julilili42/papers huggingface dataset:
Recommendations for the packaging and containerizing of bioinformatics software
2019-03-20

<ns4:p>Software Containers are changing the way scientists and researchers develop, deploy and exchange scientific software. They allow labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. However, containers and software packages should be produced under certain rules and standards in order to be reusable, compatible and easy to integrate into pipelines and analysis workflows. Here, we presented a set of recommendations developed by the BioContainers Community to produce standardized bioinformatics packages and containers. These recommendations provide practical guidelines to make bioinformatics software more discoverable, reusable and transparent. They are aimed to guide developers, organisations, journals and funders to increase the quality and sustainability of research software.</ns4:p>
Computer-supported reflective learning: how apps can foster reflection at work
2019-03-20

This paper discusses the potential of ICT to support reflective learning for professionals. We aggregated data collected in 20 field studies with 12 different applications, involving a total of 321 participants. The applications addressed individual reflection as well as collaborative reflection. Such a systematic analysis with different applications used across industry sectors and companies is unique in the current literature on computer-supported reflective learning in the workplace. Primarily, we assessed the reaction to reflection applications and their effectiveness regarding learning, behaviour change, and organisational impact. In addition, we investigated differences with respect to work experience. Results show that users had a positive reaction to the apps and perceived their use to be beneficial for their work by using them. In collaborative reflection an inexperienced employee can benefit from the experiences and perspectives of more experienced (co-)workers. In contrast, individual reflection was more profitable for more experienced workers. Notwithstanding the overall positive results, the actual implementation of reflection applications requires careful adaptation to the specific organisational and situational context, as well as introductory and accompanying measures to assure efficient and beneficial usage of the tools.
Fate of cobalt and nickel in mackinawite during diagenetic pyrite formation
2019-03-20

Abstract As iron sulfide mineral phases are important sedimentary sinks for naturally occurring or contaminant metals, it is important to know the fate of metals during the diagenetic transformation of primary sulfide minerals into more stable phases, such as pyrite (FeS2). Furthermore, the trace metal content of pyrite has been proposed as a marine paleoredox proxy. Given the diverse low-temperature diagenetic formation pathways for pyrite, this use of pyrite requires validation. We, therefore, studied nickel (Ni) and cobalt (Co) incorporation into freshly precipitated mackinawite (FeSm), and after experimental diagenesis to pyrite (FeS2) using S0 as an oxidant at 65 °C. Metal incorporation was quantified on bulk digests using ICP-OES or ICP-AES. Bulk mineralogy was characterized with micro-X-ray diffraction (micro-XRD), documenting the transformation of mackinawite to pyrite. Epoxy grain mounts were made anoxically of mackinawite and pyrite grains. We used synchrotron-based micro-X-ray fluorescence (μXRF) to map the distribution of Co and Ni, as well as to collect multiple energy maps throughout the sulfur (S) K-edge. Iron (Fe) and S K-edge micro-X-ray absorption near edge spectroscopy (μXANES) was used to identify the oxidation state and mineralogy within the experimentally synthesized and diagenetically transformed minerals, and map end-member solid phases within the grain mounts using the multiple energy maps. Metal-free FeSm transformed to pyrite, with residual FeSm detectable. Co- and Ni-containing FeSm also transformed to pyrite, but with multiple techniques detecting FeSm as well as S0, implying less complete transformation to pyrite as compared to metal-free FeSm. These results indicate that Co and Ni may inhibit transformation for FeSm to pyrite, or slow it down. Cobalt concentrations in the solid diminished by 30% during pyrite transformation, indicating that pyrite Co may be a conservative tracer of seawater or porewater Co concentrations. Nickel concentrations increased several-fold after pyrite formation, suggesting that pyrite may have scavenged Ni from the dissolution of primary FeSm grains. Nickel in pyrites thus may not be a reliable proxy for seawater or porewater metal concentrations.
International heterogeneity in the associations of new business models and broadband Internet with music revenue and piracy
2019-03-20

Broadband Internet has fundamentally changed business models in many industries. In the music industry, for instance, old business models were challenged by illegal competitors, and broadband Internet has enabled value creation through new business models. The changes that established business models experienced in the wake of broadband Internet, however, differed vastly across national markets, and these differences are not well understood. We build a conceptual framework and study the extent to which differences in economic and cultural factors are associated with different market outcomes in the wake of the proliferation of broadband Internet. Thus, we compile two unique data sets from the music industry, comprising (1) revenue data for 36 countries and 22 years and (2) piracy data for 47 countries and >2 years. We use a Bayesian multilevel model to explore between-country heterogeneity in the associations between these variables and broadband Internet adoption and business model innovations. Our results show that the negative association between broadband Internet penetration and music revenue is weaker in high-income countries, where income restrictions are less likely to drive demand towards illegitimate piracy services. In terms of cultural factors, we find that a market's response to the introduction of broadband Internet is less negative in countries scoring high on Hofstede's individualism and uncertainty avoidance dimensions. Furthermore, we find that overall revenues only recover after the latest generation of streaming services (e.g., Spotify) has been introduced, and the adoption of these services is associated with lower levels of online music piracy.
The Role of Hours Changes for the Increase in German Earnings Inequality
2019-03-20

Abstract Using data from the German Structure of Earnings Survey (GSES), this paper studies the role of changes in working hours for the increase in male and female earnings inequality between 2001 and 2010. We provide both classic decompositions of the variance of log earnings into the variances of hours, wage rates and their covariance, and decompositions based on reweighting the conditional hours distribution. Depending on the inequality measure considered, our results suggest that between 10 and 30% of the increase in male earnings inequality and 37 to 47% of the increase in female earnings inequality can be explained by changes in working hours. In addition, a large part of the inequality increase can be accounted for by changes in the composition of person and firm characteristics.
Antigen Targets for the Development of Immunotherapies in Leukemia
2019-03-20

Immunotherapeutic approaches, including allogeneic stem cell transplantation and donor lymphocyte infusion, have significantly improved the prognosis of leukemia patients. Further efforts are now focusing on the development of immunotherapies that are able to target leukemic cells more specifically, comprising monoclonal antibodies, chimeric antigen receptor (CAR) T cells, and dendritic cell- or peptide-based vaccination strategies. One main prerequisite for such antigen-specific approaches is the selection of suitable target structures on leukemic cells. In general, the targets for anti-cancer immunotherapies can be divided into two groups: (1) T-cell epitopes relying on the presentation of peptides via human leukocyte antigen (HLA) molecules and (2) surface structures, which are HLA-independently expressed on cancer cells. This review discusses the most promising tumor antigens as well as the underlying discovery and selection strategies for the development of anti-leukemia immunotherapies.
Directing‐Group‐Free C7‐Alkylations of N‐Alkylindoles Mediated by Cationic Zirconium Complexes: Role of Brønsted Acid for Catalytic Manifold
2019-03-20

Abstract Highly position selective alkylations of N‐alkylindoles at C7‐positions have been enabled by cationic zirconium complexes. The strategy provides a straightforward access to install alkyl groups at C7‐positions of indoles without a complex directing group. Mechanistic studies provided support for the importance of Brønsted acids in the catalytic manifold.
Performance of a novel high sensitivity cardiac troponin I assay in asymptomatic hemodialysis patients – evidence for sex-specific differences
2019-03-20

Abstract Background High sensitivity assays for the determination of cardiac troponin I (cTnI) are able to reliably measure cTnI far below the 99th percentile of healthy persons (hs-cTnI) and display sex-specific differences. There is uncertainty regarding the clinical utility of hs-cTnI in asymptomatic hemodialysis (HD) patients and if sex-specific differences also apply in this cohort. Methods In this multicenter study we measured hs-cTnI and sensitive cTnI (s-TnI) concentrations (both on Siemens Centaur) in 215 HD patients from a predialytic sample to determine the prevalence of elevated concentrations above the 99th percentile, the association with baseline characteristics, prognostic accuracy for death, and sex-specific differences. Results Hs-cTnI and s-cTnI concentrations were below the 99th percentile in 93% and 85% of patients with a median concentration of 12 ng/L (interquartile range 7–66) and 19 ng/L (12; 31, p &lt; 0.0001). Hs-cTnI and s-cTnI concentrations were independently associated with age (p &lt; 0.05) and ischemic cardiac disease (p &lt; 0.05), but not with residual renal function. Both hs-cTnI and s-cTnI were predictors of death after median follow-up of 2.6 years with an AUC of 0.733 and 0.744, respectively (both p &lt; 0.0001). Important sex-differences emerged for hs-cTnI, but not for s-cTnI: first, women had significantly lower hs-cTnI concentrations than men (p = 0.03); second, hs-cTnI had significantly higher prognostic accuracy for death in women than for men (AUC 0.824 vs. 0.674, p = 0.04). Conclusions The majority of HD patients have (h)s-cTnI concentrations below the 99th percentile. High normal values are predictive of death. Hs-cTnI allows to elucidate important sex-differences in HD patients with lower concentrations and higher prognostic accuracy in women.
Tunable Superconducting Two-Chip Lumped-Element Resonator
2019-03-20

We have fabricated and investigated a stacked two-chip device, consisting of\\na lumped element resonator on one chip, which is side-coupled to a coplanar\\nwaveguide transmission line on a second chip. We present a full model to\\npredict the behavior of the device dependent on the position of the lumped\\nelement resonator with respect to the transmission line. We identify different\\nregimes, in which the device can be operated. One of them can be used to tune\\nthe coupling between the two subsystems. Another regime enables frequency\\ntunability of the device, without leaving the over-coupled limit for internal\\nquality factors of about , while in the last regime the resonator\\nproperties are insensitive against small variations of the position. Finally,\\nwe have measured the transmission characteristics of the resonator for\\ndifferent positions, demonstrating a good agreement with the model.\\n
Ketamine exhibit antidepressant effect through regulating sleep-wake rhythm and synaptic homeostasis
2019-03-20

A single infusion of ketamine has sustained antidepressant effects and significantly decreases the risk of suicide, and the effects can last up for 7-10 days, but the underlying mechanism is unclear. The mechanism was reviewed underlying the antidepressant effects of ketamine, and found that ketamine may exert its antidepressant effect by regulating sleep/wake cycle, synaptic pruning, molecular pathways, and neural circuits for treatment-refractory depression.Further studies are needed to investigate the genetic, molecular mechanisms underlying the sustained antidepressant effect of ketamine, and the associated imaging findings through in vivo imaging of animals and imaging genetics techniques, explore the optimal time for administration of ketamine, and then provide accurate scientific basis for enhancing its anti-depressant effect. Key words: Ketamine; Sustained antidepressant effect; Homer1a protein; Synaptic pruning; Brain network
Wie sollten Rückmeldungen von quantitativ erfasstem Schülerfeedback (nicht) gestaltet werden?
2019-03-20

Data-based school-improvement depends on the correct and concise extraction of the information from the data through teachers. Such data are usually not provided in raw form, instead graphs are presented which encode transformed and aggregated data. Such graphs generally allow an effective extraction of the relevant information but simultaneously challenge teachers’ statistical literacy. The present study investigates this trade-off by design- based-research with private tutors. We triangulated perceived informativity and validity of interpretation (N = 83) about differently aggregated and encoded feedback on instructional quality (N = 9730) with log files from a feedback web application (N = 232). We found associations between dwelling time (on specific graphics) and the corresponding perceived informativity (positive, monotonous, quadratic) and perceived validity of interpretation (U- shaped, quadratic). Additionally there was evidence for a preference of very simple statistical coefficients and transformations (arithmetic mean, likert scale). The relevance of these results was discussed on the background of the present highly mathematics-oriented sample.
The BCS critical temperature in a weak homogeneous magnetic field
2019-03-21

We show that, within a linear approximation of BCS theory, a weak homogeneous magnetic field lowers the critical temperature by an explicit constant times the field strength, up to higher order terms. This provides a rigorous derivation and generalization of results obtained in the physics literature fromWHH theory of the upper critical magnetic field. A new ingredient in our proof is a rigorous phase approximation to control the effects of the magnetic field.
Population history from the Neolithic to present on the Mediterranean island of Sardinia: An ancient DNA perspective
2019-03-21

Abstract Recent ancient DNA studies of western Eurasia have revealed a dynamic history of admixture, with evidence for major migrations during the Neolithic and Bronze Age. The population of the Mediterranean island of Sardinia has been notable in these studies – Neolithic individuals from mainland Europe cluster more closely with Sardinian individuals than with all other present-day Europeans. The current model to explain this result is that Sardinia received an initial influx of Neolithic ancestry and then remained relatively isolated from expansions in the later Neolithic and Bronze Age that took place in continental Europe. To test this model, we generated genome-wide capture data (approximately 1.2 million variants) for 43 ancient Sardinian individuals spanning the Neolithic through the Bronze Age, including individuals from Sardinia’s Nuragic culture, which is known for the construction of numerous large stone towers throughout the island. We analyze these new samples in the context of previously generated genome-wide ancient DNA data from 972 ancient individuals across western Eurasia and whole-genome sequence data from approximately 1,500 modern individuals from Sardinia. The ancient Sardinian individuals show a strong affinity to western Mediterranean Neolithic populations and we infer a high degree of genetic continuity on the island from the Neolithic (around fifth millennium BCE) through the Nuragic period (second millennium BCE). In particular, during the Bronze Age in Sardinia, we do not find significant levels of the “Steppe” ancestry that was spreading in many other parts of Europe at that time. We also characterize subsequent genetic influx between the Nuragic period and the present. We detect novel, modest signals of admixture between 1,000 BCE and present-day, from ancestry sources in the eastern and northern Mediterranean. Within Sardinia, we confirm that populations from the more geographically isolated mountainous provinces have experienced elevated levels of genetic drift and that northern and southwestern regions of the island received more gene flow from outside Sardinia. Overall, our genetic analysis sheds new light on the origin of Neolithic settlement on Sardinia, reinforces models of genetic continuity on the island, and provides enhanced power to detect post-Bronze-Age gene flow. Together, these findings offer a refined demographic model for future medical genetic studies in Sardinia.
A <em>Galleria mellonella</em> Oral Administration Model to Study Commensal-Induced Innate Immune Responses
2019-03-21

The investigation of the immunogenic potential of commensal bacteria on the host immune system is one essential component when studying intestinal host-microbe interactions. It is well established that different commensals exhibit a different potential to stimulate the host intestinal immune system. Such investigations involve vertebrate animals, especially rodents. Since increasing ethical concerns are linked with experiments involving vertebrates, there is a high demand for invertebrate replacements models. Here, we provide a Galleria mellonella oral administration model using commensal non-pathogenic bacteria and the possible assessment of the immunogenic potential of commensals on the G. mellonella immune system. We demonstrate that G. mellonella is a useful alternative invertebrate replacement model that allows the analysis of commensals with different immunogenic potential such as Bacteroides vulgatus and Escherichia coli. Interestingly, the bacteria exhibited no killing effect on the larvae, which is similar to mammals. The immune responses of G. mellonella were comparable with vertebrate innate immune responses and involve recognition of the bacteria and production of antimicrobial molecules. We propose that G. mellonella was able to restore previous microbiota balance, which is well known from healthy mammalian individuals. Although providing comparable innate immune responses in both G. mellonella and vertebrates, G. mellonella does not harbor an adaptive immune system. Since the investigated components of the innate immune system are evolutionary conserved, the model allows a prescreening and first analysis of bacterial immunogenic properties.
WAT’s up!? – Organ-on-a-chip integrating human mature white adipose tissues for mechanistic research and pharmaceutical applications
2019-03-21

Abstract Obesity and its numerous adverse health consequences have taken on global, pandemic proportions. White adipose tissue (WAT) – a key contributor in many metabolic diseases – contributes about one fourth of a healthy human’s body mass. Despite its significance, many WAT-related pathophysiogical mechanisms in humans are still not understood, largely due to the reliance on non-human animal models. In recent years, Organ-on-a-chip (OoC) platforms have developed into promising alternatives for animal models; these systems integrate engineered human tissues into physiological microenvironment supplied by a vasculature-like microfluidic perfusion. Here, we report the development of a novel OoC that integrates functional mature human WAT. The WAT-on-a-chip is a multilayer device that features tissue chambers tailored specifically for the maintenance of 3D tissues based on human primary adipocytes, with supporting nourishment provided through perfused media channels. The platform’s capability to maintain long-term viability and functionality of WAT was confirmed by real-time monitoring of fatty acid uptake, by quantification of metabolite release into the effluent media as well as by an intact responsiveness to a therapeutic compound. The novel system provides a promising tool for wide-ranging applications in mechanistic research of WAT-related biology, in studying of pathophysiological mechanisms in obesity and diabetes, and in R&amp;D of pharmaceutical industry.
Shaping and polarizing fluorescence emission of a polycrystalline organic semiconductor film by plasmonic nanogratings
2019-03-21

The fluorescence emission properties of hybrid systems consisting of a one-dimensional gold nanowire grating and an evaporated thin film of the small molecule organic semiconductor diindenoperylene (DIP) are investigated. The optical properties of the metallic systems are dominated by their plasmonic resonances. The spectral positions of the resonances are tuned through the width of the single nanowires. Additionally, the plasmonic gratings show a strong polarization dependency due to their one-dimensionality. In contrast, the pure organic system has a polarization-independent emission between 570 and 900 nm when excited with blue light, whereas no photoluminescence can be detected from the bare plasmonic system for the same illumination conditions. For the hybrid system, the intensity, the shape of the emission spectrum, and the polarization of the emission clearly correlate with the optical properties of the plasmonic nanowires. Depending on the optical properties of the plasmonic system, different emission bands of the organic thin film can be enhanced.
Events and States
2019-03-21

Hidden event arguments, as introduced by Davidson (1967), have proven to be of significant benefit in explaining numerous combinatorial and inferential properties of natural language expressions, such that they show up virtually everywhere in present-day assumptions about linguistic structure. The chapter reviews current assumptions concerning the ontological properties of events and states and evaluates different approaches to a narrow or broad understanding of Davidsonian eventualities. A closer look into a variety of stative expressions reveals substantial differences with respect to a series of linguistic diagnostics that point towards deeper ontological differences. Acknowledging these differences leads to a differentiation of the cover notion of states into three separate ontological categories: D-states, K-states, and tropes. Once these three stative categories are disentangled and receive their proper place in the ontological universe, this not only allows the observed linguistic behavior to be accounted for, but it also sharpens our understanding of Davidsonian eventualities.
Complex formation of APP with GABAB receptors links axonal trafficking to amyloidogenic processing
2019-03-22

Abstract GABA B receptors (GBRs) are key regulators of synaptic release but little is known about trafficking mechanisms that control their presynaptic abundance. We now show that sequence-related epitopes in APP, AJAP-1 and PIANP bind with nanomolar affinities to the N-terminal sushi-domain of presynaptic GBRs. Of the three interacting proteins, selectively the genetic loss of APP impaired GBR-mediated presynaptic inhibition and axonal GBR expression. Proteomic and functional analyses revealed that APP associates with JIP and calsyntenin proteins that link the APP/GBR complex in cargo vesicles to the axonal trafficking motor. Complex formation with GBRs stabilizes APP at the cell surface and reduces proteolysis of APP to Aβ, a component of senile plaques in Alzheimer’s disease patients. Thus, APP/GBR complex formation links presynaptic GBR trafficking to Aβ formation. Our findings support that dysfunctional axonal trafficking and reduced GBR expression in Alzheimer’s disease increases Aβ formation.