity but in humus horizon described conditions in which more numerous recruits were observed.ConclusionsThe activity of soil enzymes can be used as the predictor of the establishment and advancement of oak regeneration but also could be seen as a new dimension of oak regeneration. The general density of spontaneous oak regeneration was not sufficient for the creation of new generation forest stands dominated by oak, but it is possible to use them as admixtures in new generation stands.
Dynamics and chronology of Mycoplasma hyopneumoniae strain 232 infection in experimentally inoculated swine
Authors: Almeida Henrique M. S. , Mechler-Dreibi Marina L. , Sonálio Karina , Ferreira Marcela M. , Martinelli Paulo E. B. , Gatto Igor R. H. , Maes Dominiek , Montassier Hélio J. , Oliveira Luís G. 
Published: June 2021

AbstractDirect detection of Mycoplasma hyopneumoniae through molecular tools is a growing trend for early diagnosis, highlighting the importance of knowing M. hyopneumoniae dynamics in the respiratory tract upon infection. This study focused on monitoring the infection level and its effects in different anatomic sites of the respiratory tract of experimentally infected swine in four time-points post-infection. To this end, 24 pigs were allocated to either non-inoculated group (n = 8) or inoculated group (n = 16). On day 0 post-infection (dpi), animals of the inoculated group were intratracheally inoculated with M. hyopneumoniae. Nasal swabs were collected weekly for qPCR detection of bacterial shedding. At 14, 28, 42, and 56 dpi, four animals from the inoculated group and two from the control group were necropsied. Bronchoalveolar lavage fluid (BALF) and samples from three different anatomical tracheal sections (cranial - CT, medium - MT, lower - LT) were collected for qPCR and histopathology. Bacterial loads (qPCR) in tracheal samples were: 4.47 × 102 copies∕μL (CT), 1.5 × 104- copies∕ μL (MT) and 1.4 × 104 copies∕μL (LT samples). M. hyopneumoniae quantification in BALF showed the highest load at 28 dpi (2.0 × 106 copies∕ μL). Microscopic lesions in LT samples presented the highest scores at 56 dpi and were significantly correlated with the pathogen load on 14 dpi (0.93) and 28 dpi (0.75). The greatest bacterial load of M. hyopneumoniae in CT samples and BALF was registered at 28 dpi, and it remained high in BALF and LT throughout the 56 dpi. The pathogen was able to persist during the whole experimental period, however higher estimated quantification values were registered in the lower parts of the respiratory tract, especially at 56 dpi. These findings are important for improving diagnostics, treatment, and control measures of M. hyopneumoniae infection in swine herds.
Salivary exosomal microRNAs as biomarkers for head and neck cancer detection—a literature review
Authors: Faur Cosmin Ioan , Rotaru Horatiu , Osan Ciprian , Jurj Ancuta , Roman Rares Calin , Moldovan Madalina , Chirila Magdalena , Hedesiu Mihaela 
Published: June 2021

Abstract
Background
MicroRNAs (miRs) are small, non-coding mRNA molecules which regulate cellular processes in tumorigenesis. miRs were discovered in extracellular environment and biological fluids, carrying marks of head and neck squamous cell carcinoma (HNSCC). They were also identified in abundance in salivary exosomes, in which they are protected by exosome lipid barrier against enzymatic injuries and therefore, the accuracy of exosomal miR-based cancer detection increase. This systematic review aimed to reveal and inventorize the most reliable exosomal miRNAs in saliva samples which can be used as novel biomarkers for early detection of HNSCC.

Materials and methods
A systematic literature search, according to PRISMA guideline, was performed on Pubmed and Google Academic libraries, based on specific keywords. Original articles published between 2010 and 2021 were selected. The quality of each paper was assessed using the Quality Evaluation Scoring Tool.

Results
At the end of selection process, five studies met the inclusion criteria. These studies analyzed twelve salivary exosomal miRs, presenting different methods of exosome and miR identification for HNSCC detection. A comprehensive explanation of the miR pathways of action was drawn and illustrated in this review.

Conclusion
Exosomal miRs are promising biomarkers for oral cavity and oropharyngeal cancer detection. miR-10b-5p, miR-486-5p, miR-24-3p and miR-200a stand as the most useful ones in saliva sample examination.
Effect of different soil moisture regimes on plant growth and water use efficiency of Sunflower: experimental study and modeling
Authors: Soothar Rajesh Kumar , Singha Ashutus , Soomro Shakeel Ahmed , Chachar Azhar-u-ddin , Kalhoro Faiza , Rahaman Md Arifur 
Published: June 2021

Abstract
Background
Climate change and increasing demand in non-agricultural sectors profoundly affect the availability and quality of water resources for irrigated agriculture. The FAO AquaCrop simulation model provides a sound theoretical framework to investigate crop yield response to environmental stress. This model has successfully simulated crop growth and yield as influenced by varying soil moisture environments for crops. Integrating crop models that simulate the effects of water on crop yield with targeted experimentation can facilitate the development of irrigation strategies for high yield procurement and improving farm level water management and water use efficiency (WUE) under climatic condition of District Hyderabad, Sindh, Pakistan.

Results
This study was based on completely randomized block design with three treatments including T1 (30% soil moisture depletion), T2 (50% soil moisture depletion) and T3 (70% soil moisture depletion) with three replicates. In order to determine the crop water requirements under desired treatments, the gypsum blocks were used for computing the daily soil moisture depletion. The result shows that total volume of water applied to crop under T1, T2 and T3 was 9689, 5200 and 2045 m3 ha−1, respectively. As a result, the grain yield under T1, T2 and T3 was 13.2, 12.1 and 14.3 t ha−1, respectively. These results advocate that total yield of crop under T1 and T2 was less as compared to T3. The T3 gave higher yield and WUE compared than other treatments. On the other hand, results revealed that the simulated sunflower yields showed a good agreement with their measured under T3. The simulated grain yield was 15.5 t ha−1, while the measured yield varied from 12.1 to 14.3 t ha−1. This study suggested that WUE under T3 was more as compared to T1 and T2. The results showed that the T3 gave the highest crop yield in relation to WUE and optimize yield of sunflower crop under water scarcity.

Conclusion
The Aquacrop model could very well predict crop yield and WUE at T3 under experiential region for sunflower production.
Portal venous and hepatic artery hemodynamic variation in non-alcoholic fatty liver disease
Authors: Sabry Manal , Youssef Tarek , Shaker Mohamed , Salama Mohamed Magdy , Assem Nourhan , Anwar Christina Alfons 
Published: June 2021

Abstract
Background
Non-alcoholic fatty liver disease remains asymptomatic until advanced disease, when risk factor modification and available treatment become no longer effective. Studies on hepatic vasculature can be informative about parenchymal injury and disease severity through the study of changes affecting vascular compliance. This study aimed to study portal vein and hepatic artery hemodynamic variation in non-alcoholic fatty liver and to correlate it with disease severity.

Results
This case control study included 80 participants; those were further divided into four groups; healthy volunteers and non-alcoholic fatty liver disease patients’ grade 1, 2, and 3. We did anthropometric measures, laboratory tests, transient elastography, and Doppler ultrasound for all participants, and then we collected the data and analyzed it using SPSS version 25.
Doppler findings showed that peak maximum velocity, peak minimum velocity, mean flow velocity, portal vein pulsatility index of portal vein, and hepatic artery resistivity index were significantly lower in non-alcoholic fatty liver disease patients than in healthy people. All indices were indirectly proportionate to the grade of the disease except for peak minimum velocity which was significantly lower on comparing grade 3 patients with grades 1 and 2 patients.

Conclusions
Reduction of portal flow and increase in hepatic artery flow in fatty liver correlates with disease severity and can help as a non-invasive measure in diagnosis and grading of non-alcoholic fatty liver disease.
Responses of Moringa oleifera to alteration in soil properties induced by calcium nanoparticles (CaNPs) on mineral absorption, physiological indices and photosynthetic indicators
Authors: Azeez Luqmon , Lateef Agbaje , Adetoro Rasheed O. , Adeleke Adebayo E. 
Published: June 2021

AbstractBackgroundThe application of nanofertilisers in agriculture has been widely utilised due to their distinct characteristics and negative impacts of conventional chemical fertilisers. This study thus examined the influence of calcium nanoparticles (CaNPs) on soil composition vis-à-vis performance parameters inMoringa oleiferaL exposed to water, 100 mg Ca(NO3)2kg−1soil and 100, 75 and 50 mg CaNPs kg−1soil. Soil morphology was determined with a scanning electron microscope coupled with energy dispersive x-ray (SEM-EDX) and elemental composition in both soils andM. oleiferaroots determined with inductively coupled plasma-optical emission spectrometer (ICP-OES).ResultsThe CaNP-amended soils were more crystalline, more fertile and had reduced salinity. An increase in immobilisation percentage of heavy metals, improvement in physiological parameters (percentage germination, vigour indices, relative water contents, lengths of roots and shoots) and photosynthetic efficiency inM. oleiferawere recorded.ConclusionThis study has demonstrated that CaNPs could improve soil composition for better plant performance and can act as nanofertilisers mobilising essential nutrients.Graphical abstract