bluuebunny/crossref_metadata_2025 huggingface dataset:
Simultaneous extraction of charge density dependent mobility and variable contact resistance from thin film transistors
Authors: Di Pietro Riccardo , Venkateshvaran Deepak , Klug Andreas , List-Kratochvil Emil J. W. , Facchetti Antonio , Sirringhaus Henning , Neher Dieter
Published: May 2014

A model for the extraction of the charge density dependent mobility and variable contact resistance in thin film transistors is proposed by performing a full derivation of the current-voltage characteristics both in the linear and saturation regime of operation. The calculated values are validated against the ones obtained from direct experimental methods. This approach allows unambiguous determination of gate voltage dependent contact and channel resistance from the analysis of a single device. It solves the inconsistencies in the commonly accepted mobility extraction methods and provides additional possibilities for the analysis of the injection and transport processes in semiconducting materials.
One-dimensional electronic transport at the organic charge-transfer interfaces under high pressures
Authors: Kang N. , Auban-Senzier P. , Li C. , Poulard C. , Pasquier C. R.
Published: May 2014

We have characterized the charge transport properties of the electronic state at the interface between tetrathiofulvalene and 7,7,8,8-tetracyanoquinodimethane organic crystals as a function of pressure. At low temperature and for all studied pressures, the conductance and the current through the interface exhibit a power-law dependence on both temperature and bias voltage which reveal features of quasi-one-dimensional character. The transport behavior as well as the pressure dependence of the power-law exponent is consistent with a one-dimensional Wigner crystal model. Our results demonstrate that organic heterointerfaces can provide an ideal platform for exploring the rich electronic phenomena in low-dimensional systems.
Stark shift and field ionization of arsenic donors in 28Si-silicon-on-insulator structures
Authors: Lo C. C. , Simmons S. , Lo Nardo R. , Weis C. D. , Tyryshkin A. M. , Meijer J. , Rogalla D. , Lyon S. A. , Bokor J. , Schenkel T. , Morton J. J. L.
Published: May 2014

We develop an efficient back gate for silicon-on-insulator (SOI) devices operating at cryogenic temperatures and measure the quadratic hyperfine Stark shift parameter of arsenic donors in isotopically purified 28Si-SOI layers using such structures. The back gate is implemented using MeV ion implantation through the SOI layer forming a metallic electrode in the handle wafer, enabling large and uniform electric fields up to 2 V/μm to be applied across the SOI layer. Utilizing this structure, we measure the Stark shift parameters of arsenic donors embedded in the 28Si-SOI layer and find a contact hyperfine Stark parameter of ηa = −1.9 ± 0.7 × 10−3 μm2/V2. We also demonstrate electric-field driven dopant ionization in the SOI device layer, measured by electron spin resonance.
Assessing hafnium on hafnia as an oxygen getter
Authors: O'Hara Andrew , Bersuker Gennadi , Demkov Alexander A.
Published: May 2014

Hafnium dioxide or hafnia is a wide band gap dielectric used in a range of electronic applications from field effect transistors to resistive memory. In many of these applications, it is important to maintain control over oxygen stoichiometry, which can be realized in practice by using a metal layer, specifically hafnium, to getter oxygen from the adjacent dielectric. In this paper, we employ density functional theory to study the thermodynamic stability of an interface between (100)-oriented monoclinic hafnia and hafnium metal. The nudged elastic band method is used to calculate the energy barrier for migration of oxygen from the oxide to the metal. Our investigation shows that the presence of hafnium lowers the formation energy of oxygen vacancies in hafnia, but more importantly the oxidation of hafnium through the migration of oxygen from hafnia is favored energetically.
An efficient fast response and high-gain solar-blind flexible ultraviolet photodetector employing hybrid geometry
Authors: Hussain Amreen A. , Pal Arup R. , Patil Dinkar S.
Published: May 2014

We report high performance flexible hybrid ultraviolet photodetector with solar-blind sensitivity using nanocomposite film of plasma polymerized aniline-titanium dioxide. A facile solvent-free plasma technique is used to synthesize superior quality hybrid material with high yield. The hybrid photodetector exhibited high photoconductive gain of the order of ∼105 and fast speed with response and recovery time of 22.87 ms and 34.23 ms. This is an excellent result towards getting a balance in the response speed and photoconductive gain trade-off of the photodetectors reported so far. In addition, the device has the advantages of enhanced photosensitivity ((Ilight − Idark)/Idark) of the order of ∼102 and high responsivity of ∼104 AW−1. All the merits substantiates that, to prepare hybrid material, plasma based method holds potential to be an easy way for realizing large scale nanostructured photodetectors for practical applications.
Generalized criterion for thermo-field emission driven electrical breakdown of gases
Authors: Venkattraman Ayyaswamy
Published: May 2014

Microdischarges operating in an ambient gas with both thermionic and field emission from the cathode are considered theoretically to predict pre-breakdown current density vs voltage as well as breakdown voltages. The integrals in the thermo-field current density expression lead to a breakdown criterion that does not have a simple closed-form and requires the use of optimization techniques to obtain the breakdown voltage. The breakdown voltage is shown to be a non-monotonic function of both cathode temperature and gap size. The proposed framework can be applied with no additional effort to gas breakdown driven by other cathode emission mechanisms.
Long-term microfluidic glucose and lactate monitoring in hepatic cell culture
Authors: Prill Sebastian , Jaeger Magnus S. , Duschl Claus
Published: May 2014

Monitoring cellular bioenergetic pathways provides the basis for a detailed understanding of the physiological state of a cell culture. Therefore, it is widely used as a tool amongst others in the field of in vitro toxicology. The resulting metabolic information allows for performing in vitro toxicology assays for assessing drug-induced toxicity. In this study, we demonstrate the value of a microsystem for the fully automated detection of drug-induced changes in cellular viability by continuous monitoring of the metabolic activity over several days. To this end, glucose consumption and lactate secretion of a hepatic tumor cell line were continuously measured using microfluidically addressed electrochemical sensors. Adapting enzyme-based electrochemical flat-plate sensors, originally designed for human whole-blood samples, to their use with cell culture medium supersedes the common manual and laborious colorimetric assays and off-line operated external measurement systems. The cells were exposed to different concentrations of the mitochondrial inhibitor rotenone and the cellular response was analyzed by detecting changes in the rates of the glucose and lactate metabolism. Thus, the system provides real-time information on drug-induced liver injury in vitro.
Do Artists Use Linear Perspective to Depict Visual Space?
Authors: Pepperell Robert , Haertel Manuela
Published: May 2014

The question of how to accurately depict visual space has fascinated artists, architects, scientists, and philosophers for hundreds of years. Many have argued that linear perspective, which is based on well-understood laws of optics and geometry, is the correct way to record visual space. Others have argued that linear perspective projections fail to account for important features of visual experience, and have proposed various curvilinear, subjective, and hyperbolic forms of perspective instead. In this study we compare three sets of artistic depictions of real-world scenes with linear perspective versions (photographs) of the same scenes. They include a series of paintings made by one of the authors, a selection of landscape paintings by Paul Cézanne, and a set of drawings made as part of a controlled experiment by people with art training. When comparing the artworks with the photographs depicting the same visual space, we found consistent differences. In the artworks the part of the scene corresponding to the central visual field was enlarged compared with the photograph, and the part corresponding to the peripheral field was compressed. We consider a number of factors that could explain these results.
Genotype-dependent influence of night-time vapour pressure deficit on night-time transpiration and daytime gas exchange in wheat
Authors: Schoppach Rémy , Claverie Elodie , Sadok Walid
Published: May 2014

In crop plants, accumulating evidence indicates non-marginal night-time transpiration (TRNight) that is responsive to environmental conditions, especially in semiarid areas. However, the agronomical advantages resulting from such phenomenon remain obscure. Recently, drought-tolerance strategies directly stemming from daytime TR (TRDay) responses to daytime vapour pressure deficit VPD (VPDDay) were identified in wheat (Triticum spp.), but the existence of similar strategies resulting from TRNight response to night-time VPD (VPDNight) remains to be investigated, especially that preliminary evidence on this species indicates that TRNight might be responsive to VPDNight. Our study aims at investigating such strategies among a group of diverse lines including drought-tolerant genotypes. The study revealed that: (i) TRNight can be as high as 55% that of the maximal TRDay; (ii) VPDNight is the major driver of TRNight in a genotype-dependent fashion and has an impact on following daytime gas exchange; and (iii) a strong correlation exists between TR sensitivities to VPD under night-time and daytime conditions, revealing that tolerance strategies such as conservative water use do also exist under night-time environments. Overall, this report opens the way to further phenotyping and modelling work aiming at assessing the potential of using TRNight as a trait in breeding new drought-tolerant germplasm.
Assessment of the temporal pattern of fire activity and weather variability in Lebanon
Authors: Salloum Liliane , Mitri George
Published: May 2014

The aim of this work was to investigate the yearly temporal pattern of fire activity and its relationship to weather in Lebanon during the past decade. The specific objectives were (1) to determine the start, peak and end dates of the fire season and their temporal changes throughout the years, and (2) to evaluate corresponding weather variability and its relationship to changes in fire occurrence and seasonality. First, fire seasonality was determined using fire occurrence data from 2001 to 2011. Second, the de-trended mean monthly weather variables were studied for correlation with fire occurrence between the earliest starting month and the latest ending month of the determined fire seasons. The results showed that the average length of the fire season was 146.6 days, the average start date was 14 June, and the average end date was 12 November. Fire occurrence was positively correlated with mean monthly temperatures and negatively correlated with mean monthly precipitation and mean monthly wind speed. The length of the fire season was negatively correlated with mean annual precipitation. In addition, an increasing fire occurrence risk was observed in association with high maximum temperatures and long dry seasons.
A seismologically consistent compositional model of Earth’s core
Authors: Badro James , Côté Alexander S. , Brodholt John P.
Published: May 2014

Significance

It is well known that Earth’s core is made primarily of iron, alloyed with ∼5% nickel and some lighter elements, such as carbon, oxygen, silicon, or sulfur. The amount as well as the chemistry of the light elements is poorly known and still a matter of considerable debate. In this paper we calculate the seismic signature of iron-rich light-element alloys and compare them to the seismic properties of Earth’s core. We find that oxygen is required as a major light element in the core, whereas silicon, sulfur, and carbon are not required. We also find that silicon concentration in the core cannot be higher than 4.5%, and sulfur concentration cannot be higher than 2.4%.
Active learning increases student performance in science, engineering, and mathematics
Authors: Freeman Scott , Eddy Sarah L. , McDonough Miles , Smith Michelle K. , Okoroafor Nnadozie , Jordt Hannah , Wenderoth Mary Pat
Published: May 2014

Significance

The President’s Council of Advisors on Science and Technology has called for a 33% increase in the number of science, technology, engineering, and mathematics (STEM) bachelor’s degrees completed per year and recommended adoption of empirically validated teaching practices as critical to achieving that goal. The studies analyzed here document that active learning leads to increases in examination performance that would raise average grades by a half a letter, and that failure rates under traditional lecturing increase by 55% over the rates observed under active learning. The analysis supports theory claiming that calls to increase the number of students receiving STEM degrees could be answered, at least in part, by abandoning traditional lecturing in favor of active learning.
Global view of enhancer–promoter interactome in human cells
Authors: He Bing , Chen Changya , Teng Li , Tan Kai
Published: May 2014

Significance

In eukaryotes, gene expression is controlled by short regulatory DNA sequences called enhancers. Understanding how an enhancer selects its target promoter(s) is a major challenge in the field of gene regulation. Advances in genomic technologies have enabled rapid and comprehensive identification of active promoters and enhancers for many cell types. However, there is a lack of methods to link bona fide enhancers and their target promoters. Here, we develop and integrate multiple genomic features into a statistical predictor for enhancer–promoter interactions. Systematic analyses of the predicted interactions across 12 cell types reveals several global features of enhancer–promoter communication. Our approach presents a systematic and effective strategy to decipher the mechanisms underlying enhancer and promoter communication.
Selection and constraint underlie irreversibility of tooth loss in cypriniform fishes
Authors: Aigler Sharon R. , Jandzik David , Hatta Kohei , Uesugi Kentaro , Stock David W.
Published: May 2014

Significance

The mechanisms underlying Dollo’s Law, the assertion that the evolutionary loss of complex structures is irreversible, remain poorly characterized. In principle, such mechanisms could involve the improbability either of generating the mutations required for trait reappearance or of selecting for their fixation. Whereas most attention has focused on the former mechanism, we used experimental reversal of dentition reduction in cypriniform fishes to provide evidence for the operation of both within a single system.
DELLA protein functions as a transcriptional activator through the DNA binding of the INDETERMINATE DOMAIN family proteins
Authors: Yoshida Hideki , Hirano Ko , Sato Tomomi , Mitsuda Nobutaka , Nomoto Mika , Maeo Kenichiro , Koketsu Eriko , Mitani Rie , Kawamura Mayuko , Ishiguro Sumie , Tada Yasuomi , Ohme-Takagi Masaru , Matsuoka Makoto , Ueguchi-Tanaka Miyako
Published: May 2014

Significance

Gibberellin (GA)-dependent degradation of DELLA protein, a key negative regulator, is essential for GA action. However, it is unclear how DELLA regulates downstream gene expression. Although possessing strong transactivation activity, DELLA lacks a DNA-binding domain. Therefore, a model has been proposed in which DELLA acts as a transcriptional coactivator with another transcription factor or factors containing a DNA-binding domain. Here, we show that some members of the INDETERMINATE DOMAIN (IDD) protein family are such intermediate proteins. The DELLA/IDD complex up-regulates the expression of the GA-positive regulatorSCARECROW-LIKE 3(SCL3). Meanwhile, SCL3 protein also interacts with IDD proteins to suppress its own expression. We propose that a coregulator exchange system between DELLA (as coactivator) and SCL3 (as corepressor) regulates the expression ofSCL3.
Repair of DNA double-strand breaks by templated nucleotide sequence insertions derived from distant regions of the genome
Authors: Onozawa Masahiro , Zhang Zhenhua , Kim Yoo Jung , Goldberg Liat , Varga Tamas , Bergsagel P. Leif , Kuehl W. Michael , Aplan Peter D.
Published: May 2014

Significance

We show that DNA double-strand breaks (DSBs) can be repaired by insertion of 50- to 1,000-bp sequences termed “templated-sequence insertions” (TSIs) derived from distant regions of the genome. Additional experiments indicate that the source of template for repair was primarily nuclear RNA. This mode of DNA-DSB repair by insertion is not restricted to experimentally produced breaks but also occurs at the site of spontaneous DNA DSBs in human cells. These TSIs are polymorphic in the human genome, suggesting that some TSIs occur in germ cells or embryos. Recognition of these TSIs is important in interpreting structural variations in short-read sequencing studies and provides additional polymorphic markers for population and evolution studies. This error-prone form of DNA repair may play a role in genetic diseases.
Integrating phase and composition of secondary organic aerosol from the ozonolysis of α-pinene
Authors: Kidd Carla , Perraud Véronique , Wingen Lisa M. , Finlayson-Pitts Barbara J.
Published: May 2014

Significance

The phase of atmospheric aerosol particles can have dramatic effects on reactivity, growth, oxidation, and water uptake. As such, it plays a critical role in every aspect of particle evolution. Despite this, our knowledge of the phase of secondary organic aerosol (SOA) and how it changes in relation to conditions during SOA formation, particle history, composition, relative humidity, and temperature remains poor. Recent laboratory experiments suggest that SOA, under certain circumstances, is best described as a semisolid or viscous tar. This work shows how phase/viscosity, water availability during SOA formation, and composition are interrelated and offers mechanistic insights into these relationships.
Childhood bullying involvement predicts low-grade systemic inflammation into adulthood
Authors: Copeland William E. , Wolke Dieter , Lereya Suzet Tanya , Shanahan Lilly , Worthman Carol , Costello E. Jane
Published: May 2014

Significance

Bullying is a common childhood experience that affects children at all income levels and racial/ethnic groups. Being a bully victim has long-term adverse consequences on physical and mental health and financial functioning, but bullies themselves display few ill effects. Here, we show that victims suffer from greater increases in low-grade systemic inflammation from childhood to young adulthood than are seen in others. In contrast, bullies showed lower increases in inflammation into adulthood compared with those uninvolved in bullying. Elevated systemic low-grade inflammation is a mechanism by which this common childhood social adversity may get under the skin to affect adult health functioning, even many years later.
In vitro assay using engineered yeast vacuoles for neuronal SNARE-mediated membrane fusion
Authors: Ko Young-Joon , Lee Miriam , Kang KyeongJin , Song Woo Keun , Jun Youngsoo
Published: May 2014

Significance

Although synaptic vesicle fusion plays a crucial role in neurotransmission, studies of its molecular mechanisms have relied heavily on the use of artificial liposomes reconstituted with recombinantly expressed proteins. In this study, we establish an in vitro assay using engineered yeast vacuoles bearing neuronal SNAREs for measuring neuronal SNARE-mediated membrane fusion and show that this assay provides a simple and independent means of investigating synaptic vesicle fusion mechanisms.
Helicase proteins DHX29 and RIG-I cosense cytosolic nucleic acids in the human airway system
Authors: Sugimoto Naoshi , Mitoma Hiroki , Kim Taeil , Hanabuchi Shino , Liu Yong-Jun
Published: May 2014

Significance

Different molecules act in sensing cytosolic nucleic acids derived from viruses, depending on the cell type and the virus. Epithelial cells and fibroblasts recognize viral invasion through cytosolic nucleic acid sensors and initiate antiviral immune responses by secreting cytokines. Retinoic acid-inducible gene 1 (RIG-I), a member of the DNA/RNA helicase family, plays a significant role as such a sensor. We identified DEAH (Asp-Glu-Ala-His) box polypeptide 29 (DHX29), another member of the family, as a unique cytosolic nucleic acid cosensor in human airway epithelial cells and fibroblasts. DHX29 directly bound nucleic acids, interacted with RIG-I, and triggered downstream signaling. DHX29 may be the optimal target for drug and vaccine design to control viral infections and viral-induced pathology in the airway.
Functional type 2 photosynthetic reaction centers found in the rare bacterial phylum Gemmatimonadetes
Authors: Zeng Yonghui , Feng Fuying , Medová Hana , Dean Jason , Koblížek Michal
Published: May 2014

Significance

Photosynthesis is one of the most fundamental biological processes on Earth. To date, species capable of performing (bacterio)chlorophyll-based phototrophy have been reported in six bacterial phyla. Here we report a phototrophic bacterium belonging to the rare and understudied phylum Gemmatimonadetes. This strain, isolated from a freshwater lake in the Gobi Desert, contains fully functional photosynthetic reaction centers. Its photosynthesis genes appear to originate from an ancient horizontal gene transfer from a purple phototrophic bacterium. Our findings not only demonstrate that Gemmatimonadetes represents a new phototrophic bacterial phylum, but also present, to our knowledge, the first evidence that genes for (bacterio)chlorophyll-based phototrophy can be transferred between distant bacterial phyla.
Air-stable droplet interface bilayers on oil-infused surfaces
Authors: Boreyko Jonathan B. , Polizos Georgios , Datskos Panos G. , Sarles Stephen A. , Collier C. Patrick
Published: May 2014

Significance

By suspending a lipid bilayer in an aperture or between water droplets, single-molecule transport through membrane channels can be electrically detected. To date, all suspended bilayers have been confined to fluid reservoirs. This study demonstrates that droplet interface bilayers can be created in an ambient environment using noncoalescing water droplets on an oil-infused surface. Air-stable droplet interface bilayers are easy to manipulate and electrically characterize, and could potentially allow for the biosensing of airborne molecules.
Cheating by type 3 secretion system-negative
Pseudomonas aeruginosa
during pulmonary infection
Authors: Czechowska Kamila , McKeithen-Mead Saria , Al Moussawi Khatoun , Kazmierczak Barbara I.
Published: May 2014

Significance

Bacterial pathogens frequently use type 3 secretion systems (T3SS) to counteract host immune responses to infection. T3SS expression is associated with increased virulence of
Pseudomonas aeruginosa
in humans and in animal models, but T3SS-negative bacteria often are isolated from acutely and chronically infected patients. We tested whether T3SS-negative bacteria could “cheat” during mixed infections with T3SS-positive bacteria in a murine model of acute pneumonia. Bacterial cheating occurred in the inflamed lung but only when T3SS-positive bacteria secreted the phospholipase A
2
effector, Exotoxin U. Phenotypically T3SS-expressing and –non-expressing bacteria co-exist within
P. aeruginosa
populations, suggesting that bacterial cheating might allow T3SS-negative organisms to establish themselves within a host.
Neurons in cortical area MST remap the memory trace of visual motion across saccadic eye movements
Authors: Inaba Naoko , Kawano Kenji
Published: May 2014

Significance

We found that most medial superior temporal (MST) neurons, but no middle temporal neurons, increased their firing rates when a saccade brought the location of the visual stimulus, which had been visible only before the saccade, into their receptive fields (RFs): so-called “memory remapping.” The distinctive feature of the MST neurons is that they did not respond to stimuli in their future RFs before the saccade, a response known as “predictive remapping.” In other areas (e.g., lateral intraparietal cortex, frontal eye field), neurons showing memory remapping had been recorded together with neurons showing predictive remapping, consistent with their role in guiding goal-directed motor actions such as saccades. Our finding is understandable in the view that MST has a different role, which is to perceive the visual world.
Family of prokaryote cyclic nucleotide-modulated ion channels
Authors: Brams Marijke , Kusch Jana , Spurny Radovan , Benndorf Klaus , Ulens Chris
Published: May 2014

Significance

We describe a previously unidentified family of prokaryote cyclic nucleotide-modulated ion channels. In eukaryotes, CNG channels play important roles in signal transduction as they mediate the passage of ions across the cell membrane in response to cAMP or cGMP. In this study, we demonstrate that two prokaryote homologs, AmaK and SthK, can be expressed and purified from
Escherichia coli
membranes. We reveal that SthK has functional properties that closely resemble eukaryote HCN or CNG channels. SthK is gated by cyclic AMP, but not cyclic GMP, and selects K
+
over Na
+
ions in a weakly voltage-dependent manner. Our results contribute to understanding the evolutionary origin of cyclic nucleotide-modulated ion channels and pave the way for future structural and functional studies.
Lipid flippase modulates olfactory receptor expression and odorant sensitivity in
Drosophila
Authors: Ha Tal Soo , Xia Ruohan , Zhang Haiying , Jin Xin , Smith Dean P.
Published: May 2014

Significance

The work identifies dATP8B as a critical factor for proper odorant and 11-
cis
-vaccenyl acetate pheromone sensitivity. These defects are attributed to a failure to translocate lipids, because mutants defective for dATP8B enzymatic activity do not rescue, but a functional vertebrate homolog fully rescues the pheromone detection defects. We identified abnormal localization of Or67d receptors as a likely cause for the phenotypes, and overexpression of Or67d can rescue 11-
cis
-vaccenyl acetate sensitivity and loss of spontaneous spiking in the lipid flippase mutant. We suggest dATP8B is important for lipid translocation in olfactory neurons, which in turn is important for proper subcellular trafficking of receptor subunits.
In vivo modulation of hypoxia-inducible signaling by topographical helix mimetics
Authors: Lao Brooke Bullock , Grishagin Ivan , Mesallati Hanah , Brewer Thomas F. , Olenyuk Bogdan Z. , Arora Paramjit S.
Published: May 2014

Significance

Protein–protein interactions are attractive targets for drug design due to their fundamental role in biological function. However, small molecules that selectively target the intended interactions have been difficult to access using traditional drug discovery approaches. We show that compounds that reproduce key functionality at the interface between transcription factor hypoxia-inducible factor 1α (HIF1α) and coactivator p300 (or CREB binding protein, CBP) can inhibit expression of a multitude of genes under hypoxic environments. The designed inhibitors target the chosen protein–protein interaction in a predictable manner and reduce tumor growth in mouse xenograft models.
Specificity of
O
-glycosylation in enhancing the stability and cellulose binding affinity of Family 1 carbohydrate-binding modules
Authors: Chen Liqun , Drake Matthew R. , Resch Michael G. , Greene Eric R. , Himmel Michael E. , Chaffey Patrick K. , Beckham Gregg T. , Tan Zhongping
Published: May 2014

Significance

Plant biomass decomposition has broad implications for the global carbon cycle, agriculture, and ecology, and it is primarily accomplished by fungi. Recently, research into fungal biomass degradation mechanisms has been driven by the growing biofuels industry, because enzymes from fungi are among the primary catalysts being investigated for industrial processes to convert polysaccharides into upgradeable sugars. Understanding the mechanisms used by polysaccharide-degrading enzymes and identifying means to improve their performance is of paramount importance because of the scale of enzyme production for biofuels processes. Here, we use glycoprotein synthesis and biophysical measurements to characterize the specific effects of glycosylation on ubiquitous fungal carbohydrate-binding modules for biomass degradation, which reveal key features of the importance of posttranslational modifications on enzyme function.
Compressive mapping of number to space reflects dynamic encoding mechanisms, not static logarithmic transform
Authors: Cicchini Guido Marco , Anobile Giovanni , Burr David C.
Published: May 2014

Significance

The ability to map numbers onto space is fundamental to measurement and mathematics. The mental “numberline” is an important predictor of math ability, thought to reflect an internal, native logarithmic representation of number, later becoming linearized by education. Here we demonstrate that the nonlinearity results not from a static logarithmic transformation but from dynamic processes that incorporate past history into numerosity judgments. We show strong and significant correlations between the response to the current trial and the magnitude of the previous stimuli and that subjects respond with a weighted average of current and recent stimuli, explaining completely the logarithmic-like nonlinearity. We suggest that this behavior reflects a general strategy akin to predictive coding to cope adaptively with environmental statistics.
Split-gene system for hybrid wheat seed production
Authors: Kempe Katja , Rubtsova Myroslava , Gils Mario
Published: May 2014

Significance

Global food security demands the development of new technologies to increase and secure cereal production on finite arable land without increasing water and fertilizer use. Although the use of heterosis through hybrid breeding has produced tremendous economic benefits in worldwide crop production, less than 1% of the global wheat area is planted with hybrids. One of the greatest bottlenecks in breeding hybrid wheat is the lack of an efficient sterility system to block self-pollination. This report describes a recessive system for pollination control in wheat. We demonstrate the implementation and feasibility of the system for generation and maintenance of the male-sterile parent, hybrid seed production and full restoration of fertility in the hybrid wheat seed.
Crystal structure of lipid phosphatase
Escherichia coli
phosphatidylglycerophosphate phosphatase B
Authors: Fan Junping , Jiang Daohua , Zhao Yan , Liu Jianfeng , Zhang Xuejun Cai
Published: May 2014

Significance

Phosphatases regulate many aspects of cellular function-homeostasis and signal transduction. Using X-ray crystallography methods, we determined the structure of phosphatidylglycerol-phosphate phosphatase B (PgpB) from
Escherichia coli
, a member of the type II phosphatidic acid phosphatase (PAP2) family and a homologue of human glucose-6-phosphatase, which plays a variety of physiopathological roles. Our structure of PgpB showed that the membrane-integrated and soluble members of the PAP2 family share the same catalytic mechanism. The mechanism of recognition of lipid substrates was postulated based on analyses of enzymatic activities and thermal stabilities of PgpB variants. This work presents an important structural model for studying eukaryotic PAP2s.
Immunoglobulin somatic hypermutation by APOBEC3/Rfv3 during retroviral infection
Authors: Halemano Kalani , Guo Kejun , Heilman Karl J. , Barrett Bradley S. , Smith Diana S. , Hasenkrug Kim J. , Santiago Mario L.
Published: May 2014

Significance

Antibodies are important for recovery from viral infections and vaccine efficacy. To improve the ability of antibodies to bind and neutralize viral pathogens, antibody DNA sequences undergo a mutational process driven by the enzyme activation-induced deaminase (AID). However, high levels of antibody mutations are required to potently inhibit global strains of the retrovirus HIV-1. We provide evidence that a related enzyme, apolipoprotein B mRNA-editing enzyme catalytic polypeptide 3 (APOBEC3), can also mutate antibodies during retrovirus infection, but in a different DNA sequence context compared to AID. The findings demonstrate that APOBEC3 acts as a key player in generating virus-specific neutralizing antibodies and highlight a previously unidentified mechanism for antibody diversification that could be harnessed for vaccine development.
Glutathione-dependent and -independent oxidative stress-control mechanisms distinguish normal human mammary epithelial cell subsets
Authors: Kannan Nagarajan , Nguyen Long V. , Makarem Maisam , Dong Yifei , Shih Kingsley , Eirew Peter , Raouf Afshin , Emerman Joanne T. , Eaves Connie J.
Published: May 2014

Significance

Our study reveals lineage-specific mechanisms of ROS control and associated sensitivity to oxidative DNA damage in the basal and luminal progenitor-enriched subsets of normal human mammary cells. We show that the primitive luminal cells contain more mitochondria, show greater uptake of O
2
, sustain and withstand higher levels of ROS, and have mechanisms that allow them to accrue mutagenic levels of oxidative DNA damage. These findings support a growing body of data suggesting the involvement of primitive luminal cells in the generation of human breast cancers.
Trypanosomal TAC40 constitutes a novel subclass of mitochondrial β-barrel proteins specialized in mitochondrial genome inheritance
Authors: Schnarwiler Felix , Niemann Moritz , Doiron Nicholas , Harsman Anke , Käser Sandro , Mani Jan , Chanfon Astrid , Dewar Caroline E. , Oeljeklaus Silke , Jackson Christopher B. , Pusnik Mascha , Schmidt Oliver , Meisinger Chris , Hiller Sebastian , Warscheid Bettina , Schnaufer Achim C. , Ochsenreiter Torsten , Schneider André
Published: May 2014

Significance

During cell division mitochondria and their genomes need to be transmitted to the daughter cells. In the parasitic protozoa
Trypansoma brucei
we find a unique situation. It has a single mitochondrion with a single-unit genome that is physically connected to the flagellum. Here we identify the β-barrel mitochondrial outer membrane protein TAC40 that localizes to this connection. TAC40 is essential and defines a novel subclass of mitochondrial porins that are specialized in mitochondrial genome inheritance. A comparative analysis reveals a conserved concept of a mitochondrial DNA inheritance mechanism in trypanosomes and yeast that depends on a physical linkage between mitochondrial DNA and the cytoskeleton, which is organized around a β-barrel protein of the mitochondrial porin family.
Circulating proteolytic signatures of chemotherapy-induced cell death in humans discovered by N-terminal labeling
Authors: Wiita Arun P. , Hsu Gerald W. , Lu Chuanyi M. , Esensten Jonathan H. , Wells James A.
Published: May 2014

Significance

Many chemotherapeutics function by inducing cellular apoptosis, or programmed cell death, in tumor cells. Here, using a unique enzymatically driven technology, we find that numerous protein fragments are released into the bloodstream from apoptotic cells within hours after chemotherapy. These circulating signatures of cell death, if confidently assigned to tumor cells, may form the foundation for entirely novel, rapid, and inexpensive biomarkers of chemotherapeutic efficacy. Diagnostic tests to rapidly assess cell death after treatment could serve an important role in management for many cancers.
Tolerance induction in memory CD4 T cells requires two rounds of antigen-specific activation
Authors: David Alexandria , Crawford Frances , Garside Paul , Kappler John W. , Marrack Philippa , MacLeod Megan
Published: May 2014

Significance

Autoimmune diseases are driven by immune cells that recognize self-tissues. A major goal for treatment strategies for autoimmune diseases is to turn off or tolerize self-reactive immune cells such as CD4 T cells that coordinate tissue damage in many autoimmune diseases. Autoimmune diseases are often diagnosed many years following their onset. The self-reactive CD4 T cells that must be tolerized, therefore, are previously activated or memory CD4 T cells. Little is known about whether tolerance can be induced in memory CD4 T cells. This paper demonstrates that memory CD4 T cells survive initial exposure to tolerance-inducing signals but that a second activation signal leads to cell death. This study has important implications for immunotherapeutic strategies for autoimmune diseases.
Behçet disease-associated MHC class I residues implicate antigen binding and regulation of cell-mediated cytotoxicity
Authors: Ombrello Michael J. , Kirino Yohei , de Bakker Paul I. W. , Gül Ahmet , Kastner Daniel L. , Remmers Elaine F.
Published: May 2014

Significance

To elucidate their role in Behçet disease (BD), we used imputation to analyze MHC class I (MHC-I) alleles and amino acids in a large case-control collection. Several MHC-I alleles influenced BD susceptibility, some conferring risk and others affording protection. The association of MHC-I with BD was mapped to six positions around the peptide-binding groove and to one position in the signal peptide. These residues are critical in defining the peptide-binding specificity of MHC-I molecules, and they also affect the engagement of MHC-I molecules by killer immunoglobulin-like receptors on natural killer and T cells. These data implicate peptide binding by MHC-I in BD pathogenesis and suggest that altered regulation of cytotoxic cells by MHC-I may be pathogenic in BD.
The Role of the Champlain Canal and Erie Canal as Putative Corridors for Colonization of Lake Champlain and Lake Ontario by Sea Lampreys
Authors: Eshenroder Randy L.
Published: May 2014

The origin of populations of the landlocked Sea LampreyPetromyzon marinusin Lakes Champlain and Ontario, whether by artificial canals or by natural colonization following the last ice age, is controversial, in part because the related history and ecology had been poorly documented. This situation favored a native classification for the populations in both lakes based mainly on genetics. A native classification for the Lake Champlain population was predicated on either of two erroneous dates of first record, 1841 and 1894, whereas the correct date, 1929, was much more recent and strongly supports a nonnative classification. The detection of the Sea Lamprey in Lake Champlain occurred shortly after the opening in 1916 of the Champlain Barge Canal, which opened the upper Hudson River to fish passage. The case for a native Lake Ontario population did not account for a watershed breach in 1863 between the Susquehanna River, where the Sea Lamprey had been common, and the Lake Ontario drainage. Shortly after this canal‐related connection was made, Sea Lamprey populations became abundant, nearly simultaneously, in four locations in the Lake Ontario drainage, suggesting this breach was the entry point for the founding population. The genetic distances between the landlocked populations and the Atlantic Ocean population appear to have been caused by recent bottlenecks rather than long‐term residence; a recent genetic bottleneck was detected in the Lake Ontario population. Native classifications rested, in part, on extraordinary ecological scenarios, whereas nonnative classifications are consistent with experience in the upper Great Lakes and with well‐known vectors of range expansion (canals, dam openings, watershed breaches). These findings in aggregate favor a nonnative classification of the Sea Lamprey in both lakes.
Ecological Factors Affecting Rainbow Smelt Recruitment in the Main Basin of Lake Huron, 1976–2010
Authors: O'Brien Timothy P. , Taylor William W. , Roseman Edward F. , Madenjian Charles P. , Riley Stephen C.
Published: May 2014

Rainbow SmeltOsmerus mordaxare native to northeastern Atlantic and Pacific–Arctic drainages and have been widely introduced throughout North America. In the Great Lakes region, Rainbow Smelt are known predators and competitors of native fish and a primary prey species in pelagic food webs. Despite their widespread distribution, importance as a prey species, and potential to negatively interact with native fish species, there is limited information concerning stock–recruitment relationships for Rainbow Smelt. To better understand recruitment mechanisms, we evaluated potential ecological factors determining recruitment dynamics for Rainbow Smelt in Lake Huron using data from bottom trawl catches. We specifically evaluated influence of stock size, environmental factors (water temperature, lake levels, and precipitation), and salmonine predation on the production of age‐0 recruits from 1976 to 2010. Rainbow Smelt recruitment was negatively related to stock size exceeding 10kg/ha, indicating that compensatory, density‐dependent mortality from cannibalism or intraspecific competition was an important factor related to the production of age‐0 recruits. Recruitment was positively related to spring precipitation suggesting that the amount of stream‐spawning habitat as determined by precipitation was important for the production of strong Rainbow Smelt recruitment. Additionally, density of age‐0 Rainbow Smelt was positively related to Lake TroutSalvelinus namaycushabundance. However, spawning stock biomass of Rainbow Smelt, which declined substantially from 1989 to 2010, was negatively associated with Lake Trout catch per effort suggesting predation was an important factor related to the decline of age‐2 and older Rainbow Smelt in Lake Huron. As such, we found that recruitment of Rainbow Smelt in Lake Huron was regulated by competition with or cannibalism by older conspecifics, spring precipitation influencing stream spawning habitats, and predation by Lake Trout on age‐2 and older Rainbow Smelt.
Juvenile Anadromous Salmonid Production in Upper Columbia River Side Channels with Different Levels of Hydrological Connection
Authors: Martens Kyle D. , Connolly Patrick J.
Published: May 2014

We examined the contribution of three types of side channels based on their hydrologic connectivity (seasonally disconnected, partially connected, and connected) to production of juvenile anadromous salmonids. Juvenile steelhead Oncorhynchus mykiss and Chinook Salmon O. tshawytscha were found in all three of these side channel types and in each year of the study. Upon connection with the main stem at high flows, the seasonally disconnected side channels experienced an emptying out of the previous year's fish while filling with young‐of‐year fish during the 2‐ to 4‐month period of hydrologic connection. There were no differences between the densities of juvenile steelhead and Chinook Salmon and the rate of smolts produced among the three types of side channels. Recently reintroduced Coho Salmon O. kisutch had sporadic presence and abundance in partially and connected side channels, but the smolt production rate was over two times that of steelhead and Chinook Salmon in seasonally disconnected side channels. Within seasonally disconnected side channels, young‐of‐year salmonids in deep pools (≥100cm) had greater survival than those in shallow pools (<100cm). Densities of juvenile steelhead in all side channel types were similar to those in tributaries and were higher than in main‐stem lateral margins. Juvenile Chinook Salmon densities were higher in side channels than in both tributary and main‐stem lateral margins. Our results suggest that improving quality of pool habitat within seasonally disconnected side channels can result in improved survival for juvenile anadromous salmonids during the period of disconnection. Habitat improvement in these seasonally disconnected side channels should be recognized as a worthy restoration strategy, especially when full connectivity of side channels may not be a feasible target (e.g., through lack of water availability) or when full connectivity may present too high a risk (e.g., flooding, stream capture, bank destabilization).
Estimates of Skipped Spawning in Lean and Siscowet Lake Trout in Southern Lake Superior: Implications for Stock Assessment
Authors: Sitar Shawn P. , Jasonowicz Andrew J. , Murphy Cheryl A. , Goetz Frederick W.
Published: May 2014

We found that some lean (12.2%) and siscowet (58.0%) Lake Trout Salvelinus namaycush in populations in southern Lake Superior do not reproduce each year (i.e., display “skipped spawning”) even though they have reached puberty. We measured skipped spawning in Lake Trout in southern Lake Superior and assessed its impact on reproduction by developing length‐based and age‐based ogives (i.e., probabilities of being mature). In populations in which skipped spawning is negligible, a maturity ogive can be considered equivalent to a reproduction ogive (probability of being reproductive). However, in populations in which skipped spawning is present, such as in lean and siscowet Lake Trout in southern Lake Superior, maturity and reproduction ogives are very different. We evaluated the influence of skipped spawning on a key stock assessment quantity—spawning stock biomass—by applying maturity and reproduction ogives to simulated populations. Furthermore, we evaluated whether skipped spawning was associated with lower energy reserves by testing for differences in the hepatosomatic index (HSI) according to maturity status. Our population simulations indicate that spawning stock biomass can be overestimated (8.3% for leans and 475% for siscowets) when skipped spawners are assumed to be a part of the spawning stock. An inflated reproductive potential of the population could allow for excessive fishing if quotas are based on these biased spawning stock biomass estimates. Siscowet Lake Trout that were skipping spawning had significantly lower energy reserves (assessed by HSI) than mature fish. The high incidence of skipped spawning in siscowets may be related to the reported slowed somatic growth, high population abundance, and low prey resources in southern Lake Superior, which supports the hypothesis that skipped spawning is a density‐dependent response to limited energy resources.
Pleural innate response activator B cells protect against pneumonia via a GM-CSF-IgM axis
Authors: Weber Georg F. , Chousterman Benjamin G. , Hilgendorf Ingo , Robbins Clinton S. , Theurl Igor , Gerhardt Louisa M.S. , Iwamoto Yoshiko , Quach Tam D. , Ali Muhammad , Chen John W. , Rothstein Thomas L. , Nahrendorf Matthias , Weissleder Ralph , Swirski Filip K.
Published: May 2014

Pneumonia is a major cause of mortality worldwide and a serious problem in critical care medicine, but the immunophysiological processes that confer either protection or morbidity are not completely understood. We show that in response to lung infection, B1a B cells migrate from the pleural space to the lung parenchyma to secrete polyreactive emergency immunoglobulin M (IgM). The process requires innate response activator (IRA) B cells, a transitional B1a-derived inflammatory subset which controls IgM production via autocrine granulocyte/macrophage colony-stimulating factor (GM-CSF) signaling. The strategic location of these cells, coupled with the capacity to produce GM-CSF–dependent IgM, ensures effective early frontline defense against bacteria invading the lungs. The study describes a previously unrecognized GM-CSF-IgM axis and positions IRA B cells as orchestrators of protective IgM immunity.