julilili42/papers huggingface dataset:
Monolayers of hard rods on planar substrates. II. Growth
2017-02-24

Growth of hard-rod monolayers via deposition is studied in a lattice model using rods with discrete orientations and in a continuum model with hard spherocylinders. The lattice model is treated with kinetic Monte Carlo simulations and dynamic density functional theory while the continuum model is studied by dynamic Monte Carlo simulations equivalent to diffusive dynamics. The evolution of nematic order (excess of upright particles, “standing-up” transition) is an entropic effect and is mainly governed by the equilibrium solution, rendering a continuous transition [Paper I, M. Oettel et al., J. Chem. Phys. 145, 074902 (2016)]. Strong non-equilibrium effects (e.g., a noticeable dependence on the ratio of rates for translational and rotational moves) are found for attractive substrate potentials favoring lying rods. Results from the lattice and the continuum models agree qualitatively if the relevant characteristic times for diffusion, relaxation of nematic order, and deposition are matched properly. Applicability of these monolayer results to multilayer growth is discussed for a continuum-model realization in three dimensions where spherocylinders are deposited continuously onto a substrate via diffusion.
Prophylactic nimodipine treatment and improvement in hearing outcome after vestibular schwannoma surgery: a combined analysis of a randomized, multicenter, Phase III trial and its pilot study
2017-02-24

OBJECTIVE In clinical routines, neuroprotective strategies in neurosurgical interventions are still missing. A pilot study (n = 30) and an analogously performed Phase III trial (n = 112) pointed to a beneficial effect of prophylactic nimodipine and hydroxyethyl starch (HES) in vestibular schwannoma (VS) surgery. Considering the small sample size, the data from both studies were pooled. METHODS The patients in both investigator-initiated studies were assigned to 2 groups. The treatment group (n = 70) received parenteral nimodipine (1–2 mg/hour) and HES (hematocrit 30%–35%) from the day before surgery until the 7th postoperative day. The control group (n = 72) was not treated prophylactically. Facial and cochlear nerve functions were documented preoperatively, during the inpatient care, and 1 year after surgery. RESULTS Pooled raw data were analyzed retrospectively. Intent-to-treat analysis revealed a significantly lower risk for hearing loss (Class D) 12 months after surgery in the treatment group compared with the control group (OR 0.46, 95% CI 0.22–0.97; p = 0.04). After exclusion of patients with preoperative Class D hearing, this effect was more pronounced (OR 0.38, 95% CI 0.17–0.83; p = 0.016). Logistic regression analysis adjusted for tumor size showed a 4 times lower risk for hearing loss in the treatment group compared with the control group (OR 0.25, 95% CI 0.09–0.63; p = 0.003). Facial nerve function was not significantly improved with treatment. Apart from dose-dependent hypotension (p &lt; 0.001), the study medication was well tolerated. CONCLUSIONS Prophylactic nimodipine is safe and may be recommended in VS surgery to preserve hearing. Prophylactic neuroprotective treatment in surgeries in which nerves are at risk seems to be a novel and promising concept. Clinical trial registration no.: DRKS 00000328 ( https://drks-neu.uniklinik-freiburg.de/drks_web/ )
Entropic equality for worst-case work at any protocol speed
2017-02-24

We derive an equality for non-equilibrium statistical mechanics in finite-dimensional quantum systems. The equality concerns the worst-case work output of a time-dependent Hamiltonian protocol in the presence of a Markovian heat bath. It has the form 'worst-case work = penalty—optimum'. The equality holds for all rates of changing the Hamiltonian and can be used to derive the optimum by setting the penalty to 0. The optimum term contains the max entropy of the initial state, rather than the von Neumann entropy, thus recovering recent results from single-shot statistical mechanics. Energy coherences can arise during the protocol but are assumed not to be present initially. We apply the equality to an electron box.
Wilson loop in light-front quantization
2017-02-24

Using Dirac's method for the quantization of constrained systems QED is\\ncanonically quantized in the front-form in a gauge which is the light-front\\nanalog of the Weyl gauge. From the obtained vacuum wave functional the spatial\\nWilson loop is calculated. The result known from the canonical instant-form\\nquantization or from the covariant path integral quantization is found only if\\nthe static limit is taken in a specific order. The same ambiguity\\nis also found in the static photon propagator in coordinate space.\\n
Linking above‐ and belowground traits to soil and climate variables: an integrated database on China's grassland species
2017-02-27

Abstract Knowledge of plant functional traits and trait–environment interactions is important for characterizing species strategies and understanding ecological processes. However, comprehensive field data on both above‐ and belowground traits, together with their environmental variables are scarce. Biome‐scale studies are particularly lacking. Here we present two large‐scale data sets that include functional traits of leaves and fine roots and their corresponding soil and climatic variables in China's grasslands. Leaf, fine root, and soil samples were collected in three biogeographic regions: temperate grassland on the Inner Mongolia Plateau, alpine grassland on the Tibetan Plateau, and mountain grassland in the Xinjiang mountain areas. Field data were collected over two periods. The first data set collected between 2003 and 2004 includes 13 foliar traits (leaf mass per area, LMA ; photosynthetic nitrogen use efficiency, PNUE ; water use efficiency, WUE ; stomatal conductance for water vapor, Gs; transpiration rate, TR ; mass‐ and area‐based photosynthetic capacity, Amass and Aarea; mass‐ and area‐based carbon concentrations, Cmass and Carea; nitrogen concentrations, Nmass and Narea; and phosphorus concentrations, Pmass and Parea) for 170 species at 173 sites. The second data set collected between 2006 and 2007 includes six sets of analogous traits for both leaves and fine roots (C, N, and P concentrations; leaf thickness/root diameter; specific leaf area, SLA ; specific root length, SRL ; and tissue density) for 139 species at 82 sites, along with soil attributes (soil total and organic carbon, STC and SOC ; total and available N, STN and SAN ; total and available P, STP and SAP ; pH , bulk density, and moisture). Moreover, associated information was also gathered, including geographical location (latitude, longitude, and altitude), climate (mean annual temperature, MAT ; mean annual precipitation, MAP ; growing season temperature, GST ; growing season precipitation, GSP ; potential evapotranspiration, PET ; and actual evapotranspiration, AET ) and site descriptions (vegetation and soil types). The data sets are unique because they integrate plant above‐ and belowground traits, climate, and soil factors over broad regional, elevational, and taxonomic ranges in understudied regions (e.g., the Tibetan Plateau). This is the only database on China's grassland species for unrestricted global access. These data sets will make a valuable contribution to future large‐scale trait‐based ecological studies.
Optic-nerve-transmitted eyeshine, a new type of light emission from fish eyes
2017-02-27

The generality of these factors and the lack of specifically adapted features implies that ONT eyeshine is widespread among small fish species. Nevertheless, its intensity varies considerably, depending on the specific combination and varying expression of common anatomical features. We discuss whether ONT eyeshine might affect visual performance, and speculate about possible functions such as predator detection, camouflage, and intraspecific communication.
Chimeric Autofluorescent Proteins as Photophysical Model System for Multicolor Bimolecular Fluorescence Complementation
2017-02-27

The yellow fluorescent protein (YFP) is frequently used in a protein complementation assay called bimolecular fluorescence complementation (BiFC), and is employed to visualize protein-protein interactions. In this analysis, two different, nonfluorescent fragments of YFP are genetically attached to proteins of interest. Upon interaction of these proteins, the YFP fragments are brought into proximity close enough to reconstitute their original structure, enabling fluorescence. BiFC allows for a straightforward readout of protein-protein interactions and furthermore facilitates their functional investigation by in vivo imaging. Furthermore, it has been observed that the available color range in BiFC can be extended upon complementing fragments of different proteins that are, like YFP, derived from the Aequorea victoria green fluorescent protein, thereby allowing for a multiplexed investigation of protein-protein interactions. Some spectral characteristics of "multicolor" BiFC (mcBiFC) complexes have been reported before; however, no in-depth analysis has been performed yet. Therefore, little is known about the photophysical characteristics of these mcBiFC complexes because a proper characterization essentially relies on in vitro data. This is particularly difficult for fragments of autofluorescent proteins (AFPs) because they show a very strong tendency to form supramolecular aggregates which precipitate ex vivo. In this study, this intrinsic difficulty is overcome by directly fusing the coding DNA of different AFP fragments. Translation of the genetic sequence in Escherichia coli leads to fully functional, highly soluble fluorescent proteins with distinct properties. On the basis of their construction, they are designated chimeric AFPs, or BiFC chimeras, here. Comparison of their spectral characteristics with experimental in vivo BiFC data confirmed the utility of the chimeric proteins as a BiFC model system. In this study, nine different chimeras were thoroughly analyzed at both the ensemble and the single-molecular level. The data indicates that mutations believed to be photophysically silent significantly alter the properties of AFPs.
MHC-I Ligand Discovery Using Targeted Database Searches of Mass Spectrometry Data: Implications for T-Cell Immunotherapies
2017-02-28

Class I major histocompatibility complex (MHC-I)-bound peptide ligands dictate the activation and specificity of CD8<sup>+</sup> T cells and thus are important for devising T-cell immunotherapies. In recent times, advances in mass spectrometry (MS) have enabled the precise identification of these MHC-I peptides, wherein MS spectra are compared against a reference proteome. Unfortunately, matching these spectra to reference proteome databases is hindered by inflated search spaces attributed to a lack of enzyme restriction in the searches, limiting the efficiency with which MHC ligands are discovered. Here we offer a solution to this problem whereby we developed a targeted database search approach and accompanying tool SpectMHC, that is based on a priori-predicted MHC-I peptides. We first validated the approach using MS data from two different allotype-specific immunoprecipitates for the C57BL/6 mouse background. We then developed allotype-specific HLA databases to search previously published MS data sets of human peripheral blood mononuclear cells (PBMCs). This targeted search strategy improved peptide identifications for both mouse and human ligandomes by greater than 2-fold and is superior to traditional "no enzyme" searches of reference proteomes. Our targeted database search promises to uncover otherwise missed novel T-cell epitopes of therapeutic potential.
A preferred retinal location of fixation can be induced when systematic stimulus relocations are applied
2017-02-28

Patients with central vision loss obtain visual information by fixating on an object eccentrically with a preferred retinal locus of fixation (PRL). Patients do not always choose the most efficient PRL position, and as a consequence, visual performance is not always fully exploited. This study investigates whether PRLs can be induced by applying systematic stimulus relocations. The PRL was trained using a central scotoma simulation in 15 healthy subjects. They performed different visual tasks during four sessions, after which their reading performance was evaluated. In five subjects the stimulus was relocated to the left hemifield whenever a saccade would place the stimulus on the opposite hemifield. In five different subjects the relocation was inversed: The stimulus was located in the right hemifield. The relocation was 7.5° of visual angle and it was applied horizontally. Five additional subjects naturally chose the PRL location. They were used as the control group to evaluate the development of a PRL. After training, subjects performed visual search tasks on static stimuli. Evaluation after training showed that systematic stimulus relocations can be used to influence the development of the PRL. These results might be significant for the development of training strategies for the visually impaired.
Rapid Sampling of Escherichia coli After Changing Oxygen Conditions Reveals Transcriptional Dynamics
2017-02-28

Escherichia coli is able to shift between anaerobic and aerobic metabolism by adapting its gene expression, e.g., of metabolic genes, to the new environment. The dynamics of gene expression that result from environmental shifts are limited, amongst others, by the time needed for regulation and transcription elongation. In this study, we examined gene expression dynamics after an anaerobic-to-aerobic shift on a short time scale (0.5, 1, 2, 5, and 10 min) by RNA sequencing with emphasis on delay times and transcriptional elongation rates (TER). Transient expression patterns and timing of differential expression, characterized by delay and elongation, were identified as key features of the dataset. Gene ontology enrichment analysis revealed early upregulation of respiratory and iron-related gene sets. We inferred specific TERs of 89 operons with a mean TER of 42.0 nt/s and mean delay time of 22.4 s. TERs correlate with sequence features, such as codon bias, whereas delay times correlate with the involvement of regulators. The presented data illustrate that at very short times after a shift in oxygenation, extensional changes of the transcriptome, such as temporary responses, can be observed. Besides regulation, TERs contribute to the dynamics of gene expression.
‘Living God, renew and transform us’ – 26th General Council of the World Communion of Reformed Churches, in Leipzig, Germany, 29 June to 07 July 2017
2017-02-28

This article aims at exploring the theme ‘Living God, renew and transform us’ under the following headings: the living God and the gods of death, the desolation of atheism and the sun of righteousness, just law and the fullness of life. The author relates the ‘God of Life’ to a ‘theology embracing life’. He links the ‘gods of death’ to racism, capitalism and terrorism in which we ‘encounter a new religion of death’. He points out that Christianity is a religion of joy in God and sets out to illustrate this with selected biblical texts. In the section ‘The desolation of atheism’, the author argues that modern atheism offers a ‘reduced life’. To make his point, he refers to his own personal experience and the theological ‘protest atheism’ which arose in the 19th century. The author concludes by stating that atheism offers nothing positive. In the final section, ‘The sun of righteousness, just law and the fullness of life’, the author addresses issues of justice. In referring to the Reformation doctrine on justification, the author states that the justification of victims requires confessio oris, rising up from humiliation and forgiveness.
Fast and Robust Eyelid Outline and Aperture Detection in Real-World Scenarios
2017-03-01

The correct identification of the eyelids and its aperture provide essential data to infer a subject's mental state (e.g., vigilance, fatigue, and drowsiness) and to validate or reduce the search space of other eye features (e.g., pupil, and iris). This knowledge can be used not only to improve many applications, such as eye tracking and iris recognition, but also to derive information about the user (such as, the take-over readiness of the driver in the automated driving context). In this paper, we propose a computervision-based approach to eyelids identification and aperture estimation. Evaluation was performed on an existing data set from the literature as well as on a new data set introduced in this work. The new data set contains 4000 hand-labeled eye images from 11 subjects driving in a city, these contain several challenges such as reflections, makeup, wrinkles, blinks, and changing illumination. The proposed method outperformed state-of-the-art methods by up to 16.11 percentage points in terms of average similarity to the hand-labeled eyelid outline (from 34px to 12px) and 21.7 pixels (or 7.53% of the eye image height) in terms of average eyelid aperture estimation error. The proposed method implementation runs in real time even on a single core (7ms) and is available, together with the new data set, at http://www.ti.uni-tuebingen.de/Eyelid-detection.2007.0.html.
Gene-based association studies report genetic links for clinical subtypes of frontotemporal dementia
2017-03-01

Genome-wide association studies in frontotemporal dementia showed limited success in identifying associated loci. This is possibly due to small sample size, allelic heterogeneity, small effect sizes of single genetic variants, and the necessity to statistically correct for testing millions of genetic variants. To overcome these issues, we performed gene-based association studies on 3348 clinically identified frontotemporal dementia cases and 9390 controls (discovery, replication and joint-cohort analyses). We report association of APOE and TOMM40 with behavioural variant frontotemporal dementia, and ARHGAP35 and SERPINA1 with progressive non-fluent aphasia. Further, we found the ɛ2 and ɛ4 alleles of APOE harbouring protective and risk increasing effects, respectively, in clinical subtypes of frontotemporal dementia against neurologically normal controls. The APOE-locus association with behavioural variant frontotemporal dementia indicates its potential risk-increasing role across different neurodegenerative diseases, whereas the novel genetic associations of ARHGAP35 and SERPINA1 with progressive non-fluent aphasia point towards a potential role of the stress-signalling pathway in its pathophysiology.
Red fluorescence of the triplefinTripterygion delaisiis increasingly visible against background light with increasing depth
2017-03-01

The light environment in water bodies changes with depth due to the absorption of short and long wavelengths. Below 10 m depth, red wavelengths are almost completely absent rendering any red-reflecting animal dark and achromatic. However, fluorescence may produce red coloration even when red light is not available for reflection. A large number of marine taxa including over 270 fish species are known to produce red fluorescence, yet it is unclear under which natural light environment fluorescence contributes perceptively to their colours. To address this question we: (i) characterized the visual system of Tripterygion delaisi, which possesses fluorescent irides, (ii) separated the colour of the irides into its reflectance and fluorescence components and (iii) combined these data with field measurements of the ambient light environment to calculate depth-dependent perceptual chromatic and achromatic contrasts using visual modelling. We found that triplefins have cones with at least three different spectral sensitivities, including differences between the two members of the double cones, giving them the potential for trichromatic colour vision. We also show that fluorescence contributes increasingly to the radiance of the irides with increasing depth. Our results support the potential functionality of red fluorescence, including communicative roles such as species and sex identity, and non-communicative roles such as camouflage.
Following Eye Gaze Activates a Patch in the Posterior Temporal Cortex That Is not Part of the Human “Face Patch” System
2017-03-01

Abstract Humans follow another person’s eye gaze to objects of interest to the other, thereby establishing joint attention, a first step toward developing a theory of the other’s mind. Previous functional MRI studies agree that a “gaze-following patch” (GFP) of cortex close to the posterior superior temporal sulcus (STS) is specifically implicated in eye gaze-following. The location of the GFP is in the vicinity of the posterior members of the core face-processing system that consists of distinct patches in ventral visual cortex, the STS, and frontal cortex, also involved in processing information on the eyes. To test whether the GFP might correspond to one of the posterior face patches, we compared the pattern of blood oxygenation level–dependent (BOLD) imaging contrasts reflecting the passive vision of static faces with the one evoked by shifts of attention guided by the eye gaze of others. The viewing of static faces revealed the face patch system. On the other hand, eye gaze-following activated a cortical patch (the GFP) with its activation maximum separated by more than 24 mm in the right and 19 mm in the left hemisphere from the nearest face patch, the STS face area (FA). This segregation supports a distinct function of the GFP, different from the elementary processing of facial information.
When Less Is More: Constructing a Parsimonious Concept of Interstate Peace for Quantitative Analysis
2017-03-01

Peace researchers have recently started to develop datasets that allow distinguishing between different levels of interstate peace. In this article, I first argue that existing conceptualizations and measurements suffer—to varying degrees—from two major specification problems: on the one hand, they face problems of what I call "ontological underload," as they do not include all essential constitutive dimensions. On the other hand, they face problems of "ontological overload," as they integrate factors as endogenous dimensions that should better be understood as exogenous causes of different levels of peace. I propose a new concept P* that avoids both problems. P* is based on a profound and parsimonious ontology that allows for straightforward theory formulation and empirical analysis. It incorporates three dimensions—behavior, expectations, and duration/stability—that allow us to differentiate between different levels of interstate peace. In this article, I also discuss how P* can be operationalized for a dataset of 126 dyads.
A new ex vivo model for optimizing distribution of therapeutic aerosols: the (inverted) bovine urinary bladder
2017-03-01

Abstract Background Development of Pressurized IntraPeritoneal Aerosol Chemotherapy (PIPAC) requires adequate preclinical models. Methods The model should be easy to use, reproducible and cost-effective. It should have a volume similar to the human abdominal cavity, and an oval shape. The inner surface should be lined with serosa. The model should allow pharmacological and biological analysis, including histology. No living animals should be used. Results The fresh urinary bladder is explanted from an adult bovine in the slaughterhouse. A 4-cm incision is performed into the bladder neck. The bladder can be inverted through the incision, which allows exposition of the serosa on its inner side. A balloon trocar is inserted through the incision and a ligature placed, ensuring full tightness. The therapeutic capnoperitoneum is installed. The bovine bladder has a volume somewhat smaller (2–3 L) than the human abdominal cavity (3–5 L). Costs are minimal. There is no significant bacteriological contamination. Manipulation is simple. Conclusions The (inverted) bovine urinary bladder is an innovative and versatile ex vivo model for optimizing drug delivery with therapeutic aerosols both onto the mucosa or the serosa. This model can be used for pharmaceutical Quality-by-Design approaches and will replace a large number of experiments in the animal.