bluuebunny/crossref_metadata_2025_split huggingface dataset:
Architecture, process, and environmental diversity in a late Cretaceous slope channel system
Authors: Kneller Benjamin , Bozetti Guilherme , Callow Richard , Dykstra Mason , Hansen Larissa , Kane Ian , Li Pan , McArthur Adam , Catharina Amanda Santa , Dos Santos Thisiane , Thompson Philip 
Published: January 2020

ABSTRACT
Arroyo San Fernando, on the Pacific coast of Baja California, Mexico, provides a superb view of the architecture of a Maastrichtian active margin slope channel system and the record of its evolution through a third-order sea-level cycle. The succession is organized into architectural building blocks (channel-complex sets) consisting of a channel belt with an axial region and a channel-belt margin of terraces and internal levees. The channel belt is confined by an external levee on one side and by an erosion surface into the slope on the other. Each channel-complex set can be subdivided into three stages of evolution: Stage I consists of highly amalgamated coarse-grained channel complexes, Stage II consists of gravelly meander belts with marginal and stratigraphically intervening thin-bedded turbidites, and Stage III consists of mudstones representing abandonment. This succession is associated with repeated and therefore predictable changes in architecture, facies distribution, inferred seafloor morphology, and sedimentary process. We describe variability in the sedimentology, ichnology, palynology, provenance, and inferred sedimentary processes between and within these architectural elements. Channel formation and fill are attributed to erosion, sediment transport, and deposition by turbidity currents and lesser debris flows. Ichnology indicates enhanced oxygenation and supply of organic material, substrate type, and turbidity within the channel belt; the axial region can be differentiated from the terraces by differing response to turbidity-current intensity. Levee environments show ichnological gradients away from the channel towards background slope. Palynology reflects confinement of the supply of terrigenous material to the channel belt, but is also indicative of stratification within the turbidity-currents, as is the distribution of heavy minerals. Provenance is from the extinct part of the continental-margin arc to the east, via high-gradient gravelly streams and across a steep shoreline, with direct supply of coastal material to deep water. Architectural hierarchy bears comparison with other slope channel systems, but in common with them the fill represents only a small fraction of the time that the system was active.
Gender Differences in Treatments and Interventions Received for Children and Adolescents with Cerebral Palsy
Authors: Josenby Annika Lundkvist , Czuba Tomasz , Schmidt Ann I Alriksson 
Published: January 2020

Abstract
Background: In the Swedish population-based follow-up program and national quality registry for individuals with cerebral palsy (CPUP), physiotherapy (PT) and occupational therapy (OT) treatments are regularly recorded along with functional status. By Swedish law, all citizens irrespective of personal characteristics or socioeconomic status have the right to receive healthcare and medical treatments as applicable. Previous research has shown gender differences in treatments and interventions received by children with cerebral palsy (CP). The purpose of this study was to examine differences in treatments and interventions by gender and place of birth in children and adolescents participating in CPUP. Methods: This was a cross-sectional registry study. Data from the latest PT (n = 2635) and OT assessment forms (n = 3480) in CPUP were extracted for individuals aged 0-17 years. Logistic regressions were used to assess the relationships between the outcome variables and gender and place of birth (including an interaction term gender X place of birth), adjusted for age, Gross Motor Function Classification System (GMFCS) levels and spasticity scores for PT interventions and Manual Ability Classification System (MACS) for OT interventions. Results: Results are presented as odds ratios [95% confidence intervals] and p-values. Girls were significantly more likely to have spinal braces than boys; 1.54 [1.07, 2.22] p<0.05, a significant interaction with place of birth indicated fewer spinal braces prescribed to children born outside of the Nordic countries; 0.20 [0.079, 0.53] p<0.001. Girls were less likely to have undergone selective dorsal rhizotomy (SDR); 0.49 [0.25, 0.94] p<0.05. Individuals born outside of the Nordic countries, were significantly less likely to have received intrathecal baclofen (ITB) 0.27 [0.074, 0.98] p<0.05. Conclusions: Of the treatments prescribed, gender differences were observed for spinal braces and having undergone SDR. A statistically significant difference based on place of birth was noted for spinal bracing and having received ITB treatment. Other PT and OT treatments were associated with age, levels of spasticity, and functional severity as classified with the GMFCS and the MACS. Increased awareness of differences based on gender, and where a child is born, could be obtained by inter- and intraprofessional discussions.
Efficacy of continuous epidural infusion with epidural electric stimulation compared to that of conventional continuous epidural infusion for acute herpes zoster management: A retrospective study﻿
Authors: Lee Chung Hun , Choi Sang Sik , Lee Mi Kyoung , Lee Yeon Joo , Park Jong Sun 
Published: January 2020

Abstract
Background: Continuous epidural infusions are commonly used in clinical settings to reduce the likelihood of transition to postherpetic neuralgia via pain control. The purpose of this study was to compare the efficacy of conventional continuous epidural infusion to that of continuous epidural infusion in which the catheter is guided by electric stimulation to areas with neurological damage for the treatment of zoster-related pain and prevention of postherpetic neuralgia.Methods: We analyzed the medical records of 114 patients in this study. The patients were divided into two groups: contrast (conventional continuous epidural infusion) and stimulation (continuous epidural infusion with epidural electric stimulation). In the contrast group, the position of the epidural catheter was confirmed using contrast medium alone, whereas in the stimulation group, the site of herpes zoster infection was identified through electric stimulation using a guidewire in the catheter. Clinical efficacy was assessed using a numerical rating scale (pain score) up to 6 months after the procedures. We compared the percentage of patients who showed complete remission (pain score less than 2 and no further medication) in each group. We also investigated whether the patients required additional interventional treatment due to insufficient pain control during the 6-month follow-up period after each procedure.Results: After adjusting for confounding variables, the pain score was significantly lower in the stimulation group than in the contrast group for 6 months after the procedure. After adjustment, the odds of complete remission were 1.9-times higher in the stimulation group than in the contrast group (95% confidence interval [CI]: 0.81-4.44, P = 0.14). Patients in the contrast group were significantly more likely to require other interventions within 6 months of the procedure than patients in the stimulation group (odds ratio: 3.62, 95% CI: 1.17-11.19, P = 0.03).Conclusion: Epidural drug administration to specific spinal segments using electric stimulation catheters may be more helpful than conventional continuous epidural infusion for improving pain and preventing postherpetic neuralgia in the acute phase of herpes zoster.
Immune Classification for the PD-L1 Expression and Tumour-Infiltrating Lymphocytes in Colorectal Adenocarcinoma
Authors: Noh Byeong-Joo , Kwak Jae Young , Eom Dae-Woon 
Published: January 2020

Abstract
Background

Colorectal adenocarcinoma is the third most common cancer worldwide and a leading cause of cancer-related death. The recent emergence of diverse immunotherapeutic agents has made it crucial to interpret a complex tumour microenvironment intermingled with tumour-infiltrating immune cells to predict the immunotherapeutic response rate. However, in colorectal adenocarcinoma, studies are lacking that provide detailed analyses of programmed death-ligand 1 (PD-L1) and tumour-infiltrating lymphocytes (TIL) to elucidate their prognostic values and to identify immunotherapy-targetable subgroups, preferably with multiple immune-related biomarkers. In the present study, we categorize colorectal adenocarcinomas into four types of tumour immune microenvironments according to PD-L1 expression and TIL, analyse their prognostic values, and propose an immunotherapy-targetable subgroup.Methods

Formalin-fixed, paraffin-embedded tissue samples of surgically resected primary colorectal adenocarcinomas (n = 489) were obtained and arrayed on tissue microarray blocks. Immunohistochemical stains for PD-L1, programmed cell death protein 1 (PD-1), cluster of differentiation 8 (CD8), and microsatellite instability (MSI) were performed and evaluated.Results

Tumour microenvironment immune type (TMIT) I (PD-L1-positive tumour cells and CD8-high TIL) and type II (PD-L1-negative tumour cells and CD8-low TIL) showed the best and worst prognoses, respectively. PD-L1 overexpression was significantly associated with MSI status. PD-L1 immunoreactivity was positively correlated with TIL having CD8 or PD-1 overexpression.Conclusions

TMIT I subgroup showed stronger CD8/PD-L1/PD-1 signalling interaction compared to the other TMIT. Therefore, we propose that the TMIT I subgroup is a candidate TMIT to predict effective response rate for existing immune checkpoint inhibitors and determine targetable subgroups for emerging therapies.
Comparative analysis of somatic variant calling on matched FF and FFPE WGS samples
Authors: Brienen Louise de Schaetzen van , Larmuseau Maarten , Eecken Kim Van der , De Ryck Frederic , Robbe Pauline , Schuh Anna , Fostier Jan , Ost Piet , Marchal Kathleen 
Published: January 2020

Abstract

Background. Research grade Fresh Frozen (FF) DNA material is not yet routinely collected in clinical practice. Many hospitals, however, collect and store Formalin Fixed Paraffin Embedded (FFPE) tumor samples. Consequently, the sample size of whole genome cancer cohort studies could be increased tremendously by including FFPE samples, although the presence of artefacts might obfuscate the variant calling. To assess whether FFPE material can be used for cohort studies, we performed an in-depth comparison of somatic SNVs called on matching FF and FFPE Whole Genome Sequence (WGS) samples extracted from the same tumor.
Results. We first compared the calls between an FF and an FFPE from a metastatic prostate tumor, showing that on average 50% of the calls in the FF are recovered in the FFPE sample, with notable differences between variant callers. Combining the variants of the different callers using a simple heuristic increases both the precision and the sensitivity of the variant calling. Validating the heuristic on nine additional matched FF-FFPE samples, resulted in an average F1-score of 0.58 and an outperformance of any of the individual callers. In addition, we could show that part of the discrepancy between the FF and the FFPE samples can be attributed to intra-tumor heterogeneity (ITH).
Conclusion. This study illustrates that when using the correct variant calling strategy, the majority of clonal SNVs can be recovered in an FFPE sample with high precision and sensitivity. These results suggest that somatic variants derived from WGS of FFPE material can be used in cohort studies.
Decomposing the educational inequalities in the factors associated with severe acute malnutrition among under-five children in Low- and Middle-Income Countries
Authors: Fagbamigbe Adeniyi Francis , Kandala Ngianga- Bakwin , Uthman Olalekan 
Published: January 2020

Abstract
Background: Low- and Middle-Income Countries (LMIC) have remained plagued with the burden of severe acute malnutrition (SAM). The decomposition of the educational inequalities in SAM across individual, neighbourhood and national level characteristics in LMIC have not been explored. This study aims to decompose educational-related inequalities in the development of SAM among under-five children in LMIC and identify the risk factors that contribute to the inequalities. Methods: We pooled successive secondary data from the Demographic and Health Survey (DHS) conducted between 2010 and 2018 in 51 LMIC. We analysed data of 532,680 under-five children nested within 55,823 neighbourhoods. Severe acute malnutrition was the outcome variable while the literacy status of mothers was the main exposure variable. The explanatory variables cut across the individual-, household and neighbourhood-level factors of the mother-child pair. Oaxaca-Blinder decomposition method was used at p=0.05. Results: Mothers with no formal education ranged from 0.1 % in Armenia and Kyrgyz to as much as 86.1 % in Niger. The overall prevalence of SAM in the group of children whose mothers had no education was 5.8 % compared with 4.2 % among those whose mothers were educated, this varied within each country. Fourteen countries (Cameroon(p=0.000), Chad(p=0.000), Comoro(p=0.047), Burkina Faso(p=0.000), Ethiopia(p=0.000), India(p=0.000), Kenya(p=0.000), Mozambique(p=0.012), Namibia(p=0.001), Nigeria(p=0.000), Pakistan(p=0.000), Senegal(p=0.003), Togo(p=0.013), and Timor Leste(p=0.000) had statistically significant pro-illiterate inequality while no country showed statistically significant pro-literate inequality. We found significant differences in SAM prevalence across child’s age(p=0.000), child’s sex(p=0.000), maternal age(p=0.001), household wealth quintile(p=0.001), mother’s access to media(p=0.001), birth weight(p=0.000) and neighbourhood socioeconomic status disadvantage(p=0.000). On the average, neighbourhood socioeconomic status disadvantage, location of residence were the most important factors in most countries. Other contributors to the explanation of educational inequalities are birth weight, maternal age and toilet type. Conclusions: SAM is prevalent in most LMIC with wide educational inequalities. Educational inequalities in SAM was explained by individual, household and community-level factors. Promotion of women education should be strengthened as better education among women will close the gaps and reduce the burden of SAM generally. We recommend further studies of other determinate causes of inequalities in severe acute malnutrition in LMIC.
Associations between maternal BMI, breastfeeding practices and infant anthropometric status in Colombia; secondary analysis of ENSIN 2010.
Authors: Aldana-Parra Fanny , Olaya Gilma , Fewtrell Mary 
Published: January 2020

Abstract
• Background: Maternal malnutrition and infant feeding mode impact short and long term infant and child morbidity and mortality. The period of lactation may provide an opportunity to modulate the risk of disease later in life. Our aim was to estimate the effect of maternal body mass index (BMI) and infant feeding mode, particularly breastfeeding practices, on the anthropometric status of children under two years in Colombia.
Experiences, views and needs of first-time fathers in pregnancy related care: a qualitative study in south-east Nigeria.
Authors: Onyeze-Joe Chiemeka , Godin Isabelle 
Published: January 2020

Abstract
Background Given the relevance of paternal involvement in maternal care, there is a need to prepare first-time fathers to participate in pregnancy and childbirth actively. This study explores the experiences and needs of first-time fathers and the influence of these on their involvement during pregnancy and childbirth in Nigeria. Methods A descriptive qualitative study was conducted. Semi-structured interviews with 50 men recruited from rural and urban workplaces, hospitals, and markets, generated data used to explore the experiences, views and needs of first-time fathers’ in pregnancy-related care in south-east Nigeria. All data were transcribed and analysed using thematic analysis. Results Six major themes were identified: gender roles, antenatal involvement, care costs and delivery choices, need to be informed, dealing with emotions, and dealing with the delivery day. A key finding was that inexperience, cultural beliefs and perceptions of gender norms greatly influenced the support provided by first-time fathers to their spouses, and the support they received from their social support networks. Two primary needs were identified: need to be informed and the need to know about the cost of care in health settings. First-time fathers acknowledged the role of information on their decision making and final choices. Conclusion Findings reveal the influence of gender norms, beliefs, and social support on first-time fathers’ involvement in pregnancy and childbirth. This study also highlights the urgent need to provide informational support for first-time fathers and presents insights into what hospitals can do to achieve this need. Keywords: male involvement, first-time fathers, pregnancy, qualitative, Nigeria
Genomic and transcriptomic survey of an endophytic fungus Calcarisporium arbuscula NRRL 3705 and potential overview of its secondary metabolites
Authors: Cheng Jintao , Cao Fei , Chen Xinai , Li Yongquan , Mao Xuming 
Published: January 2020

Abstract
Background: Endophytic fungi can produce many active secondary metabolites, which are important resources of natural medicines. However, there is currently little understanding of endophytic fungi at the omics levels. Calcarisporium arbuscula, an endophytic fungus from the healthy fruit of Russulaceae, can produce a variety of secondary metabolites with anti-cancer, anti-nematode and antibiotic bioactivities. Comprehensive survey of the endophytic fungi genome and transcriptome will help to understand their capacity to biosynthesize secondary metabolites and lay the foundation for the development of these precious resources.Results: In this study，we reported the high-quality genome sequence of a strain C. arbuscula NRRL 3705 based on Single Molecule Real-Time sequencing technology. The genome of this fungus is over 45 Mb in size, relatively larger than other typical filamentous fungi, and comprises 10,001 predictable genes, encoding at least 762 secretory-proteins, 386 carbohydrate-active enzymes and 177 P450 enzymes. 398 virulence factors and 228 genes related to pathogen-host interactions were also predicted in this fungus. Moreover, 65 secondary metabolite biosynthetic gene clusters were revealed, including the gene cluster for mycotoxins aurovertins. In addition, several gene clusters were predicted to produce various mycotoxins, including aflatoxin, alternariol, destruxin, citrinin and isoflavipucine. Notably, two independent gene clusters were shown possibly involved in the biosynthesis of alternariol. Furthermore, RNA-Seq assay showed that only the expression of aurovertin gene cluster is much stronger than the housekeeping genes under laboratory conditions, consistent with that aurovertins are the predominant metabolites. The gene expression of the remaining 64 gene clusters for compound backbone biosynthesis was all lower than the housekeeping genes, which might partially explain poor production of other secondary metabolites in this fungus.Conclusions: Our omics data along with bioinformatics analysis indicated that C. arbuscula NRRL 3705 contains a large number of biosynthetic gene clusters and has a huge potential to produce profound secondary metabolites. This work also provides the basis for development of endophytic fungi as a new resource of natural products with promising biological activities.
Does Xpert MTB/RIF Assay Give Rifampicin Resistance Results Without Identified Mutation? Review of Cases from Addis Ababa, Ethiopia.
Authors: Alemu Ayinalem , Tadesse Mengistu , Seid Getachew , Mollalign Helina , Eshetu Kirubel , Sinshaw Waganeh , Abebaw Yeshiwork , Amare Misikir , Dagne Biniyam , Diriba Getu , Yenew Bazezew , Getu Melak , Zerihun Betselot 
Published: January 2020

Abstract
Background: Xpert® MTB/RIF assay is currently used in Ethiopia for the rapid diagnosis of Mycobacterium tuberculosis (MTB) and mutations that confer Rifampicin resistance. Rifampicin resistance is determined based on any mutation in the 81 bp of rpoB gene using five overlapping probes represented as Probe A (codons 507–511), Probe B (codons 512–518), Probe C (codons 518–523), Probe D (codons 523–529) and Probe E (codons 529–533). In this review, we assessed the frequency of missed probe types for Rifampicin Resistance results. Methods: Data were reviewed from specimens received and tested using Xpert® MTB/RIF assay at Ethiopian National Tuberculosis Reference Laboratory, in Addis Ababa from 15 July 2016 to 31 December 2018 retrospectively. All archived data were reviewed carefully to describe missed probe types and the quantity of DNA in the sample. Results: A total of 100 specimens were reported as MTB Detected Rifampicin Resistance Detected by Xpert® MTB/RIF assay. More than half (55%) of these results were reported from male patients. The median age was 28.0 years (5 months to 88 years). Majorities (62%) of the cases were detected from sputum. Among the total of 38 extrapulmonary samples, lymph node aspirates were accounted for 50% (19/38). The most common mutations (81.0%) were found in the Probe E region followed by Probe D (10.0%), and Probe B (3.0%). Mutations in Probe A and Probe C regions were not observed. However, six (6.0%) Rifampicin resistance cases were found without any missed probe type. The delta Ct max is ≥4.3. No specimen yielded Rifampicin resistance associated with more than one probe failure or mutation combinations. Conclusion: Mutations associated with Probe E (codons 529–533) region were identified as the commonest rpoB gene mutations. The Rifampicin resistance results found without any identified missing probe needs further study. The lower DNA amount was observed in extrapulmonary specimens compared with sputum. Keywords: Rifampicin-resistance, Molecular Beacon, DNA probes, Xpert® MTB/RIF Assay