julilili42/papers huggingface dataset:
Is Africa prepared for tackling the COVID-19 (SARS-CoV-2) epidemic. Lessons from past outbreaks, ongoing pan-African public health efforts, and implications for the future
2020-02-28

Soon after the novel coronavirus, SARS-CoV-2 (2019-nCoV), was first identified in a cluster of patients with pneumonia (Li et al., 2020), in the Chinese city of Wuhan on 31 December 2019, rapid human to human transmission was anticipated (Hui et al., 2020). The fast pace of transmission is wreaking havoc and stirring media hype and public health concern (Ippolito et al., 2020) globally. When the World Health Organization (WHO) declared the disease, (now officially named COVID-19) a Public Health Emergency of International Concern (PHEIC) on 31st January 2020 (WHO, 2020a), the Director General Dr Tedros Ghebreyesus justified the decision by stating that WHOs greatest concern was the potential for the virus to spread to countries with weaker health systems. Repeated outbreaks of other preventable emerging and re-emerging infectious diseases with epidemic potential have taken their toll on the health systems of many African countries. The devastating 2014–2016 Ebola Virus Epidemic (WHO, 2020b) in West Africa, demonstrated how ill-prepared the affected countries were to rapidly identify the infection and halt transmission (WHO, 2020d, Largent, 2016, Hoffman and Silverberg, 2018, Omoleke et al., 2016). Similarly, the smoldering remnants of the 2018–19 Ebola Virus outbreak in the Democratic Republic of Congo, have demonstrated even for health services with considerable experience of dealing with a certain emerging pathogen, geography and sociopolitical instability, can hamper the response (Aruna et al., 2019).
AQDS and Redox-Active NOM Enables Microbial Fe(III)-Mineral Reduction at cm-Scales
2020-02-28

Redox-active organic molecules such as anthraquinone-2,6-disulfonate (AQDS) and natural organic matter (NOM) can act as electron shuttles thus facilitating electron transfer from Fe(III)-reducing bacteria (FeRB) to terminal electron acceptors such as Fe(III) minerals. In this research, we examined the length scale over which this electron shuttling can occur. We present results from agar-solidified experimental incubations, containing either AQDS or NOM, where FeRB were physically separated from ferrihydrite or goethite by 2 cm. Iron speciation and concentration measurements coupled to a diffusion-reaction model highlighted clearly Fe(III) reduction in the presence of electron shuttles, independent of the type of FeRB. Based on our fitted model, the rate of ferrihydrite reduction increased from 0.07 to 0.19 μmol d<sup>-1</sup> with a 10-fold increase in the AQDS concentration, highlighting a dependence of the reduction rate on the electron-shuttle concentration. To capture the kinetics of Fe(II) production, the effective AQDS diffusion coefficient had to be increased by a factor of 9.4. Thus, we postulate that the 2 cm electron transfer was enabled by a combination of AQDS molecular diffusion and an electron hopping contribution from reduced to oxidized AQDS molecules. Our results demonstrate that AQDS and NOM can drive microbial Fe(III) reduction across 2 cm distances and shed light on the electron transfer process in natural anoxic environments.
Binding and electronic level alignment of π-conjugated systems on metals
2020-02-28

We review the binding and energy level alignment of π-conjugated systems on metals, a field which during the last two decades has seen tremendous progress both in terms of experimental characterization as well as in the depth of theoretical understanding. Precise measurements of vertical adsorption distances and the electronic structure together with ab initio calculations have shown that most of the molecular systems have to be considered as intermediate cases between weak physisorption and strong chemisorption. In this regime, the subtle interplay of different effects such as covalent bonding, charge transfer, electrostatic and van der Waals interactions yields a complex situation with different adsorption mechanisms. In order to establish a better understanding of the binding and the electronic level alignment of π-conjugated molecules on metals, we provide an up-to-date overview of the literature, explain the fundamental concepts as well as the experimental techniques and discuss typical case studies. Thereby, we relate the geometric with the electronic structure in a consistent picture and cover the entire range from weak to strong coupling.
Distinct organization of two cortico-cortical feedback pathways
2020-02-28

Abstract Neocortical feedback is critical for processes like attention, prediction, and learning. A mechanistic understanding of its function requires deciphering its cell-type wiring logic. Recent studies revealed a disinhibitory circuit between motor and sensory areas in mice, where feedback preferentially targets vasointestinal peptide-expressing interneurons, in addition to pyramidal cells. It is unknown whether this circuit motif is a general cortico-cortical feedback organizing principle. Combining multiple simultaneous whole-cell recordings with optogenetics we found that in contrast to this wiring rule, feedback between the hierarchically organized visual areas (lateral-medial to V1) preferentially activated somatostatin-expressing interneurons. Functionally, both feedback circuits temporally sharpened feed-forward excitation by eliciting a transient increase followed by a prolonged decrease in pyramidal firing rate under sustained feed-forward input. However, under feed-forward transient input, the motor-sensory feedback facilitated pyramidal cell bursting while visual feedback increased spike time precision. Our findings argue for multiple feedback motifs implementing different dynamic non-linear operations.
Mass spectrometry-based identification of a B-cell maturation antigen-derived T-cell epitope for antigen-specific immunotherapy of multiple myeloma
2020-02-28

Abstract The B-cell maturation antigen (BCMA) is currently being evaluated as promising tumor-associated surface antigen for T-cell-based immunotherapy approaches, such as CAR T cells and bispecific antibodies, in multiple myeloma (MM). Cytotoxic T cells bearing BCMA-specific T-cell receptors might further allow targeting HLA-presented antigens derived from the intracellular domain of BCMA. By analyzing a mass spectrometry-acquired immunopeptidome dataset of primary MM samples and MM cell lines for BCMA-derived HLA ligands, we identified the naturally presented HLA-B*18-restricted ligand P(BCMA) B*18 . Additionally, P(BCMA) B*18 was identified on primary CLL samples, thereby expanding the range for possible applications. P(BCMA) B*18 induced multifunctional BCMA-specific cells de novo from naïve CD8 + T cells of healthy volunteers. These T cells exhibited antigen-specific lysis of autologous peptide-loaded cells. Even in the immunosuppressive context of MM, we detected spontaneous memory T-cell responses against P(BCMA) B*18 in patients. By applying CTLA-4 and PD-1 inhibition in vitro we induced multifunctional P(BCMA) B*18 -specific CD8 + T cells in MM patients lacking preexisting BCMA-directed immune responses. Finally, we could show antigen-specific lysis of autologous peptide-loaded target cells and even MM.1S cells naturally presenting P(BCMA) B*18 using patient-derived P(BCMA) B*18 -specific T cells. Hence, this BCMA-derived T-cell epitope represents a promising target for T-cell-based immunotherapy and monitoring following immunotherapy in B-cell malignancy patients.
The role of disc torques in forming resonant planetary systems
2020-02-28

Context. The most accurate method for modelling planetary migration and hence the formation of resonant systems is using hydrodynamical simulations. Usually, the force (torque) acting on a planet is calculated using the forces from the gas disc and the star, while the gas accelerations are computed using the pressure gradient, the star, and the planet’s gravity, ignoring its own gravity. For a non-migrating planet the neglect of the disc gravity results in a consistent torque calculation while for a migrating case it is inconsistent. Aims. We aim to study how much this inconsistent torque calculation can affect the final configuration of a two-planet system. We focus on low-mass planets because most of the multi-planetary systems, discovered by the Kepler survey, have masses around ten Earth masses. Methods. Performing hydrodynamical simulations of planet–disc interaction, we measured the torques on non-migrating and migrating planets for various disc masses as well as density and temperature slopes with and without considering the self-gravity of the disc. Using this data, we found a relation that quantifies the inconsistency, used this relation in an N -body code, and performed an extended parameter study modelling the migration of a planetary system with different planet mass ratios and disc surface densities, to investigate the impact of the torque inconsistency on the architecture of the planetary system. Results. Not considering disc self-gravity produces an artificially larger torque on the migrating planet that can result in tighter planetary systems. The deviation of this torque from the correct value is larger in discs with steeper surface density profiles. Conclusions. In hydrodynamical modelling of multi-planetary systems, it is crucial to account for the torque correction, otherwise the results favour more packed systems. We examine two simple correction methods existing in the literature and show that they properly correct this problem.
Analyzing phonetic data with generalized additive mixed models
2020-02-28

This chapter provides a user's guide to analysing phonetic data with the Generalized Additive Model (GAM). We show how GAMs can be used to capture the different kinds of nonlinear effects and patterns that are ubiquitous in phonetic data. To illustrate how GAMs work, we present analyses of three datasets of Taiwan Mandarin, addressing nonlinearities in time series of experimental response times, in F0 contours, and in the geographic distribution of sociophonetic variation. By building models incrementally, we clarify the kinds of problem that arise at various stages of analysis, and show how these can be addressed within the GAM framework. In our analyses, we also show how variation between individual speakers can be accounted for.
X-ray standing waves reveal lack of OH termination at hydroxylated ZnO(0001) surfaces
2020-02-28

The vertical adsorption distances of the planar conjugated organic molecule 3,4,9,10-perylenetetracarboxylic diimide (PTCDI) on hydroxylated ZnO(0001), determined with the x-ray standing wave technique (XSW), are at variance with adsorption geometries simulated with density functional theory for surface-structure models that consider terminating OH, whereas good agreement is found for PTCDI in direct contact with the topmost Zn layer. The consequential assignment of OH to subsurface sites is supported by additional, independent XSW and energy scanned photoelectron diffraction data and calls for a reconsideration of the prevalent surface models with important implications for the understanding of ZnO(0001) surfaces.
Heteromolecular Bilayers on a Weakly Interacting Substrate: Physisorptive Bonding and Molecular Distortions of Copper–Hexadecafluorophthalocyanine
2020-02-28

Heteromolecular bilayers of π-conjugated organic molecules on metals, considered as model systems for more complex thin film heterostructures, are investigated with respect to their structural and electronic properties. By exploring the influence of the organic-metal interaction strength in bilayer systems, we determine the molecular arrangement in the physisorptive regime for copper-hexadecafluorophthalocyanine (F<sub>16</sub>CuPc) on Au(111) with intermediate layers of 5,7,12,14-pentacenetetrone and perylene-3,4,9,10-tetracarboxylic diimide. Using the X-ray standing wave technique to distinguish the different molecular layers, we show that these two bilayers are ordered following their deposition sequence. Surprisingly, F<sub>16</sub>CuPc as the second layer within the heterostructures exhibits an inverted intramolecular distortion compared to its monolayer structure.
Effects of a dissipative coupling to the momentum of a particle in a double well potential
2020-02-28

Double well potentials offer the possibility of coherent state preparation and therefore constitute important building blocks in the analysis of quantum information and quantum engineering devices. Here we present a study of the coherent tunneling in a parabolic double well potential in presence of different dissipative interactions. Specifically, we investigate the effects of an environmental coupling to the momentum and/or to the position of a particle in the potential. Using the semiclassical approximation to calculate instanton paths in Euclidean time, we find that momentum dissipation enhances the coherent tunnel splitting. In presence of both types of dissipation, the momentum dissipation shifts the critical coupling strength of the dissipative phase transition induced by the position dissipation.
Allogeneic Hematopoietic Stem Cell Transplantation in a Rare Case of Tonsillar Mast Cell Sarcoma
2020-02-28

Mast cell sarcoma comprises a rare aggressive mast cell neoplasia with histological, clinical, and genetic features distinct from other mast cell neoplasm. Until now, prognosis is still poor due to high rates of progression to mast cell leukemia and failure of conventional chemotherapies. Our here presented first report about successful allogeneic hematopoietic stem cell transplantation leading to remission in a case of tonsillar MCS represents a promising potential curative treatment option for this rare and often fatal disease.
A novel Ataxin-3 knock-in mouse model mimics the human SCA3 disease phenotype including neuropathological, behavioral, and transcriptional abnormalities
2020-02-28

Abstract Background Spinocerebellar ataxia type 3 is the most common autosomal dominant inherited ataxia worldwide and is caused by a CAG repeat expansion in the Ataxin-3 gene resulting in a polyQ expansion in the corresponding protein. The disease is characterized by neuropathological (aggregate formation, cell loss), phenotypical (gait instability, body weight reduction), and specific transcriptional changes in affected brain regions. So far, there is no mouse model available representing all the different aspects of the disease, yet highly needed to gain a better understanding of the disease pathomechanism. Methods Here, we characterized a novel Ataxin-3 knock-in mouse model, expressing either a heterozygous or homozygous expansion of 304 CAG/CAAs in the murine Ataxin-3 locus using biochemical, behavioral, and transcriptomic approaches. Further, we compared the transcriptional changes of the knock-in mice to those found in human SCA3 patients, to evaluate the comparability of our model. Results The novel Ataxin-3 knock-in mouse is characterized by the expression of a polyQ-expansion in the murine Ataxin-3 protein, leading to massive aggregate formation, especially in brain regions known to be vulnerable in SCA3 patients, and impairment of Purkinje cells. Along these neuropathological changes, mice showed a reduction in body weight accompanied by gait and balance instability. Transcriptomic analysis of cerebellar tissue revealed age-dependent differential expression, enriched for genes attributed to myelinating oligodendrocytes. Comparing these transcriptional changes with those found in cerebellar tissue of SCA3 patients, we discovered an overlap of differentially expressed genes pointing towards similar gene expression perturbances in several genes linked to myelin sheaths and myelinating oligodendrocytes. Conclusion The novel Ataxin-3 knock-in model shares neuropathological, behavioral, and transcriptomic features with human SCA3 patients and, therefore, represents an ideal model to investigate early-onset developments, therapy studies, or longitudinal biomarker alterations.
Intraspecific variation in land use-related functional traits inPlantago lanceolata
2020-02-28

Abstract Background and aims Intraspecific variation in functional traits is essential for the evolutionary success of organisms. The co-variation between trait variation and environment, as well as between different traits, can help us to understand which ecological factors drive habitat adaptation, and to what extent adaptation may be constrained by trait correlations and trade-offs. In managed grasslands, plants experience a combination of competition, recurrent biomass removal and nutrient pulses. Each of these ecological challenges requires specific plant tolerances, and populations should locally adapt if intraspecific variation exists in these traits. Methods We studied variation in land use-related traits in the common grassland plant Plantago lanceolata . In a common environment, we quantified the competitive ability ( R *), clipping tolerance and responses to a nitrogen pulse of plants from 54 populations with different land use intensities across Germany. Key results We found significant population differentiation in competitive ability but there was little evidence that trait variation was related to land use intensity. There was a positive relationship between competitive ability and clipping tolerance at the population level, indicating a genetic, and possibly functional, link between these two traits. In contrast, clipping tolerance and nitrogen responses were negatively correlated at the levels of plant individuals, indicating a physiological trade-off between plant responses to these two land-use processes. Conclusions Our results show that there is substantial intraspecific variation in some of the key functional traits for plant success in managed grasslands, and that rapid evolution and adaptation is therefore possible in these traits.
Arabic Literature of the North Caucasian Naqshbandiyya in the 19th Century
2020-02-28

Abstract This article analyses the Sufi treatise al-Ādāb al-marḍiyya fī l-ṭarīqa al-naqshbandiyya written by the Daghestanian Naqshbandī shaykh Jamāl al-Dīn al-Ghāzīghumūqī (d. 1866/67), the Sufi master, companion and father-in-law of Imām Shāmil (d. 1871). After providing an outline of the life and activities of Shaykh Jamāl al-Dīn I will examine the concepts, persons, and practices treated in his Ādāb which not only provide valuable insights regarding the mystical orientation of the Sufi shaykh, but the North Caucasian Naqshbandiyya during the anti-Russian jihād movement in the 19th century. My aim is to illustrate that this document indicates no or in a minor degree references to the Khālidiyya branch of the Naqshbandiyya. This leads me to the assumption that in the case of the Daghestanian Naqshbandiyya in the 19th century, we have a premature, i.e. not developed form of the Khālidiyya.
Does anti-acid treatment influence disease progression in SSc-ILD? Data form the German SSc-network
2020-02-28

Background: Gastroesophageal reflux (GER) is common in SSc and thus treatment with anti-acid therapy (AAT) is frequent. An association between GER and SSc-ILD progression has been hypothesized. However, outcomes of AAT on disease progression in SSc-ILD has only sparsely been studied.
Long term outcomes of immunmodulatory drugs in SSc-ILD – data rom the German SSc network
2020-02-28

Background: Data from prospective clinical trials support the use of immunomodulatory therapies (IT) for treatment of SSc-ILD. However, outcomes for SSc-ILD in respect to IT use in large real-life cohorts has only sparsely been reported.
Faculty Opinions recommendation of LINGO1 is a regulatory subunit of large conductance, Ca2+-activated potassium channels.
2020-02-28

LINGO1 is a transmembrane protein that is up-regulated in the cerebellum of patients with Parkinson's disease (PD) and Essential Tremor (ET). Patients with additional copies of the LINGO1 gene also present with tremor. Pharmacological or genetic ablation of large conductance Ca2+-activated K+ (BK) channels also result in tremor and motor disorders. We hypothesized that LINGO1 is a regulatory BK channel subunit. We show that 1) LINGO1 coimmunoprecipitated with BK channels in human brain, 2) coexpression of LINGO1 and BK channels resulted in rapidly inactivating BK currents, and 3) LINGO1 reduced the membrane surface expression of BK channels. These results suggest that LINGO1 is a regulator of BK channels, which causes a "functional knockdown" of these currents and may contribute to the tremor associated with increased LINGO1 levels.Copyright © 2020 the Author(s). Published by PNAS. PMID: 31932443
Molecular surveillance of the Pfmdr1 N86Y allele among Congolese pregnant women with asymptomatic malaria
2020-02-28

<title>Abstract</title> Background: Malaria in pregnancy is associated with considerable morbidity and mortality Regular surveillance of artemisinin−based combination therapy tolerance or resistance molecular makers is vital for effective malaria treatment, control and eradication programmes. P. falciparum multiple drug resistance-1 gene ( Pfmdr1 ) N86Y mutation is associated with reduced susceptibility to lumefantrine . This study assessed the prevalence of Pfmdr1 N86Y in Brazzaville, Republic of Congo. Methods: A total 1001 of P. falciparum− infected blood samples obtained from asymptomatic malaria pregnant women having a normal child delivery at the Madibou Integrated Health Center were analysed. Pfmdr1 N86Y genotyping was conducted using PCR-Restriction fragment length polymorphism (RFLP). Results: The wild type Pfmdr1 N86 allele was predominant (&gt;68 %) in this study whereas a few isolates carrying the either the mutant allele ( Pfmdr1 86Y) alone or both alleles (mixed genotype). The dominance of the wildtype allele ( pfmdr1 N86) indicates the plausible decline P. falciparum susceptibility to lumefantrine. Conclusion: This study gives an update on the prevalence of Pfmdr1 N86Y alleles in Brazzaville, Republic of Congo. It also raises concern on the imminent emergence of resistance against artemether−lumefantrine in this setting. Our study underscores the importance to regular artemether−lumefantrine efficacy monitoring to inform malaria control programme of the Republic of Congo.
Mining Big Data in Education: Affordances and Challenges
2020-03-01

The emergence of big data in educational contexts has led to new data-driven approaches to support informed decision making and efforts to improve educational effectiveness. Digital traces of student behavior promise more scalable and finer-grained understanding and support of learning processes, which were previously too costly to obtain with traditional data sources and methodologies. This synthetic review describes the affordances and applications of microlevel (e.g., clickstream data), mesolevel (e.g., text data), and macrolevel (e.g., institutional data) big data. For instance, clickstream data are often used to operationalize and understand knowledge, cognitive strategies, and behavioral processes in order to personalize and enhance instruction and learning. Corpora of student writing are often analyzed with natural language processing techniques to relate linguistic features to cognitive, social, behavioral, and affective processes. Institutional data are often used to improve student and administrational decision making through course guidance systems and early-warning systems. Furthermore, this chapter outlines current challenges of accessing, analyzing, and using big data. Such challenges include balancing data privacy and protection with data sharing and research, training researchers in educational data science methodologies, and navigating the tensions between explanation and prediction. We argue that addressing these challenges is worthwhile given the potential benefits of mining big data in education.