julilili42/papers huggingface dataset:
COVID‐19 Vaccine‐Associated Cerebral Venous Thrombosis in Germany
2021-07-20

Objective We aimed to estimate the incidence of cerebral sinus and venous thrombosis (CVT) within 1 month from first dose administration and the frequency of vaccine‐induced immune thrombotic thrombocytopenia (VITT) as the underlying mechanism after vaccination with BNT162b2, ChAdOx1, and mRNA‐1273, in Germany. Methods A web‐based questionnaire was e‐mailed to all departments of neurology. We requested a report of cases of CVT occurring within 1 month of a COVID‐19 vaccination. Other cerebral events could also be reported. Incidence rates of CVT were calculated by using official statistics of 9 German states. Results A total of 45 CVT cases were reported. In addition, 9 primary ischemic strokes, 4 primary intracerebral hemorrhages, and 4 other neurological events were recorded. Of the CVT patients, 35 (77.8%) were female, and 36 (80.0%) were younger than 60 years. Fifty‐three events were observed after vaccination with ChAdOx1 (85.5%), 9 after BNT162b2 (14.5%) vaccination, and none after mRNA‐1273 vaccination. After 7,126,434 first vaccine doses, the incidence rate of CVT within 1 month from first dose administration was 0.55 (95% confidence interval [CI] = 0.38–0.78) per 100,000 person‐months (which corresponds to a risk of CVT within the first 31 days of 0.55 per 100,000 individuals) for all vaccines and 1.52 (95% CI = 1.00–2.21) for ChAdOx1 (after 2,320,535 ChAdOx1 first doses). The adjusted incidence rate ratio was 9.68 (95% CI = 3.46–34.98) for ChAdOx1 compared to mRNA‐based vaccines and 3.14 (95% CI = 1.22–10.65) for females compared to non‐females. In 26 of 45 patients with CVT (57.8%), VITT was graded highly probable. Interpretation Given an incidence of 0.02 to 0.15 per 100,000 person‐months for CVT in the general population, these findings point toward a higher risk for CVT after ChAdOx1 vaccination, especially for women. ANN NEUROL 2021;90:627–639
Preparation and Characterization of Electrospun Polylactic Acid (PLA) Fiber Loaded with Birch Bark Triterpene Extract for Wound Dressing
2021-07-20

Abstract Drug-loaded electrospun fibers have attracted increasing attention as a promising wound dressing material due to their capability of preventing from infections and inflammation and maintaining an appropriate environment for wound healing. In this study, polylactic acid (PLA), which is widely used in wound management, was chosen as electrospinnable polymer. A triterpene extract (TE) from the outer bark of birch known for its anti-inflammatory, antiviral, antibacterial, and wound healing effects was chosen to produce TE-loaded PLA electrospun fibers for wound dressing. A binary solvent system of dichloromethane (DCM) and dimethyl sulfoxide (DMSO) was employed, and the ratio of the solvents was optimized for preparing smooth and uniform fibers. The morphology of TE-loaded PLA electrospun fibers was investigated by scanning electron microscopy (SEM). The entrapment of TE in PLA fibers was confirmed by confocal laser scanning microscopy (CLSM). Differential scanning calorimetry (DSC) and X-ray diffraction (XRD) were used to analyze the solid state of TE in PLA fibers. The release behavior of TE was assayed by a shaking flask method for a period of 96 h. The results revealed that TE-loaded electrospun PLA microfibers could be reliably prepared and are promising future candidates in wound therapy.
The extrafoveal preview paradigm as a measure of predictive, active sampling in visual perception
2021-07-20

A key feature of visual processing in humans is the use of saccadic eye movements to look around the environment. Saccades are typically used to bring relevant information, which is glimpsed with extrafoveal vision, into the high-resolution fovea for further processing. With the exception of some unusual circumstances, such as the first fixation when walking into a room, our saccades are mainly guided based on this extrafoveal preview. In contrast, the majority of experimental studies in vision science have investigated "passive" behavioral and neural responses to suddenly appearing and often temporally or spatially unpredictable stimuli. As reviewed here, a growing number of studies have investigated visual processing of objects under more natural viewing conditions in which observers move their eyes to a stationary stimulus, visible previously in extrafoveal vision, during each trial. These studies demonstrate that the extrafoveal preview has a profound influence on visual processing of objects, both for behavior and neural activity. Starting from the preview effect in reading research we follow subsequent developments in vision research more generally and finally argue that taking such evidence seriously leads to a reconceptualization of the nature of human visual perception that incorporates the strong influence of prediction and action on sensory processing. We review theoretical perspectives on visual perception under naturalistic viewing conditions, including theories of active vision, active sensing, and sampling. Although the extrafoveal preview paradigm has already provided useful information about the timing of, and potential mechanisms for, the close interaction of the oculomotor and visual systems while reading and in natural scenes, the findings thus far also raise many new questions for future research.
Natural History of Polymerase Gamma–Related Ataxia
2021-07-20

ABSTRACT Background Mutations in the mitochondrial DNA polymerase gamma are causing a wide phenotypic spectrum including ataxia as one of the most common presentations. Objective The objective of this study was to determine the course of disease of polymerase gamma–related ataxia. Methods In a prospective natural history study, we assessed 24 adult ataxia patients with biallelic polymerase gamma mutations for (1) severity of cerebellar dysfunction using the Scale for the Assessment and Rating of Ataxia score, (2) presence of nonataxia signs using the Inventory of Non‐Ataxia Symptoms, (3) gray‐ and white‐matter changes in brain MRI, and (4) findings in nerve conduction studies. Results Assessment included follow‐up visits up to 11.6 years. The Scale for the Assessment and Rating of Ataxia showed a mean annual increase of 1.02 ± 0.78 points/year. Disease progression was faster in patients with age at onset ≤ 30 years (1.5 Scale for the Assessment and Rating of Ataxia points/year) than with later onset (0.5 points/year); P = 0.008. The Inventory of Non‐Ataxia Symptoms count increased by 0.30 ± 0.4 points/year. External ophthalmoplegia, brain stem oculomotor signs, areflexia, and sensory deficits were the most common nonataxic features. On MRI cerebellar atrophy was mild. T2 signal alterations affected mostly cerebellar white matter, middle cerebellar peduncles, thalamus, brain stem, and occipital and frontal white matter. Within 4 years, progression was primarily observed in the context of repeated epileptic seizures. Nerve conduction studies revealed axonal sensory peripheral neuropathy with mild motor nerve involvement. Exploratory sample size calculation implied 38 patients per arm as sufficient to detect a reduction of progression by 50% in hypothetical interventions within a 1‐year trial. Conclusion The results recommend the Scale for the Assessment and Rating of Ataxia as a primary outcome measure for future interventional trials in polymerase gamma–related ataxia. © 2021 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society
Performance and scaling behavior of bioinformatic applications in virtualization environments to create awareness for the efficient use of compute resources
2021-07-20

The large amount of biological data available in the current times, makes it necessary to use tools and applications based on sophisticated and efficient algorithms, developed in the area of bioinformatics. Further, access to high performance computing resources is necessary, to achieve results in reasonable time. To speed up applications and utilize available compute resources as efficient as possible, software developers make use of parallelization mechanisms, like multithreading. Many of the available tools in bioinformatics offer multithreading capabilities, but more compute power is not always helpful. In this study we investigated the behavior of well-known applications in bioinformatics, regarding their performance in the terms of scaling, different virtual environments and different datasets with our benchmarking tool suite BOOTABLE . The tool suite includes the tools BBMap, Bowtie2, BWA, Velvet, IDBA, SPAdes, Clustal Omega, MAFFT, SINA and GROMACS. In addition we added an application using the machine learning framework TensorFlow. Machine learning is not directly part of bioinformatics but applied to many biological problems, especially in the context of medical images (X-ray photographs). The mentioned tools have been analyzed in two different virtual environments, a virtual machine environment based on the OpenStack cloud software and in a Docker environment. The gained performance values were compared to a bare-metal setup and among each other. The study reveals, that the used virtual environments produce an overhead in the range of seven to twenty-five percent compared to the bare-metal environment. The scaling measurements showed, that some of the analyzed tools do not benefit from using larger amounts of computing resources, whereas others showed an almost linear scaling behavior. The findings of this study have been generalized as far as possible and should help users to find the best amount of resources for their analysis. Further, the results provide valuable information for resource providers to handle their resources as efficiently as possible and raise the user community’s awareness of the efficient usage of computing resources.
How Have Researchers Acknowledged and Controlled for Academic Work Activity When Measuring Medical Students’ Internet Addiction? A Systematic Literature Review
2021-07-20

Internationally, medical students’ Internet Addiction (IA) is widely studied. As medical students use the Internet extensively for work, we asked how researchers control for work-related Internet activity, and the extent to which this influences interpretations of “addiction” rates. A search of PubMed, CINAHL, Web of Science, Scopus, and Google Scholar was conducted on the search phrase of “medical students” and “internet addiction” in March 2020. In total, 98 studies met our criteria, 88 (90%) used Young’s Internet Addiction Test, and the studies’ IA rates ranged widely. Little note was taken of work-related activity, and, when discussed, had little to no impact on the interpretation of Internet “addiction”. Studies seldom accounted for work-related activities, researcher bias appears to influence their position, “usage” appears conflated with “addiction”, and correlations between “addiction” and negative behaviours are frequently confused with one-way causation. In spite of IA’s not being officially recognised, few researchers questioned its validity. While IA may exist among medical students, its measurement is flawed; given the use of the Internet as a crucial medical education tool, there is the risk that conscientious students will be labelled “addicted”, and poor academic performance may be attributed to this “addiction”.
Bacteria Involved in Thiosulfate Reduction Coupled with Anaerobic Ammonium Oxidation in the Critical Zone Groundwater
2021-07-20

Studies are limited on microbial-driven sulfurous species reduction coupled with anaerobic ammonium oxidation (Sammox) in a water environment. In this study, thiosulfate-driven Sammox bacteria from Ningbo Critical Zone Observatory (CZO) groundwater, Zhejiang Province, China were enriched and analyzed. The results showed that all three groundwater samples contained bacteria with sulfur reduction, sulfide oxidation-dependent denitrification, and nitrogen fixation abilities. At the genus level, Arcobacter, Flavobacterium, Hydrogenophaga, Gemmobacter, Pseudomonas, and Methylophilus have higher abundance in three samples. Proteobacteria accounted for a large proportion at the phylum level in all groundwater samples, and are often found in the sulfate reduction coupled with the ammonium oxidation process. Sammox can be performed by synergistic action of bacteria, which may convert ammonium to nitrite and thiosulfate to sulfide. Arcobacter was the dominant bacteria in the medium to remove nitrite and thiosulfate/sulfide. Sammox may also be performed by a single bacterium, belonging to Planctomycetes, Verrucomicrobia, and Chlamydiae superphylum. Overall, bacterial-mediated Sammox exists in the environment of CZO groundwater.
Expansion of the mutational spectrum of BMPER leading to diaphanospondylodysostosis and description of the associated disease process
2021-07-20

Abstract Background Diaphanospondylodysostosis (DSD) is a rare congenital, lethal skeletal disorder caused by recessively inherited mutations in the BMPER gene, which encodes the bone morphogenetic protein‐binding endothelial cell precursor‐derived regulator. The most prominent features of DSD are missing ossification of the axial skeleton, rib abnormalities and thoracic hypoplasia/insufficiency, as well as intralobar nephrogenic rests within the kidneys. Methods We report on the case of a 22‐month‐old patient with DSD where trio‐exome sequencing was performed. Results Genetic testing revealed a homozygous nonsense variant c.1577G&gt;A (p.Trp526*) in the BMPER gene, leading to a premature stop in protein translation. Both parents are asymptomatic carriers for the BMPER variant, which has not been described in the literature before. Conclusions Our findings expand the genotypic and phenotypic spectrum of BMPER variants leading to DSD.
ASO Visual Abstract: Relevance of Preoperative Identification of Adamkiewicz Artery in Posterior Mediastinal Pediatric Tumors
2021-07-20

Injury of the artery of Adamkiewicz (AKA) may lead to spinal cord ischemia and severe neurologic complications.We analyzed the importance of preoperative identification of the AKA by spinal digital subtraction angiography (DSA) for the therapeutic procedure in children with posterior mediastinal tumors (https://doi.org/10.1245/s10434-021-10381-8). Thirty-six children with posterior mediastinal tumors were evaluated for surgery at our clinic.In ten children with left-sided or bilateral tumor localized at vertebral level T8 to L1, the most probable location of the artery, spinal DSA was performed during preoperative workup to assess AKA.The AKA was identified in all cases, and proximity to the tumor was detected in four patients, in three of whom the planned surgery was changed to irradiation.No complications occurred during spinal DSA or surgery.
Organic Matter from Redoximorphic Soils Accelerates and Sustains Microbial Fe(III) Reduction
2021-07-21

Microbial reduction of Fe(III) minerals is a prominent process in redoximorphic soils and is strongly affected by organic matter (OM). We herein determined the rate and extent of microbial reduction of ferrihydrite (Fh) with either adsorbed or coprecipitated OM by <i>Geobacter sulfurreducens</i>. We focused on OM-mediated effects on electron uptake and alterations in Fh crystallinity. The OM was obtained from anoxic soil columns (effluent OM, efOM) and included-unlike water-extractable OM-compounds released by microbial activity under anoxic conditions. We found that organic molecules in efOM had generally no or only very low electron-accepting capacity and were incorporated into the Fh aggregates when coprecipitated with Fh. Compared to OM-free Fh, adsorption of efOM to Fh decelerated the microbial Fe(III) reduction by passivating the Fh surface toward electron uptake. In contrast, coprecipitation of Fh with efOM accelerated the microbial reduction, likely because efOM disrupted the Fh structure, as noted by Mössbauer spectroscopy. Additionally, the adsorbed and coprecipitated efOM resulted in a more sustained Fe(III) reduction, potentially because efOM could have effectively scavenged biogenic Fe(II) and prevented the passivation of the Fh surface by the adsorbed Fe(II). Fe(III)-OM coprecipitates forming at anoxic-oxic interfaces are thus likely readily reducible by Fe(III)-reducing bacteria in redoximorphic soils.
Virotherapy in Germany—Recent Activities in Virus Engineering, Preclinical Development, and Clinical Studies
2021-07-21

Virotherapy research involves the development, exploration, and application of oncolytic viruses that combine direct killing of cancer cells by viral infection, replication, and spread (oncolysis) with indirect killing by induction of anti-tumor immune responses. Oncolytic viruses can also be engineered to genetically deliver therapeutic proteins for direct or indirect cancer cell killing. In this review—as part of the special edition on “State-of-the-Art Viral Vector Gene Therapy in Germany”—the German community of virotherapists provides an overview of their recent research activities that cover endeavors from screening and engineering viruses as oncolytic cancer therapeutics to their clinical translation in investigator-initiated and sponsored multi-center trials. Preclinical research explores multiple viral platforms, including new isolates, serotypes, or fitness mutants, and pursues unique approaches to engineer them towards increased safety, shielded or targeted delivery, selective or enhanced replication, improved immune activation, delivery of therapeutic proteins or RNA, and redirecting antiviral immunity for cancer cell killing. Moreover, several oncolytic virus-based combination therapies are under investigation. Clinical trials in Germany explore the safety and potency of virotherapeutics based on parvo-, vaccinia, herpes, measles, reo-, adeno-, vesicular stomatitis, and coxsackie viruses, including viruses encoding therapeutic proteins or combinations with immune checkpoint inhibitors. These research advances represent exciting vantage points for future endeavors of the German virotherapy community collectively aimed at the implementation of effective virotherapeutics in clinical oncology.
Postictal Psychosis in Epilepsy: A Clinicogenetic Study
2021-07-21

Objective Psychoses affecting people with epilepsy increase disease burden and diminish quality of life. We characterized postictal psychosis, which comprises about one quarter of epilepsy‐related psychoses, and has unknown causation. Methods We conducted a case–control cohort study including patients diagnosed with postictal psychosis, confirmed by psychiatric assessment, with available data regarding epilepsy, treatment, psychiatric history, psychosis profile, and outcomes. After screening 3,288 epilepsy patients, we identified 83 with psychosis; 49 had postictal psychosis. Controls were 98 adults, matched by age and epilepsy type, with no history of psychosis. Logistic regression was used to investigate clinical factors associated with postictal psychosis; univariate associations with a p value &lt; 0.20 were used to build a multivariate model. Polygenic risk scores for schizophrenia were calculated. Results Cases were more likely to have seizure clustering (odds ratio [OR] = 7.59, p &lt; 0.001), seizures with a recollected aura (OR = 2.49, p = 0.013), and a family history of psychiatric disease (OR = 5.17, p = 0.022). Cases showed predominance of right temporal epileptiform discharges (OR = 4.87, p = 0.007). There was no difference in epilepsy duration, neuroimaging findings, or antiseizure treatment between cases and controls. Polygenic risk scores for schizophrenia in an extended cohort of postictal psychosis cases (n = 58) were significantly higher than in 1,366 epilepsy controls ( R 2 = 3%, p = 6 × 10 −3 ), but not significantly different from 945 independent patients with schizophrenia ( R 2 = 0.1% , p = 0.775). Interpretation Postictal psychosis occurs under particular circumstances in people with epilepsy with a heightened genetic predisposition to schizophrenia, illustrating how disease biology (seizures) and trait susceptibility (schizophrenia) may interact to produce particular outcomes (postictal psychosis) in a common disease. ANN NEUROL 2021;90:464–476
LDL-AURIS: a computational model, grounded in error-driven learning, for the comprehension of single spoken words
2021-07-21

A computational model for the comprehension of single spoken words is presented that builds on an earlier model using discriminative learning. Real-valued features are extracted from the speech signal instead of discrete features. Vectors representing word meanings using one-hot encoding are replaced by real-valued semantic vectors. Instead of incremental learning with Rescorla-Wagner updating, we use linear discriminative learning, which captures incremental learning at the limit of experience. These new design features substantially improve prediction accuracy for unseen words, and provide enhanced temporal granularity, enabling the modelling of cohort-like effects. Visualisation with t-SNE shows that the acoustic form space captures phone-like properties. Trained on 9 h of audio from a broadcast news corpus, the model achieves recognition performance that approximates the lower bound of human accuracy in isolated word recognition tasks. LDL-AURIS thus provides a mathematically-simple yet powerful characterisation of the comprehension of single words as found in English spontaneous speech.
The Theory, Practice, and Ethical Challenges of Designing a Diversity-Aware Platform for Social Relations
2021-07-21

Diversity-aware platform design is a paradigm that responds to the ethical\\nchallenges of existing social media platforms. Available platforms have been\\ncriticized for minimizing users' autonomy, marginalizing minorities, and\\nexploiting users' data for profit maximization. This paper presents a design\\nsolution that centers the well-being of users. It presents the theory and\\npractice of designing a diversity-aware platform for social relations. In this\\napproach, the diversity of users is leveraged in a way that allows like-minded\\nindividuals to pursue similar interests or diverse individuals to complement\\neach other in a complex activity. The end users of the envisioned platform are\\nstudents, who participate in the design process. Diversity-aware platform\\ndesign involves numerous steps, of which two are highlighted in this paper: 1)\\ndefining a framework and operationalizing the "diversity" of students, 2)\\ncollecting "diversity" data to build diversity-aware algorithms. The paper\\nfurther reflects on the ethical challenges encountered during the design of a\\ndiversity-aware platform.\\n