julilili42/papers huggingface dataset:
High Frequency of Drug Resistance Mutations in the HBV Genome in ART-Experienced HIV-Coinfected Patients in Southwestern Nigeria
2018-10-01

Background HBV and HIV infections are highly endemic in sub-Saharan Africa and Nigeria while HBV–HIV coinfection is not uncommon. Antiretroviral (ART)-treatment for HIV can affect HBV whereby antiviral resistance mutations in the HBV genome can be selected. Here, we determined the prevalence of resistance mutations among ART-experienced and ART-naive HIV–HBV-coinfected patients in southwestern Nigeria. Methods A total of 81 serum samples from HBV–HIV-coinfected patients who were either ART-naive or received lamivudine (3TC)-containing ART-therapy and HBV-monoinfected patients were analysed. Hepatitis B surface antigen (HBsAg) was detected using ELISA. HBV-positive samples were confirmed by PCR amplification of the surface and polymerase regions. Mutations conferring drug resistance to HBV were analysed by direct sequencing. Phylogenetic analysis was performed to identify the HBV genotype. Results Of the 81 HBsAg-positive samples, 27 had detectable HBV DNA by real-time PCR with mean viral loads of 6.77 log IU/ml. Phylogenetic analyses showed a predominance of HBV genotype E. A high prevalence (22.2%; 6/27) of HBV resistance mutations among ART-experienced HBV–HIV-coinfected patients was detected. However, a relatively high selection rate of resistance mutations in drug-naive HIV–HBV-coinfected (3.7%; 1/27) and in HBV-monoinfected patients, potential drug resistance mutations (7.4%; 2/27) were also observed. HBV polymerase amino acid substitutions found included rtV173L, rtL180M, rtM204V, rtK212R, rtS213T, rtV214A, rtL229V and rtP237A/S. Conclusions Drug resistant mutations were detected frequently in ART-experienced HIV–HBV patients. Well-coordinated antiviral therapy for HIV patients coinfected with HBV should include proper HBV diagnosis and resistance testing to minimize the emergence and spread of antiviral drug resistance.
VAPLI: Novel Visual Abstraction for Protein-Lipid Interactions
2018-10-01

Molecular visualization of molecular dynamics data commonly uses representative surfaces of varying resolution to depict protein molecules while a variety of geometric shapes, from lines to spheres, are often used to represent atoms and inter-atomic bonds. In general, the aim of molecular visualization is focused on efficiently rendering atoms or molecules themselves, while the interaction space between them is less explored. Furthermore, with naive approaches rendering every molecule, the particles overlap so that significant interaction details are obscured due to clutter. Contrary to common approaches, our work focuses on the interaction between lipids and proteins and the area in which this occurs, the - lipid - membrane. To do so, we introduce a novel abstract interaction space for Protein-Lipid Interaction (PLI). The cylindrical abstraction simplifies perception and computation of PLI. It does so by using a local projection of PLI onto a cylindrical geometry. This also addresses the challenge of visualizing complex, time-dependent interactions between these molecules. We propose a fast GPU-based implementation that maps lipid-constituents involved in the interaction onto the abstract protein interaction space. The tool provides interactive rendering of PLI for 336,260 particles over almost 2,000 time-steps. The result is a great simplification of this complex Protein-Lipid Interaction leading to both better perception and new insight for computational biologists.
Personal Recollections of James H. Cone
2018-10-01

On the occasion of James H. Cone’s death in April 2018, his long-time colleague Jürgen Moltmann reflects on the many decades of their theological and personal friendship, from their initial meeting in 1970 to their last get-together in 2015. With deep personal gratitude, Moltmann speaks about the counseling role, which Cone assumed for him in the United States context for many years, and shares important moments in their common effort to develop a liberating theology for all humankind. After Moltmann’s “Personal Recollections of Wolfhart Pannenberg,” published in Theology Today 72:1 (2015): 11–14, this is another valuable testimony of twentieth-century theological history.
Three different ways of training ultrasound student-tutors yield significant and comparable gains in tutee's scanning-skills – Weiterentwicklung curricularer Ultraschallkurs Innere Medizin um Notfallsonografie
2018-10-01

Many medical universities rely these days on trained student tutors to enable faculty-wide undergraduate ultrasound training. However, there is neither consensus on an optimal method nor any developed and agreed standard in the training of these student tutors. Usually internships and courses are employed which both have a specific set of advantages and disadvantages. We conducted a prospective quasi-randomized study to assess the effects of three types of tutor training on the resulting improvement in scanning skills of their tutees.
Implications and methods for co-existing automotive radar and communication systems
2018-10-01

5G mobile communication systems allow small cells with low latencies and high data rates by increasing the carrier frequency. Implemented for vehicle-to-vehicle (V2V) or other vehicle related (V2x) communication, it supports progress in safe automated driving. Spectrum sharing of V2x and radar reduces hardware efforts and costs. Here, we compare radar and communication systems and analyze the impact of their co-existence on a commercial automotive radar system. Besides orthogonal frequency division multiplexing (OFDM), we consider two pulse based communication systems. The analysis is performed using interference models and a sensor model that was validated with real world measurements. We further suggest a sub-Nyquist V2x receiver using noise modulated pulses to mitigate interference on automotive radar systems. Its pulsed shape reduces the interference duration significantly compared to communication systems using OFDM.
Resection of a Petroclival Meningioma via the Endoscope-Assisted Retrosigmoid Approach: 2-D Operative Video
2018-10-01

Abstract We present a case of a petroclival meningioma that was resected through an endoscope-assisted retrosigmoid approach via corridors above and below the facial-vestibulocochlear nerve complex. The patient is a 61-year-old female with complaints of left-sided hypesthesia and neuralgia of the infraorbital and zygomatic region, intermittent periorbital myokymia, and a slight facial palsy (HB II). This 2D video demonstrates the operative technique, anatomical and surgical nuances of the skull base approach and microdissection of the tumor from the critical neurovascular structures. A gross total resection was achieved. The patient’s facial and trigeminal symptoms resolved completely within a few weeks. At 2 year follow up there was no indication of residual or recurrence. In summary, the retrosigmoid approach with endoscopic assistance is an important and powerful tool in the armamentarium for the microsurgical management of meningiomas of the lateroventral skullbase of the posterior fossa. The link to the video can be found at: https://youtu.be/Px4XIRDoALc.
Concentric Circles and Spiral Configurations for Large Correlator Arrays in Radio Astronomy
2018-10-01

Abstract Aperture synthesis arrays are commonly used in radio astronomy to take images of radio point sources, with the planned Square Kilometre Array (SKA) being the most common example. One approach to enhancing the quality of the images is to optimize an antenna array configuration in a possible SKA implementation. An ideal arrangement must ensure optimal configurations to capture a clear image by either decreasing the sidelobe level (SLL) in the l–m domain or increasing the sampled data in the spatial-frequency domain. In this paper a novel configuration is considered to optimize the array by considering all possible observation situations through the positions of the antenna array elements via a mathematical model that we call geometrical method (GM). To demonstrate its efficiency, the technique is applied to developing an optimal configuration for the elements of the Giant Metrewave Radio Telescope (GMRT). The effect of these changes, particularly in the forms of circular and spiral arrangements, is discussed. It is found that a spiral configuration results in fewer overlapping samples than the number of antennas placed along three arms of the GMRT with fewer than 11% and 27% overlapping samples in the snapshot and 6 hr tracking observations, respectively. Finally, the spiral configuration reduces the first SLL from −13.01 dB, using the arms of the current GMRT configuration, to −15.64 dB.
Hermeneutics of Resistance in Marion’s Phenomenology of Givenness
2018-10-01

Abstract My goal in this paper is to investigate the role of the subject in Jean-Luc Marion’s phenomenology aided by his interpretation of the Kantian categories in ‟Being Given” and ‟In Excess”. I shall relate Marion’s hypothetical saturation of the Kantian categories to the suspension of the I-identity. The inner mechanism of this suspension will be shown to consist in a critical resistance to an excessive intuition that is defined by a failed attempt at the conceptualizing of intuitions. This failure shall manifest the saturated phenomenon as a counter-experience. The critical resistance to an excessive intuition acts as a temporary activity of the subject leading to its role as interpreter inscribed in an infinite hermeneutic. Based on this I argue that Marion’s subject is not destroyed by an excessive intuition but is only called upon to investigate a phenomenon from a multitude of perspectives. I hold this to be of the essence for Marion, as it explains the possibility of interpreting and experiencing the given as a given during the encounter with the given in which both the subject as well as the given become manifest. I shall argue thus that the recourse to Kant further clarifies Marion’s account of a critical, resistant subject. However, this does not mean that I am arguing for Kant’s categories, but that I hold them to have an important explanatory role for Marion’s phenomenology.
Reliability of Novel Ceramic Encapsulation Materials for Electronic Packaging
2018-10-01

Abstract Enhancements on power electronic systems with reduced chip area and miniaturized passive components are subject of several research activities in academics and industry. To realize such future electronic devices, it is necessary to incorporate wide bandgap semiconductor technology such as silicon carbide and gallium nitride operating at higher temperatures. Therefore, the development of novel materials with high thermal conductivities and stability, withstanding harsh environments up to 300°C is of major interest. Especially, polymeric encapsulation materials have to be improved because of common degradation effects above 175°C. Ceramic (nonpolymeric) materials with thermal conductivities above 5 W/(m·K) already illustrated promising results for the encapsulation of power electronics. The present work illustrates recent developments and improvements on novel ceramic encapsulation materials, which finally avoid critical interactions with the chip surface. Furthermore, advances in reliability will be discussed in terms of passed high-temperature reverse bias and humidity tests correlated with relevant material properties.
Comment on Dumoulin FL et al. Full-thickness resection with an over-the-scope device: possible translocation of adenoma tissue in a case of an incomplete resection at the appendix
2018-10-01

Letter to: Full-thickness resection with an over-the-scope device: possible translocation of adenoma tissue in a case of an incomplete resection at the appendixEndosc Int Open 2018; 06(05): E622-E624DOI: 10.1055/a-0589-9850
Multiobjective optimization reveals distinct cancer-testis antigen patterns by primary site and human papilloma virus status in head and neck squamous cell carcinoma
2018-10-01

Background: Most previous vaccination attempts in cancer immunotherapy have been focused on a single antigen. Consequently, the expression of the selected antigen needs to be determined before trial inclusion resulting in a high screening failure rate. The establishment of a multi-antigen vaccine may improve the coverage of potential patients, especially if the selected antigens are semipersonalized for clinical patient subgroups. Methods: Analysis and Visualization of Alteration Data (AVATAR), a novel bioinformatic software tool for multi-objective optimization of large datasets, was used to analyze publicly available datasets of transcriptome data from The Cancer Genome Atlas (TCGA) and a dataset from Gene Expression Omnibus (GSE 40774). Cancer-testis antigens (CTA) were selected as model antigens for multi-objective optimization based on the primary tumor site and HPV-status. Dichotomized data were pooled and edited resulting in a cohort of 865 patients, of which 125 were HPV-positive (HPV+). Primary tumor sites included were oral cavity (n = 208), oropharynx (n = 150) and larynx (n = 208). Results: Selecting 10 CTA genes for the whole cohort results in a coverage of 89.3%. When optimizing gene selections for each primary tumor site, distinct 10-gene-selections are revealed improving the coverage in the respective group markedly. Antigen selections overlap only to a minor degree with the solutions for all patients or other patient groups. Even in predominantly HPV- primary sites such as OC and L, antigen selections are remarkably different from each other. When optimizing for HPV-status, distinct selections were found for optimal coverage in the respective patient group overlapping only in one gene. Conclusions: AVATAR can be used to identify antigen selections with optimal coverage within a specified patient group. A semi-personalized antigen selection based on multi-objective optimization may be a useful strategy to plan trials for antigen-specific vaccination. Legal entity responsible for the study: University Medical Center Ulm. Funding: Deutsche Forschungsgemeinschaft (GRK2254). Disclosure: S. Laban: Advisory board member: AstraZeneca, Merck Sharp & Dohme; Lecture fees: Bristol-Myers Squibb, Merck Serono. G. Völkel, H. Kestler, J. Kraus: Developers of Analysis and Visualization of Alteration Data (AVATAR) software. T.K. Hoffmann: Advisory board member: MSD, Merck Serono. H.-G. Rammensee: Cofounder and shareholder: Immatics, CureVac, Synimmune. P.J. Schuler: Advisory board member: Bristol-Myers Squibb. All other authors have declared no conflicts of interest.
FV 697. Biallelic Mutations in SCYL1 Cause CALFAN-Syndrome (Cholestasis, Acute Liver Failure, and Neurodegeneration), A Congenital Disorder of Intracellular Trafficking with a Variable Neurological Phenotype
2018-10-01

Background and Objectives: Biallelic mutations in SCYL1 were recently identified as the molecular cause of “spinocerebellar ataxia, autosomal recessive 21” within a study of patients with ataxia. SCYL1 is involved in retrograde transport scaffolding for key components of coat protein complex I coats and regulating Golgi morphology. Inborn errors of intracellular trafficking, such as NBAS deficiency, are an emerging group of diseases associated with a syndromal multisystemic phenotype mainly involving brain and liver. So far, very little is known regarding the phenotypic spectrum and pathomechanism of SCYL1 deficiency.
P 968. Vitamine B6-Dependent Epilepsy in a 14-Year-Old Girl with Drug-Resistant Seizures and Recurring Status Epilepticus
2018-10-01

Background: Vitamine B6–dependent respectively pyridoxine-dependent epilepsy, in most cases caused by homozygous or compound heterozygous mutations in the ALDH7A1 gene, is a rare neurometabolic disease which usually begins in the first day of life. Only the immediate treatment with pyridoxine can stop the seizures.
Is eSport a ‘real’ sport? Reflections on the spread of virtual competitions
2018-10-02

In recent years, eSport has become widely popular; so much in fact that it could become a part of the Olympic Games in 2024. A huge variety of competitive electronic games exist; among the best-kno...
Estimating Visual Focus of Attention in Multiparty Meetings using Deep Convolutional Neural Networks
2018-10-02

Convolutional neural networks (CNNs) are employed to estimate the visual focus of attention (VFoA), also called gaze direction , in multiparty face-to-face meetings on the basis of multimodal nonverbal behaviors including head pose, direction of the eyeball, and presence/absence of utterance. To reveal the potential of CNNs, we focus on aspects of multimodal and multiparty fusion including individual/group models, early/late fusion, and robustness when using inputs from image-based trackers. In contrast to the individual model that separately targets each person specific to one's seat, the group model aims to jointly estimate the gaze directions of all participants. Experiments confirmed that the group model outperformed the individual model especially in predicting listeners' VFoA when the inputs did not include eyeball directions. This result indicates that the group CNN model can implicitly learn underlying conversation structures, e.g., the listeners' gazes converge on the speaker. When the eyeball direction feature is available, both models outperformed the Bayes models used for comparison. In this case, the individual model was superior to the group model, particularly in estimating the speaker's VFoA. Moreover, it was revealed that in group models, two-stage late fusion, which integrates an individual features first, and multiparty features second, outperformed other structures. Furthermore, our experiment confirmed that image-based tracking can provide a comparable level of performance to that of sensor-based measurements. Overall, the results suggest that the CNN is a promising approach for VFoA estimation.
Sacrificing Cinderella: will giving up Religious Education help to establish a more promising successor?
2018-10-02

This article discusses the recent report of the Commission on Religious Education on “Religion and Worldviews“. While it praises the report for its honest critical evaluation of the current situation of Religious Education in England as well as for the effort of improving this situation by suggesting far-reaching amendments at a systemic level, the article also raises a number of critical questions. These questions refer to the relationship between state and religion, to problems arising from the ill-defined term ‘worldview’, to unresolved problems concerning teacher education in the area of worldviews as well as to the lack of attention to research on Religious Education in the report. Altogether it does not appear necessary to give up the subject of Religious Education in order to improve the situation and not enough good reasons have been presented for switching to a new subject which, in other countries, has in fact created many new problems.
Predicting ADHD Risk from Touch Interaction Data
2018-10-02

This paper presents a novel approach for automatic prediction of risk of ADHD in schoolchildren based on touch interaction data. We performed a study with 129 fourth-grade students solving math problems on a multiple-choice interface to obtain a large dataset of touch trajectories. Using Support Vector Machines, we analyzed the predictive power of such data for ADHD scales. For regression of overall ADHD scores, we achieve a mean squared error of 0.0962 on a four-point scale (R2 = 0.5667). Classification accuracy for increased ADHD risk (upper vs. lower third of collected scores) is 91.1%.
Chronic linaclotide treatment reduces colitis-induced neuroplasticity and reverses persistent bladder dysfunction
2018-10-03

Irritable bowel syndrome (IBS) patients suffer from chronic abdominal pain and extraintestinal comorbidities, including overactive bladder (OAB) and interstitial cystitis/painful bladder syndrome (IC-PBS). Mechanistic understanding of the cause and time course of these comorbid symptoms is lacking, as are clinical treatments. Here, we report that colitis triggers hypersensitivity of colonic afferents, neuroplasticity of spinal cord circuits, and chronic abdominal pain, which persists after inflammation. Subsequently, and in the absence of bladder pathology, colonic hypersensitivity induces persistent hypersensitivity of bladder afferent pathways, resulting in bladder-voiding dysfunction, indicative of OAB/IC-PBS. Daily administration of linaclotide, a guanylate cyclase-C (GC-C) agonist that is restricted to and acts within the gastrointestinal tract, reverses colonic afferent hypersensitivity, reverses neuroplasticity-induced alterations in spinal circuitry, and alleviates chronic abdominal pain in mice. Intriguingly, daily linaclotide administration also reverses persistent bladder afferent hypersensitivity to mechanical and chemical stimuli and restores normal bladder voiding. Linaclotide itself does not inhibit bladder afferents, rather normalization of bladder function by daily linaclotide treatment occurs via indirect inhibition of bladder afferents via reduced nociceptive signaling from the colon. These data support the concepts that cross-organ sensitization underlies the development and maintenance of visceral comorbidities, while pharmaceutical treatments that inhibit colonic afferents may also improve urological symptoms through common sensory pathways.
Cardiac Myxoma and Cerebrovascular Events: A Retrospective Cohort Study
2018-10-03

<b>Background:</b> Cardiac myxoma (CM) is the most frequent, cardiac benign tumor and is associated with enhanced risk for cerebrovascular events (CVE). Although surgical CM excision is the only curative treatment to prevent CVE recurrence, in recent reports conservative treatment with antiplatelet or anticoagulant agents in high-risk patients with CM-related CVE has been discussed. <b>Methods:</b> Case records at the University Hospital of Tübingen between 2005 and 2017 were screened to identify patients with CM-related CVE. Clinical features, brain and cardiac imaging findings, histological reports, applied treatments and long-term neurological outcomes were assessed. <b>Results:</b> 52 patients with CM were identified and among them, 13 patients with transient ischemic attack, ischemic stroke or retinal ischemia were included to the (to our knowledge) largest reported retrospective study of CM-related CVE. In all identified patients, CVE was the first manifestation of CM; 61% suffered ischemic stroke, 23% transient ischemic attack and 15% retinal ischemia. In 46% of the patients, CVE occurred under antiplatelet or anticoagulation treatment, while 23% of the patients developed recurrent CVE under bridging-antithrombotic-therapy prior to CM surgical excision. Prolonged time interval between CVE and CM-surgery was significantly associated with CVE recurrence (<i>p</i> = 0.021). One patient underwent i.v. thrombolysis, followed by thrombectomy, with good post-interventional outcome and no signs of hemorrhagic transformation. <b>Discussion:</b> Our results suggest that antiplatelet or anticoagulation treatment is no alternative to cardiac surgery in patients presenting with CM-related CVE. We found significantly prolonged time-intervals between CVE and CM surgery in patients with recurrent CVE. Therefore, we suggest that the waiting- or bridging-interval with antithrombotic therapy until curative CM excision should be kept as short as possible. Based on our data and review of the literature, we suggest that in patients with CM-related CVE, i.v. thrombolysis and/or endovascular interventions may present safe and efficacious acute treatments.