bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using an artificial neural network to map cancer common data elements to the biomedical research integrated domain group model in a semi-automated manner
Authors: Renner Robinette , Li Shengyu , Huang Yulong , van der Zijp-Tan Ada Chaeli , Tan Shaobo , Li Dongqi , Kasukurthi Mohan Vamsi , Benton Ryan , Borchert Glen M. , Huang Jingshan , Jiang Guoqian 
Published: December 2019

AbstractBackgroundThe medical community uses a variety of data standards for both clinical and research reporting needs. ISO 11179 Common Data Elements (CDEs) represent one such standard that provides robust data point definitions. Another standard is the Biomedical Research Integrated Domain Group (BRIDG) model, which is a domain analysis model that provides a contextual framework for biomedical and clinical research data. Mapping the CDEs to the BRIDG model is important; in particular, it can facilitate mapping the CDEs to other standards. Unfortunately, manual mapping, which is the current method for creating the CDE mappings, is error-prone and time-consuming; this creates a significant barrier for researchers who utilize CDEs.MethodsIn this work, we developed a semi-automated algorithm to map CDEs to likely BRIDG classes. First, we extended and improved our previously developed artificial neural network (ANN) alignment algorithm. We then used a collection of 1284 CDEs with robust mappings to BRIDG classes as the gold standard to train and obtain the appropriate weights of six attributes in CDEs. Afterward, we calculated the similarity between a CDE and each BRIDG class. Finally, the algorithm produces a list of candidate BRIDG classes to which the CDE of interest may belong.ResultsFor CDEs semantically similar to those used in training, a match rate of over 90% was achieved. For those partially similar, a match rate of 80% was obtained and for those with drastically different semantics, a match rate of up to 70% was achieved.DiscussionOur semi-automated mapping process reduces the burden of domain experts. The weights are all significant in six attributes. Experimental results indicate that the availability of training data is more important than the semantic similarity of the testing data to the training data. We address the overfitting problem by selecting CDEs randomly and adjusting the ratio of training and verification samples.ConclusionsExperimental results on real-world use cases have proven the effectiveness and efficiency of our proposed methodology in mapping CDEs with BRIDG classes, both those CDEs seen before as well as new, unseen CDEs. In addition, it reduces the mapping burden and improves the mapping quality.
Parameter, noise, and tree topology effects in tumor phylogeny inference
Authors: Tomlinson Kiran , Oesper Layla 
Published: December 2019

Abstract
Background
Accurate inference of the evolutionary history of a tumor has important implications for understanding and potentially treating the disease. While a number of methods have been proposed to reconstruct the evolutionary history of a tumor from DNA sequencing data, it is not clear how aspects of the sequencing data and tumor itself affect these reconstructions.

Methods
We investigate when and how well these histories can be reconstructed from multi-sample bulk sequencing data when considering only single nucleotide variants (SNVs). Specifically, we examine the space of all possible tumor phylogenies under the infinite sites assumption (ISA) using several approaches for enumerating phylogenies consistent with the sequencing data.

Results
On noisy simulated data, we find that the ISA is often violated and that low coverage and high noise make it more difficult to identify phylogenies. Additionally, we find that evolutionary trees with branching topologies are easier to reconstruct accurately. We also apply our reconstruction methods to both chronic lymphocytic leukemia and clear cell renal cell carcinoma datasets and confirm that ISA violations are common in practice, especially in lower-coverage sequencing data. Nonetheless, we show that an ISA-based approach can be relaxed to produce high-quality phylogenies.

Conclusions
Consideration of practical aspects of sequencing data such as coverage or the model of tumor evolution (branching, linear, etc.) is essential to effectively using the output of tumor phylogeny inference methods. Additionally, these factors should be considered in the development of new inference methods.
Water spirits within the fishers’ worldview: implications for fishing management in Northeast Brazil
Authors: da Silva André Bastos , Lopes João Batista , Figueiredo Luciano Silva , de Barros Roseli Farias Melo , Souto Wedson Medeiros Silva , Alencar Nelson Leal , Lopes Clarissa Gomes Reis 
Published: December 2019

Abstract
Background
Historically, aquatic environments are linked to the worldview of many local people, where there is an interconnection between the natural world, the supernatural, and the social organization. In this study, we provided a discussion on how the supernatural beings that inhabit the freshwater systems interact with artisanal fishers and fishing resources in the riverine community of Parnaíba River middle course, in Mid North of Northeast Brazil. We also provided the implications of these interactions on the fisher’s behaviors and how the acculturation process (e.g., introduction of new religions) can affect the fishers’ worldview.

Method
The selection of participants was done through intentional sampling. The content qualitative analysis was carried out to interpret the data from semi-structured interviews with 29 artisanal fishers.

Results
The mythical representations that inhabit the aquatic environments in the surveyed area were as follows: Mãe d’ água, Cabeça de cuia, Muleque d’água, Visage, Piratinga, Sucuiuiu, and Luz e Arco-íris. These beings have distinctions regarding the form and attributions and can be associated with seasonality (temporal markers) and specific habitats (spatial markers). The respect and fear feeling of the mythical beings were striking among the fishers interviewed. For instance, we have record offering practices in order to obtain protection and success during the fisheries. These practices suggest that there may be local conservationist habits in fisheries management. However, the advancement of urbanization and the introduction of new religions that deny the existence of mythical entities are factors that can generate the acculturation process among the fishers.

Conclusions
It is therefore necessary to carry out more studies in the surveyed area in order to evaluate the existence of possible patterns in the relationship between fisher and mythical beings. This information could confirm the role of mythical beings as environmental regulators. Consequently, it could be considered in the conservationist policies of fishery resources, reinforcing the importance of local knowledge and cultural factors for fishing management approaches.
The BMP signaling pathway enhances the osteoblastic differentiation of bone marrow mesenchymal stem cells in rats with osteoporosis
Authors: Zhao Bin , Xing Gengyan , Wang Aiyuan 
Published: December 2019

Abstract
Background
This study was conducted with the aim of exploring the effect of the BMP signaling pathway on osteoblastic differentiation in rat bone marrow mesenchymal stem cells (rBMSCs) in rats with osteoporosis (OP).

Methods
The bilateral ovaries of female SD rats were resected for the establishment of a rat OP model. The osteoblastic differentiation of isolated rBMSCs was identified through osteogenic induction. Adipogenetic induction and flow cytometry (FCM) were used to detect adipogenic differentiation and the expression of rBMSC surface markers. The rBMSCs were grouped into the blank group, NC group, si-BMP2 group, and oe-BMP2 group. The expression levels of key factors and osteogenesis-related factors were determined by Western blot and quantitative real-time polymerase chain reaction (qRT-PCR). The formation of calcified nodules was observed by alizarin red staining. ALP activity was measured by alkaline phosphatase staining.

Results
The rats with OP had greater weight but decreased bone mineral density (BMD) than normal rats (all P < 0.01). The rBMSCs from rats with OP were capable of osteoblastic differentiation and adipogenic differentiation and showed high expression of CD44 (91.3 ± 2.9%) and CD105 (94.8 ± 2.1%). Compared with the blank group, the oe-BMP2 group had elevated BMP-2 and Smad1 levels and an increase in calcified nodules and ALP-positive staining areas (all P < 0.05). Moreover, the expression levels of Runx2, OC, and OPN in the oe-BMP2 group were relatively higher than those in the blank group (all P < 0.05). The findings in the si-BMP2 group were opposite to those in the oe-BMP2 group.

Conclusion
BMP signaling pathways activated by BMP-2 can promote the osteoblastic differentiation of rBMSCs from rats with OP.
Cell-specific expression of Epac2 in the subventricular and subgranular zones
Authors: Seo Hyunhyo , Lee Kyungmin 
Published: December 2019

Abstract
Aim
cAMP signal transduction cascade activation is important in regulating neurogenesis in adult rodents by increasing the proliferation of newborn cells. Although the ventricular-subventricular zone (V-SVZ) and subgranular zone (SGZ) both contain large populations of neural stem/precursor cells; it remains unclear whether an alternative target of cAMP, the exchange protein directly activated by cAMP (Epac2), is involved in adult neurogenesis in the V-SVZ and SGZ. Here, we investigated the cell-specific expression of Epac2 protein in the V-SVZ and SGZ of the adult mouse brain.

Methods
Immunohistochemical analyses were performed using antibodies against Epac2, glial fibrillary acidic protein (GFAP), doublecortin (DCX), and beta-catenin, to examine the co-localization of Epac2 protein and neural stem/precursor cells in the V-SVZ and SGZ in three 8-week-old male mice.

Results
In the V-SVZ of the lateral ventricle, most GFAP-positive adult neural stem cells (NSC, defined as type B cells) and 75% of DCX-positive migrating neuroblasts (type A cells) expressed Epac2 proteins. Ninety-three percent of beta-catenin-positive ependymal cells (type E cells), which are in direct contact with NSCs and the ventricles, also expressed Epac2 protein. Similarly, in the SGZ of the hippocampus, Epac2-immunopositive signals were shown by 83% of GFAP-positive radial-glia-like NSCs (type 1 cells), 86% of DCX-positive transiently amplifying cells (type 2 and type 3 cells), and 71% of DCX-positive immature neurons. The present data suggest that a PKA-independent cAMP signaling pathway via Epac2 may be party to adult neurogenesis in the V-SVZ and the SGZ.
Preliminary effect and feasibility of physiotherapy with strength training and protein-rich nutritional supplement in combination with anabolic steroids in cross-continuum rehabilitation of patients with hip fracture: protocol for a blinded randomized controlled pilot trial (HIP-SAP1 trial)
Authors: Hulsbæk Signe , Ban Ilija , Aasvang Tobias Kvanner , Jensen Jens-Erik Beck , Kehlet Henrik , Foss Nicolai Bang , Bandholm Thomas , Kristensen Morten Tange 
Published: December 2019

Abstract
Background
A 2014 Cochrane review evaluating the effect of anabolic steroids after hip fracture concluded that the quality of the studies was insufficient to draw conclusions on the effects and recommended further high-quality trials in the field. Therefore, the aim of this pilot trial is to determine the preliminary effect and feasibility of a 12-week multimodal intervention consisting of physiotherapy (with strength training), protein-rich nutritional supplement and anabolic steroid on knee-extension muscle strength and function 14 weeks after hip fracture surgery.

Methods
We plan to conduct a randomized, placebo-controlled pilot trial with 48 patients operated for acute hip fracture. The patients are randomized (1:1) to either (1) physiotherapy with protein-rich nutritional supplement plus anabolic steroid or (2) physiotherapy with protein-rich nutritional supplement plus placebo. Outcome assessments will be carried out blinded at baseline (3–10 days after surgery) and at 14 weeks after entering the trial. Primary outcome is the change from baseline to follow-up in maximal isometric knee-extension muscle strength in the fractured limb. Secondary outcomes are physical performance test, patient-reported outcomes, and measures of body composition.

Discussion
If the trial is found feasible and the results show an indication of anabolic steroid being a relevant addition to further enhance the recovery of muscle strength and function in an enhanced recovery after surgery program, this trial will constitute the basis of a larger confirmatory trial.

Trial registration
ClinicalTrials.gov, NCT03545347. Preregistered on 4 June 2018.
Effect of a community-based intervention for cardiovascular risk factor control on stroke mortality in rural Gadchiroli, India: study protocol for a cluster randomised controlled trial
Authors: Kalkonde Yogeshwar , Deshmukh Mahesh , Nila Sindhu , Jadhao Sunil , Bang Abhay 
Published: December 2019

AbstractBackgroundStroke has emerged as a leading cause of death in rural India. However, well-tested healthcare interventions to reduce stroke mortality in rural under-resourced settings are lacking. The aim of this study is to evaluate the effect of a community-based preventive intervention on stroke mortality in rural Gadchiroli, India.MethodsThe study is a two-arm, parallel group, cluster randomised controlled trial in which 32 villages will be randomised to the intervention and the enhanced usual care (EUC) arm. In the intervention arm, individuals ≥50 years of age will be screened for hypertension, diabetes and stroke by trained Community Health Workers (CHWs). Screened individuals who are positive will be referred to a mobile outreach clinic which will visit the intervention villages periodically. A physician in the clinic will confirm the diagnosis, provide guideline-based treatment and follow up patients. The CHWs will make home visits once a month to ensure medication compliance and counsel patients to reduce salt consumption and quit tobacco and alcohol. In the EUC arm, households will be provided information on the ill effects of tobacco use and steps to quit it. Individuals from both the arms will have access to the government’s national programme for the prevention and control of non-communicable diseases, where treatment for hypertension, diabetes and preventive treatment after stroke is available at the nearest primary health centres (PHCs). The intervention will be implemented for 3.5 years. The primary outcome will be a reduction in stroke mortality in the last 2.5 years of the intervention.DiscussionThis trial will provide important information regarding the feasibility and effect of a community-based preventive intervention package on stroke mortality in a rural under-resourced setting and can inform India’s non-communicable diseases prevention and control programme. If successful, such an intervention can be scaled up in the rural regions of India and other countries.Trial registrationClinical Trials Registry of India:CTRI/2015/12/006424. Registered on 8 December 2015.
Pretreatment for biorefineries: a review of common methods for efficient utilisation of lignocellulosic materials
Authors: Galbe Mats , Wallberg Ola 
Published: December 2019

AbstractThe implementation of biorefineries based on lignocellulosic materials as an alternative to fossil-based refineries calls for efficient methods for fractionation and recovery of the products. The focus for the biorefinery concept for utilisation of biomass has shifted, from design of more or less energy-driven biorefineries, to much more versatile facilities where chemicals and energy carriers can be produced. The sugar-based biorefinery platform requires pretreatment of lignocellulosic materials, which can be very recalcitrant, to improve further processing through enzymatic hydrolysis, and for other downstream unit operations. This review summarises the development in the field of pretreatment (and to some extent, of fractionation) of various lignocellulosic materials. The number of publications indicates that biomass pretreatment plays a very important role for the biorefinery concept to be realised in full scale. The traditional pretreatment methods, for example, steam pretreatment (explosion), organosolv and hydrothermal treatment are covered in the review. In addition, the rapidly increasing interest for chemical treatment employing ionic liquids and deep-eutectic solvents are discussed and reviewed. It can be concluded that the huge variation of lignocellulosic materials makes it difficult to find a general process design for a biorefinery. Therefore, it is difficult to define “the best pretreatment” method. In the end, this depends on the proposed application, and any recommendation of a suitable pretreatment method must be based on a thorough techno-economic evaluation.
Upgrading of efficient and scalable CRISPR–Cas-mediated technology for genetic engineering in thermophilic fungus Myceliophthora thermophila
Authors: Liu Qian , Zhang Yongli , Li Fangya , Li Jingen , Sun Wenliang , Tian Chaoguang 
Published: December 2019

AbstractBackgroundThermophilic filamentous fungusMyceliophthora thermophilahas great capacity for biomass degradation and is an attractive system for direct production of enzymes and chemicals from plant biomass. Its industrial importance inspired us to develop genome editing tools to speed up the genetic engineering of this fungus. First-generation CRISPR–Cas9 technology was developed in 2017 and, since then, some progress has been made in thermophilic fungi genetic engineering, but a number of limitations remain. They include the need for complex independent expression cassettes for targeting multiplex genomic loci and the limited number of available selectable marker genes.ResultsIn this study, we developed anAcidaminococcussp. Cas12a-based CRISPR system for efficient multiplex genome editing, using a single-array approach inM. thermophila. These CRISPR–Cas12a cassettes worked well for simultaneous multiple gene deletions/insertions. We also developed a new simple approach for marker recycling that relied on the novel cleavage activity of the CRISPR–Cas12a system to make DNA breaks in selected markers. We demonstrated its performance by targeting nine genes involved in the cellulase production pathway inM. thermophilavia three transformation rounds, using two selectable markersneoandbar. We obtained the nonuple mutant M9 in which protein productivity and lignocellulase activity were 9.0- and 18.5-fold higher than in the wild type. We conducted a parallel investigation using our transient CRISPR–Cas9 system and found the two technologies were complementary. Together we called themCRISPR–Cas-assistedmarkerrecyclingtechnology (Camr technology).ConclusionsOur study described new approaches (Camr technology) that allow easy and efficient marker recycling and iterative stacking of traits in the same thermophilic fungus strain either, using the newly established CRISPR–Cas12a system or the established CRISPR–Cas9 system. This Camr technology will be a versatile and efficient tool for engineering, theoretically, an unlimited number of genes in fungi. We expect this advance to accelerate biotechnology-oriented engineering processes in fungi.
Aminorex identified in horse urine following consumption of Barbarea vulgaris; a preliminary report
Authors: Maylin George , Fenger Clara , Machin Jacob , Kudrimoti Sucheta , Eisenberg Rodney , Green Jonathan , Tobin Thomas 
Published: December 2019

Abstract
Background
Aminorex, (RS)-5- Phenyl-4,5-dihydro-1,3-oxazol-2-amine, is an amphetamine-like anorectic and in the United States a Drug Enforcement Administration [DEA] Schedule 1 controlled substance. Aminorex in horse urine is usually present as a metabolite of Levamisole, an equine anthelmintic and immune stimulant. Recently, Aminorex identifications have been reported in horse urine with no history or evidence of Levamisole administration. Analysis of the urine samples suggested a botanical source, directing attention to the Brassicaceae plant family, with their contained GlucoBarbarin and Barbarin as possible sources of Aminorex. Since horsepersons face up to a 1 year suspension and a $10,000.00 fine for an Aminorex identification, the existence of natural sources of Aminorex precursors in equine feedstuffs is of importance to both individual horsepersons and the industry worldwide.

Results
Testing the hypothesis that Brassicaceae plants could give rise to Aminorex identifications in equine urine we botanically identified and harvested flowering Kentucky Barbarea vulgaris, (“Yellow Rocket”) in May 2018 in Kentucky and administered the plant orally to two horses. Analysis of post-administration urine samples yielded Aminorex, showing that consumption of Kentucky Barbarea vulgaris can give rise to Aminorex identifications in equine urine.

Conclusions
Aminorex has been identified in post administration urine samples from horses fed freshly harvested flowering Kentucky Barbarea vulgaris, colloquially “Yellow Rocket”. These identifications are consistent with occasional low concentration identifications of Aminorex in equine samples submitted for drug testing. The source of these Aminorex identifications is believed to be the chemically related Barbarin, found as its precursor GlucoBarbarin in Kentucky Barbarea vulgaris and related Brassicaceae plants worldwide.
Prevalence of adjustment disorder among cancer patients, and the reach, effectiveness, cost-utility and budget impact of tailored psychological treatment: study protocol of a randomized controlled trial
Authors: van Beek Florie E. , Wijnhoven Lonneke M. A. , Jansen Femke , Custers José A. E. , Aukema Eline J. , Coupé Veerle M. H. , Cuijpers Pim , van der Lee Marije L. , Lissenberg-Witte Birgit I. , Wijnen Ben , Prins Judith B. , Verdonck-de Leeuw Irma M. 
Published: December 2019

AbstractBackgroundInformation on the prevalence of adjustment disorders among cancer patients and the value of psychological interventions in this group of patients is limited. This study investigates the prevalence of adjustment disorders among cancer patients as well as the reach, effectiveness, cost-utility and budget impact of a tailored psychological intervention.MethodThis study consists of two parts. Part 1 is an observational study among a representative group of mixed cancer patients after cancer treatment on the prevalence of adjustment disorder as well as the uptake (i.e. reach) of psychological treatment. In Part 2, patients diagnosed with an adjustment disorder are invited to participate in a randomized controlled trial. Patients will be randomized to the intervention (access to the tailored psychological intervention) or control group (waitlist period of 6 months). The psychological intervention consists of three modules: one module containing psycho-education (3 sessions, all patients) and two additional modules (maximum of 6 sessions per module) provided as continuum, in case needed. Module 2 and 3 can consist of several evidence-based interventions (e.g. group interventions, mindfulness, eHealth) The primary outcome is psychological distress (HADS). Secondary outcomes are mental adjustment to cancer (MAC) and health-related quality of life (EORTC QLQ-C30). To assess the cost-utility and budget impact, quality of life (EQ-5D-5 L) and costs (iMCQ and iPCQ) will be measured. Measures will be completed at baseline and 3 and 6-months after randomization.DiscussionThis study will provide data of the prevalence of adjustment disorders and the reach, effectiveness, cost-utility and budget impact of a tailored psychological intervention.Trial registrationNetherlands Trial Register identifier:NL7763. Registered on 3 June 2019.