julilili42/papers huggingface dataset:
Molecular Recognition and Visual Detection of G‐Quadruplexes by a Dicarbocyanine Dye
2015-08-11

Abstract The interactions of a dicarbocyanine dye 3,3′‐diethylthiadicarbocyanine, DiSC 2 (5) , with DNA G‐quadruplexes were studied by means of a combination of various spectroscopic techniques. Aggregation of excess dye as a result of its positive charge is promoted by the presence of the polyanionic quadruplex structure. Specific high‐affinity binding to the parallel quadruplex of the MYC promoter sequence involves stacking of DiSC 2 (5) on the external G‐tetrads; the 5′‐terminal tetrad is the favored binding site. Significant energy transfer between DNA and the dye in the UV spectral region is observed upon DiSC 2 (5) binding. The transfer efficiency strongly depends on the DNA secondary structure as well as on the G‐quadruplex topology. These photophysical features enable the selective detection of DNA quadruplexes through sensitized DiSC 2 (5) fluorescence in the visible region.
The Symmetric Nature of Evaluative Memory Associations
2015-08-11

Changing attitudes by repeated co-occurrences of initially neutral stimuli (conditioned stimuli [CSs]) with affective entities (unconditioned stimuli [USs]) is called evaluative conditioning (EC). The vast majority of EC procedures in the literature are “forward” in nature, presenting the CS before the US. Scant empirical research into the issue has argued that forward procedures are more effective than backward procedures, but this research suffers from methodological issues while a meta-analysis indicated no difference. Two experiments show that backward conditioning procedures are equally effective in changing attitudes as forward conditioning procedures. Memory measures show that memory associations are equally strong from the CSs to the USs as from the USs to the CSs, irrespective of the presentation order (forward vs. backward) of the stimuli. Together the data support the proposition that the associations generated by EC are symmetric and bidirectional, rather than unidirectional, in nature.
Identification of a Novel Immunodominant HLA-B*07
2015-08-11

Adenovirus infections of immunocompromised patients, particularly following allogeneic hematopoietic stem cell transplantation, are associated with morbidity and mortality. Immunotherapy by adoptive transfer of hexon-specific and penton-specific T cells has been successfully applied, but many approaches are impeded by the low number of HLA class I-restricted adenoviral peptide epitopes described to date. We use a novel method to identify naturally presented adenoviral peptide epitopes from infected human cells, ectopically expressing defined HLA, using peptide elution and liquid chromatography-mass spectrometry analysis. We show that the previously described HLA-A*01:01-restricted peptide epitope LTDLGQNLLY from hexon protein is naturally presented, and demonstrate the functionality of LTDLGQNLLY-specific T cells. We further identify a novel immunodominant HLA-B*07:02-restricted peptide epitope VPATGRTLVL from protein 13.6 K, and demonstrate the high proliferative, cytotoxic, and IFN-γ-producing capacity of peptide-specific T cells. Lastly, LTDLGQNLLY-specific T cells can be detected ex vivo following adoptive transfer therapy, and LTDLGQNLLY-specific and VPATGRTLVL-specific T cells have memory phenotypes ex vivo. Given their proliferative and cytotoxic capacity, such epitope-specific T cells are promising candidates for adoptive T-cell transfer therapy of adenovirus infection.
Modified gravity in three dimensional metric-affine scenarios
2015-08-11

We consider metric-affine scenarios where a modified gravitational action is sourced by electrovacuum fields in a three dimensional space-time. Such scenarios are supported by the physics of crystalline structures with microscopic defects and, in particular, those that can be effectively treated as bi-dimensional (like graphene). We first study the case of theories, finding deviations near the center as compared to the solutions of General Relativity. We then consider Born-Infeld gravity, which has raised a lot of interest in the last few years regarding its applications in astrophysics and cosmology, and show that new features always arise at a finite distance from the center. Several properties of the resulting space-times, in particular in presence of a cosmological constant term, are discussed.
On the limits of language influences on numerical cognition – no inversion effects in three-digit number magnitude processing in adults
2015-08-12

The inversion of number words influences numerical cognition even in seemingly non-verbal tasks, such as Arabic number comparison. However, it is an open question whether inversion of decades and units also influences number processing beyond the two-digit number range. The current study addresses this question by investigating compatibility effects in both German- (a language with inverted) and English-speaking (a language with non-inverted number words) university students (mean age 22 years) in a three-digit number comparison task. We observed reliable hundred-decade as well as hundred-unit compatibility effects for three-digit number comparison. This indicates that, comparable two-digit numbers, three-digit numbers are processed in a parallel decomposed fashion. However, in contrast to previous results on two-digit numbers as well as on childrenâs processing of three-digit numbers, no reliable modulation of these compatibility effects through language was observed in adults. The present data indicate that inversion-related differences in multi-digit number processing are limited. They seem to be restricted to the number range involving those digits being inverted (i.e., tens and units in two-digit numbers) but do not generalize to neighboring digits. Possible reasons for this lack of generalization are discussed.
Organizer, observer and participant
2015-08-12

Public participation has become an important issue in science and technology studies as well as in politics. Procedures creating such multi-actor spaces of public participation are usually discussed under the label "participatory technology assessment" (pTA). PTA is considered to be a possible and promising way to foster direct interaction between members of the general public (lay people), organized interest groups, scientific experts, and sometimes also policy makers. Over the last ten years pTA has been utilized in many European countries, but also elsewhere in the world. However, there are vast differences regarding participatory methods. Abels and Bora propose a typology differentiating among seven different types of procedures. These seven types adopt divergent approaches with regard to the participants involved (who), the ways and means of participation (how) and the supposed functions of public participation (what for). The paper investigates the role social scientists play in pTA. It argues that social scientists can act in three different roles: as organizers of pTA, as scientific observers and as participants. The last role can take two different directions. Social scientists can be involved in pTA as "regular" scientific experts, or they can serve as "translators" in the complicated communication among social groups. It is this role as translator that is considered to be most innovative and worth exploring in the theory and praxis of pTA.
A Single-Strand Annealing Protein Clamps DNA to Detect and Secure Homology
2015-08-13

Repair of DNA breaks by single-strand annealing (SSA) is a major mechanism for the maintenance of genomic integrity. SSA is promoted by proteins (single-strand-annealing proteins [SSAPs]), such as eukaryotic RAD52 and λ phage Redβ. These proteins use a short single-stranded region to find sequence identity and initiate homologous recombination. However, it is unclear how SSAPs detect homology and catalyze annealing. Using single-molecule experiments, we provide evidence that homology is recognized by Redβ monomers that weakly hold single DNA strands together. Once annealing begins, dimerization of Redβ clamps the double-stranded region and nucleates nucleoprotein filament growth. In this manner, DNA clamping ensures and secures a successful detection for DNA sequence homology. The clamp is characterized by a structural change of Redβ and a remarkable stability against force up to 200 pN. Our findings not only present a detailed explanation for SSAP action but also identify the DNA clamp as a very stable, noncovalent, DNA-protein interaction.
An enigmatic crocodyliform tooth from the bauxites of western Hungary suggests hidden mesoeucrocodylian diversity in the Early Cretaceous European archipelago
2015-08-13

Background. The Cretaceous of southern Europe was characterized by an archipelago setting with faunas of mixed composition of endemic, Laurasian and Gondwanan elements. However, little is known about the relative timing of these faunal influences. The Lower Cretaceous of East-Central Europe holds a great promise for understanding the biogeographic history of Cretaceous European biotas because of the former proximity of the area to Gondwana (as part of the Apulian microcontinent). However, East-Central European vertebrates are typically poorly known from this time period. Here, we report on a ziphodont crocodyliform tooth discovered in the Lower Cretaceous (Albian) Alsópere Bauxite Formation of Olaszfalu, western Hungary. Methods. The morphology of the tooth is described and compared with that of other similar Cretaceous crocodyliforms. Results. Based on the triangular, slightly distally curved, constricted and labiolingually flattened crown, the small, subequal-sized true serrations on the carinae mesially and distally, the longitudinal fluting labially, and the extended shelves along the carinae lingually the tooth is most similar to some peirosaurid, non-baurusuchian sebecosuchian, and uruguaysuchid notosuchians. In addition, the paralligatorid Wannchampsus also possesses similar anterior teeth, thus the Hungarian tooth is referred here to Mesoeucrocodylia indet. Discussion. Supposing a notosuchian affinity, this tooth is the earliest occurrence of the group in Europe and one of the earliest in Laurasia. In case of a paralligatorid relationship the Hungarian tooth would represent their first European record, further expanding their cosmopolitan distribution. In any case, the ziphodont tooth from the Albian bauxite deposit of western Hungary belongs to a group still unknown from the Early Cretaceous European archipelago and therefore implies a hidden diversity of crocodyliforms in the area.
Cell death of spinal cord ED1+cells in a rat model of multiple sclerosis
2015-08-13

Infiltration of macrophages into the central nervous system and activation of microglia are hallmarks of multiple sclerosis and its animal model-experimental autoimmune encephalomyelitis (EAE). Cell death in EAE has been demonstrated as an essential mechanism in the local regulation of the inflammatory reaction, but also as one of the major factors contributing to the destruction of the nervous tissue. The focus of this study was on detection of cell death among ED1(+) cells (macrophages/activated microglia) in the spinal cord of Dark Agouti rats at the peak of EAE. Cell death was assessed using the TUNEL assay and immunostaining for cleaved caspase 3, as markers for cell death in general and "classical" apoptosis, respectively. Major infiltrates of immune cells were detected both in white matter and gray matter of spinal cords in rats at the disease peak. ED1, TUNEL, and caspase 3 positive cells were detected within, but also outside the infiltrates. There were more dying ED1(+) cells in white matter than in gray matter, both in the general population and in infiltrated regions. The observed discrepancy in the proportion of dying ED1(+) cells in spinal cord gray and white matter indicated that in EAE rat macrophages/microglia within gray matter are less prone to cell death induction. This is of special interest in the context of the increasingly appreciated contribution of spinal cord gray matter inflammation to multiple sclerosis pathogenesis. Our findings suggest that activated macrophages/microglia of gray matter are less susceptible to cell death induction. Alternatively, it can be assumed that intrinsic cell death-inductive mechanisms of nervous tissue differ in white and gray matter. Thus, further research on the gray matter macrophages/microglia cell death during EAE is warranted. They should be aimed at identification of the reasons for the observed differences and finding suitable ways to stimulate gray matter activated macrophages/microglia death.
Point-of-Care Testing of Coagulation in Patients Treated With Non–Vitamin K Antagonist Oral Anticoagulants
2015-08-14

Background and Purpose— Specific coagulation assays for non–vitamin K antagonist oral anticoagulants (NOAC) are relatively slow and often lack availability. Although specific point-of-care tests (POCT) are currently not available, NOAC are known to affect established coagulation POCT. This study aimed at determining the diagnostic accuracy of the CoaguChek POCT to rule out relevant concentrations of rivaroxaban, apixaban, and dabigatran in real-life patients. Methods— We consecutively enrolled 60 ischemic stroke patients newly started on NOAC treatment and obtained blood samples at 6 prespecified time points. Samples were tested using the CoaguChek POCT, laboratory-based coagulation assays (prothrombin time and activated partial thromboplastin time, anti-Xa test and Hemoclot), and liquid chromatography–tandem mass spectrometry for direct determination of NOAC concentrations. Results— Three hundred fifty-six blood samples were collected. The CoaguChek POCT strongly correlated ( r =0.82 P &lt;0.001) with rivaroxaban concentrations but did not accurately detect dabigatran or apixaban. If used to estimate the presence of low rivaroxaban concentrations, POCT was superior to predictions based on normal prothrombin time and activated partial thromboplastin time values even if sensitive reagents were used. POCT-results ≤1.0 predicted rivaroxaban concentrations &lt;32 and &lt;100 ng/mL with a specificity of 90% and 96%, respectively. Conclusions— If anti-Xa test is not available, we propose the use of the CoaguChek POCT to guide thrombolysis decisions after individual risk assessment in rivaroxaban-treated patients having acute ischemic stroke. Clinical Trial Registration— URL: http://www.clinicaltrials.gov . Unique identifier: NCT02371044.
Prophylactic nimodipine treatment for cochlear and facial nerve preservation after vestibular schwannoma surgery: a randomized multicenter Phase III trial
2015-08-14

OBJECT A pilot study of prophylactic nimodipine and hydroxyethyl starch treatment showed a beneficial effect on facial and cochlear nerve preservation following vestibular schwannoma (VS) surgery. A prospective Phase III trial was undertaken to confirm these results. METHODS An open-label, 2-arm, randomized parallel group and multicenter Phase III trial with blinded expert review was performed and included 112 patients who underwent VS surgery between January 2010 and February 2013 at 7 departments of neurosurgery to investigate the efficacy and safety of the prophylaxis. The surgery was performed after the patients were randomly assigned to one of 2 groups using online randomization. The treatment group (n = 56) received parenteral nimodipine (1–2 mg/hr) and hydroxyethyl starch (hematocrit 30%–35%) from the day before surgery until the 7th postoperative day. The control group (n = 56) was not treated prophylactically. RESULTS Intent-to-treat analysis showed no statistically significant effects of the treatment on either preservation of facial nerve function (35 [67.3%] of 52 [treatment group] compared with 34 [72.3%] of 47 [control group]) (p = 0.745) or hearing preservation (11 [23.4%] of 47 [treatment group] compared with 15 [31.2%] of 48 [control group]) (p = 0.530) 12 months after surgery. Since tumor sizes were significantly larger in the treatment group than in the control group, logistic regression analysis was required. The risk for deterioration of facial nerve function was adjusted nearly the same in both groups (OR 1.07 [95% CI 0.34–3.43], p = 0.91). In contrast, the risk for postoperative hearing loss was adjusted 2 times lower in the treatment group compared with the control group (OR 0.49 [95% CI 0.18–1.30], p = 0.15). Apart from dose-dependent hypotension (p &lt; 0.001), no clinically relevant adverse reactions were observed. CONCLUSIONS There were no statistically significant effects of the treatment. Despite the width of the confidence intervals, the odds ratios may suggest but do not prove a clinically relevant effect of the safe study medication on the preservation of cochlear nerve function after VS surgery. Further study is needed before prophylactic nimodipine can be recommended in VS surgery.
Comparing L1 and L2 speakers using articulography
2015-08-14

This study uses articulography, the measurement of the position of tongue and lips during speech, as a tool to quantitatively assess the differences between pronunciations of native and non-native (Dutch) speakers of English. In our study, we focus on two pairs of English sound contrasts: /s/-/ʃ / and /t/-/θ/. Our analysis focuses on the anterior-posterior position of the tongue tip during the pronunciation of minimal pairs containing the contrasting sounds. Our results indicate that the contrast between /s / and /ʃ / made by the Dutch L2 speakers is slightly reduced compared to the contrast produced by the English L1 speakers. For the contrast /t/-/θ/, our findings show that while native English speakers clearly produce this contrast, Dutch speakers do not. Our results line up with earlier studies on the basis of acoustic data, and also illustrate that articulography is a suitable method of investigating pronunciation differences between first and second language speakers.
A high-precision sampling scheme to assess persistence and transport characteristics of micropollutants in rivers
2015-08-15

Increasing numbers of organic micropollutants are emitted into rivers via municipal wastewaters. Due to their persistence many pollutants pass wastewater treatment plants without substantial removal. Transport and fate of pollutants in receiving waters and export to downstream ecosystems is not well understood. In particular, a better knowledge of processes governing their environmental behavior is needed. Although a lot of data are available concerning the ubiquitous presence of micropollutants in rivers, accurate data on transport and removal rates are lacking. In this paper, a mass balance approach is presented, which is based on the Lagrangian sampling scheme, but extended to account for precise transport velocities and mixing along river stretches. The calculated mass balances allow accurate quantification of pollutants' reactivity along river segments. This is demonstrated for representative members of important groups of micropollutants, e.g. pharmaceuticals, musk fragrances, flame retardants, and pesticides. A model-aided analysis of the measured data series gives insight into the temporal dynamics of removal processes. The occurrence of different removal mechanisms such as photooxidation, microbial degradation, and volatilization is discussed. The results demonstrate, that removal processes are highly variable in time and space and this has to be considered for future studies. The high precision sampling scheme presented could be a powerful tool for quantifying removal processes under different boundary conditions and in river segments with contrasting properties.
On-Surface Synthesis of BN-Substituted Heteroaromatic Networks
2015-08-17

We report on the bottom-up fabrication of BN-substituted heteroaromatic networks achieved by surface-assisted polymerization and subsequent cyclodehydrogenation of specifically designed BN-substituted precursor monomers based on a borazine core structural element. To get insight into the cyclodehydrogenation pathway and the influence of molecular flexibility on network quality, two closely related precursor monomers with different degrees of internal cyclodehydrogenation have been employed. Scanning tunneling microscopy shows that, for both monomers, surface-assisted cyclodehydrogenation allows for complete monomer cyclization and the formation of covalently interlinked BN-substituted polyaromatic hydrocarbon networks on the Ag(111) surface. In agreement with experimental observations, density functional theory calculations reveal a significantly lower energy barrier for the cyclodehydrogenation of the conformationally more rigid precursor monomer, which is also reflected in a higher degree of long-range order of the obtained heteroaromatic network. Our proof-of-concept study will allow for the fabrication of atomically precise substitution patterns within BNC heterostructures.
Magnetic field evolution in superconducting neutron stars
2015-08-17

The presence of superconducting and superfluid components in the core of mature neutron stars calls for the rethinking of a number of key magnetohydrodynamical notions like resistivity, the induction equation, magnetic energy and flux-freezing. Using a multifluid magnetohydrodynamics formalism, we investigate how the magnetic field evolution is modified when neutron star matter is composed of superfluid neutrons, type-II superconducting protons and relativistic electrons. As an application of this framework, we derive an induction equation where the resistive coupling originates from the mutual friction between the electrons and the vortex/fluxtube arrays of the neutron and proton condensates. The resulting induction equation allows the identification of two time-scales that are significantly different from those of standard magnetohydrodynamics. The astrophysical implications of these results are briefly discussed.
The δ 18 O signatures of HCl ‐extractable soil phosphates: methodological challenges and evidence of the cycling of biological P in arable soil
2015-08-17

Summary Soil phosphates exchange oxygen atoms rapidly with soil water once recycled by intracellular enzymes, thereby approaching an equilibrium δ 18 O P signature that depends on ambient temperature and the δ 18 O W signature of soil water. We hypothesized that in the topsoil, phosphates reach this equilibrium δ 18 O P signature even if amended by different fertilizers. In the subsoil, however, there might be phosphates with a smaller δ 18 O P value than that represented by the isotopic equilibrium value, a condition that could exist in the case of limited biological P cycling only. We tested these hypotheses for the HCl ‐extractable P pool of the Hedley fractionation scheme of arable soil in Germany, which integrates over extended time‐scales of the soil P cycle. We sampled several types of fertilizer, the surface soil that received these fertilizer types and composites from a Haplic Luvisol depth profile under long‐term agricultural practice. Organic fertilizers had significantly smaller δ 18 O P values than mineral fertilizers. Intriguingly, the fields fertilized organically also tended to have smaller δ 18 O P signatures than other types of surface soil, which calls into question full isotopic equilibrium at all sites. At depths below 50 cm, the soil δ 18 O P values were even depleted relative to the values calculated for isotopic equilibrium. This implies that HCl ‐extractable phosphates in different soil horizons are of different origins. In addition, it supports the assumption that biological cycling of P by intracellular microbial enzymes might have been relatively inefficient in the deeper subsoil. At depths of 50–80 cm, there was a transition zone of declining δ 18 O P values, which might be regarded as the first evidence that the degree of biological P cycling changed at this depth interval.