julilili42/papers huggingface dataset:
Charge carrier mobilities in organic semiconductor crystals based on the spectral overlap
2016-07-02

The prediction of substance‐related charge‐transport properties is important for the tayloring of new materials for organic devices, such as organic solar cells. Assuming a hopping process, the Marcus theory is frequently used to model charge transport. Here another approach, which is already widely used for exciton transport, is adapted to charge transport. It is based on the spectral overlap of the vibrational donor and acceptor spectra. As the Marcus theory it is derived from Fermi's Golden rule, however, it contains less approximations, as the molecular vibrations are treated quantum mechanically. In contrast, the Marcus theory reduces all vibrational degrees of freedom to one and treats its influence classically. The approach is tested on different acenes and predicts most of the experimentally available hole mobilities in these materials within a factor of 2. This represents a significant improvement to values obtained from Marcus theory which is qualitatively correct but frequently overestimates the mobilities by factors up to 10. Furthermore, the charge‐transport properties of two derivatives of perylene bisimide are investigated. © 2016 Wiley Periodicals, Inc.
Is this my voice or yours? The role of emotion and acoustic quality in self-other voice discrimination in schizophrenia
2016-07-03

These results suggest that abnormalities in higher order processes (evaluation of the salience of a speech stimulus) modulate impaired self-other voice discrimination in schizophrenia. Abnormal processing of negative self-generated speech may play a role in the experience of AVH.
Peierls substitution for magnetic Bloch bands
2016-07-03

We consider the one-particle Schrödinger operator in two dimensions with a periodic potential and a strong constant magnetic field perturbed by slowly varying, nonperiodic scalar and vector potentials [math] and [math] for [math] . For each isolated family of magnetic Bloch bands we derive an effective Hamiltonian that is unitarily equivalent to the restriction of the Schrödinger operator to a corresponding almost invariant subspace. At leading order, our effective Hamiltonian can be interpreted as the Peierls substitution Hamiltonian widely used in physics for nonmagnetic Bloch bands. However, while for nonmagnetic Bloch bands the corresponding result is well understood, both on a heuristic and on a rigorous level, for magnetic Bloch bands it is not clear how to even define a Peierls substitution Hamiltonian beyond a formal expression. The source of the difficulty is a topological obstruction: in contrast to the nonmagnetic case, magnetic Bloch bundles are generically not trivializable. As a consequence, Peierls substitution Hamiltonians for magnetic Bloch bands turn out to be pseudodifferential operators acting on sections of nontrivial vector bundles over a two-torus, the reduced Brillouin zone. Part of our contribution is the construction of a suitable Weyl calculus for such pseudodifferential operators. ¶ As an application of our results we construct a new family of canonical one-band Hamiltonians [math] for magnetic Bloch bands with Chern number [math] that generalizes the Hofstadter model [math] for a single nonmagnetic Bloch band. It turns out that [math] is isospectral to [math] for any [math] and all spectra agree with the Hofstadter spectrum depicted in his famous (black and white) butterfly. However, the resulting Chern numbers of subbands, corresponding to Hall conductivities, depend on [math] and [math] , and thus the models lead to different colored butterflies.
Proteome-wide measurement of non-canonical bacterial mistranslation by quantitative mass spectrometry of protein modifications
2016-07-05

Abstract The genetic code is virtually universal in biology and was likely established before the advent of cellular life. The extent to which mistranslation occurs is poorly understood and presents a fundamental question in basic research and production of recombinant proteins. Here we used shotgun proteomics combined with unbiased protein modification analysis to quantitatively analyze in vivo mistranslation in an E. coli strain with a defect in the editing mechanism of leucyl-tRNA synthetase. We detected the misincorporation of a non-proteinogenic amino acid norvaline on 10% of all measured leucine residues under microaerobic conditions and revealed preferential deployment of a tRNA Leu (CAG) isoacceptor during norvaline misincorporation. The strain with the norvalylated proteome demonstrated a substantial reduction in cell fitness under both prolonged aerobic and microaerobic cultivation. Unlike norvaline, isoleucine did not substitute for leucine even under harsh error-prone conditions. Our study introduces shotgun proteomics as a powerful tool in quantitative analysis of mistranslation.
Probing Corticospinal Recruitment Patterns and Functional Synergies with Transcranial Magnetic Stimulation
2016-07-05

Combining IO curves and different pulse waveforms may provide complementary information on neural circuit dynamics and corticospinal recruitment patterns of synergistic muscles and their neuroplastic modulation.
Eradication of methicillin resistantStaphylococcus aureusdetected for the first time in cystic fibrosis: A single center observational study
2016-07-05

Summary Objective To retrospectively identify CF patients with methicillin resistant Staphylococcus aureus (MRSA) and to assess the long‐term success of an eradication scheme introduced in 2002 for all newly colonized patients. Patients All microbiological results from all 505 CF patients followed between 2002 and 2012 were analyzed focusing on the detection of MRSA. Methods Retrospective patient record analysis of MRSA positive CF patients regarding eradication and clinical outcome. Results We identified 57 patients with MRSA, mean age 15.3 years (range: 0.6–36.9, incidence 0.9%/year). Of these, nine patients were lost to follow‐up; seven chronically colonized patients were excluded from the intervention. Eradication was suggested to all patients, 37/41 gave their consent to the following two‐step approach: (i) dual iv antibiotic treatment over 3 weeks, accompanied by hygienic directives and topical therapy for 5 days followed by a 6‐week period with dual oral antibiotic therapy and inhalation with vancomycin. (ii) Each new MRSA detection was treated with 6 weeks inhalation of vancomycin and topical therapy for 5 days. Long‐term eradication was rated by the microbiological status in the third year after first detection. MRSA was eradicated in 31 of 37 patients (84%) whose clinical course was stable (mean FEV1 one year before MRSA 80.4%, 3 years after MRSA 81.0%). Conclusions MRSA colonization mandates complex and expensive hygienic measures which are not well accepted by patients. Therefore, MRSA eradication is desirable. Intensive therapy regimens may be successful in patients with CF and might help to maintain a stable clinical course. Pediatr Pulmonol. 2016;51:1010–1019. © 2016 Wiley Periodicals, Inc.
Using Surface Scans for the Evaluation of Halogen Bonds toward the Side Chains of Aspartate, Asparagine, Glutamate, and Glutamine
2016-07-05

Using halogen-specific Connolly type molecular surfaces, we herein invented a new type of surface-based interaction analysis employed for the study of halogen bonding toward model systems of biologically relevant carboxylates (ASP/GLU) and carboxamides (ASN/GLN). Database mining and statistical assessment of the PDB revealed that such interactions are widely underrepresented at the moment. We observed important distance-dependent adaptions of the binding modes of halobenzenes from a preferential oxygen-directed to a bifurcated interaction geometry of the carboxylate. In addition, halogen···π contacts perpendicular to the nitrogen atom of the carboxamide become increasingly important for the lighter halogens. Our analysis on a MP2/TZVPP level of theory is backed by CCSD(T)/CBS reference calculations. To put the vast interaction energies into perspective, we also performed COSMO-RS calculations of the solvation free energy. Facilitating the visualization of our results mapped onto any binding site of choice, we aim to inspire more design studies showcasing these underrepresented interactions.
Heavy neutrino impact on the triple Higgs coupling
2016-07-05

We present the first calculation of the one-loop corrections to the triple\\nHiggs coupling in the framework of a simplified 3+1 Dirac neutrino model, that\\nis three light neutrinos plus one heavy neutrino embedded in the Standard Model\\n(SM). The triple Higgs coupling is a key parameter of the scalar potential\\ntriggering the electroweak symmetry-breaking mechanism in the SM. The impact of\\nthe heavy neutrino can be as large as to for parameter points\\nallowed by the current experimental constraints depending on the tightness of\\nthe perturbative bound. This can be probed at the high-luminosity LHC, at\\nfuture electron-positron colliders and at the Future Circular Collider in\\nhadron-hadron mode, an envisioned 100 TeV machine. Our calculation, being\\ndone in the mass basis, can be extended to any model using the neutrino portal.\\nIn addition, the effects that we have calculated are expected to be enhanced if\\nadditional heavy fermions with large Yukawa couplings are included, as in\\nlow-scale seesaw mechanisms.\\n
Two-variable Logic with a Between Relation
2016-07-05

We study an extension of FO2[<], first-order logic interpreted in finite words, in which formulas are restricted to use only two variables. We adjoin to this language two-variable atomic formulas that say, 'the letter a appears between positions x and y'. This is, in a sense, the simplest property that is not expressible using only two variables.
Replication of Polymer‐Based Peptide Microarrays by Multi‐Step Transfer
2016-07-05

Abstract Peptide microarrays serve as a high‐throughput tool for the readout of protein–peptide interactions. We present a multi‐step purification of high‐complexity peptide microarrays by transfer to specialized surfaces. Only correctly synthesized peptides are transferred from the synthesis surface to various substrates where they can be immobilized by a variety of different anchor molecules. Here, we demonstrate the transfer to rigid streptavidin, epoxide, gold, and azide surfaces. The reported method reduces the cost of purified peptide array production through the reproduction of one array several times.
Neandertal cannibalism and Neandertal bones used as tools in Northern Europe
2016-07-06

Abstract Almost 150 years after the first identification of Neandertal skeletal material, the cognitive and symbolic abilities of these populations remain a subject of intense debate. We present 99 new Neandertal remains from the Troisième caverne of Goyet (Belgium) dated to 40,500–45,500 calBP. The remains were identified through a multidisciplinary study that combines morphometrics, taphonomy, stable isotopes, radiocarbon dating and genetic analyses. The Goyet Neandertal bones show distinctive anthropogenic modifications, which provides clear evidence for butchery activities as well as four bones having been used for retouching stone tools. In addition to being the first site to have yielded multiple Neandertal bones used as retouchers, Goyet not only provides the first unambiguous evidence of Neandertal cannibalism in Northern Europe, but also highlights considerable diversity in mortuary behaviour among the region’s late Neandertal population in the period immediately preceding their disappearance.
Predicting hand function after hemidisconnection
2016-07-06

Hemidisconnections (i.e. hemispherectomies or hemispherotomies) invariably lead to contralateral hemiparesis. Many patients with a pre-existing hemiparesis, however, experience no deterioration in motor functions, and some can still grasp with their paretic hand after hemidisconnection. The scope of our study was to predict this phenomenon. Hypothesizing that preserved contralateral grasping ability after hemidisconnection can only occur in patients controlling their paretic hands via ipsilateral corticospinal projections already in the preoperative situation, we analysed the asymmetries of the brainstem (by manual magnetic resonance imaging volumetry) and of the structural connectivity of the corticospinal tracts within the brainstem (by magnetic resonance imaging diffusion tractography), assuming that marked hypoplasia or Wallerian degeneration on the lesioned side in patients who can grasp with their paretic hands indicate ipsilateral control. One hundred and two patients who underwent hemidisconnections between 0.8 and 36 years of age were included. Before the operation, contralateral hand function was normal in 3/102 patients, 47/102 patients showed hemiparetic grasping ability and 52/102 patients could not grasp with their paretic hands. After hemidisconnection, 20/102 patients showed a preserved grasping ability, and 5/102 patients began to grasp with their paretic hands only after the operation. All these 25 patients suffered from pre- or perinatal brain lesions. Thirty of 102 patients lost their grasping ability. This group included all seven patients with a post-neonatally acquired or progressive brain lesion who could grasp before the operation, and also all three patients with a preoperatively normal hand function. The remaining 52/102 patients were unable to grasp pre- and postoperatively. On magnetic resonance imaging, the patients with preserved grasping showed significantly more asymmetric brainstem volumes than the patients who lost their grasping ability. Similarly, these patients showed striking asymmetries in the structural connectivity of the corticospinal tracts. In summary, normal preoperative hand function and a post-neonatally acquired or progressive lesion predict a loss of grasping ability after hemidisconnection. A postoperatively preserved grasping ability is possible in hemiparetic patients with pre- or perinatal lesions, and this is highly likely when the brainstem is asymmetric and especially when the structural connectivity of the corticospinal tracts within the brainstem is asymmetric.
In Planta Single-Molecule Pull-Down Reveals Tetrameric Stoichiometry of HD-ZIPIII:LITTLE ZIPPER Complexes
2016-07-06

Abstract Deciphering complex biological processes markedly benefits from approaches that directly assess the underlying biomolecular interactions. Most commonly used approaches to monitor protein-protein interactions typically provide nonquantitative readouts that lack statistical power and do not yield information on the heterogeneity or stoichiometry of protein complexes. Single-molecule pull-down (SiMPull) uses single-molecule fluorescence detection to mitigate these disadvantages and can quantitatively interrogate interactions between proteins and other compounds, such as nucleic acids, small molecule ligands, and lipids. Here, we establish SiMPull in plants using the HOMEODOMAIN LEUCINE ZIPPER III (HD-ZIPIII) and LITTLE ZIPPER (ZPR) interaction as proof-of-principle. Colocalization analysis of fluorophore-tagged HD-ZIPIII and ZPR proteins provides strong statistical evidence of complex formation. In addition, we use SiMPull to directly quantify YFP and mCherry maturation probabilities, showing these differ substantially from values obtained in mammalian systems. Leveraging these probabilities, in conjunction with fluorophore photobleaching assays on over 2000 individual complexes, we determined HD-ZIPIII:ZPR stoichiometry. Intriguingly, these complexes appear as heterotetramers, comprising two HD-ZIPIII and two ZPR molecules, rather than heterodimers as described in the current model. This surprising result raises new questions about the regulation of these key developmental factors and is illustrative of the unique contribution SiMPull is poised to make to in planta protein interaction studies.
Code coverage for any kind of test in any kind of transcompiled cross-platform applications
2016-07-06

Code coverage is a widely used measure to determine how thoroughly an application is tested. There are many tools available for different languages. However, to the best of our knowledge, most of them focus on unit testing and ignore end-to-end tests with ui- or web tests. Furthermore, there is no support for determining code coverage of transcompiled cross-platform applications. This kind of application is written in one language, but compiled to and executed in a different programming language. Besides, it may run on a different platform. In this paper, we propose a new code coverage testing method that calculates the code coverage of any kind of test (unit-, integration- or ui-/web-test) for any type of (transcompiled) applications (desktop, web or mobile application). Developers obtain information about which parts of the source code are uncovered by tests. The basis of our approach is generic and may be applied in numerous programming languages based on an abstract syntax tree. We present our approach for any-kind-applications developed in Java and evaluate our tool on a web application created with Google Web Toolkit, on standard desktop applications, and on some small Java applications that use the Swing library to create user interfaces. Our results show that our tool is able to judge the code coverage of any kind of test. In particular, our tool is independent of the unit- or ui-/web test-framework in use. The runtime performance is promising although it is not as fast as already existing tools in the area of unit-testing.
Identifying Referents in Emily Dickinson’s ‘If it had no pencil’
2016-07-06

In our work, we combine linguistic and literary methods in the analysis of poetry. Our analysis is based on the assumption that leaving possibilities open and ambiguities unresolved have been intended by the author in order to enable individual choices regarding the interpretation of the poem. We shall illustrate our methods through the analysis of Emily Dickinson’s ‘If it had no pencil’. Locally, we look at semantic structures and phenomena (such as mismatches or ambiguities) within the text. Globally, we look at biographical and intertextual information which might help to illuminate Dickinson’s special use of certain words by going beyond the text. This approach systematically reveals which meaning components can be identified by a strict semantic analysis of the poem and which components are more flexible and require additional information. It can therefore be specified what the source of different interpretations is, and which of them can be considered plausible.
Regional differences in health, diet and weaning patterns amongst the first Neolithic farmers of central Europe
2016-07-07

Abstract Across much of central Europe, the Linearbandkeramik (LBK) represents the first Neolithic communities. Arising in Transdanubia around 5500 cal. BC the LBK spread west to the Rhine within two to three hundred years, carrying elements of a mixed agricultural economy and a relatively homogeneous material culture. Colonisation of new regions during this progress would have required economic adaptations to varied ecological conditions within the landscape. This paper investigates whether such adaptation at a local scale affected health patterns and altered the dietary habits of populations that otherwise shared a common cultural and biological origin. Analysis of non-specific stress (linear enamel hypoplasia, porotic hyperostosis, cribra orbitalia) within five LBK populations from across central Europe in conjunction with published carbon and nitrogen stable isotope data from each site revealed a high prevalence of porotic hyperostosis and cribra orbitalia in western populations that was associated with a lower animal protein intake. Hypoplastic enamel was more frequently observed in eastern populations however, and may reflect geographic differences in childhood morbidity and mortality as a result of variation in social practices relating to weaning. Local socio-economic adaptations within the LBK were therefore an important factor in the exposure of populations to non-specific stress.
Mandarin Lexical Tone Acquisition in Cochlear Implant Users With Prelingual Deafness: A Review
2016-07-07

Purpose The purpose of this review article is to synthesize evidence from the fields of developmental linguistics and cochlear implant technology relevant to the production and perception of Mandarin lexical tone in cochlear implant users with prelingual deafness. The aim of this review was to identify potential factors that determine outcomes for tonal-language speaking cochlear implant users and possible directions for further research. Method A computerized database search of MEDLINE, CINAHL, Academic Search Premier, Web of Science, and Google Scholar was undertaken in June and July 2014. Search terms used were lexical tone AND tonal language, speech development AND/OR speech production AND/OR speech perception AND cochlear implants, and pitch perception AND cochlear implants, anywhere in the title or abstract. Conclusion Despite the demonstrated limitations of pitch perception in cochlear implant users, there is some evidence that typical production and perception of lexical tone is possible by cochlear implant users with prelingual deafness. Further studies are required to determine the factors that contribute to better outcomes to inform rehabilitation processes for cochlear implant users in tonal-language environments.
Effects of cue modality and emotional category on recognition of nonverbal emotional signals in schizophrenia
2016-07-07

Our results confirmed that perceptual impairments can be observed for vocal as well as facial cues conveying various social and emotional connotations. The observed differences in severity of impairments with most severe deficits for alluring expressions might be related to specific difficulties in recognizing the complex social emotional information of interpersonal intentions as compared to "basic" emotional states. Therefore, future studies evaluating perception of nonverbal cues should consider a broader range of social and emotional signals beyond basic emotions including attitudes and interpersonal intentions. Identifying specific domains of social perception particularly prone for misunderstandings in patients with schizophrenia might allow for a refinement of interventions aiming at improving social functioning.
Geochemical Characterization of Four Quaternary Obsidian Sources and Provenance of Obsidian Artifacts from the Middle Stone Age Site of Gademotta, Main Ethiopian Rift
2016-07-07

Twenty‐six Middle Stone Age obsidian artifacts from the Gademotta Formation were instrumentally characterized by energy dispersive X‐ray fluorescence. Analysis of artifacts from the type locality enabled sampling of a greater time depth while avoiding the uncertainties in previous results on artifacts sampled from a “disturbed” context at Kulkuletti. Moreover, the analysis here of source samples from Alutu, Worja, and the previously unstudied Bora and Ficke sources in the broader region offers a better understanding of prehistoric lithic raw material procurement. The local Worja source, an aphyric obsidian excellent for tool production, substantially dominates the assemblage. Bora, another aphyric obsidian in the wider region, is also present, but not common. The vitrophyric Ficke and Alutu obsidian sources with abundant sanidine phenocrysts were not present in the archaeological assemblage, and likely did not compete with Worja and Bora for tool production. At least one artifact appears to be from an as yet unknown source, thus confirming results of previous studies. A few artifacts share similar geochemical composition with the Worja and Bora sources, thus highlighting the complexity of obsidian source studies in this part of the rift where multiple geographically close sources may share similar crustal material.