bluuebunny/crossref_metadata_2025_split huggingface dataset:
Physiology and evolution of nitrate acquisition in Prochlorococcus
Authors: Berube Paul M , Biller Steven J , Kent Alyssa G , Berta-Thompson Jessie W , Roggensack Sara E , Roache-Johnson Kathryn H , Ackerman Marcia , Moore Lisa R , Meisel Joshua D , Sher Daniel , Thompson Luke R , Campbell Lisa , Martiny Adam C , Chisholm Sallie W 
Published: October 2014

Abstract
Prochlorococcus is the numerically dominant phototroph in the oligotrophic subtropical ocean and carries out a significant fraction of marine primary productivity. Although field studies have provided evidence for nitrate uptake by Prochlorococcus, little is known about this trait because axenic cultures capable of growth on nitrate have not been available. Additionally, all previously sequenced genomes lacked the genes necessary for nitrate assimilation. Here we introduce three Prochlorococcus strains capable of growth on nitrate and analyze their physiology and genome architecture. We show that the growth of high-light (HL) adapted strains on nitrate is ∼17% slower than their growth on ammonium. By analyzing 41 Prochlorococcus genomes, we find that genes for nitrate assimilation have been gained multiple times during the evolution of this group, and can be found in at least three lineages. In low-light adapted strains, nitrate assimilation genes are located in the same genomic context as in marine Synechococcus. These genes are located elsewhere in HL adapted strains and may often exist as a stable genetic acquisition as suggested by the striking degree of similarity in the order, phylogeny and location of these genes in one HL adapted strain and a consensus assembly of environmental Prochlorococcus metagenome sequences. In another HL adapted strain, nitrate utilization genes may have been independently acquired as indicated by adjacent phage mobility elements; these genes are also duplicated with each copy detected in separate genomic islands. These results provide direct evidence for nitrate utilization by Prochlorococcus and illuminate the complex evolutionary history of this trait.
Kinesin-14 and kinesin-5 antagonistically regulate microtubule nucleation by γ-TuRC in yeast and human cells
Authors: Olmsted Zachary T. , Colliver Andrew G. , Riehlman Timothy D. , Paluh Janet L. 
Published: October 2014

AbstractBipolar spindle assembly is a critical control point for initiation of mitosis through nucleation and organization of spindle microtubules and is regulated by kinesin-like proteins. In fission yeast, the kinesin-14 Pkl1 binds the γ-tubulin ring complex (γ-TuRC) microtubule-organizing centre at spindle poles and can alter its structure and function. Here we show that kinesin-14 blocks microtubule nucleation in yeast and reveal that this inhibition is countered by the kinesin-5 protein, Cut7. Furthermore, we demonstrate that Cut7 binding to γ-TuRC and the Cut7 BimC domain are both required for inhibition of Pkl1. We also demonstrate that a yeast kinesin-14 peptide blocks microtubule nucleation in two human breast cancer cell lines, suggesting that this mechanism is evolutionarily conserved. In conclusion, using genetic, biochemical and cell biology approaches we uncover antagonistic control of microtubule nucleation at γ-TuRC by two kinesin-like proteins, which may represent an attractive anti-mitotic target for cancer therapies.
Area‐efficient method to approximate two minima for LDPC decoders
Authors: Jung Jaehwan , Lee Youngjoo , Park In‐Cheol 
Published: October 2014

A simple yet effective method is proposed to reduce the hardware complexity of min‐sum‐based low‐density parity‐check (LDPC) decoders. The proposed method finds the second minimum from the last four candidates of the first minimum, and can be implemented with only a few hardware components. In the case of 64 inputs, the proposed method reduces the comparators and 2‐to‐1 multiplexers by 48 and 64% compared to the conventional method that finds two exact minima.
High‐performance HfO2/ZrO2/IGZO thin‐film transistors deposited using atmospheric pressure plasma jet
Authors: Wu Chien‐Hung , Chang Kow‐Ming , Hsu Hsin‐Yu 
Published: October 2014

An atmospheric pressure plasma jet (APPJ) deposition technology that is employed for the preparation of transparent oxide semiconductors film using an eco‐friendly water‐based metal salt solution as a precursor is presented. Through the use of APPJ indium–gallium–zinc‐oxide (IGZO) film as the channel material and a high‐k dielectric HfO2/ZrO2 gate stack, IGZO‐based transparent thin‐film transistors (TFTs) were fabricated and characterised. The HfO2/ZrO2/IGZO‐TFTs by APPJ demonstrated excellent electrical characteristics, including a low Vth of 0.63 V, a small subthreshold swing of 0.37 V/dec, a high mobility of 40 cm2/V‐s and a large Ion/Ioff ratio of 7 × 108.
Compact microstrip triplexer based on twist‐modified asymmetric split‐ring resonators
Authors: Huang Yongjun , Wen Guangjun , Li Jian 
Published: October 2014

On the basis of strong mixed couplings of two adjacent modified asymmetric split‐ring resonators (SRRs), a compact microstrip filter unit is designed and its triplexer application is experimentally demonstrated by properly arranging the layout of three different sized filter units. The cross size of the proposed triplexer is only 20 × 16 mm. Both experimental and numerical results are obtained, which agree quite well with each other. The results show that such triplexer exhibits three quite close channels (2.15/2.95/3.80 GHz) and the isolations for all the three output ports are <20 dB. The proposed triplexer can be flexibly integrated in the miniaturised multi‐frequency/model radio frequency/microwave circuits.
Wideband power amplifier for two‐way radio applications via real‐frequency technique
Authors: Aridas N.K. , Yarman B.S. , Chacko P. 
Published: October 2014

The requirements of two‐way radio applications in the wideband operating frequency are stringent, particularly for the power amplifier (PA) design. A novel design method for a wideband PA matching network for two‐way radio applications is proposed. The design method begins with identifying an initial guess of the matching network from the theoretical analysis, followed by a practical design methodology to realise the design in the compact form factor and low cost implementation. Experimental results demonstrated an output power of ∼7 W and an efficiency of about 65%, demonstrated high power performance (including stable operation and ruggedness) from 270 to 560 MHz running at a low DC supply of 7.2 V (with LDMOS device technology).
Scaling laws governing stochastic growth and division of single bacterial cells
Authors: Iyer-Biswas Srividya , Wright Charles S. , Henry Jonathan T. , Lo Klevin , Burov Stanislav , Lin Yihan , Crooks Gavin E. , Crosson Sean , Dinner Aaron R. , Scherer Norbert F. 
Published: October 2014

Significance
Growth and division of individual cells are the fundamental events underlying many biological processes, including the development of organisms, the growth of tumors, and pathogen–host interactions. Quantitative studies of bacteria can provide insights into single-cell growth and division but are challenging owing to the intrinsic noise in these processes. Now, by using a unique combination of measurement and analysis technologies, together with mathematical modeling, we discover quantitative features that are conserved across physiological conditions. These universal behaviors reflect the physical principle that a single timescale governs noisy bacterial growth and division despite the complexity of underlying molecular mechanisms.
Unconscious information changes decision accuracy but not confidence
Authors: Vlassova Alexandra , Donkin Chris , Pearson Joel 
Published: October 2014

SignificanceOne of the more intriguing but controversial ideas in psychology is that unconscious information can influence our decisions without us even knowing it. Here, we explicitly tested these controversial ideas with a novel behavioral task and computational models of decision-making. We report that unconscious information can be accumulated in a similar manner but less effectively than conscious information. However, unlike conscious information, unconscious information does not seem to boost decision confidence. Our findings cannot be accounted for using existing models of priming or adaptation.
Benchmarking all-atom simulations using hydrogen exchange
Authors: Skinner John J. , Yu Wookyung , Gichana Elizabeth K. , Baxa Michael C. , Hinshaw James R. , Freed Karl F. , Sosnick Tobin R. 
Published: October 2014

Significance
Molecular dynamics simulations have recently become capable of observing multiple protein unfolding and refolding events in a single-millisecond–long trajectory. This major advance produces atomic-level information with nanosecond resolution, a feat unmatched by experimental methods. Such simulations are being extensively analyzed to assess their description of protein folding, yet the results remain difficult to validate experimentally. We apply a combination of hydrogen exchange, NMR, and other techniques to test the simulations with a resolution of single H-bonds. Several significant discrepancies between the simulations and experimental data were uncovered for regions of the energy surface outside of the native basin. This comparison yields suggestions for improving the force fields and provides a general method for experimentally validating folding simulations.
DLK1/PREF1 regulates nutrient metabolism and protects from steatosis
Authors: Charalambous Marika , Da Rocha Simao Teixeira , Radford Elizabeth Jane , Medina-Gomez Gema , Curran Scott , Pinnock Scarlett B. , Ferrón Sacri R. , Vidal-Puig Antonio , Ferguson-Smith Anne C. 
Published: October 2014

Significance
Hepatosteatosis or nonalcoholic fatty liver disease (NAFLD) is an important health problem affecting approximately 20% of the population of the United States and is associated with cardiovascular risk factors such as insulin resistance and obesity. Using a Delta-like homologue (Dlk1) [also known as preadipocyte factor 1 (Pref1)] transgenic model, we identified a new player in the growth hormone (GH) signaling pathway that, when overexpressed, is protective against obesity and hepatosteatosis. Because the dosage of circulating DLK1 is naturally elevated in early life and during pregnancy, we believe that our transgenic model mimics endogenous mechanisms of DLK1-mediated GH signaling modulation that are used during periods of metabolic stress to protect from steatosis and alter fuel utilization in the whole organism.
Sensing nerve injury at the axonal ER: Activated Luman/CREB3 serves as a novel axonally synthesized retrograde regeneration signal
Authors: Ying Zhengxin , Misra Vikram , Verge Valerie M. K. 
Published: October 2014

Significance
Peripheral nerve injury often occurs at axonal sites remote from the neuronal cell bodies. Information about these remote injuries must be accurately relayed back to the cell body as part of the reprogramming that occurs to transition the neuron to a regenerating state. We provide new insights into how the axonal endoplasmic reticulum (ER) proximal to the injury site generates a critical regeneration signal in sensory neurons. This involves injury-triggered activation and synthesis of an intraaxonal, ER transmembrane transcription factor, Luman/cAMP response element binding protein 3, that is retrogradely transported back into the nucleus. Manipulation of axon-derived Luman expression in injured sensory neurons reveals an important role for Luman in regulation of the intrinsic elongating form of axonal growth associated with the regeneration state.
p100/IκBδ sequesters and inhibits NF-κB through kappaBsome formation
Authors: Tao Zhihua , Fusco Amanda , Huang De-Bin , Gupta Kushol , Young Kim Daniel , Ware Carl F. , Van Duyne Gregory D. , Ghosh Gourisankar 
Published: October 2014

SignificanceNF-κB activation pathways program cells to induce various activities including survival and inflammation. NF-κB activation requires inhibitor IκB degradation. Two of the IκB proteins, p100 and p105, are also the precursors of two NF-κB proteins, p52 and p50. The mechanism by which the p100 inhibits NF-κB remains elusive. The X-ray structure of the C-terminal domain of p100 reveals tetrameric organization and an essential function of tetramerization in sequestering four NF-κB molecules in a subunit-independent manner. Such broader nonspecific NF-κB inhibition by p100 contrasts with the functions of other IκB proteins. A host of genetic mutations linked to excessive p100 processing derail homeostatic NF-κB activity. Our work provides a molecular framework to understand homeostatic regulation of p100 function.
Membrane-enabled dimerization of the intrinsically disordered cytoplasmic domain of ADAM10
Authors: Deng Wei , Cho Sungyun , Su Pin-Chuan , Berger Bryan W. , Li Renhao 
Published: October 2014

Significance
Transmembrane receptors often dimerize to facilitate signaling across the cell membrane. Here we show that the intrinsically disordered cytoplasmic domain of a disintegrin and metalloprotease (ADAM)10, an important transmembrane protease, can acquire structure and dimerize when it is adjoined to a transmembrane helix and thus placed near the membrane surface. This study is, to our knowledge, the first report of a transmembrane helix enabling dimerization of an adjacent intrinsically disordered sequence, which not only advances our understanding of the activation mechanism of ADAM protease, but also provides novel insights on the principles of membrane–protein interactions and their roles in transmembrane signaling.
Stretch-activated ion channel Piezo1 directs lineage choice in human neural stem cells
Authors: Pathak Medha M. , Nourse Jamison L. , Tran Truc , Hwe Jennifer , Arulmoli Janahan , Le Dai Trang T. , Bernardis Elena , Flanagan Lisa A. , Tombola Francesco 
Published: October 2014

Significance
Stem cells make lineage-choice decisions based on a combination of internal and external signals, including mechanical cues from the surrounding environment. Here we show that Piezo1, an ion channel opened by membrane tension, plays an important role in transducing matrix mechanical information to intracellular pathways affecting differentiation in neural stem cells. Piezo1 activity influences whether neural stem cells differentiate along a neuronal or astrocytic lineage. One of the barriers to successful neural stem cell transplantation therapy for neurological disorders lies in directing the fate of transplanted cells. Pharmacological agents aimed at modulating Piezo1 activity may be useful in directing the fate of transplanted neural stem cells toward the desired lineage.
Preservation of viral genomes in 700-y-old caribou feces from a subarctic ice patch
Authors: Ng Terry Fei Fan , Chen Li-Fang , Zhou Yanchen , Shapiro Beth , Stiller Mathias , Heintzman Peter D. , Varsani Arvind , Kondov Nikola O. , Wong Walt , Deng Xutao , Andrews Thomas D. , Moorman Brian J. , Meulendyk Thomas , MacKay Glen , Gilbertson Robert L. , Delwart Eric 
Published: October 2014

Significance
Knowledge of ancient viruses is limited due to their low concentration and poor preservation in ancient specimens. Using a viral particle-associated nucleic acid enrichment approach, we genetically characterized one complete DNA and one partial RNA viral genome from a 700-y-old fecal sample preserved in ice. Using reverse genetics, we reconstituted the DNA virus, which replicated and systemically spread in a model plant species. Under constant freezing conditions, encapsidated viral nucleic acids may therefore be preserved for centuries. Our finding indicates that cryogenically preserved materials can be repositories of ancient viral nucleic acids, which in turn allow molecular genetics to regenerate viruses to study their biology.
Human population reduction is not a quick fix for environmental problems
Authors: Bradshaw Corey J. A. , Brook Barry W. 
Published: October 2014

Significance
The planet’s large, growing, and overconsuming human population, especially the increasing affluent component, is rapidly eroding many of the Earth’s natural ecosystems. However, society’s only real policy lever to reduce the human population humanely is to encourage lower per capita fertility. How long might fertility reduction take to make a meaningful impact? We examined various scenarios for global human population change to the year 2100 by adjusting fertility and mortality rates (both chronic and short-term interventions) to determine the plausible range of outcomes. Even one-child policies imposed worldwide and catastrophic mortality events would still likely result in 5–10 billion people by 2100. Because of this demographic momentum, there are no easy ways to change the broad trends of human population size this century.
Unconscious discrimination of social cues from eye whites in infants
Authors: Jessen Sarah , Grossmann Tobias 
Published: October 2014

Significance
The human eye with its prominent white sclera is thought to facilitate social and cooperative interactions among humans. While there is evidence for brain mechanisms that allow for the unconscious detection of eye cues in adults, it is not known whether this ability of the human brain emerges early in ontogeny and can therefore be considered a key feature of human social functioning. The current study provides neural evidence for the unconscious detection of emotion and gaze cues from the sclera in 7-mo-old infants. Our findings demonstrate the existence of fast, efficient, and reliable social cue detection mechanisms in the human infant brain that likely provide a vital foundation for the development of social interactive skills.
Size limits of self-assembled colloidal structures made using specific interactions
Authors: Zeravcic Zorana , Manoharan Vinothan N. , Brenner Michael P. 
Published: October 2014

Significance
Nature uses hierarchical assembly to make complex structures such as biomolecules, virus shells, and microtubules with high fidelity. Today a key challenge is to translate this process to artificial systems, which hinges on understanding the fundamental questions of efficiency and scalability of self-assembly. Although self-assembly has been studied for decades, the principles behind it and its fundamental and practical limits are still largely unknown. In this paper we establish size limitations for assembling structures of controlled size and shape out of colloidal particles with specific interactions. Inspired by simulations of structures with highly variable shapes and sizes, we develop an understanding of yield through a general theory of excited states that compete with the desired structure in assembly.
Timing and heterogeneity of mutations associated with drug resistance in metastatic cancers
Authors: Bozic Ivana , Nowak Martin A. 
Published: October 2014

Significance
Metastatic dissemination to surgically inaccessible sites is the major cause of death in cancer patients. Targeted therapies, often initially effective against metastatic disease, invariably fail due to resistance. We use mathematical modeling to study heterogeneity of resistance to treatment and describe for the first time, to our knowledge, the entire ensemble of resistant subclones present in metastatic lesions. We show that radiographically detectable metastatic lesions harbor multiple resistant subclones of comparable size and compare our predictions to clinical data on resistance-associated mutations in colorectal cancer patients. Our model provides important information for the development of second-line treatments that aim to inhibit known resistance mutations.
Stochastic nanoroughness modulates neuron–astrocyte interactions and function via mechanosensing cation channels
Authors: Blumenthal Nils R. , Hermanson Ola , Heimrich Bernd , Shastri V. Prasad 
Published: October 2014

Significance
The role of soluble signals in neural differentiation and neurodegeneration is well established. However, the impact of nanotopography imposed by macromolecules within brain tissue on neuronal function and pathologies is not fully appreciated. We have discovered that nanoroughness can modulate the function of hippocampal neurons and their relationship with astrocytes. Inhibition of mechanosensing cation channels including Piezo-1, whose distribution is altered by nanotopography, abrogates the effects imposed by nanotopography and the association of neurons with astrocytes. The finding that regions of amyloid plaque buildup in Alzheimer’s involve changes to tissue nanoroughness provides a link between nanoscale physical cues and loss of function in neurons and may have implications in uncovering the factors that promote neurodegenerative diseases.
Direct and indirect punishment among strangers in the field
Authors: Balafoutas Loukas , Nikiforakis Nikos , Rockenbach Bettina 
Published: October 2014

Significance
Why do humans cooperate in one-time interactions with strangers? The most prominent explanations for this long-standing puzzle rely on punishment of noncooperators, but differ in the form punishment takes. In models of direct punishment, noncooperators are punished directly at personal cost, whereas indirect reciprocity assumes that punishment is indirect by withholding rewards. To resolve the persistent debate on which model better explains cooperation, we conduct the first field experiment, to our knowledge, on direct and indirect punishment among strangers in real-life interactions. We show that many people punish noncooperators directly but prefer punishing indirectly by withholding help when possible. The occurrence of direct and indirect punishment in the field shows that both are key to understanding the evolution of human cooperation.
Structural basis for translational surveillance by the large ribosomal subunit-associated protein quality control complex
Authors: Lyumkis Dmitry , Oliveira dos Passos Dario , Tahara Erich B. , Webb Kristofor , Bennett Eric J. , Vinterbo Staal , Potter Clinton S. , Carragher Bridget , Joazeiro Claudio A. P. 
Published: October 2014

Significance
All organisms have systems in place to ensure that aberrant nascent polypeptide chains are promptly dealt with before being released from ribosomes and posing harm to the cell. The ribosome-associated quality control complex (RQC), composed of the Ltn1 E3 ubiquitin ligase catalytic subunit and cofactors, has become a paradigm for understanding quality control in eukaryotes. However, exactly how RQC functions has remained unknown. Here, we determine the structure of the 60S subunit-bound RQC complex. The data provide critical insights into how RQC is able to selectively target aberrant nascent chains, while ignoring nascent chains in normally translating ribosomes. Furthermore, the structure shows the architecture of a ribosome-bound E3 ligase poised to mark nascent chains for degradation.
Functional conservation despite structural divergence in ligand-responsive RNA switches
Authors: Boerneke Mark A. , Dibrov Sergey M. , Gu Jing , Wyles David L. , Hermann Thomas 
Published: October 2014

Significance
RNA viruses, including the human pathogenic hepatitis C virus (HCV), use a structured untranslated region of their genome to hijack host cell ribosomes for the synthesis of viral proteins. These genome regions are termed internal ribosome entry site (IRES) elements and are encoded by distinct sequences in different viruses but share common functional RNA motifs. This study shows that viral IRES elements contain conformationally flexible RNA switches, whose state can be captured by the binding of a common ligand. Conformational switching plays a role in the function of the IRES elements. These new RNA switches are smaller than previously discovered “riboswitches” and may be the simplest form of ligand-responsive mechanical modules in nucleic acids.