bluuebunny/crossref_metadata_2025_split huggingface dataset:
Green synthesised‐gold nanoparticles in photothermal therapy of breast cancer
Authors: Yee Foo Yiing , Saw Wen Shang , Periasamy Vengadesh , Chong Wu Yi , Abd Malek Sri Nurestri , Tayyab Saad 
Published: January 2019

In this work, the use of gold nanoparticles (AuNPs), synthesised using Curcuma mangga (CM) extract in photothermal killing of breast cancer (MCF‐7) cells is demonstrated. CM‐AuNPs showed higher photothermal heating efficiency compared to citrate‐AuNPs upon irradiation with a 532 nm laser. In addition, treatment of MCF‐7 cells with CM‐AuNPs coupled with laser irradiation for 120 s was found to significantly reduce (72%) the cell viability compared to about 13%, obtained with citrate‐AuNPs. Results from flow cytometry showed that the CM‐AuNP‐dependent photothermal‐induced MCF‐7 cells death was triggered mainly by apoptosis mechanism. All these results suggested the potential use of CM‐AuNPs as therapeutic agents in cancer therapy.
Delivering blended bioinformatics training in resource-limited settings: a case study on the University of Khartoum H3ABioNet node
Authors: Ahmed Azza E , Awadallah Ayah A , Tagelsir Mawada , Suliman Maram A , Eltigani Atheer , Elsafi Hassan , Hamdelnile Basil D , Mukhtar Mohamed A , Fadlelmola Faisal M 
Published: January 2019

Abstract

Motivation
Delivering high-quality distance-based courses in resource-limited settings is a challenging task. Besides the needed infrastructure and expertise, effective delivery of a bioinformatics course could benefit from hands-on sessions, interactivity and problem-based learning approaches.

Results
In this article, we discuss the challenges and best practices in delivering bioinformatics training in resource-limited settings taking the example of hosting and running a multiple-delivery online course, Introduction to Bioinformatics, that was developed by the H3ABioNet Education and Training working group and delivered in 27 remote classrooms across Africa in 2017. We take the case of the University of Khartoum classrooms. Believing that our local setting is similar to others in less-developed countries, we also reflect upon aspects like classroom environment and recruitment of students to maximize outcomes.
Evaluation of ontology structural metrics based on public repository data
Authors: Franco Manuel , Vivo Juana María , Quesada-Martínez Manuel , Duque-Ramos Astrid , Fernández-Breis Jesualdo Tomás 
Published: January 2019

Abstract
The development and application of biological ontologies have increased significantly in recent years. These ontologies can be retrieved from different repositories, which do not provide much information about quality aspects of the ontologies. In the past years, some ontology structural metrics have been proposed, but their validity as measurement instrument has not been sufficiently studied to date. In this work, we evaluate a set of reproducible and objective ontology structural metrics. Given the lack of standard methods for this purpose, we have applied an evaluation method based on the stability and goodness of the classifications of ontologies produced by each metric on an ontology corpus. The evaluation has been done using ontology repositories as corpora. More concretely, we have used 119 ontologies from the OBO Foundry repository and 78 ontologies from AgroPortal. First, we study the correlations between the metrics. Second, we study whether the clusters for a given metric are stable and have a good structure. The results show that the existing correlations are not biasing the evaluation, there are no metrics generating unstable clusterings and all the metrics evaluated provide at least reasonable clustering structure. Furthermore, our work permits to review and suggest the most reliable ontology structural metrics in terms of stability and goodness of their classifications.
Availability: http://sele.inf.um.es/ontology-metrics
Parental IBD and Long-term Health Outcomes in the Offspring
Authors: Nørgård Bente Mertz , Jølving Line Riis , Larsen Michael Due , Friedman Sonia 
Published: January 2019

Abstract
For decades, the research on reproductive consequences in women with inflammatory bowel disease (IBD) has focused on short-term outcomes, including adverse pregnancy outcomes (eg, abruptio placenta, placenta previa, preeclampsia/eclampsia) and adverse birth outcomes (eg, small for gestational age, preterm birth, and congenital malformations). The long-term health outcomes of the children of parents with IBD have been studied to a much lesser extent, and there is a critical research gap in understanding the influence of parental IBD on long-term outcomes. In this review, we propose the reasons for this lack of evidence and highlight the weakest areas of the research on the impact of parental IBD on offspring health. We will focus on health outcomes in children of parents with IBD from an age of 1 year through childhood, adolescence, and adulthood.
A fully mixed finite element method for the coupling of the Stokes and Darcy–Forchheimer problems
Authors: Almonacid Javier A , Díaz Hugo S , Gatica Gabriel N , Márquez Antonio 
Published: January 2019

Abstract
In this paper we introduce and analyze a fully mixed formulation for the nonlinear problem given by the coupling of the Stokes and Darcy–Forchheimer equations with the Beavers–Joseph–Saffman condition on the interface. This new approach yields non-Hilbert normed spaces and a twofold saddle point structure for the corresponding operator equation, whose continuous and discrete solvabilities are analyzed by means of a suitable abstract theory developed for this purpose. In particular, feasible choices of finite element subspaces include PEERS of the lowest order for the stress of the fluid, Raviart–Thomas of the lowest order for the Darcy velocity, piecewise constants for the pressures and continuous piecewise linear elements for the vorticity. An a priori error estimates and associated rates of convergence are derived, and several numerical results illustrating the good performance of the method are reported.
On Rogers–Shephard Type Inequalities for General Measures
Authors: Alonso-Gutiérrez David , Hernández Cifre María A , Roysdon Michael , Yepes Nicolás Jesús , Zvavitch Artem 
Published: January 2019

Abstract
In this paper we prove a series of Rogers–Shephard type inequalities for convex bodies when dealing with measures on the Euclidean space with either radially decreasing densities or quasi-concave densities attaining their maximum at the origin. Functional versions of classical Rogers–Shephard inequalities are also derived as consequences of our approach.
Multi-centric evaluation of the online MSI platform for the identification of cryptic and rare species of Aspergillus by MALDI-TOF
Authors: Imbert Sébastien , Normand Anne Cécile , Gabriel Frédéric , Cassaing Sophie , Bonnal Christine , Costa Damien , Lachaud Laurence , Hasseine Lilia , Kristensen Lise , Schuttler Christine , Raberin Hélène , Brun Sophie , Hendrickx Marijke , Stubbe Dirk , Piarroux Renaud , Fekkar Arnaud 
Published: January 2019

AbstractThe taxonomy of Aspergillus species has recently been revolutionized with the introduction of cryptic species and section concepts. However, their species-level identification in routine laboratories remains a challenge. The aim of this study was to prospectively assess the identification accuracy of cryptic species of Aspergillus in various laboratories using the mass spectrometry identification (MSI) platform, an independent and freely accessible online mass spectrometry database. Over a 12-month period, when a select set of MSI users identified cryptic species, they were contacted and requested to send the isolates to our laboratory for sequence-based identification. Sequence and MSI identification results were then compared. During the study period, 5108 Aspergillus isolates were identified using MSI including 1477 (28.9%) cryptic species. A total of 245 isolates that corresponded to 56 cryptic species and 13 sections were randomly selected for DNA sequencing confirmation. Agreement between the two methods was 99.6% at the section level and 66.1% at the species level. However, almost all discrepancies (72/83, 86.7%) were misidentifications between closely related cryptic species belonging to the same section. Fifty-one isolates from noncryptic species were also identified, thus yielding 100% and 92.2% agreement at the section and species level, respectively. Although the MSI fungus database is a reliable tool to identify Aspergillus at the section level, the database still requires adjustment to correctly identify rare or cryptic species at the species level. Nevertheless, the application properly differentiated between cryptic and sensu stricto species in the same section, thus alerting on possible specific isolate characteristics.
First detection of the pre-biotic molecule glycolonitrile (HOCH2CN) in the interstellar medium
Authors: Zeng S , Quénard D , Jiménez-Serra I , Martín-Pintado J , Rivilla V M , Testi L , Martín-Doménech R 
Published: January 2019

ABSTRACT
Theories of a pre-RNA world suggest that glycolonitrile (HOCH2CN) is a key species in the process of ribonucleotide assembly, which is considered as a molecular precursor of nucleic acids. In this Letter, we report the first detection of this pre-biotic molecule in the interstellar medium by using ALMA data obtained at frequencies between 86.5 GHz and 266.5 GHz toward the Solar-type protostar IRAS16293–2422 B. A total of 15 unblended transitions of HOCH2CN were identified. Our analysis indicates the presence of a cold (T$\rm _{ex}$ = 24 ± 8 K) and a warm (T$\rm _{ex}$ = 158 ± 38 K) component meaning that this molecule is present in both the inner hot corino and the outer cold envelope of IRAS16293 B. The relative abundance with respect to H2 is (6.5 ± 0.6) × 10−11 and ≥(6 ± 2) × 10−10 for the warm and cold components, respectively. Our chemical modelling seems to underproduce the observed abundance for both the warm and cold component under various values of the cosmic ray ionization rate (ζ). Key gas phase routes for the formation of this molecule might be missing in our chemical network.
Intrinsic and regulated properties of minimally edited trypanosome mRNAs
Authors: Tylec Brianna L , Simpson Rachel M , Kirby Laura E , Chen Runpu , Sun Yijun , Koslowsky Donna J , Read Laurie K 
Published: January 2019

AbstractMost mitochondrial mRNAs in kinetoplastids require extensive uridine insertion/deletion editing to generate translatable open reading frames. Editing is specified by trans-acting gRNAs and involves a complex machinery including basal and accessory factors. Here, we utilize high-throughput sequencing to analyze editing progression in two minimally edited mRNAs that provide a simplified system due their requiring only two gRNAs each for complete editing. We show that CYb and MURF2 mRNAs exhibit barriers to editing progression that differ from those previously identified for pan-edited mRNAs, primarily at initial gRNA usage and gRNA exchange. We demonstrate that mis-edited junctions arise through multiple pathways including mis-alignment of cognate gRNA, incorrect and sometimes promiscuous gRNA utilization and inefficient gRNA anchoring. We then examined the roles of accessory factors RBP16 and MRP1/2 in maintaining edited CYb and MURF2 populations. RBP16 is essential for initiation of CYb and MURF2 editing, as well as MURF2 editing progression. In contrast, MRP1/2 stabilizes both edited mRNA populations, while further promoting progression of MURF2 mRNA editing. We also analyzed the effects of RNA Editing Substrate Binding Complex components, TbRGG2 and GAP1, and show that both proteins modestly impact progression of editing on minimally edited mRNAs, suggesting a novel function for GAP1.
Amygdala and Hypothalamus: Historical Overview With Focus on Aggression
Authors: Gouveia Flavia Venetucci , Hamani Clement , Fonoff Erich Talamoni , Brentani Helena , Alho Eduardo Joaquim Lopes , de Morais Rosa Magaly Campêlo Borba , de Souza Aline Luz , Rigonatti Sérgio Paulo , Martinez Raquel C R 
Published: January 2019

Abstract
Aggressiveness has a high prevalence in psychiatric patients and is a major health problem. Two brain areas involved in the neural network of aggressive behavior are the amygdala and the hypothalamus. While pharmacological treatments are effective in most patients, some do not properly respond to conventional therapies and are considered medically refractory. In this population, surgical procedures (ie, stereotactic lesions and deep brain stimulation) have been performed in an attempt to improve symptomatology and quality of life. Clinical results obtained after surgery are difficult to interpret, and the mechanisms responsible for postoperative reductions in aggressive behavior are unknown. We review the rationale and neurobiological characteristics that may help to explain why functional neurosurgery has been proposed to control aggressive behavior.
Dutch
Authors: Corver Norbert , van Koppen Marjo 
Published: January 2019

AbstractThis chapter discusses ellipsis in Dutch and the dialects of Dutch. It provides detailed information on the major types of ellipsis as they have been presented in Part III of this handbook: gapping and stripping, predicate ellipsis (VP-ellipsis and pseudogapping), Conjunction Reduction and Right-Node Raising, sluicing, fragments, nominal ellipsis, Comparative Deletion, and Null Complement Anaphora. It discusses the main insights from the literature as well as new observations with respect to these constructions. The final section shows that the Dutch dialects display an enormous amount of variation concerning ellipsis constructions. In particular, it examines the variation in NP-ellipsis with possessive, demonstrative, and adjectival remnants and variation with respect to sluicing.
James on Percepts, Concepts, and the Function of Cognition
Authors: O’Shea James R. 
Published: January 2019

Abstract
Central to both James’s earlier psychology and his later philosophical views was a recurring distinction between percepts and concepts. The distinction evolved and remained fundamental to his thinking throughout his career as he sought to come to grips with its fundamental nature and significance. This chapter focuses initially on James’s early attempt to articulate the distinction in his 1885 article “The Function of Cognition.” This will highlight a key problem to which James continued to return throughout his later philosophical work on the nature of our cognition, including in his famous “radical empiricism” and metaphysics of “pure experience” (neutral monism) around the turn of the century. We shall find that James grappled insightfully but ambivalently with the perceptual and conceptual dimensions of the “given” and the “knowledge relation” or “cognitive relation,” as he called it—or what, following Franz Brentano, philosophers would later call our object-directed thought or intentionality more generally.
Analysis of Kneeling by Medical Imaging Shows the Femur Moves Back to the Posterior Rim of the Tibial Plateau, Prompting Review of the Concave-Convex Rule
Authors: Scarvell Jennie M , Hribar Nicola , Galvin Catherine R , Pickering Mark R , Perriman Diana M , Lynch Joseph T , Smith Paul N 
Published: January 2019

Abstract

Background
Physical therapists assess joint movement by observation and palpation. New imaging technologies that enable vision of bones and joints during functional activities can be used to analyze joint kinematics and review traditional assumptions.

Purpose
The purpose was to measure relations between flexion, rotation, and translation at the knee and to validate these visually.

Design
This was a prospective, observational study.

Methods
Twenty-five healthy participants aged &gt;45 years (13 males) knelt from upright kneeling to full flexion with the foot free. Fluoroscopy recorded movement at 30 frames per second of x-ray. A computed tomography scan provided 3-dimensional data, which were registered to the fluoroscopy frames to provide a moving model. Motion in 6 degrees of freedom was analyzed for coupling of movements.

Results
Mean (standard deviation) flexion reached by participants was 142 (6)° in kneeling. Posterior femoral translation was coupled to flexion (r = 0.96). From 90° to 150° flexion, the femur translated posteriorly by 36 (3) mm to finish 23 (3) mm posterior to the center of the tibia at 150° flexion. From 90° to 150° flexion, the femur externally rotated from 8 (6)° to 16 (5)°. Flexion was coupled to rotation (r = 0.47). Abduction was &lt;3° and lateral translation was &lt;3 mm. Visually, the femur appeared to translate posteriorly until the femoral condyles rested on the posterior rim of the tibial plateau with concurrent external rotation so that the popliteal fossa aligned with the posterior margin of the medial tibial plateau.

Limitations
A limitation of the study is that knee flexion can include squat and lunge as well as kneeling.

Conclusion
Deep flexion requires femoral posterior translation and external rotation. These findings invite review of the concave-convex rule as it might apply to manual therapy of the knee.
Stakeholder perceptions of scientific knowledge in policy processes: A Peruvian case-study of forestry policy development
Authors: Ramirez Luisa F , Belcher Brian M 
Published: January 2019

Abstract
There is a need to better understand how scientific knowledge is used in decision-making. This is especially true in the Global South where policy processes often occur under high political uncertainty and where a shift toward multilevel governance and decision-making brings new opportunities and challenges. This study applies knowledge-policy models to analyse a forestry research project that succeeded in influencing national policy-making. We investigate how decisions were made, what factors affected and shaped the policy process, and how scientific knowledge was used. The results highlight the complexity of policy processes and the related challenges in crossing the science-policy interface. Perceptions of scientific knowledge differed greatly among stakeholders, and those perceptions strongly influenced how scientific knowledge was valued and used. The findings suggest a need for researchers to better understand the problem context to help design and implement research that will more effectively inform decision-making.
Effect of Intra-arterial Nimodipine on Cerebral Oxygen Saturation and Systemic Hemodynamic Indices in Patients With Cerebral Vasospasm: A Prospective Cohort Study
Authors: Sriganesh Kamath , Venkataramaiah Sudhir , Palaniswamy Sangeetha R. , Ramalingaiah Arvinda H. 
Published: January 2019

Background:
Intra-arterial nimodipine (IaN) is used in the management of cerebral vasospasm after aneurysmal subarachnoid hemorrhage (aSAH). The impact of IaN therapy on regional cerebral oxygen saturation (rScO2) assessed by near infra-red spectroscopy, and dynamic cardiac indices, is currently unknown. This study assessed the effect of IaN on rScO2 and systemic hemodynamic indices during IaN therapy for cerebral vasospasm after aSAH.

Methods:
This prospective cohort study was conducted in 20 patients over sixteen month period after ethics committee approval and informed consent. Patients with angiographic evidence of vasospasm received IaN 3mg over 30 minutes in the spastic vessels. Data regarding rScO2 heart rate (HR), mean blood pressure (MBP) cardiac index (CI), stroke volume index (SVI), stroke volume variation (SVV), and total peripheral resistance index (TPRI) were collected during IaN treatment. The primary outcome measure was change in rScO2 after IaN therapy.

Results:
There was no significant change from baseline in ipsilateral and contralateral rScO2 after IaN administration (mean difference [MD], 0.2; 95% confidence interval [CI], −2.1 to 1.6; P=0.804, and 1.3; −1.1 to 3.8; P=0.276, respectively). There was a significant decrease in MBP and TPRI (MD, −12.4; 95% CI, −6.6 to −18.2; P<0.001, and −674.3; −374.9 to −973.7; P<0.001, respectively) and increase in SVI and CI (MD, 7.5; 95% CI, 14.4 to 0.6; P=0.035 and 0.7; 0.9 to 0.4; P<0.001, respectively) after IaN therapy. HR and SVV were unchanged.

Conclusions:
IaN for aSAH-related cerebral vasospasm did not improve rScO2 but was associated with significant systemic hemodynamic effects, including a decrease in MBP and TPRI. These hemodynamic changes might offset any potential effects of IaN to improve rScO2.
Effect of Amputation Level on Quality of Life and Subjective Function in Children
Authors: McQuerry Jessica , Gammon Lee , Carpiaux Aaron , Talwalkar Vishwas , Iwinski Henry , Walker Janet , Jacobs Cale A. , Muchow Ryan 
Published: January 2019

Background:
Our aim was to discern whether children with amputations have differences in subjective function based on amputation level. We hypothesized that children with more proximal amputations would report poorer function and quality of life.

Methods:
An IRB-approved, retrospective chart review of patients aged 0 to 21 years old with lower extremity amputations was performed. Demographic information, type of amputation, type of prosthesis, and the Pediatric Outcomes Data Collection Instrument (PODCI) was collected from parents and children (above 10 y old). Patients were divided into 4 groups based on the level of amputation (ankle; transtibial; knee; transfemoral), and PODCI scores were compared between groups. PODCI subscores were also compared between unilateral versus bilateral amputations, high-demand versus low-demand prostheses, and congenital versus acquired amputations.

Results:
We identified 96 patients for analysis (39 ankle, 21 transtibial, 27 knee, and 9 transfemoral amputations). The sports/physical functioning subscale of the PODCI showed the only statistically significant difference between amputation level and outcome with ankle-level amputations reporting higher scores than knee-level amputations (parent: 78.3±16.4 vs. 60.0±25.3, P=0.006; child: 87.4±15.3 vs. 65.4±31.5, P=0.03). Although not significantly different from either the ankle, knee, or transfemoral groups, patients with transtibial amputations reported intermediate scores (parent: 68.5±27.5; child: 78.9±25.5). There were no significant differences among amputation level for PODCI transfers, pain/comfort, global function, or happiness subscales. In subgroup analysis, same-level congenital amputees had similar scores to acquired amputees (P>0.05). When compared with unilateral knee amputations patients, patients with bilateral knee amputations had significantly worse transfer (62.4 vs. 88.3; P=0.02), sports/physical functioning (34.2 vs. 66.2; P=0.01), and global domains (58.4 vs. 80.5; P=0.02).

Conclusions:
Subjective sports and physical functioning of pediatric amputees were significantly worse after knee amputation when compared with ankle-level amputations. Although not statistically significant at all levels, our data suggest a graded decline in sports/physical functioning with higher level amputations. Amputation level did not affect pain, happiness, or basic mobility.

Level of Evidence:
Level III.