julilili42/papers huggingface dataset:
How do various maize crop models vary in their responses to climate change factors?
2014-01-07

Abstract Potential consequences of climate change on crop production can be studied using mechanistic crop simulation models. While a broad variety of maize simulation models exist, it is not known whether different models diverge on grain yield responses to changes in climatic factors, or whether they agree in their general trends related to phenology, growth, and yield. With the goal of analyzing the sensitivity of simulated yields to changes in temperature and atmospheric carbon dioxide concentrations [ CO 2 ], we present the largest maize crop model intercomparison to date, including 23 different models. These models were evaluated for four locations representing a wide range of maize production conditions in the world: Lusignan (France), Ames ( USA ), Rio Verde (Brazil) and Morogoro (Tanzania). While individual models differed considerably in absolute yield simulation at the four sites, an ensemble of a minimum number of models was able to simulate absolute yields accurately at the four sites even with low data for calibration, thus suggesting that using an ensemble of models has merit. Temperature increase had strong negative influence on modeled yield response of roughly −0.5 Mg ha −1 per °C. Doubling [ CO 2 ] from 360 to 720 μmol mol −1 increased grain yield by 7.5% on average across models and the sites. That would therefore make temperature the main factor altering maize yields at the end of this century. Furthermore, there was a large uncertainty in the yield response to [ CO 2 ] among models. Model responses to temperature and [ CO 2 ] did not differ whether models were simulated with low calibration information or, simulated with high level of calibration information.
Facial affect perception and mentalizing abilities in female patients with persistent somatoform pain disorder
2014-01-07

Abstract Background Numerous studies have demonstrated a robust link between alexithymic traits and somatic complaints in patients suffering from psychosomatic disorders, while less is known about disease‐related impairments in the processing of affective social information. Deficits in emotion recognition can lead to misinterpretations of social signals and induce distress in interpersonal interactions. This, in turn, might contribute to somatoform symptomatology in affected individuals. The aim of the present study was to investigate basal facial affect recognition as well as higher‐order cognitive mind‐reading skills in order to further clarify the association between alexithymia and the processing of social affective information in a homogenous sample of patients suffering from somatoform pain. Methods We employed a series of animated morph clips that gradually displayed the onset and development of the six basic emotional expressions to investigate facial affect perception in a female sample of patients diagnosed with persistent somatoform pain disorder ( PSPD ) and matched healthy controls. In addition, all participants were presented with the M ovie for the A ssessment of S ocial C ognition to explore mind‐reading abilities. Results Specifically impaired mentalizing skills and increased alexithymic traits were observed in PSPD , while emotional facial expression recognition appeared to be intact in these patients. Conclusions PSPD subjects tend to overattribute inappropriate affective states to others, which could be the consequence of the inability to adequately experience and express their own emotional reactions. This cognitive bias might lead to the experience of poor psychosocial functioning and has the potential to negatively impact the course and outcome of this psychopathology.
‘Inner voices’: the cerebral representation of emotional voice cues described in literary texts
2014-01-07

While non-verbal affective voice cues are generally recognized as a crucial behavioral guide in any day-to-day conversation their role as a powerful source of information may extend well beyond close-up personal interactions and include other modes of communication such as written discourse or literature as well. Building on the assumption that similarities between the different 'modes' of voice cues may not only be limited to their functional role but may also include cerebral mechanisms engaged in the decoding process, the present functional magnetic resonance imaging study aimed at exploring brain responses associated with processing emotional voice signals described in literary texts. Emphasis was placed on evaluating 'voice' sensitive as well as task- and emotion-related modulations of brain activation frequently associated with the decoding of acoustic vocal cues. Obtained findings suggest that several similarities emerge with respect to the perception of acoustic voice signals: results identify the superior temporal, lateral and medial frontal cortex as well as the posterior cingulate cortex and cerebellum to contribute to the decoding process, with similarities to acoustic voice perception reflected in a 'voice'-cue preference of temporal voice areas as well as an emotion-related modulation of the medial frontal cortex and a task-modulated response of the lateral frontal cortex.
Seleno groups control the energy-level alignment between conjugated organic molecules and metals
2014-01-07

The charge injection from metallic electrodes into hole transporting layers of organic devices often suffers from deviations from vacuum-level alignment at the interface. Even for weakly interacting cases, Pauli repulsion causes an interface dipole between the metal and conjugated organic molecules (COMs) (so called “push-back” or “cushion” effect), which leads notoriously to an increase of the hole injection barrier. On the other hand, for chalcogenol self assembled monolayers (SAMs) on metal surfaces, chemisorption via the formation of chalcogen-metal bonds is commonly observed. In these cases, the energy-level alignment is governed by chalcogen-derived interface states in the vicinity of the metal Fermi-level. In this work, we present X-ray and ultraviolet photoelectron spectroscopy data that demonstrate that the interfacial energy-level alignment mechanism found for chalcogenol SAMs also applies to seleno-functionalized COMs. This can be exploited to mitigate the push-back effect at metal contacts, notably also when COMs with low ionization energies are employed, permitting exceedingly low hole injection barriers, as shown here for the interfaces of tetraseleno-tetracene with Au(111), Ag(111), and Cu(111).
Microstructure of Bentonite in Iron Ore Green Pellets
2014-01-07

Abstract Sodium-activated calcium bentonite is used as a binder in iron ore pellets and is known to increase strength of both wet and dry iron ore green pellets. In this article, the microstructure of bentonite in magnetite pellets is revealed for the first time using scanning electron microscopy. The microstructure of bentonite in wet and dry iron ore pellets, as well as in distilled water, was imaged by various imaging techniques (e.g., imaging at low voltage with monochromatic and decelerated beam or low loss backscattered electrons) and cryogenic methods (i.e., high pressure freezing and plunge freezing in liquid ethane). In wet iron ore green pellets, clay tactoids (stacks of parallel primary clay platelets) were very well dispersed and formed a voluminous network occupying the space available between mineral particles. When the pellet was dried, bentonite was drawn to the contact points between the particles and formed solid bridges, which impart strength to the solid compact.
A recurrent 11q aberration pattern characterizes a subset of MYC-negative high-grade B-cell lymphomas resembling Burkitt lymphoma
2014-01-08

Key Points A subset of lymphomas with gene expression and pathological characteristics of Burkitt lymphomas but absence of MYC translocation does exist. These lymphomas carry chr 11q proximal gains and telomeric losses, suggesting co-deregulation of oncogenes and tumor suppressor genes.
Localization and Functionality of the Inflammasome in Neutrophils
2014-01-08

Neutrophils represent the major fraction of circulating immune cells and are rapidly recruited to sites of infection and inflammation. The inflammasome is a multiprotein complex that regulates the generation of IL-1 family proteins. The precise subcellular localization and functionality of the inflammasome in human neutrophils are poorly defined. Here we demonstrate that highly purified human neutrophils express key components of the NOD-like receptor family, pyrin domain containing 3 (NLRP3), and absent in melanoma 2 (AIM2) inflammasomes, particularly apoptosis-associated speck-like protein containing a CARD (ASC), AIM2, and caspase-1. Subcellular fractionation and microscopic analyses further showed that inflammasome components were localized in the cytoplasm and also noncanonically in secretory vesicle and tertiary granule compartments. Whereas IL-1β and IL-18 were expressed at the mRNA level and released as protein, highly purified neutrophils neither expressed nor released IL-1α at baseline or upon stimulation. Upon inflammasome activation, highly purified neutrophils released substantially lower levels of IL-1β protein compared with partially purified neutrophils. Serine proteases and caspases were differentially involved in IL-1β release, depending on the stimulus. Spontaneous activation of the NLRP3 inflammasome in neutrophils in vivo affected IL-1β, but not IL-18 release. In summary, these studies show that human neutrophils express key components of the inflammasome machinery in distinct intracellular compartments and release IL-1β and IL-18, but not IL-1α or IL-33 protein. Targeting the neutrophil inflammasome may represent a future therapeutic strategy to modulate neutrophilic inflammatory diseases, such as cystic fibrosis, rheumatoid arthritis, or sepsis.
The Mechanism of Gold(I)‐Catalyzed Hydroalkoxylation of Alkynes: An Extensive Experimental Study
2014-01-08

Abstract An extensive experimental study of the mechanism of gold(I)‐catalyzed hydroalkoxylation of internal alkynes has been conducted by using NMR spectroscopy. This study was focused on the organogold intermediates, observations of actual catalytic intermediates in situ, and the reaction kinetics that are involved in this reaction. Based on the experimental results, a complete mechanistic picture was established, including on‐ and off‐cycle processes that explain the role of diaurated species. We have shown that gold‐catalyzed hydroalkoxylation of internal alkynes is a reaction that requires only one gold atom for the catalytic cycle, disproving a recent hypothesis regarding the involvement of cooperative gold catalysis.
Anisotropy of singlet exciton diffusion in organic semiconductor crystals from ab initio approaches
2014-01-08

Due to its importance for the function of organic optoelectronic devices, accurate simulations of the singlet exciton diffusion are crucial to predict the performance of new materials. We present a protocol which allows for the efficient directional analysis of exciton transport with high-level ab initiomethods. It is based on an alternative to the frequently employed rate equation since the latter was found to be erroneous in some cases. The new approach can be used in combination with the master equation which is considerably faster than the corresponding Monte Carlo approach. The long-range character of the singlet exciton coupling is taken into account by an extrapolation scheme. The approach is applied to singlet exciton diffusion in those substances where these quantities are experimentally best established: naphthalene and anthracene. The high quality of the crystals, furthermore, diminish uncertainties arising from the geometrical structures used in the computations. For those systems, our new approach provides exciton diffusion lengths L for naphthalene and anthracene crystals which show an excellent agreement with their experimental counterparts. For anthracene, for example, the computed L value in a direction is computed to 58 nm while the experimental value is 60 ± 10 nm.
Dopamine Reduction in the Substantia Nigra of Parkinson's Disease Patients Confirmed by In Vivo Magnetic Resonance Spectroscopic Imaging
2014-01-08

Reduced N-acetylaspartate and dopamine concentrations result from progressive degeneration of dopamine-producing neurons within the substantia nigra pars compacta. Decreased creatine levels can be interpreted as impaired energy metabolism due to mitochondrial dysfunction. Lower glutathione concentrations might be a cause or consequence of oxidative stress. Furthermore, slightly increased glutamine+glutamate and γ-aminobutyric acid levels are expected based on post mortem data in Parkinson's disease. To the best of our knowledge, this is the first non-invasive confirmation of these metabolic changes.
α2δ3 Is Essential for Normal Structure and Function of Auditory Nerve Synapses and Is a Novel Candidate for Auditory Processing Disorders
2014-01-08

The auxiliary subunit α 2 δ3 modulates the expression and function of voltage-gated calcium channels. Here we show that α 2 δ3 mRNA is expressed in spiral ganglion neurons and auditory brainstem nuclei and that the protein is required for normal acoustic responses. Genetic deletion of α 2 δ3 led to impaired auditory processing, with reduced acoustic startle and distorted auditory brainstem responses. α 2 δ3 −/− mice learned to discriminate pure tones, but they failed to discriminate temporally structured amplitude-modulated tones. Light and electron microscopy analyses revealed reduced levels of presynaptic Ca 2+ channels and smaller auditory nerve fiber terminals contacting cochlear nucleus bushy cells. Juxtacellular in vivo recordings of sound-evoked activity in α 2 δ3 −/− mice demonstrated impaired transmission at these synapses. Together, our results identify a novel role for the α 2 δ3 auxiliary subunit in the structure and function of specific synapses in the mammalian auditory pathway and in auditory processing disorders.
Solute carrier transporter and drug-related nephrotoxicity: the impact of proximal tubule cell models for preclinical research
2014-01-08

In vitro cell culture models (e.g., continuous and primary renal cell lines, polarized cell monolayers) represent valuable tools for early assessment of the nephrotoxic potential of drugs. Since SLC transporters contribute to drug excretion in a large part, in vitro cell culture models might be very helpful to study transport pathways and/or potential drug-drug interactions at an early stage of the drug development process to predict nephrotoxic effects.
Sodium Lignosulfonate Induced Vaterite Calcium Carbonate with Multilayered Structure
2014-01-08

Abstract Sodium lignosulfonate (SL), a byproduct of the pulping industry, was used as a stabilizer for the mineralization of CaCO 3 . In a calcium acetate–urea–water system, the direct aging of the aqueous solution of calcium acetate and urea resulted in the formation of mixed aragonite and vaterite phases or a pure aragonite phase depending on the aging time. However, SL was introduced into the calcium acetate–urea–water system to markedly stabilize the formation of a thermodynamically unstable vaterite phase. Various morphologies of vaterite structures were observed by adjusting the concentration of urea and SL as well as the aging time. Based on these results, ion exchange, carbonate attacking the calcium(II) ions, aggregations of SL‐stabilized primary CaCO 3 particles through oriented attachment and Ostwald ripening, as well as mesoscale self‐assembly were proposed as mechanisms to elucidate the formation of various morphologies.
Mondegreens and Soramimi as a Method to Induce Misperceptions of Speech Content – Influence of Familiarity, Wittiness, and Language Competence
2014-01-08

Expectations and prior knowledge can strongly influence our perception. In vision research, such top-down modulation of perceptual processing has been extensively studied using ambiguous stimuli, such as reversible figures. Here, we propose a novel method to address this issue in the auditory modality during speech perception by means of Mondgreens and Soramimi which represent song lyrics with the potential for misperception within one or across two languages, respectively. We demonstrate that such phenomena can be induced by visual presentation of the alternative percept and occur with a sufficient probability to exploit them in neuroscientific experiments. Song familiarity did not influence the occurrence of such altered perception indicating that this tool can be employed irrespective of the participants' knowledge of music. On the other hand, previous knowledge of the alternative percept had a strong impact on the strength of altered perception which is in line with frequent reports that these phenomena can have long-lasting effects. Finally, we demonstrate that the strength of changes in perception correlated with the extent to which they were experienced as amusing as well as the vocabulary of the participants as source of potential interpretations. These findings suggest that such perceptional phenomena might be linked to the pleasant experience of resolving ambiguity which is in line with the long-existing theory of Hermann von Helmholtz that perception and problem-solving recruit similar processes.
Design and Synthesis of Tricyclic JAK3 Inhibitors with Picomolar Affinities as Novel Molecular Probes
2014-01-08

Abstract The Janus kinase (JAK) signaling pathway is of particular importance in the pathology of inflammatory diseases and oncological disorders, and the inhibition of Janus kinase 3 (JAK3) with small molecules has proven to provide therapeutic immunosuppression. A novel class of tricyclic JAK inhibitors derived from the 3‐methyl‐1,6‐dihydrodipyrrolo[2,3‐ b :2′,3′‐ d ]pyridine scaffold was designed based on the tofacitinib–JAK3 crystal structure by applying a rigidization approach. A convenient synthetic strategy to access the scaffold via an intramolecular Heck reaction was developed, and a small library of inhibitors was prepared and characterized using in vitro biochemical as well as cellular assays. IC 50 values as low as 220 p M could be achieved with selectivity for JAK3 over other JAK family members. Both activity and selectivity were confirmed in a cellular STAT phosphorylation assay, providing also first‐time data for tofacitinib. Our novel inhibitors may serve as tool compounds and useful probes to explore the role of JAK3 inhibition in pharmacodynamics studies.
Correction: Screening for Protein-DNA Interactions by Automatable DNA-Protein Interaction ELISA
2014-01-08

DNA-binding proteins (DBPs), such as transcription factors, constitute about 10% of the protein-coding genes in eukaryotic genomes and play pivotal roles in the regulation of chromatin structure and gene expression by binding to short stretches of DNA.Despite their number and importance, only for a minor portion of DBPs the binding sequence had been disclosed.Methods that allow the de novo identification of DNA-binding motifs of known DBPs, such as protein binding microarray technology or SELEX, are not yet suited for high-throughput and automation.To close this gap, we report an automatable DNA-protein-interaction (DPI)-ELISA screen of an optimized double-stranded DNA (dsDNA) probe library that allows the high-throughput identification of hexanucleotide DNA-binding motifs.In contrast to other methods, this DPI-ELISA screen can be performed manually or with standard laboratory automation.Furthermore, output evaluation does not require extensive computational analysis to derive a binding consensus.We could show that the DPI-ELISA screen disclosed the full spectrum of binding preferences for a given DBP.As an example, AtWRKY11 was used to demonstrate that the automated DPI-ELISA screen revealed the entire range of in vitro binding preferences.In addition, protein extracts of AtbZIP63 and the DNA-binding domain of AtWRKY33 were analyzed, which led to a refinement of their known DNA-binding consensi.Finally, we performed a DPI-ELISA screen to disclose the DNA-binding consensus of a yet uncharacterized putative DBP, AtTIFY1.A palindromic TGATCA-consensus was uncovered and we could show that the GATC-core is compulsory for AtTIFY1 binding.This specific interaction between AtTIFY1 and its DNA-binding motif was confirmed by in vivo plant one-hybrid assays in protoplasts.Thus, the value and applicability of the DPI-ELISA screen for de novo binding site identification of DBPs, also under automatized conditions, is a promising approach for a deeper understanding of gene regulation in any organism of choice.
On the origin of cyclotron lines in the spectra of X-ray pulsars
2014-01-08

\\nCyclotron resonance scattering features are observed in the spectra of some X-ray pulsars and show significant changes in the line energy with the pulsar luminosity. In a case of bright sources, the line centroid energy is anti-correlated with the luminosity. Such a behaviour is often associated with the onset and growth of the accretion column, which is believed to be the origin of the observed emission and the cyclotron lines. However, this scenario inevitably implies large gradient of the magnetic field strength within the line-forming region, and it makes the formation of the observed line-like features problematic. Moreover, the observed variation of the cyclotron line energy is much smaller than could be anticipated for the corresponding luminosity changes. We argue that a more physically realistic situation is that the cyclotron line forms when the radiation emitted by the accretion column is reflected from the neutron star surface. The idea is based on the facts that a substantial part of column luminosity is intercepted by the neutron star surface and the reflected radiation should contain absorption features. The reflection model is developed and applied to explain the observed variations of the cyclotron line energy in a bright X-ray pulsar V 0332+53 over a wide range of luminosities.\\n
Electron Transfer from Humic Substances to Biogenic and Abiogenic Fe(III) Oxyhydroxide Minerals
2014-01-09

Microbial humic substance (HS) reduction and subsequent abiotic electron transfer from reduced HS to poorly soluble Fe(III) (oxyhydr)oxides, a process named electron shuttling, significantly increases microbial Fe(III) mineral reduction rates. However, the importance of electron shuttling in nature and notably the electron transfer from HS to biogenic Fe(III) (oxyhydr)oxides have thus far not been determined. In this study, we have quantified the rate and extent of electron transfer from reduced and nonreduced Pahokee Peat humic acids (PPHA) and fresh soil organic matter (SOM) extracts to both synthetic and environmentally relevant biogenic Fe(III) (oxyhydr)oxides. We found that biogenic Fe(III) minerals were reduced faster and to an equal or higher degree than their abiogenic counterparts. Differences were attributed to differences in crystallinity and the association of bacterial biomass with biogenic minerals. Compared to purified PPHA, SOM extract transferred fewer electrons per milligram of carbon and electron transfer was observed only to poorly crystalline ferrihydrite but not to more crystalline goethite. This indicates a difference in redox potential distribution of the redox-active functional groups in extracted SOM relative to the purified PPHA. Our results suggest that HS electron shuttling can also contribute to iron redox processes in environments where biogenic Fe(III) minerals are present.