bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNA Transcription and Splicing Errors as a Source of Cancer Frameshift Neoantigens for Vaccines
Authors: Shen Luhui , Zhang Jian , Lee HoJoon , Batista Milene Tavares , Johnston Stephen Albert 
Published: October 2019

AbstractThe success of checkpoint inhibitors in cancer therapy is largely attributed to activating the patient’s immune response to their tumor’s neoantigens arising from DNA mutations. This realization has motivated the interest in personal cancer vaccines based on sequencing the patient’s tumor DNA to discover neoantigens. Here we propose an additional, unrecognized source of tumor neoantigens. We show that errors in transcription of microsatellites (MS) and mis-splicing of exons create highly immunogenic frameshift (FS) neoantigens in tumors. The sequence of these FS neoantigens are predictable, allowing creation of a peptide array representing all possible neoantigen FS peptides. This array can be used to detect the antibody response in a patient to the FS peptides. A survey of 5 types of cancers reveals peptides that are personally reactive for each patient. This source of neoantigens and the method to discover them may be useful in developing cancer vaccines.
Selective bacterial colonization processes on polyethylene waste samples in an abandoned landfill site
Authors: Puglisi Edoardo , Romaniello Francesco , Galletti Serena , Boccaleri Enrico , Frache Alberto , Cocconcelli Pier Sandro 
Published: October 2019

AbstractThe microbial colonization of plastic wastes has been extensively studied in marine environments, while studies on aged terrestrial wastes are scarce, and mostly limited to the isolation of plastic-degrading microorganisms. Here we have applied a multidisciplinary approach involving culturomics, next-generation sequencing analyses and fine-scale physico-chemical measurements to characterize plastic wastes retrieved in landfill abandoned for more than 35 years, and to assess the composition of bacterial communities thriving as biofilms on the films’ surfaces. All samples were characterized by different colors but were all of polyethylene; IR and DSC analyses identified different level of degradation, while FT-Raman spectroscopy and X-ray fluorescence further assessed the degradation level and the presence of pigments. Each plastic type harbored distinct bacterial communities from the others, in agreement with the differences highlighted by the physico-chemical analyses. Furthermore, the most degraded polyethylene films were found to host a bacterial community more similar to the surrounding soil as revealed by both α- and β-diversity NGS analyses. This work confirms the novel hypothesis that different polyethylene terrestrial waste samples select for different bacterial communities, and that structure of these communities can be correlated with physico-chemical properties of the plastics, including the degradation degree.
GM2-GM3 gangliosides ratio is dependent on GRP94 through down-regulation of GM2-AP cofactor in brain metastasis cells
Authors: Bedia Carmen , Badia Miriam , Muixí Laia , Levade Thierry , Tauler Romà , Sierra Angels 
Published: October 2019

AbstractGRP94 is an ATP-dependent chaperone able to regulate pro-oncogenic signaling pathways. Previous studies have shown a critical role of GRP94 in brain metastasis (BrM) pathogenesis and progression. In this work, an untargeted lipidomic analysis revealed that some lipid species were altered in GRP94-deficient cells, specially GM2 and GM3 gangliosides. The catalytic pathway of GM2 is affected by the low enzymatic activity of β-Hexosaminidase (HexA), responsible for the hydrolysis of GM2 to GM3. Moreover, a deficiency of the GM2-activator protein (GM2-AP), the cofactor of HexA, is observed without alteration of gene expression, indicating a post-transcriptional alteration of GM2-AP in the GRP94-ablated cells. One plausible explanation of these observations is that GM2-AP is a client of GRP94, resulting in defective GM2 catabolic processing and lysosomal accumulation of GM2 in GRP94-ablated cells. Overall, given the role of gangliosides in cell surface dynamics and signaling, their imbalance might be linked to modifications of cell behaviour acquired in BrM progression. This work indicates that GM2-AP could be an important factor in ganglioside balance maintenance. These findings highlight the relevance of GM3 and GM2 gangliosides in BrM and reveal GM2-AP as a promising diagnosis and therapeutic target in BrM research.
Highly durable and flexible gallium-based oxide conductive-bridging random access memory
Authors: Gan Kai-Jhih , Liu Po-Tsun , Chien Ta-Chun , Ruan Dun-Bao , Sze Simon M. 
Published: October 2019

AbstractThe flexible conductive-bridging random access memory (CBRAM) device using a Cu/TiW/Ga2O3/Pt stack is fabricated on polyimide substrate with low thermal budget process. The CBRAM devices exhibit good memory-resistance characteristics, such as good memory window (>105), low operation voltage, high endurance (>1.4 × 102 cycles), and large retention memory window (>105). The temperature coefficient of resistance in the filament confirms that the conduction mechanism observed in the Ga2O3 layer is similar with the phenomenon of electrochemical metallization (ECM). Moreover, the performance of CBRAM device will not be impacted during the flexibility test. Considering the excellent performance of the CBRAM device fabricated by low-temperature process, it may provide a promising potential for the applications of flexible integrated electronic circuits.
Classification of Articulator Movements and Movement Direction from Sensorimotor Cortex Activity
Authors: Salari E. , Freudenburg Z. V. , Branco M. P. , Aarnoutse E. J. , Vansteensel M. J. , Ramsey N. F. 
Published: October 2019

AbstractFor people suffering from severe paralysis, communication can be difficult or nearly impossible. Technology systems called brain-computer interfaces (BCIs) are being developed to assist these people with communication by using their brain activity to control a computer without any muscle activity. To benefit the development of BCIs that employ neural activity related to speech, we investigated if neural activity patterns related to different articulator movements can be distinguished from each other. We recorded with electrocorticography (ECoG), the neural activity related to different articulator movements in 4 epilepsy patients and classified which articulator participants moved based on the sensorimotor cortex activity patterns. The same was done for different movement directions of a single articulator, the tongue. In both experiments highly accurate classification was obtained, on average 92% for different articulators and 85% for different tongue directions. Furthermore, the data show that only a small part of the sensorimotor cortex is needed for classification (ca. 1 cm2). We show that recordings from small parts of the sensorimotor cortex contain information about different articulator movements which might be used for BCI control. Our results are of interest for BCI systems that aim to decode neural activity related to (actual or attempted) movements from a contained cortical area.
Combined Near-Infrarred Light Transillumination and Direct Digital Radiography Increases Diagnostic In Approximal Caries
Authors: Melo Maria , Pascual Agustin , Camps Isabel , Ata-Ali Fadi , Ata-Ali Javier 
Published: October 2019

AbstractThe objective of this study was to evaluate the clinical ability of Near-Infrared Light-Transillumination (NILT) for approximal dentinal caries detection and to compare with direct digital-radiography (DDR), as well as to determine whether the combination of both techniques improves the diagnostic capacity of the lesions. From 88 patients (over 18 years), 138 posterior teeth (76 molars and 62 premolars), that had approximal caries reached into dentine determined by DDR, were included. Lesion extension and DDR images were scored as follows: D0 = sound surface, D1/D2 = caries restricted to the outer/inner-half of the enamel, and D3/4 = caries restricted to the outer/inner-half of the dentin. Opening of the approximal surface using 0.5 mm-in-diameter diamond-bar was used as gold-standard. The lesion extension was then determined by the following criteria: no dentinal caries (D0/1/2) or dentinal caries (D3/4). Seventy-one lesions were D3 and 67 lesions were D4. Sensitivities of overall/D3/D4 were 98.0/95.7/100.0 (NILT) and 100/100/100 (DDR), respectively. Correlations with gold-standard were 0.92 (NILT) and 0.42 (DDR), respectively. The correlation increased to 0.97 (p = 0.045) on combining NILT and DDR. There was no difference in sensitivity between the methods (p > 0.05); but was differences in the correlation (p < 0.01). It can be concluded that NILT showed sensitivity similar to that of DDR and higher correlation than DDR for approximal dentinal caries detection. Accordingly, it may be used to monitor the progression of caries without exposing the patient to ionizing radiation, this being of particular interest in growing patients and in pregnant women. In this respect, NILT can be an effective diagnostic tool adjunctive to bitewing radiographs in detecting approximal dentinal caries. The combination of NILT and DDR represents an increase in the diagnosis of approximal lesions The proposed diagnostic protocol comprises visual examination, followed by NILT and DDR only if the former technique detects approximal caries.
Liquid biopsy: one cell at a time
Authors: Lim Su Bin , Di Lee Wen , Vasudevan Jyothsna , Lim Wan-Teck , Lim Chwee Teck 
Published: October 2019

AbstractAs an alternative target to surgically resected tissue specimens, liquid biopsy has gained much attention over the past decade. Of the various circulating biomarkers, circulating tumor cells (CTCs) have particularly opened new windows into the metastatic cascade, with their functional, biochemical, and biophysical properties. Given the extreme rarity of intact CTCs and the associated technical challenges, however, analyses have been limited to bulk-cell strategies, missing out on clinically significant sources of information from cellular heterogeneity. With recent technological developments, it is now possible to probe genetic material of CTCs at the single-cell resolution to study spatial and temporal dynamics in circulation. Here, we discuss recent transcriptomic profiling efforts that enabled single-cell characterization of patient-derived CTCs spanning diverse cancer types. We further highlight how expression data of these putative biomarkers have advanced our understanding of metastatic spectrum and provided a basis for the development of CTC-based liquid biopsies to track, monitor, and predict the efficacy of therapy and any emergent resistance.
A retrospective impact analysis of the WannaCry cyberattack on the NHS
Authors: Ghafur S. , Kristensen S. , Honeyford K. , Martin G. , Darzi A. , Aylin P. 
Published: October 2019

AbstractA systematic analysis of Hospital Episodes Statistics (HES) data was done to determine the effects of the 2017 WannaCry attack on the National Health Service (NHS) by identifying the missed appointments, deaths, and fiscal costs attributable to the ransomware attack. The main outcomes measured were: outpatient appointments cancelled, elective and emergency admissions to hospitals, accident and emergency (A&E) attendances, and deaths in A&E. Compared with the baseline, there was no significant difference in the total activity across all trusts during the week of the WannaCry attack. Trusts had 1% more emergency admissions and 1% fewer A&E attendances per day during the WannaCry week compared with baseline. Hospitals directly infected with the ransomware, however, had significantly fewer emergency and elective admissions: a decrease of about 6% in total admissions per infected hospital per day was observed, with 4% fewer emergency admissions and 9% fewer elective admissions. No difference in mortality was noted. The total economic value of the lower activity at the infected trusts during this time was £5.9 m including £4 m in lost inpatient admissions, £0.6 m from lost A&E activity, and £1.3 m from cancelled outpatient appointments. Among hospitals infected with WannaCry ransomware, there was a significant decrease in the number of attendances and admissions, which corresponded to £5.9 m in lost hospital activity. There was no increase in mortality reported, though this is a crude measure of patient harm. Further work is needed to appreciate the impact of a cyberattack or IT failure on care delivery and patient safety.
Engaging the Articulators Enhances Perception of Concordant Visible Speech Movements
Authors: Masapollo Matthew , Guenther Frank H. 
Published: October 2019

PurposeThis study aimed to test whether (and how) somatosensory feedback signals from the vocal tract affect concurrent unimodal visual speech perception.MethodParticipants discriminated pairs of silent visual utterances of vowels under 3 experimental conditions: (a) normal (baseline) and while holding either (b) a bite block or (c) a lip tube in their mouths. To test the specificity of somatosensory–visual interactions during perception, we assessed discrimination of vowel contrasts optically distinguished based on their mandibular (English /ɛ/–/æ/) or labial (English /u/–French /u/) postures. In addition, we assessed perception of each contrast using dynamically articulating videos and static (single-frame) images of each gesture (at vowel midpoint).ResultsEngaging the jaw selectively facilitated perception of the dynamic gestures optically distinct in terms of jaw height, whereas engaging the lips selectively facilitated perception of the dynamic gestures optically distinct in terms of their degree of lip compression and protrusion. Thus, participants perceived visible speech movements in relation to the configuration and shape of their own vocal tract (and possibly their ability to produce covert vowel production–like movements). In contrast, engaging the articulators had no effect when the speaking faces did not move, suggesting that the somatosensory inputs affected perception of time-varying kinematic information rather than changes in target (movement end point) mouth shapes.ConclusionsThese findings suggest that orofacial somatosensory inputs associated with speech production prime premotor and somatosensory brain regions involved in the sensorimotor control of speech, thereby facilitating perception of concordant visible speech movements.Supplemental Materialhttps://doi.org/10.23641/asha.9911846
From grains to pebbles: the influence of size distribution and chemical composition on dust emission properties
Authors: Ysard N. , Koehler M. , Jimenez-Serra I. , Jones A. P. , Verstraete L. 
Published: October 2019

Context. The size and chemical composition of interstellar dust grains are critical in setting the dynamical, physical, and chemical evolution of all the media in which they are present. Thanks to facilities such as the Atacama Large Millimeter/submillimeter Array (ALMA) and, in the future, the Square Kilometer Array (SKA), thermal emission in the (sub)millimetre to centimetre domain has become a very convenient way to trace grain properties.
Aims. Our aim is to understand the influence of the composition and size distribution of dust grains on the shape of their spectral energy distribution (peak position, spectral index) in dense interstellar regions such as molecular clouds, prestellar cores, young stellar objects, and protoplanetary discs.
Methods. Starting from the optical constants defined in The Heterogeneous dust Evolution Model for Interstellar Solids (THEMIS) for amorphous hydrogenated carbon grains and amorphous silicates in addition to water ice, we defined six material mixtures that we believe are representative of the expected dust composition in dense interstellar regions. The optical properties of 0.01 μm to 10 cm grains were then calculated with effective medium and Mie theories. The corresponding spectral energy distributions were subsequently calculated for isolated clouds either externally heated by the standard interstellar radiation field alone or in addition to an internal source.
Results. The three main outcomes of this study are as follows. Firstly, the dust mass absorption coefficient strongly depends on both grain composition and size distribution potentially leading to errors in dust mass estimates by factors up to ~3 and 20, respectively. Secondly, it appears almost impossible to retrieve the grain composition from the (sub)millimetre to centimetre thermal emission shape alone as its spectral index for λ ≳ 3 mm does not depend on dust composition. Thirdly, using the “true” dust opacity spectral index to estimate grain sizes may lead to erroneous findings as the observed spectral index can be highly modified by the dust temperature distribution along the line of sight, which depends on the specific heating source and on the geometry of the studied interstellar region.
Conclusions. Based on the interpretation of only the spectral shape of (sub)millimetre to centimetre observational data, the determination of the dust masses, compositions, and sizes are highly uncertain.
Definition of the Response to Initial Therapy with Radioiodine in Patients with Differentiated Thyroid Carcinoma: Basal or Stimulated Thyroglobulin?
Authors: Rosario Pedro Weslley , Mourão Gabriela Franco , Calsolari Maria Regina 
Published: October 2019

AbstractBasal thyroglobulin (b-Tg) measured with second-generation assay or stimulated Tg (s-Tg) can be used to define the response to therapy of differentiated thyroid carcinoma. However, they do not always define the same category and guidelines do not establish “if” or “when” s-Tg needs to be obtained. We studied 304 patients without clinically apparent disease or disease detected by neck ultrasonography and without anti-Tg antibodies 9–12 months after therapy. Based on b-Tg, 196 patients had an excellent response and 108 had an indeterminate response. Based on s-Tg, a change in category occurred in 10.2% of the patients with an initial excellent response (all to indeterminate response) and in half the patients with an initial indeterminate response (44.4% to excellent response and 5.5% to biochemical incomplete response). One case of recurrence was observed among patients with an initial excellent response but whose response changed to indeterminate after s-Tg, while no disease was detected among those who remained in the initial category; however, this difference was not significant. In patients with an initial indeterminate response, no recurrence was detected among those whose response changed to excellent after s-Tg, while 11.1 and 33.3% of those who remained in the initial category or whose response changed to biochemical incomplete, respectively, had structural disease. This study suggest that, in low- or intermediate-risk patients, s-Tg better defines the response to therapy with 131I when it is classified as indeterminate based on b-Tg using second-generation assay. However, s-Tg is not necessary when b-Tg defines the response as excellent.
Perspective on Idiopathic Subchondral, Osteochondral, and Chondral Lesions with Emphasis on the Knee
Authors: Fischer Wolfgang 
Published: October 2019

AbstractSubchondral, osteochondral, and chondral lesions of unknown cause are often encountered, especially in the knee joint. These are mainly idiopathic bone marrow edema syndrome, osteochondrosis dissecans, and cartilage delaminations. The literature on these diseases is sparse and often confusing and inconsistent. Because there is little evidence, this article was written as a perspective on these conditions. It offers an overview of the literature with personal comments and opinions based on observations from many years of clinical practice. The main goal is to highlight clinically important features and provide a practical guide for dealing with various magnetic resonance imaging findings in everyday work. The article also discusses several terms commonly used in relation to these diseases and their differential diagnoses.
Top-Ten Tips for Imaging the Brachial Plexus with Ultrasound and MRI
Authors: Griffith James F. , Lalam Radhesh Krishna 
Published: October 2019

AbstractWhen it comes to examining the brachial plexus, ultrasound (US) and magnetic resonance imaging (MRI) are complementary investigations. US is well placed for screening most extraforaminal pathologies, whereas MRI is more sensitive and accurate for specific clinical indications. For example, MRI is probably the preferred technique for assessment of trauma because it enables a thorough evaluation of both the intraspinal and extraspinal elements, although US can depict extraforaminal neural injury with a high level of accuracy. Conversely, US is probably the preferred technique for examination of neurologic amyotrophy because a more extensive involvement beyond the brachial plexus is the norm, although MRI is more sensitive than US for evaluating muscle denervation associated with this entity. With this synergy in mind, this review highlights the tips for examining the brachial plexus with US and MRI.
Top-Ten Tips for Dual-Energy CT in MSK Radiology
Authors: Walstra Frances E. , Hickle Jonathan , Duggan Peter , Alsharhan Rashid , Murray Nicolas , Mallinson Paul , Munk Peter , Ouellette Hugue 
Published: October 2019

Dual-energy computed tomography (DECT) has the potential to detect musculoskeletal pathology with greater sensitivity than conventional CT alone at no additional radiation dose to the patient. It therefore has the potential to reduce the need for further diagnostic imaging or procedures (e.g., joint aspirations in the case of gout or magnetic resonance imaging to confirm undisplaced fractures).DECT is a well-established technique for the detection of gout arthropathy. Multiple newer applications have shown clinical potential including bone marrow edema detection and metal artifact reduction. Collagen analysis, bone marrow lesion detection, and iodine mapping in CT arthrography are areas of possible future application and development.This article outlines 10 tips on the use of DECT imaging of the musculoskeletal system, explaining the technique and indications with practical suggestions to help guide the radiologist.
Cartilage Imaging in Osteoarthritis
Authors: Alizai Hamza , Walter William , Khodarahmi Iman , Burke Christopher J. 
Published: October 2019

AbstractOsteoarthritis (OA) is the most common joint disease in the United States. The prevalence of OA is rising due to an aging population and increasing rates of obesity. Magnetic resonance imaging (MRI) allows an incomparable noninvasive assessment of all joint structures. Irreversible and progressive degradation of the articular cartilage remains the hallmark feature of OA. To date, attempts at developing disease-modifying drugs or biomechanical interventions for treating OA have proven unsuccessful. MRI-based cartilage imaging techniques have continued to advance, however, and will likely play a central role in the development of these joint preservation methods of the future. In this narrative review, we describe clinical MR image acquisition and assessment of cartilage. We discuss the semiquantitative cartilage scoring methods used in research. Lastly, we review the quantitative MRI techniques that allow assessment of changes in the biochemical composition of cartilage, even before the morphological changes are evident.