bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automatic group-wise whole-brain short association fiber bundle labeling based on clustering and cortical surface information
Authors: Vázquez Andrea , López-López Narciso , Houenou Josselin , Poupon Cyril , Mangin Jean-François , Ladra Susana , Guevara Pamela 
Published: January 2020

Abstract
Background: Diffusion MRI is the preferred non-invasive in vivo modality for the study of brain white matter connections. Tractography datasets contain 3D streamlines that can be analyzed to study the main brain white matter tracts. Fiber clustering methods have been used to automatically regroup similar fibers into clusters. However, due to inter-subject variability and artifacts, the resulting clusters are difficult to process for finding common connections across subjects, specially for superficial white matter. Methods: We present an automatic method for labeling of short association bundles on a group of subjects. The method is based on an intra-subject fiber clustering that generates compact fiber clusters. Posteriorly, the clusters are labeled based on the cortical connectivity of the fibers, taking as reference the Desikan-Killiany atlas, and named according to their relative position along one axis. Finally, two different strategies were applied and compared for the labeling of inter-subject bundles: a matching with the Hungarian algorithm, and a well-known fiber clustering algorithm, called QuickBundles. Results: Individual labeling was executed over four subjects, with an execution time of 3.6 minutes. An inspection of individual labeling based on a distance measure, showed good correspondence among the four tested subjects. Two inter-subject labeling were successfully implemented and applied to 20 subjects, and compared using a set of distance thresholds, ranging from a conservative value of 10 mm to a moderate value of 21 mm. Hungarian algorithm led to high correspondence, but low reproducibility for all the thresholds, with 96 seconds of execution time. QuickBundles led to better correspondence, reproducibility and short execution time of 9 seconds. Hence, the whole processing for the inter-subject labeling over 20 subjects takes 1.17 hours. Conclusion: We implemented a method for the automatic labeling of short bundles in individuals, based on an intra-subject clustering and the connectivity of the clusters with the cortex. The labels provide useful information for the visualization and analysis of individual connections, what is very difficult without any additional information. Furthermore, we provide two fast inter-subject bundle labeling methods. The obtained clusters could be used for performing manual or automatic connectivity analysis in individuals or across subjects. Keywords: fiber labeling; clustering; fiber bundle; tractography; superficial white matter
Genes gained and lost during the evolution and domestication of Brassica napus
Authors: Zhou Hong , Ye Xueling , Ma Yanling , Hu Haiyan , Wei Yuming , Youliang Zheng , Liu Yaxi , Liu Chunji 
Published: January 2020

Abstract
Background: Brassica napus is one of the most important sources of vegetable oil for human nutrition and biofuel. It is an allotetraploid formed about 7500 years ago by hybridization between B. rapa and B. oleracea. Results from earlier studies show that the allopolyploidization process was accompanied by rapid and intensive changes and abundant homoeologous exchanges between the subgenomes have been accumulated during its short history of evolution. Results: By comparing differences between 19 artificially synthesized and 30 natural genotypes, we assessed possible changes in gene ratio, diversity and functional groups during the evolution and domestication of this species. This comparison revealed that gene ratio and diversity between the two subgenomes have hardly changed. However, large numbers of genes have been lost and many new genes gained. Compared with the artificial genotypes, the natural ones contain much lower proportions of genes conferring resistance and tolerance to biotic and abiotic stresses but much higher proportions of genes associated with seeds development and metabolic processes. The diploid donor for the A subgenome of B. napus contributed more genes involved in agronomic traits and the C subgenome donor contributed more genes related to cellular development and metabolic process. Conclusions: Our results show that genes conditioning resistance and tolerance to both biotic and abiotic stresses have suffered stronger selection during the evolution and domestication of B. napus, and that changes in different aspects including gene content and genome size in the allotetraploid are not random but dictated by its two diploid donors.
Genome-centric metagenomic insights into the impact of alkaline/acid and thermal sludge pre-treatment on digestion sludge microbiome
Authors: Wang Shanquan , Liang Zhiwei , Shi Jiangjian , Wang Chen , Li Junhui , He Zhili 
Published: January 2020

Abstract
Background: Wastewater treatment generates large amounts of waste activated sludge (WAS), which mainly consist of recalcitrant microbial cells and particulate organic matter. WAS pre-treatment is an effective way to destabilize sludge floc structure and release cellular macromolecules and other organic matter for improvement of digestion efficiency. Nonetheless, impacts of WAS pre-treatment on the complex digestion sludge microbiome, as well as mechanistic insight into how sludge pre-treatment improve digestion performance, remain to be elucidated. Results: In this study, genome-centric metagenomic approach was employed to investigate the digestion sludge microbiome in four methanogenic sludge digesters with different feeding sludge: APAD, WAS pre-treated with 0.25 mol/L alkaline/acid; HS-APAD, WAS pre-treated with 0.8 mol/L alkaline/acid; Thermal-AD, thermal pre-treated WAS; Control-AD, fresh WAS. We retrieved 254 metagenomic-assembled genomes (MAGs) to identify the key functional populations involved in methanogenic digestion process. These MAGs span 28 phyla with 69 of them as yet-to-be-cultivated lineages, and 30 novel lineages were characterized with metabolic potential associated with hydrolysis and fermentation. Interestingly, functional populations involving carbohydrate digestion were overrepresented in APAD and HS-APAD, while lineages related to protein and lipid fermentation were overrepresented in Thermal-AD, reflecting different digestion substrates released from alkaline/acid and thermal pre-treatments. Of the three major functional populations, i.e., fermentative bacteria, acetogenic syntrophs and methanogens, significant correlations between genome sizes of the fermentative bacteria and their abundance were observed, particularly in the APAD and HS-APAD with improved digestion performance. Conclusion: These genome-centric metagenomic insights advance our understanding of sludge pre-treatment on digestion sludge microbiomes, shedding light on future optimization of methanogenic sludge digestion and resource recovery.
Hygiene Hypothesis: Association between Hygiene and Asthma among Preschool Children in Lebanon
Authors: Hallit Souheil , Sacre Hala , Kheir Nelly , Hobeika Eva , Hallit Rabih , Waked Mirna , Salameh Pascale 
Published: January 2020

Abstract
Background Our objective was the validation of a scale to assess the hygiene hypothesis and the link between hygiene, and asthma among 3 to 5 years old Lebanese children in preschool.Methods Between November 2018 and March 2019, this cross-sectional study was carried out, enrolled 515 preschool children’ asthma and potential risk factors, including hygiene, were assessed using a standardized questionnaire. A specific hygiene hypothesis related scale was generated and validated for this purpose.Results Items related to the hygiene hypothesis scale have led to a convergence over a nine factors solution, having over than 1 Eigenvalue, which explains the variance total of 65.86%. Cronbach’s alpha values corresponding to the hygiene hypothesis related scale (0.696) was deemed acceptable. The backward logistic regression, taking as dependent variable the asthma’s presence or absence in child, showed that living in prairie (ORa=2.42), playing outside (ORa=2.80), having respiratory problems (ORa=4.18), attending a kindergarten (ORa=2.76), and having a sister with seasonal allergy (ORa=6.86) had significant association with increased odds of occurrence of children’s asthma. The hygiene hypothesis related score was not found to be associated with increased asthma odds (p=0.663).Conclusion Current findings suggested that home cleaning and personal cleanliness were not correlated with asthma in preschool children. Future studies will require more in-depth analyses of microbial exposure, allowing proper identification of unequivocal species and functional characteristics.
In vitro evaluation of novel Zeolite-hydroxyapatite blended scaffold for dental tissue engineering
Authors: Mohandesnezhad Sanam , Alizadeh Effat , Pilehvar-Soltanahmadi Yunes , Davaran Soodabeh , Goodarzi Arash , Khatamian Masoumeh , Zarghami Nosratollah , Samiei Mohammad , Aghazadeh Marzieh , akbarzadeh abolfazl 
Published: January 2020

Abstract
Main purpose of tissue engineering is creating appropriate conditions for the regeneration of tissues. Dental pulp-derived stem cells due to differentiation capacity and angiogenic properties have potential to regenerate dental pulp tissue. In the current experimental study poly caprolactone and poly L-lactic acid were synthesized by ring-opening polymerization method. The nano-hydroxyapatite and Zeolite were obtained by hydrothermal method. Morphological features and crystals properties of nHA and Zeolite were studied by X-ray diffraction. Nanofibers were fabricated using electrospinning method and investigated by FT-IR spectroscopy. DPSCs obtained from human source and proliferation and viability of them on electrospun scaffolds were evaluated by MTT assay. Also, the adhesion and proliferation of hDPSCs were investigated by SEM. The results showed that hDPSCs have the most viability and proliferation on the 1 st , 7 th , 14 th days on PCL-PLA/Zeolite scaffolds and maximum on the 3 rd day on PCL-PLA/nHA scaffolds. On the days of 7 th and 14 th , cell growth on scaffolds containing both nHA and Zeolite is better than sample that nHA is used alone with PCL-PLA. Briefly, by these results can be understand that Zeolite is a good agent in bone and tooth tissue engineering applications. More studies requires to investigate Zeolite effect on scaffold properties.
Shifting Demographics and Comorbidity Burden in Chinese Urban Patients With Chronic Hepatitis B, 2013 and 2016
Authors: Hou Jinlin , Chen Wendong , Ying Han , Wang Lei , Lee I-Heng Emma , Hsu Ling-I , Xie Dongying , Yin Xueru , Hou Fengqin , Yang Yida 
Published: January 2020

Abstract
Background: The long-term safety of anti-hepatitis B virus (HBV) therapies is critical to assess, particularly in the context of aging chronic hepatitis B (CHB) populations and accumulating comorbidities. HBV is common and clinically consequential in China; however, the demographics and comorbidity burden of this population have not been fully characterized.Aim: To characterize changes in demographics and comorbidity burden of urban Chinese patients with CHB between 2013 and 2016. Methods: The China Health Insurance Research Association (CHIRA) annual urban health insurance claims database from 2013 and 2016 was used to identify adults with ≥1 ICD-10 code for CHB. Descriptive analyses were conducted to compare age and comorbidities distributions between 2013 and 2016.Results: Median age increased from 40 in 2013 (N=14,545) to 44 in 2016 (N=11,648) (P<0.001). The proportion of patients aged >45 years increased significantly from 40.3% in 2013 to 49% in 2016 (P<0.001). Significant increases in multiple comorbidities were observed, including hypertension (9.4% to 14.5%), hyperlipidemia (4.7% to 7.0%), and cardiovascular disease (5.7% to 10%) (P<0.001 for all comparisons). Increases were also observed in renal impairment (8.8% to 10.0%; P<0.001) and osteoporosis and/or pathologic nontraumatic bone fracture (3.8% to 7.3%; P<0.001). Conclusions: Even over the short interval assessed in this study, there was a significant shift in the characteristics of urban CHB patients in China. Aging of the population was accompanied by significant increases in the percentage of patients having potentially concerning comorbidities. Careful selection of treatment options and comorbidity monitoring should be considered when managing Chinese patients with CHB.
Physiological Effects of the Combined Stresses of Freeze-thaw, Acid Precipitation and Deicing Salt on Alfalfa Seedlings
Authors: Bao Guozhang , Tang Wenyi , An Qirui , Liu Yaoxin , Tian Jiaqi , Zhao Nan , Zhu Saning 
Published: January 2020

Abstract
BackgroundIn the early spring of northern China, the combined stresses of freeze-thaw, deicing salt and acid deposition are the main ecological threats to the urban turf ecosystem. ResultsWe studied changes in the Malondialdehyde (MDA), protein, soluble sugar, proline and chlorophyll contents of DongMu No. 1seedlings of 8 treatment combination groups which are imposed by freeze-thaw (F), acid rain (A) and deicing salt (D). An increasing in MDA content showed that the membrane system of seedlings was damaged under combined stress (F+A+D). The changes indicated that under the adverse conditions, the proline and soluble sugar contents increased obviously with the accumulation of MDA in the plants, while the chlorophyll content decreased significantly.ConclusionPlants can alleviate the damage caused by stress by increasing soluble sugars and by regulating the proline content to maintain osmotic balance.
Identification and analysis of CYP450 supergene family members from the transcriptome of Aralia elata (Miq.) Seem reveal candidate genes for triterpenoid saponins biosynthesis
Authors: Cheng Yao , Liu Hanbing , Tong Xuejiao , Zhang Xin , Li Dalong , Jiang Xinmei , Yu Xihong 
Published: January 2020

Abstract
BackgroundMembers of the cytochrome P450 (CYP450) gene superfamily have been shown to play essential roles in regulating secondary metabolites biosynthesis. However, the systematic identification and bioinformatics analysis of CYP450s have not been reported in Aralia elata (Miq.) Seem, a highly valued medicinal plant. ResultsIn the present study we conducted the RNA-sequencing (RNA-seq) analysis of the leaves, stems, and roots of A. elata, yielding 66,713 total unigenes. Following the annotation and classification of these unigenes, we were able to identify two pathways and 19 putative genes associated with the synthesis of triterpenoid saponins in these plants, with qRT-PCR subsequently being used to validate these gene expression patterns. Scanning with the CYP450 model from Pfam resulted in the identification of 111 full-length and 143 partial-length CYP450s, with the full-length CYP450s being further clustered into 7 clans and 36 families. Through phylogenetic and conserved motif analyses, we were further able to group these CYP450 proteins into two primary branches: A-type (53%) and non-A type (47%). We further conducted representative protein sequence alignment for these CYP450 family members, with secondary elements being assigned in light of the recently published Arabidopsis CYP90B1 structure. Using the available sequence information, we further identified predicted substrate recognition sites (SRSs) and substrate binding sites within these putative proteins.We further assessed the expression patterns of these 111 CYP450 genes across A. elata tissues, with 12 members of this gene family being selected at random for qRT-PCR validation. From these data, we identified CYP716A295 and CYP716A296 as the candidate genes most likely to be associated with oleanolic acid synthesis, while CYP72A763 was identified as being the most likely to play a role in hederagenin biosynthesis. Finally, we assessed the subcellular localization of these CYP450 proteins within Arabidopsis protoplasts, highlighting the fact that they localize to the endoplasmic reticulum.ConclusionsThis study presents a systematic analysis of the CYP450 gene family in A. elata and provided a foundation for further functional characterization of CYP450 genes.
Predictive factors for myocardial infarction in pre-hospital emergency care
Authors: Ilczak Tomasz P , Ćwiertnia Michał , Kawecki Marek , Mikulska Monika , Waksmańska Wioletta , Rak Małgorzata , Bobiński Rafał 
Published: January 2020

Abstract
Background: Identifying predictive factors based on procedures carried out by emergency medical teams may speed up the diagnosis of AMI. By shortening the time between the onset of the pain and the initiation of coronary reperfusion, patient prognosis can be improved Methods: The study was conducted on residents of the Bielsko-Biała district, served by state ambulance service Medical Response Teams (MRT). The patients were assigned to the following groups: Group A (n = 338) - patients with chest pain in whom infarction with elevation of the ST segment (ST-ACS) was diagnosed on the basis of an ECG, Group B (n=300) - patients with chest pain in whom an infarction was not diagnosed. A factor structural test for the studied parameters was used to determine their significance. An odds ratio (OR) was established for statistically significant parameters, and multi-dimensional logistic regression analysis was conducted. The significance of the odds ratios (OR) was estimated for individual risk factors based on 95% confidence intervals (CI). Results: It can be stated with 95% probability that the significant parameters: Male (p=0.00001), Age 51-70(p=0.00307), Breathing rate less than 12/min(p=0.02711), Pulse below 60 min (p=0.00165), Edemas (p=0.00075), Moist skin(p<0.01), Sinus rhythm (p=0.00004), Additional ventricular beats(p=0.00133) increase the risk of myocardial infraction. Conclusion: Identifying the predictors of myocardial infarction specific to pre-hospital emergency care is essential for improving the detection of AMI and shortening the time between calls to the MRT and the initiation of coronary reperfusion.
Efficacy of Parent-Infant-Psychotherapy with mothers with postpartum mental disorder: study protocol of the randomized controlled trial as part of the SKKIPPI project.
Authors: Mattheß Janna , Eckert Melanie , Richter Katharina , Koch Gabriele , Reinhold Thomas , Vienhues Petra , Berghöfer Anne , Roll Stephanie , Keil Thomas , Schlensog-Schuster Franziska , von Klitzing Kai , Ludwig-Körner Christiane , Kuchinke Lars 
Published: January 2020

Abstract
Background: After the birth of a child, many mothers and fathers experience postpartum mental disorders like depression, anxiety, obsessive-compulsive disorder, stress or other illnesses. This endangers the establishment of attachment between the children and their primary caregivers. Early problems in parent-child interaction can have adverse long-term effects on the family and the child’s well-being. In order to prevent a transgenerational transmission of mental disorders, it is necessary to evaluate psychotherapeutic interventions that target psychologically burdened parents of infants or toddlers. The aim of this trial is to investigate the efficacy of Parent-Infant-Psychotherapy (PIP) for mothers with postpartum mental disorder and their infants (0-12 month).Methods: In this open randomized controlled intervention trial 180 mother-infant dyads will be included and randomly allocated to 12 sessions of PIP or care as usual. The interventions take place either in inpatient adult psychiatric departments or in outpatient settings with home visits. The primary outcome is the maternal sensitivity assessed by the Sensitivity subscale of the Emotional Availability Scale (EAS) through videotaped dyadic play-interactions after 6 weeks. Secondary outcomes are maternal attachment (AAI) and reflective functioning, psychopathology, maternal stress, infant development and attachment after 6 weeks and 12 months. In addition, resource usage and associated costs will be measured. Discussion: There is increasing demand for well-controlled studies on psychotherapeutic interventions in the postpartum period that do not only focus on particular risk groups. This RCT represents one of the first studies to investigate the efficacy of PIP in inpatient psychiatric departments and outpatient care centres in Germany. The results will fill knowledge gaps on the factors contributing to symptom reduction in postpartum mental disorders and improvements in mother-child relationships and help developing preventive and therapeutic strategies for the fragmented German health care system.Trial registration: German Register for Clinical Trials: DRKS00016353.
Intravenous iron isomaltoside versus oral iron supplementation for treatment of iron deficiency in pregnancy: protocol for a randomised, comparative, open-label trial
Authors: Markova Veronika , Hansen Rebecka , Thomsen Lars Lykke , Pinborg Anja Bisgaard , Moos Torben , Holm Charlotte 
Published: January 2020

Abstract
Background: Iron deficiency is common in pregnancy. If left untreated iron deficiency can lead to iron deficiency anaemia. The prevalence of iron deficiency increases through the trimesters which means that women with iron deficiency in the beginning of pregnancy have a great risk of developing iron deficiency anaemia during pregnancy. Standard treatment is oral iron in individualized intensified doses based on screening values in 1st trimester. Maternal symptoms of iron deficiency and iron deficiency anaemia include fatigue, reduced physical performance, and Restless Legs Syndrome. Severe anaemia may cause dizziness, dyspnea, palpitation, orthostatism, syncope and it decreases the woman’s ability to cope with blood loss during delivery. It may compromise contractility in the uterine musculature increasing the risk for prolonged labor, caesarean section and postpartum haemorrhage. Foetal iron deficiency may cause low birthweight and adversely affect foetal and early childhood brain development with long term deficits.Methods: In this randomised comparative, open-label, single-centre, phase IV trial, 200 pregnant women between 14 and 21 weeks of gestation, who have iron deficiency after 4 weeks of standard treatment will be randomised 1:1 to either a single 1000 milligram dose of intravenously administered ferric derisomaltose/iron isomaltoside 1000 or a fixed dose of 100 milligrams oral ferrous fumarate containing 60 milligrams ascorbic acid. The primary endpoint is to prevent iron deficiency anaemia defined by a low level of haemoglobin throughout the trial. Other endpoints include other haematological indices of iron deficiency and anaemia, clinical outcomes by questionnaires and collection of adverse events. Explorative endpoints by medical record follow-up include complications up to 7 days after delivery.Discussion: This trial will contribute evidence on how to prevent iron deficiency anaemia which is a condition related to maternal and neonatal morbidity. The trial population represents a clinical reality, where pregnant women often have sustained iron deficiency despite an increased oral iron dose. Thus, this evidence can be used to consider the optimal 2nd line of treatment in iron deficient pregnant women.Trial registration: This trial is registered 3 May 2017 in European Union Drug Regulating Authorities Clinical Trials Database: 2017-000776-29 and 15 June 2017 at ClinicalTrials.gov: NCT03188445.