bluuebunny/crossref_metadata_2025_split huggingface dataset:
A multicenter retrospective study of heterogeneous tissue aggregates obstructing ventricular catheters explanted from patients with hydrocephalus
Authors: Hariharan Prashant , Sondheimer Jeffrey , Petroj Alexandra , Gluski Jacob , Jea Andrew , Whitehead William E. , Sood Sandeep , Ham Steven D. , Rocque Brandon G. , Marupudi Neena I. , McAllister James P. , Limbrick David , Del Bigio Marc R. , Harris Carolyn A. 
Published: July 2021

Abstract
Background
Implantation of ventricular catheters (VCs) to drain cerebrospinal fluid (CSF) is a standard approach to treat hydrocephalus. VCs fail frequently due to tissue obstructing the lumen via the drainage holes. Mechanisms driving obstruction are poorly understood. This study aimed to characterize the histological features of VC obstructions and identify links to clinical factors.

Methods
343 VCs with relevant clinical data were collected from five centers. Each hole on the VCs was classified by degree of tissue obstruction after macroscopic analysis. A subgroup of 54 samples was analyzed using immunofluorescent labelling, histology and immunohistochemistry.

Results
61.5% of the 343 VCs analyzed had tissue aggregates occluding at least one hole (n = 211) however the vast majority of the holes (70%) showed no tissue aggregates. Mean age at which patients with occluded VCs had their first surgeries (3.25 yrs) was lower than in patients with non-occluded VCs (5.29 yrs, p < 0.02). Mean length of time of implantation of occluded VCs, 33.22 months was greater than for non-occluded VCs, 23.8 months (p = 0.02). Patients with myelomeningocele had a greater probability of having an occluded VC (p = 0.0426). VCs with occlusions had greater numbers of macrophages and astrocytes in comparison to non-occluded VCs (p < 0.01). Microglia comprised only 2–6% of the VC-obstructing tissue aggregates. Histologic analysis showed choroid plexus occlusion in 24%, vascularized glial tissue occlusion in 24%, prevalent lymphocytic inflammation in 29%, and foreign body giant cell reactions in 5% and no ependyma.

Conclusion
Our data show that age of the first surgery and length of time a VC is implanted are factors that influence the degree of VC obstruction. The tissue aggregates obstructing VCs are composed predominantly of astrocytes and macrophages; microglia have a relatively small presence.
Image analysis for the automatic phenotyping of Orobanche cumana tubercles on sunflower roots
Authors: Le Ru A. , Ibarcq G. , Boniface M.- C. , Baussart A. , Muños S. , Chabaud M. 
Published: July 2021

Abstract
Background
The parasitic plant Orobanche cumana is one of the most important threats to sunflower crops in Europe. Resistant sunflower varieties have been developed, but new O. cumana races have evolved and have overcome introgressed resistance genes, leading to the recurrent need for new resistance methods. Screening for resistance requires the phenotyping of thousands of sunflower plants to various O. cumana races. Most phenotyping experiments have been performed in fields at the later stage of the interaction, requiring time and space. A rapid phenotyping screening method under controlled conditions would need less space and would allow screening for resistance of many sunflower genotypes. Our study proposes a phenotyping tool for the sunflower/O. cumana interaction under controlled conditions through image analysis for broomrape tubercle analysis at early stages of the interaction.

Results
We optimized the phenotyping of sunflower/O. cumana interactions by using rhizotrons (transparent Plexiglas boxes) in a growth chamber to control culture conditions and Orobanche inoculum. We used a Raspberry Pi computer with a picamera for acquiring images of inoculated sunflower roots 3 weeks post inoculation. We set up a macro using ImageJ free software for the automatic counting of the number of tubercles. This phenotyping tool was named RhizOSun. We evaluated five sunflower genotypes inoculated with two O. cumana races and showed that automatic counting of the number of tubercles using RhizOSun was highly correlated with manual time-consuming counting and could be efficiently used for screening sunflower genotypes at the tubercle stage.

Conclusion
This method is rapid, accurate and low-cost. It allows rapid imaging of numerous rhizotrons over time, and it enables image tracking of all the data with time kinetics. This paves the way toward automatization of phenotyping in rhizotrons that could be used for other root phenotyping, such as symbiotic nodules on legumes.
Management of chronic knee pain caused by postsurgical or posttraumatic neuroma of the infrapatellar branch of the saphenous nerve
Authors: Regev G. J. , Ben Shabat D. , Khashan M. , Ofir D. , Salame K. , Shapira Y. , Kedem R. , Lidar Z. , Rochkind S. 
Published: July 2021

Abstract
Purpose
Injury to the infrapatellar branch of the saphenous nerve (IBSN) is a relatively common complication after knee surgery, which can interfere with patient satisfaction and functional outcome. In some cases, injury to the IBSN can lead to formation of a painful neuroma. The purpose of this study was to report the results of surgical treatment in a series of patients with IBSN painful neuroma.

Methods
We retrospectively identified 37 patients who underwent resection of IBSN painful neuroma at our institution, after failure of non-operative treatment for a minimum of 6 months. Injury to the IBSN resulted from prior orthopedic surgery, vascular surgery, tumor resection, trauma, or infection. Leg pain and health-related quality of life were measured using the numeric rating scale (NRS) and EuroQol 5 dimensions (EQ-5D) questionnaire, respectively. Clinically meaningful improvement in leg pain was defined as reduction in NRS by at least 3 points. Predictors of favorable and unfavorable surgical outcome were investigated using multivariable logistic regression analysis.

Results
Patient-reported leg pain, health-related quality of life, and overall satisfaction with the surgical outcome were obtained at 94 ± 52.9 months after neuroma surgery. Postoperative patient-reported outcomes were available for 25 patients (68% of the cohort), of whom 20 patients (80.0%) reported improvement in leg pain, 17 patients (68.0%) reported clinically meaningful improvement in leg pain, and 17 patients (68%) reported improvement in health-related quality of life. The average NRS pain score improved from 9.43 ± 1.34 to 5.12 ± 3.33 (p < 0.01) and the average EQ-5D functional score improved from 10.48 ± 2.33 to 7.84 ± 2.19 (p < 0.01). Overall patient reported satisfaction with the surgical outcome was good to excellent for 18 patients (72.0%). Older age, multiple prior orthopedic knee surgeries, and failed prior attempts to resect an IBSN neuroma were associated with non-favorable surgical outcome.

Conclusion
We conclude that surgical intervention is efficacious for appropriately selected patients suffering from IBSN painful neuroma.
Mobilisation of emergency services for chemical incidents in Sweden - a multi-agency focus group study
Authors: Westman Anton , Saveman Britt-Inger , Björnstig Ulf , Hylander Johan , Gyllencreutz Lina 
Published: July 2021

Abstract
Background
In chemical incidents, infrequent but potentially disastrous, the World Health Organization calls for inter-organizational coordination of actors involved. Multi-organizational studies of chemical response capacities are scarce. We aimed to describe chemical incident experiences and perceptions of Swedish fire and rescue services, emergency medical services, police services, and emergency dispatch services personnel.

Methods
Eight emergency service organizations in two distinct and dissimilar regions in Sweden participated in one organization-specific focus group interview each. The total number of respondents was 25 (7 females and 18 males). A qualitative inductive content analysis was performed.

Results
Three types of information processing were derived as emerging during acute-phase chemical incident mobilization: Unspecified (a caller communicating with an emergency medical dispatcher), specified (each emergency service obtaining organization-specific expert information), and aligned (continually updated information from the scene condensed and disseminated back to all parties at the scene). Improvable shortcomings were identified, e.g. randomness (unspecified information processing), inter-organizational reticence (specified information processing), and downprioritizing central information transmission while saving lives (aligned information processing).

Conclusions
The flow of information may be improved by automation, public education, revised dispatcher education, and use of technical resources in the field. Future studies should independently assess these mechanism’s degree of impact on mobilisation of emergency services in chemical incidents.
Trends in clinical trial registration in sub-Saharan Africa between 2010 and 2020: a cross-sectional review of three clinical trial registries
Authors: Edem Bassey , Onwuchekwa Chukwuemeka , Wariri Oghenebrume , Nkereuwem Esin , Nkereuwem Oluwatosin O. , Williams Victor 
Published: July 2021

Abstract
Objective
Prospective registration of clinical trials is an ethical, scientific, and legal requirement that serves several functions, including minimising research wastage and publication bias. Sub-Saharan Africa (SSA) is increasingly hosting clinical trials over the past few years, and there is limited literature on trends in clinical trial registration and reporting in SSA. Therefore, we set out to determine the trends in clinical trials registered in SSA countries between 2010 and July 2020.

Methods
A cross-sectional study design was used to describe the type of clinical trials that are conducted in SSA from 1 January 2010 to 31 July 2020. The registries searched were ClinicalTrials.gov (CTG), the Pan African Clinical Trials Register (PACTR), and the International Standard Randomized Controlled Trial Number (ISRCTN). Data were extracted into Excel and imported into STATA for descriptive analysis.

Results
CTG had the highest number of registered trials at 2622, followed by PACTR with 1501 and ISRCTN with 507 trials. Trials were observed to increase gradually from 2010 and peaked at 2018–2019. Randomised trials were the commonest type, accounting for at least 80% across the three registries. Phase three trials investigating drugs targeted at infections/infestations were the majority. Few completed trials had their results posted: 58% in ISRCTN and 16.5% in CTG, thus suggesting reporting bias.

Conclusion
Despite the gradual increase in clinical trials registered during the period, recent trends suggest a drop in the number of trials registered across the region. Strengthening national and regional regulatory capacity will improve clinical trial registration and minimise reporting bias in completed clinical trials.
Role of Plasmodium berghei ookinete surface and oocyst capsule protein, a novel oocyst capsule-associated protein, in ookinete motility
Authors: Nakayama Kazuhiko , Kimura Yuta , Kitahara Yu , Soga Akira , Haraguchi Asako , Hakozaki Jun , Sugiyama Makoto , Kusakisako Kodai , Fukumoto Shinya , Ikadai Hiromi 
Published: July 2021

Abstract
Background
Plasmodium sp., which causes malaria, must first develop in mosquitoes before being transmitted. Upon ingesting infected blood, gametes form in the mosquito lumen, followed by fertilization and differentiation of the resulting zygotes into motile ookinetes. Within 24 h of blood ingestion, these ookinetes traverse mosquito epithelial cells and lodge below the midgut basal lamina, where they differentiate into sessile oocysts that are protected by a capsule.

Methods
We identified an ookinete surface and oocyst capsule protein (OSCP) that is involved in ookinete motility as well as oocyst capsule formation.

Results
We found that knockout of OSCP in parasite decreases ookinete gliding motility and gradually reduces the number of oocysts. On day 15 after blood ingestion, the oocyst wall was significantly thinner. Moreover, adding anti-OSCP antibodies decreased the gliding speed of wild-type ookinetes in vitro. Adding anti-OSCP antibodies to an infected blood meal also resulted in decreased oocyst formation.

Conclusion
These findings may be useful for the development of a transmission-blocking tool for malaria.

Graphical abstract
Abnormal methylation characteristics predict chemoresistance and poor prognosis in advanced high-grade serous ovarian cancer
Authors: Feng Li-yuan , Yan Bing-bing , Huang Yong-zhi , Li Li 
Published: July 2021

AbstractBackgroundPrimary or acquired chemoresistance is a key link in the high mortality rate of ovarian cancer. There is no reliable method to predict chemoresistance in ovarian cancer. We hypothesized that specific methylation characteristics could distinguish chemoresistant and chemosensitive ovarian cancer patients.MethodsIn this study, we used 450 K Infinium Methylation BeadChip to detect the different methylation CpGs between ovarian cancer patients. The differential methylation genes were analyzed by GO and KEGG Pathway bioinformatics analysis. The candidate CpGs were confirmed by pyrosequencing. The expression of abnormal methylation gene was identified by QRT-PCR and IHC. ROC analysis confirmed the ability to predict chemotherapy outcomes. Prognosis was evaluated using Kaplan–Meier.ResultsIn advanced high-grade serous ovarian cancer, 8 CpGs (ITGB6:cg21105318, cg07896068, cg18437633; NCALD: cg27637873, cg26782361, cg16265707; LAMA3: cg20937934, cg13270625) remained hypermethylated in chemoresistant patients. The sensitivity, specificity and AUC of 8 CpGs (ITGB6:cg21105318, cg07896068, cg18437633; NCALD: cg27637873, cg26782361, cg16265707; LAMA3: cg20937934, cg13270625) methylation to predict chemotherapy sensitivity were 63.60–97.00%, 46.40–89.30% and 0.774–0.846. PFS of 6 candidate genes (ITGB6:cg21105318, cg07896068; NCALD: cg27637873, cg26782361, cg16265707; LAMA3: cg20937934) hypermethylation patients was significantly shorter. The expression of NCALD and LAMA3 in chemoresistant patients was lower than that of chemosensitive patients. Spearman analysis showed that NCALD and LAMA3 methylations were negatively correlated with their expression.ConclusionsAs a new biomarker of chemotherapy sensitivity, hypermethylation of NCALD and LAMA3 is associated with poor PFS in advanced high-grade serous ovarian cancer. In the future, further research on NCALD and LAMA3 will be needed to provide guidance for clinical stratification of demethylation therapy.
First discovery of nautilids from the Albian–Cenomanian succession of the Koppeh Dagh Basin, NE Iran
Authors: Sharifi Javad , Tajika Amane , Mohammadabadi Alireza , Tabari Abkuh Mohammad Hossein 
Published: July 2021

AbstractThe Aitamir Formation, situated in the Koppeh Dagh Basin in the northeast of Iran, is known for its well-exposed Albian-to-Cenomanian succession. Although geologists previously documented a number of macro- and microfossils, no nautilids had been discovered until now to our knowledge. Here, we present lower Albian and middle Cenomanian nautilids from the Koppeh Dagh Basin for the first time. This discovery is also the first record of Cretaceous nautilids from Iran. We identified the specimens asEutrephoceras clementianum(d’Orbigny 1840),E.sublaevigatum(d’Orbigny 1850),E.bouchardianum(d’Orbigny 1840) andEutrephocerassp. These specimens occur in horizons situated between several ammonite-bearing levels, which allowed us to more precisely constrain age estimates for the recovered nautilid specimens.E.clementianumcould not be dated precisely but likely comes from between late Aptian ammonite indexHypacanthoplites uhligiand middle AlbianHoplites(Hoplites)baylei.E. sublaevigatumoccurs just above the late Albian ammonitesMariella bergeriandSemenoviceras michalskiiand below theMantelliceras mantelliZone. At the upper part of the section,E.bouchardianumandEutrephocerassp. were collected from lower Albian beds, which correspond to theMantelliceras mantelliandMantelliceras dixoniizones. These new findings contribute to our knowledge of the geographical distribution and stratigraphic range of Albian–Cenomanian nautilid species.
Circulating miR-146a as a possible candidate biomarker in the indeterminate phase of Chagas disease
Authors: Ballinas-Verdugo Martha Alicia , Jiménez-Ortega Rogelio Frank , Martínez-Martínez Eduardo , Rivas Nancy , Contreras-López Erick Abraham , Carbó Roxana , Sánchez Fausto , Bojalil Rafael , Márquez-Velasco Ricardo , Sánchez-Muñoz Fausto , Alejandre-Aguilar Ricardo 
Published: July 2021

Abstract
Background
Chagas disease is considered important and presents intense inflammatory and fibrotic processes induced by the perpetuation of the parasite in the affected tissues and organs. Therefore, it is necessary to inquire about the host defense and attack mechanisms to have a more detailed knowledge about Chagas disease. MicroRNAs are found in blood, tissues and extracellular vesicles. These small regulators of gene expression are involved in physiological and pathological processes in both mammals and parasites. Several microRNAs have deregulated expression in chagasic heart disease, although little is known about their extracellular expression. Our main objective was to evaluate the involvement of miR-21, miR-146a and miR-155 in several samples from mice infected with the TcI Ninoa strain from the acute and indeterminate phases. We also explored a potential functional association of the selected microRNAs using STRING software. This software identified 23 pathways associated with Trypanosoma cruzi infection. In addition, eleven genes were identified through bioinformatics analysis, and we found that SMAD family member 5 was downregulated in both phases. This gene serves as a mediator in the TGF-β signaling pathway. Thus, forty female mice of the CD1 strain were distributed into 4 groups and the expression levels of miR-21, miR-146a and miR-155 were measured in samples of heart tissue, total plasma and plasma extracellular vesicles by quantitative real-time polymerase chain reaction.

Results
Overexpression of miR-21, miR-146a and miR-155 was observed in heart and plasma in both phases. Moreover, in extracellular vesicles miR-21 and miR-146a were also overexpressed in the acute phase, whereas in the indeterminate chronic phase we found only miR-146a up-regulated.

Conclusions
The expression of inflammatory microRNAs miR-21, miR-146a and miR-155 were up-regulated in each of the samples from acutely and chronically infected mice. The relevant finding was that miR-146a was up-regulated in each sample in both phases; therefore, this miRNA could be a possible candidate biomarker in Chagas disease.
Dietary intake and food behaviours of Senegalese adolescent girls
Authors: Giguère-Johnson Madélie , Ward Stéphanie , Ndéné Ndiaye Aminata , Galibois Isabelle , Blaney Sonia 
Published: July 2021

AbstractBackgroundMalnutrition is a public health concern in low- and middle-income countries. In Senegal, 35% of adolescent girls are undernourished and 56% are anemic.MethodsThis study assessed the dietary intake of 14–18-year-old adolescent girls in Dakar, Senegal. Specifically, the study 1) assessed their intake in energy, fibre, macro- and micronutrients, 2) described the types and the quality of the foods they consume, and 3) assessed some of their eating behaviours. Dietary intake was measured using three non-consecutive 24-h recalls from 136 adolescent girls attending two colleges. Energy and nutrient intakes were measured and compared to recommendations. Foods were classified by food group and by whether they were healthy or unhealthy. Adolescents’ daily intake (g) of fruits and vegetables, as well as the proportion of girls who ate breakfast and who consumed three meals a day were calculated.ResultsSodium intake was high, while fibre intake was low. On average, 40% of the adolescents’ total energy intake came from fats. Mean intakes of zinc and calcium were higher on the weekend than on weekdays, while the opposite was observed for sodium. Eighty-three percent of adolescents had an inadequate intake of iron and 99% were at risk of calcium deficiency. Approximately 60% of the foods consumed were classified as healthy, however, the majority came from grains.ConclusionsAdolescent nutrition deserves attention given the poor quality of their dietary intake which may put them at risk of malnutrition and chronic diseases. These findings may be used to help improve programs targeting Senegalese adolescent girls’ nutrition.
A guide to do randomized controlled trials in the field of otolaryngology
Authors: Zamzam Sameh M. , Abdel-Aziz Mosaad , Atef Ahmed , Abdel-Naseer Usama , Hamoda Mostafa , Salah Mohamed , Dewidar Hazem , Elsharkawy Louay , Abdelmalek Mena E. 
Published: July 2021

Abstract
Background
Randomized controlled trials (RCTs) are prospective comparative studies in which study groups are allocated randomly to intervention or serve as controls. RCT is the mainstay to achieve evidence in the literature in clinical research. A RCT is the main research design to study the effect of an intervention and the only way to confirm the value of a new treatment.

Main body
RCT also gives the way to generate meta-analyses and systematic reviews giving a stronger evidence for clinical practice. Evidence-based medicine (EBM) is crucial for safe, effective, and standardized patient care. Although there is an agreement on the importance of performing RCT, it can be challenging to do it efficiently including different aspects like study design, funding, randomization, blinding, follow-up, data analysis, statistics, generalization of results, and reporting of quality of the studies.

Conclusion
In this article, we gave a comprehensive review for RCT in otolaryngology discussing their importance, advantages, and drawbacks, types, steps, challenges, reporting their quality and their prevalence in the literature.
CBCT image artefacts generated by implants located inside the field of view or in the exomass
Authors: Demirturk Kocasarac Husniye , Koenig Lisa J , Ustaoglu Gulbahar , Oliveira Matheus Lima , Freitas Deborah Queiroz 
Published: July 2021

Objectives: To compare artefacts in cone-beam computed tomography (CBCT) arising from implants of different materials located either inside the field of view (FOV) or in the exomass, and to test different image-acquisition parameters to reduce them. Methods: CBCT scans of a human mandible prepared with either a titanium, titanium–zirconium, or zirconia implant were acquired with the Planmeca ProMax utilizing FOV sizes of 8 × 5 cm and 4 × 5 cm, which placed the implant inside the FOV (8 × 5 cm) or in the exomass (4 × 5 cm). The scanning parameters considered three conditions of metal artefact reduction (MAR), disabled, low, and high, and 2 kVp levels (80 and 90). The standard deviation (SD) of grey values of regions of interest was obtained. The effects of implant material, implant position, MAR condition, kVp level, and their interactions were evaluated by Analysis of Variance (α = 5%). Results: The zirconia implant produced the highest SD values (more heterogeneous grey values, corresponding to greater artefact expression), followed by titanium–zirconium, and titanium. In general, implants in the exomass produced images with higher SD values than implants inside the FOV. MAR was effective in decreasing SD values, especially from the zirconia implant, only when the implant was inside the FOV. Images with 80 kVp had higher SD values than those with 90 kVp, regardless of the other factors (p < 0.05). Conclusions: Implants in the exomass lead to greater artefact expression than when they are inside the FOV. Special attention should be paid to scanning parameters that reduce metal-related artefacts, such as MAR activation and increasing kVp. This is especially important with a zirconia implant inside the FOV.