bluuebunny/crossref_metadata_2025_split huggingface dataset:
Geophysical investigation of road failure the case of the main street of Alue Naga, Banda Aceh, Indonesia
Authors: Syukri M , Taib A M , Fadhli Z , Safitri R 
Published: September 2020

Abstract
A geophysical investigation has been conducted on the road to assess the subsurface soil characteristics. The study investigates the causes of road failure around the body of the damaged roads in the main street of Alue Naga, Syiah Kuala, Banda Aceh to determine the variations of rocks charge ability and resistivity value of the subsurface of the study area. The method employed for this study was 2D Electrical Resistivity and Induced Polarization (IP) method with using Wenner-Schlumberger array. Two profiles covering a distance of 100 meters each were established parallel to the road pavement along the stable and unstable sections of the road. Data were collected along the two profiles using ABEM Terra meter SAS 4000. The observed field data were processed and inverted using 2-D modelling inversion algorithm (RES2DINV Software). The result shows the presence of low resistivity and charge ability value at several parts of both line 1 and line 2. Both lines observed the 0-1.73 msec of charge ability value and <1 ohm.m of resistivity value; those values were interpreted as alluvium. In conclusion, the low resistivity and charge ability value present that the area investigation was a layer of permeable, especially in the central part which was cohesive, and led to the instability and weakness of the load-carrying capacity.
Rapid (FLASH-FLIM) imaging of protoporphyrin IX in a lipid mixture using a CMOS based widefield fluorescence lifetime imaging camera in real time for margin demarcation applications
Authors: Sagoo Kulwinder , Cumberbatch Nathan , Holland Adam , Hungerford Graham 
Published: September 2020

Abstract
The fluorescence from protoporphyrin IX (PpIX) has been employed to characterise cellular activity and assist in the visualisation of tumour cells. Its formation can be induced by 5-aminolevulonic acid (5-ALA) which is metabolised by tumour cells to form PpIX. The PpIX is localised within the cells, rather than spreading into the vascular system. This, plus its photophysics, exhibits potential in photodynamic therapy. Hence its study and the ability to rapidly image its localisation is of importance, especially in the field of fluorescence guided surgery. This has led to investigations using tissue phantoms and widefield intensity imaging. Aggregation or the presence of photoproducts can alter PpIX emission, which has implications using widefield imaging and a broad wavelength range detection. The use of the fluorescence lifetime imaging (FLIM) is therefore advantageous as it can distinguish between the emissive species as they exhibit different fluorescence lifetimes. Here we use PpIX in a construct consisting of lipid mixture (Intralipid), employed to simulate fat content and optical scattering, in a gellan gum matrix. PpIX in intralipid in aqueous solution was injected into the gellan host to form inclusions. The samples are imaged using commercial widefield TCSPC camera based on a sensor chip with 192 × 128 pixels. Each pixel contains both detection and photon timing enabling the Fluorescence Lifetime Acquisition by Simultaneous Histogramming (FLASH). This ‘FLASH-FLIM’ approach enables widefield fluorescence lifetime images, displayed in real time to be acquired, which has potential for use in visualising tumour boundaries.
Influence of surface modification of carbon fiber based on magnetron sputtering technology on mechanical properties of carbon fiber composites
Authors: Yang Li , Xia Hong , Xu Zhenzhen , Lihua Zou , Ni Qingqing 
Published: September 2020

Abstract
To improve the interfacial performance of carbon fiber (CF) and epoxy resin, the surface of CF was modified using magnetron sputtering technology, and a CF epoxy resin (CFER) composite was prepared using injection molding technology. The influence of magnetron sputtering technology on the surface properties of CF was investigated by scanning electron microscopy (SEM), atomic force microscopy (AFM), and dynamic contact angle analysis (DCAA). The influence of the surface modification of the CFs by magnetron sputtering on the mechanical and interfacial properties of CF composites was analyzed by testing the tensile and bending properties of the CFER composites. The results indicated that the surface morphology of CF can be modified by magnetron sputtering, and a nano sized carbon film was deposited on the surface of the CFs. The morphology of the carbon film on the surface of the CFs was different from that on the silicon pellet. The surface roughness of the CF increased after it was modified by magnetron sputtering. The surface wettability of the CFs may be improved by increasing the surface free energy of the fiber owing to the deposition of the carbon film. Tests of the tensile and bending properties of the CFER composites showed that the surface modification of CFs by magnetron sputtering can effectively improve the mechanical properties of the CFER composites, which not only improves the tensile strength and bending strength, but also increases the tensile modulus and bending modulus. The SEM images showed that the interfacial adhesion between the modified CF and the epoxy resin was significantly improved. The stress–strain curves showed that the failure mode of the CFER composite modified by magnetron sputtering CF surface changed, and a stress yield phenomenon was observed.
su(2)

spin s representations via

CP2s

sigma models*
Authors: Goldstein Piotr P , Grundland A Michel , Escobar-Ruiz Adrian M 
Published: September 2020

Abstract
We establish and analyze a new relationship between the matrix functions describing spin fields of a spin s, where

2
s
∈

Z

+

, and

C

P

2
s

two-dimensional Euclidean sigma models. The spin matrices are constructed from the rank-1 Hermitian projectors of the sigma models or from the anti-Hermitian immersion functions of their soliton surfaces in the

su
(
2
s
+
1
)

algebra. We provide a geometric interpretation of this construction. For the spin fields which can be represented as linear combinations of the generalized Pauli matrices, we find the dynamics equation satisfied by their coefficients. This equation is identical to the stationary equation of a two-dimensional Heisenberg model. We show that the same holds for matrices congruent to the generalized Pauli matrices through any coordinate-independent unitary linear transformation. These properties allow for new interpretations of the spins as compositions of more elementary objects. They also open up the possibility of future applications of the sigma models to the situations which depend on spin behaviour, including spintronics, spin glasses and quantum computing.
Electronic properties of one-dimensional pentacene crystals
Authors: Nappi C , Romeo F , Sarnelli E 
Published: September 2020

Abstract
The electronic properties of an infinite row of freestanding, aligned side-by-side, pentacene molecules are derived as a function of the intermolecular overlap integral and the chemical potential shift. We use a semiclassical approximation and a first principles tight binding method to obtain conductance and mobility of this one-dimensional crystal as a function of temperature and gate voltage. For two values of the intermolecular overlap, energy bands show a metallic behavior. For all the other values, a bandgap is present and evolves with the intermolecular overlap following a typical modulation. The magnitude of the scattering parameters estimated by the observed conductivity is coherent with the existing literature values. These findings could be relevant for the implementation of organic-based sensors.
Novel t(1;8)(p31.3;q21.3) NFIA-RUNX1T1 Translocation in an Infant Erythroblastic Sarcoma
Authors: King Rebecca L , Siaghani Parwiz J , Wong Katy , Edlefsen Kerstin , Shane Lisa , Howard Matthew T , Reichard Kaaren K , Mai Ming , Viswanatha David S , Greipp Patricia T , Goble Tony A , Ruiz Maritza , Hara Harneet 
Published: September 2020

Abstract

Objectives
Pure erythroid leukemia (PEL) is exceptionally rare in the pediatric setting. Four pediatric PEL cases with t(1;16)(p31;q24) NFIA-CBFA2T3 were reported previously. We present a case of an infant with PEL presenting with erythroblastic sarcoma and harboring a novel t(1;8)(p31.3;q21.3) NFIA-RUNX1T1 fusion detected by RNA sequencing and conventional karyotype.

Methods
Bone marrow (BM) and abdominal mass biopsies from the patient were evaluated with extensive immunohistochemical, flow cytometric, cytogenetic, and molecular studies.

Results
The patient was a female infant who presented between 2 and 5 months of age with cytopenias and an enlarging abdominal mass. Blasts in the BM and abdominal mass expressed CD71 and CD117 with focal expression of CD43, E-cadherin, epithelial membrane antigen, and hemoglobin A. They were negative for additional myeloid, lymphoid, and nonhematolymphoid markers. These findings were most consistent with PEL and erythroblastic sarcoma. RNA sequencing revealed the novel NFIA-RUNX1T1 fusion.

Conclusions
Along with the previously reported PELs with NFIA-CBFA2T3 fusions, we describe a subset of PELs that occur in children, that frequently display extramedullary disease, and that harbor rearrangements of NFIA with core binding factor genes. We hypothesize that, together, these cases represent a rare but distinct clinicopathologic group of pediatric PELs with recurrent genetic abnormality.
Strengthening Laboratory Diagnostic Capacity to Support Cancer Care in Uganda
Authors: Niyonzima Nixon , Wannume Henry , Kadhumbula Sylivestor , Wasswa Hassan , Osinde Godfrey , Mulumba Yusuf , Tusabe Tobias , Kalungi Samuel , Orem Jackson 
Published: September 2020

Abstract

Objectives
An accurate cancer diagnosis is critical to providing quality care to patients with cancer. We describe the results of a laboratory improvement process that started in 2017 to improve access to cancer diagnostics at the Uganda Cancer Institute (UCI). The overall objective of the project was to build capacity for the provision of quality and timely laboratory diagnostics to support cancer care in Uganda.

Methods
A phased multistep approach was used to improve laboratory capacity, including staff training, additional staff recruitment, equipment overhaul, and optimization of the supply chain.

Results
The program led to the establishment of a pathology laboratory that handled 5,700 tissue diagnoses in 2019. Immunohistochemistry services are now offered routinely. Turnaround time for histopathology has also reduced from an average of 7 to 14 days to 5.4 days. The main clinical laboratory has also increased both the test volume and the test capacity, with the additional establishment of a molecular diagnostics laboratory.

Conclusions
Our project shows a pathway to the improvement of laboratory diagnostic capacity in cancer care centers in sub-Saharan Africa (SSA). Improved laboratory diagnostic capacity is critical to improving cancer care in SSA and more rational use of targeted therapies.
General Practice Patients’ Readiness to be Treated With Brief Intervention to Reduce Alcohol Consumption: A Cross-Sectional Study With Between-Subject Design
Authors: Fankhaenel Thomas , Mueller Anna-Maria , Frese Thomas 
Published: September 2020

Abstract

Aims
To treat excessive alcohol consumption, general practices (GPs) are recommended to use non-directive implementation strategies. Directive implementation, however, may be perceived by general practice patients as something positive because of possibly indicating higher GP engagement and a more consistent treatment. In our study, we aimed to assess the readiness of patients to be treated with BI in the hypothetical event of excessive alcohol consumption either by a GP using non-directive recommendations according to WHO or by a GP using directive instructions. Additionally, we assessed the patients’ dispositional readiness to disclose alcohol-associated personal information, termed alcohol consumption self-disclosure, in order to analyze its influence on their readiness to be treated with brief intervention (BI).

Methods
When consulting their GP, a convenience sample of general practice patients was asked by questionnaire. By means of a between-subject design, they were asked for the readiness to be treated either with non-directive BI or with directive BI. Repeated-measure ANCOVA was used to analyze the main- and interaction effects.

Results
A sample of 442 general practice patients preferred the non-directive BI, F(1, 423) = 5.56, P &lt; 0.05. We found moreover a two-way interaction between implementation and alcohol consumption self-disclosure, F(1, 423) = 18.89, P &lt; 0.001, showing that only patients with low self-disclosure preferred the non-directive BI, t(428) = 3.99, P &lt; 0.001.

Conclusions
Future research should investigate the reasons for the patients’ preference for the non-directive BI and may develop strategies to overcome the possibly low readiness of general practice patients to be treated with BI.
PheWAS-ME: a web-app for interactive exploration of multimorbidity patterns in PheWAS
Authors: Strayer Nick , Shirey-Rice Jana K , Shyr Yu , Denny Joshua C , Pulley Jill M , Xu Yaomin 
Published: September 2020

AbstractSummaryElectronic health records (EHRs) linked with a DNA biobank provide unprecedented opportunities for biomedical research in precision medicine. The Phenome-wide association study (PheWAS) is a widely used technique for the evaluation of relationships between genetic variants and a large collection of clinical phenotypes recorded in EHRs. PheWAS analyses are typically presented as static tables and charts of summary statistics obtained from statistical tests of association between a genetic variant and individual phenotypes. Comorbidities are common and typically lead to complex, multivariate gene–disease association signals that are challenging to interpret. Discovering and interrogating multimorbidity patterns and their influence in PheWAS is difficult and time-consuming. We present PheWAS-ME: an interactive dashboard to visualize individual-level genotype and phenotype data side-by-side with PheWAS analysis results, allowing researchers to explore multimorbidity patterns and their associations with a genetic variant of interest. We expect this application to enrich PheWAS analyses by illuminating clinical multimorbidity patterns present in the data.Availability and implementationA demo PheWAS-ME application is publicly available at https://prod.tbilab.org/phewas_me/. Sample datasets are provided for exploration with the option to upload custom PheWAS results and corresponding individual-level data. Online versions of the appendices are available at https://prod.tbilab.org/phewas_me_info/. The source code is available as an R package on GitHub (https://github.com/tbilab/multimorbidity_explorer).Supplementary informationSupplementary data are available at Bioinformatics online.
Learning graph representations of biochemical networks and its application to enzymatic link prediction
Authors: Jiang Julie , Liu Li-Ping , Hassoun Soha 
Published: September 2020

Abstract

Motivation
The complete characterization of enzymatic activities between molecules remains incomplete, hindering biological engineering and limiting biological discovery. We develop in this work a technique, enzymatic link prediction (ELP), for predicting the likelihood of an enzymatic transformation between two molecules. ELP models enzymatic reactions cataloged in the KEGG database as a graph. ELP is innovative over prior works in using graph embedding to learn molecular representations that capture not only molecular and enzymatic attributes but also graph connectivity.

Results
We explore transductive (test nodes included in the training graph) and inductive (test nodes not part of the training graph) learning models. We show that ELP achieves high AUC when learning node embeddings using both graph connectivity and node attributes. Further, we show that graph embedding improves link prediction by 30% in area under curve over fingerprint-based similarity approaches and by 8% over support vector machines. We compare ELP against rule-based methods. We also evaluate ELP for predicting links in pathway maps and for reconstruction of edges in reaction networks of four common gut microbiota phyla: actinobacteria, bacteroidetes, firmicutes and proteobacteria. To emphasize the importance of graph embedding in the context of biochemical networks, we illustrate how graph embedding can guide visualization.

Availability and implementation
The code and datasets are available through https://github.com/HassounLab/ELP.
Social Policy and State–Community Relationships: Storm over Forest Rights in India
Authors: Sengupta Sohini , Jha Manish K 
Published: September 2020

Abstract
Social Policy is concerned with minimising poverty and inequality through redistribution of goods and services. In the twentieth century, after the Second World War, European parliamentary democracies enlarged its ambit by making social policy an important instrument to create equality setting the benchmark for other countries. For the new independent countries in the global South, such as India, social policy followed different trajectories. In the aftermath of independence, India relied on preventive instruments to address the effects of famine, de-industrialisation and high levels of deprivation. Despite achieving high economic growth and rapid poverty reduction in the following decades, its dependence on targeted poverty reduction programme has remained. Recently, there has been some attempt to replace these strategies by rights-based programmes supported by legal framework advocated by civil society groups. Through a case study of The Scheduled Tribes and Other Traditional Forest Dwellers (Recognition of Forest Rights) Act, 2006 (referred to as FRA 2006), this article analyses the successes and failures in realising the goal of linking welfare provisions with the ideas of social citizenship and democratic rights. The article finds widening gulf in the interests of state actors and local community arising from the compromised interpretation of the social justice vision enshrined in FRA.
BACE inhibition causes rapid, regional, and non-progressive volume reduction in Alzheimer’s disease brain
Authors: Sur Cyrille , Kost James , Scott David , Adamczuk Katarzyna , Fox Nick C , Cummings Jeffrey L , Tariot Pierre N , Aisen Paul S , Vellas Bruno , Voss Tiffini , Mahoney Erin , Mukai Yuki , Kennedy Matthew E , Lines Christopher , Michelson David , Egan Michael F 
Published: September 2020

Abstract
In the phase 3 EPOCH trial (Clinicaltrials.gov; NCT01739348), treatment with the BACE inhibitor verubecestat failed to improve cognition in patients with mild-to-moderate Alzheimer’s disease, but was associated with reduced hippocampal volume after 78 weeks as assessed by MRI. The aims of the present exploratory analyses were to: (i) characterize the effect of verubecestat on brain volume by evaluating the time course of volumetric MRI changes for a variety of brain regions; and (ii) understand the mechanism through which verubecestat might cause hippocampal (and other brain region) volume loss by assessing its relationship to measures of amyloid, neurodegeneration, and cognition. Participants were aged 55–85 years with probable Alzheimer’s disease dementia and a Mini Mental State Examination score ≥15 and ≤26. MRIs were obtained at baseline and at Weeks 13, 26, 52 and 78 of treatment. MRIs were segmented using Freesurfer and analysed using a tensor-based morphometry method. PET amyloid data were obtained with 18F-flutemetamol (Vizamyl®) at baseline and Week 78. Standardized uptake value ratios were generated with subcortical white matter as a reference region. Neurofilament light chain in the CSF was assessed as a biomarker of neurodegeneration. Compared with placebo, verubecestat showed increased MRI brain volume loss at Week 13 with no evidence of additional loss through Week 78. The verubecestat-related volumetric MRI loss occurred predominantly in amyloid-rich brain regions. Correlations between amyloid burden at baseline and verubecestat-related volumetric MRI reductions were not significant (r = 0.05 to 0.26, P-values &gt; 0.27). There were no significant differences between verubecestat and placebo in changes from baseline in CSF levels of neurofilament light chain at Week 78 (increases of 7.2 and 14.6 pg/ml for verubecestat versus 19.7 pg/ml for placebo, P-values ≥ 0.1). There was a moderate correlation between volumetric MRI changes and cognitive decline in all groups including placebo at Week 78 (e.g. r = −0.45 to −0.55, P &lt; 0.001 for whole brain), but the correlations were smaller at Week 13 and significant only for the verubecestat groups (e.g. r = −0.15 and −0.11, P &lt; 0.04 for whole brain). Our results suggest that the verubecestat-associated MRI brain volume loss is not due to generalized, progressive neurodegeneration, but may be mediated by specific effects on BACE-related amyloid processes.
Electrophysiology of the Human Superior Temporal Sulcus during Speech Processing
Authors: Nourski Kirill V , Steinschneider Mitchell , Rhone Ariane E , Kovach Christopher K , Banks Matthew I , Krause Bryan M , Kawasaki Hiroto , Howard Matthew A 
Published: September 2020

AbstractThe superior temporal sulcus (STS) is a crucial hub for speech perception and can be studied with high spatiotemporal resolution using electrodes targeting mesial temporal structures in epilepsy patients. Goals of the current study were to clarify functional distinctions between the upper (STSU) and the lower (STSL) bank, hemispheric asymmetries, and activity during self-initiated speech. Electrophysiologic properties were characterized using semantic categorization and dialog-based tasks. Gamma-band activity and alpha-band suppression were used as complementary measures of STS activation. Gamma responses to auditory stimuli were weaker in STSL compared with STSU and had longer onset latencies. Activity in anterior STS was larger during speaking than listening; the opposite pattern was observed more posteriorly. Opposite hemispheric asymmetries were found for alpha suppression in STSU and STSL. Alpha suppression in the STS emerged earlier than in core auditory cortex, suggesting feedback signaling within the auditory cortical hierarchy. STSL was the only region where gamma responses to words presented in the semantic categorization tasks were larger in subjects with superior task performance. More pronounced alpha suppression was associated with better task performance in Heschl’s gyrus, superior temporal gyrus, and STS. Functional differences between STSU and STSL warrant their separate assessment in future studies.