bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contributions of a unique β-clamp to substrate recognition illuminates the molecular basis of exolysis in ferulic acid esterases
Authors: Gruninger Robert J. , Cote Chris , McAllister Tim A. , Abbott D. Wade 
Published: March 2016

Lignocellulosic biomass is a promising renewable resource; however, deconstruction of this material is still the rate-limiting step. Major obstacles in the biocatalytic turnover of lignocellulose are ester-linked decorations that prevent access to primary structural polysaccharides. Enzymes targeting these esters represent promising biotools for increasing bioconversion efficiency. Ruminant livestock are unique in their ability to degrade lignocellulose through the action of their gut microbiome. The anaerobic fungi (phylum Neocallimastigomycota) are key members of this ecosystem that express a large repertoire of carbohydrate-active enzymes (CAZymes) with little sequence identity with characterized CAZymes [Lombard, Golaconda, Drula, Coutinho and Henrissat (2014) Nucleic Acids Res. 42, D490–D495]. We have identified a carbohydrate esterase family 1 (CE1) ferulic acid esterase (FAE) belonging to Anaeromyces mucronatus (AmCE1/Fae1a), and determined its X-ray structure in both the presence [1.55 Å (1 Å=0.1 nm)] and absence (1.60 Å) of ferulic acid. AmCE1 adopts an α/β-hydrolase fold that is structurally conserved with bacterial FAEs, and possesses a unique loop, termed the β-clamp, that encloses the ligand. Isothermal titration calorimetry reveals that substrate binding is driven by enthalpic contributions, which overcomes a large entropic penalty. A comparative analysis of AmCE1 with related enzymes has uncovered the apparent structural basis for differential FAE activities targeting cross-linking ferulic acid conjugates compared with terminal decorations. Based on comparisons to structurally characterized FAEs, we propose that the β-clamp may define the structural basis of exolytic activities in FAEs. This provides a structure-based tool for predicting exolysis and endolysis in CE1. These insights hold promise for rationally identifying enzymes tailored for bioconversion of biomass with variations in cell wall composition.
Effect of moisture and thermal degradation on the activation energy of oil–paper insulation in frequency domain spectroscopy measurement
Authors: Gao Jun , Yang Lijun , Wang Youyuan , Liu Xiao , Du Yongyong , Yao Renyun 
Published: March 2016

Frequency domain spectroscopy (FDS) is widely used to diagnose the condition of transformer oil–paper insulation. However, FDS measurements are highly temperature dependent. The master curve technique is the most common method to remove the temperature effect on FDS, but the reliability of this method is largely dependent on the value of the activation energy, which can be affected by moisture content and thermal degradation degree. To understand the effects of these two factors on the activation energy, FDS measurements at different temperatures were performed on oil‐impregnated pressboards with different thermal degradation degrees and moisture contents. The activation energies of the pressboards were calculated using the Arrhenius equation. Results show that they vary between 0.88 and 1.06 eV along with thermal degradation degree and moisture. The two‐way ANOVA indicates that the effects of these two factors on activation energy are not significant at 95% confidence level when the degree of polymerisation (DP) changes from 415 to 1300 and when the moisture does not exceed 4%. The average activation energy (0.95 eV) can be utilised to generalise the Arrhenius equation to better eliminate the temperature effects. Finally, FDS measurements on a model transformer are performed to verify the effectiveness of the proposed technique.
Measurement of the dynamic response of MEMS thermal actuators based on blurred still images by wavelet transform
Authors: Li Xiuyuan , Zhao Yulong , Hu Tengjiang , Cheng Rongjun , Bai Yingwei 
Published: March 2016

A novel method to experimentally determine the dynamic response of MEMS thermal actuators based on blurred still images of motion is presented. The apex displacement of thermal actuators proves to be a first‐order linear system, whose dynamic response is depended on the system coefficient. In the frequency domain, the system coefficient of actuators excited by sinusoidal wave can be obtained from the fitted curve of vibration amplitude against frequency. An improved wavelet transform detection algorithm is proposed to acquire the vibration amplitude from blurred images taken by an ordinary camera. Compared with the conventional optical measurement method, the proposed method uses only still images instead of complex laser and optical reflecting systems, which has great potential for wide application. For the actuator in this study, the measured response time by blurred images and high‐speed camera method are 14.87 and 15.25 ms with a deviation of 2.5%, which indicates the proposed method can obtain sufficient accurate results without sophisticated equipment and high cost.
2.1 C—C and C—X Bond Formation by Allylic C—H Activation
Authors: Liu G. , Chen P. 
Published: March 2016

AbstractThis chapter documents recent studies into allylic functionalization via C—H activation processes catalyzed by metals such as palladium, rhodium, ruthenium, copper, and iron. The focus is on the formation of C—C, C—N, and C—O bonds reported in the last two decades, but more recent developments involving the formation of other C—X bonds, such as C—F and C—Si are also highlighted.
2.4 C—C Bond Formation Using Radicals
Authors: Chan W.-W. , Yu W.-Y. 
Published: March 2016

AbstractDirect C>—H carbo-functionalization of (hetero)aromatic rings, as an atom-efficient route for regioselective C>—C bond formation, is receiving current attention. In this review, radical coupling of unfunctionalized (het)arenes for C>—C bond formation is described. Recent progress on the palladium-catalyzed regioselective C>—H acylation of arenes with acyl radicals, as well as the transition-metal-free C>—H arylation using aryl radicals, are presented. Some remarkable advances in the Minisci-type radical C>—H alkylation of heterocycles are also discussed.
2.5 C—C Bond Formation by Double C—H Activation
Authors: Xia J.-B. , You S. 
Published: March 2016

AbstractThis chapter focuses on transition-metal-catalyzed aryl—aryl bond-forming reactions via double C—H activation. Biaryl scaffolds have received much attention as a privileged structure broadly found in biologically active natural products, pharmaceuticals, agrochemicals, and functional molecules in material sciences, etc. Transition-metal-catalyzed cross-coupling reactions are the most general and efficient methods to synthesize biaryls, but both coupling partners need to be preactivated in transition-metal-catalyzed cross-coupling reactions when compared with simple arenes. Over the past decade, significant advances have been made in transition-metal-catalyzed biaryl synthesis using simple arenes as substrates via C—H activation. This chapter summarizes representative examples of transition-metal-catalyzed biaryl synthesis using two simple arenes as substrates via double C—H activation.
2.6 C—C Bond Formation by C—H Carboxylation or Carbonylation
Authors: Zhang H. , Liu C. , Lei A. 
Published: March 2016

AbstractThe direct C—H carbonylation or carboxylation involving carbon monoxide is an ideal and environmentally friendly method toward the synthesis of carboxylic acids and derivatives. Within this emerging area, a number of significant examples have been reported, which are summarized in this chapter. Additionally, the recent progress on C—H carboxylation utilizing carbon dioxide is included in this review.
2.12 C—B Bond Formation by Arene C—H Activation
Authors: Ros A. , Fernandez R. , Lassaletta J. M. 
Published: March 2016

AbstractThis chapter provides a survey of the most useful available methodologies for the direct borylation of arenes and hetarenes, which proceed in all cases via a C—H activation event mediated by transition metals such as rhodium, iridium, or palladium. The borylation reactions have been organized into two main groups: (1) direct borylations with regioselectivity mainly controlled by steric factors, and (2) site-selective borylation, with regioselectivity driven by directing effects.
Discrete gene replication events drive coupling between the cell cycle and circadian clocks
Authors: Paijmans Joris , Bosman Mark , ten Wolde Pieter Rein , Lubensky David K. 
Published: March 2016

Significance
Huygens famously showed that two mechanically connected clocks tend to tick in synchrony. We uncovered a generic mechanism that can similarly phase-lock two rhythmic systems present in many living cells: the cell cycle and the circadian clock. DNA replication during the cell cycle causes protein synthesis rates to show sharp, periodic jumps that can entrain the clock. To faithfully keep time in the face of these disturbances, circadian clocks must incorporate specific insulating mechanisms. We argue that, in cyanobacteria, the presence of multiple, identical chromosome copies and the clock’s core protein-modification oscillator together play this role. Our results shed new light on the complex factors that constrain the design of biological clocks.
Defects in lysosomal maturation facilitate the activation of innate sensors in systemic lupus erythematosus
Authors: Monteith Andrew J. , Kang SunAh , Scott Eric , Hillman Kai , Rajfur Zenon , Jacobson Ken , Costello M. Joseph , Vilen Barbara J. 
Published: March 2016

SignificanceActivation of innate sensors by self-antigen contributes to autoimmunity, although how intracellular sensors are chronically exposed to self-antigen has remained unknown. Here, we identify a previously unidentified defect in which lupus-prone macrophages fail to mature the lysosome, promoting the accumulation of apoptotic debris-containing IgG–immune complexes (IgG-ICs). Interestingly, macrophages from other autoimmune diseases accumulate IgG-ICs, indicating that lysosomal defects may underlie multiple autoimmune diseases. Furthermore, the prolonged intracellular residency chronically activates Toll-like receptors and permeabilizes the phagolysosomal membrane, allowing activation of cytosolic sensors. These findings identify lysosomal maturation as a unique defect in MRL/lpr mice that impacts multiple events known to underlie SLE, including pathogenic cytokine secretion.
Conditional vulnerability of plant diversity to atmospheric nitrogen deposition across the United States
Authors: Simkin Samuel M. , Allen Edith B. , Bowman William D. , Clark Christopher M. , Belnap Jayne , Brooks Matthew L. , Cade Brian S. , Collins Scott L. , Geiser Linda H. , Gilliam Frank S. , Jovan Sarah E. , Pardo Linda H. , Schulz Bethany K. , Stevens Carly J. , Suding Katharine N. , Throop Heather L. , Waller Donald M. 
Published: March 2016

Significance
Human activities have elevated nitrogen (N) deposition and there is evidence that deposition impacts species diversity, but spatially extensive and context-specific estimates of N loads at which species losses begin remain elusive. Across a wide range of climates, soil conditions, and vegetation types in the United States, we found that 24% of >15,000 sites were susceptible to N deposition-induced species loss. Grasslands, shrublands, and woodlands were susceptible to species losses at lower loads of N deposition than forests, and susceptibility to species losses increased in acidic soils. These findings are pertinent to the protection of biodiversity and human welfare and should be considered when establishing air quality standards.
Coastal landforms and accumulation of mangrove peat increase carbon sequestration and storage
Authors: Ezcurra Paula , Ezcurra Exequiel , Garcillán Pedro P. , Costa Matthew T. , Aburto-Oropeza Octavio 
Published: March 2016

Significance
Despite their small height and stunted appearance, mangroves along the desert coasts of Baja California have compensated for sea-level rise during the last two millennia by accreting on their own root remains. In doing so, they have accumulated very large amounts of carbon in their sediments (900–3,000 Mg C/ha), often higher than that accumulated under tall, lush, tropical mangrove forests. Mangroves represent the largest carbon sink per unit area in Mexico’s northern drylands. Our results highlight the global importance of mangrove conservation in this region.
Oral activity of a nature-derived cyclic peptide for the treatment of multiple sclerosis
Authors: Thell Kathrin , Hellinger Roland , Sahin Emine , Michenthaler Paul , Gold-Binder Markus , Haider Thomas , Kuttke Mario , Liutkevičiūtė Zita , Göransson Ulf , Gründemann Carsten , Schabbauer Gernot , Gruber Christian W. 
Published: March 2016

Significance
Multiple sclerosis (MS) imposes substantial economic burdens on patients, their families, and society. Until now, there are few therapies available, but often unattractive parenteral application or severe side effects are serious issues. This study highlights the use of circular peptides as orally active T-cell-specific immunosuppressive therapeutics against the MS model experimental autoimmune encephalomyelitis, without inducing major adverse effects. Our work provides a proof of principle that nature-derived cyclic peptides serve as oral active therapeutics, utilizing their intrinsic bioactivity and stable three-dimensional structure. Cyclotides are considered a combinatorial peptide library and they can be anticipated to complement the existing collections of natural products that are used in drug discovery.
Global fishery prospects under contrasting management regimes
Authors: Costello Christopher , Ovando Daniel , Clavelle Tyler , Strauss C. Kent , Hilborn Ray , Melnychuk Michael C. , Branch Trevor A. , Gaines Steven D. , Szuwalski Cody S. , Cabral Reniel B. , Rader Douglas N. , Leland Amanda 
Published: March 2016

Significance
What would extensive fishery reform look like? In addition, what would be the benefits and trade-offs of implementing alternative approaches to fisheries management on a worldwide scale? To find out, we assembled the largest-of-its-kind database and coupled it to state-of-the-art bioeconomic models for more than 4,500 fisheries around the world. We find that, in nearly every country of the world, fishery recovery would simultaneously drive increases in food provision, fishery profits, and fish biomass in the sea. Our results suggest that a suite of approaches providing individual or communal access rights to fishery resources can align incentives across profit, food, and conservation so that few trade-offs will have to be made across these objectives in selecting effective policy interventions.
Spatial patterns of cutaneous vibration during whole-hand haptic interactions
Authors: Shao Yitian , Hayward Vincent , Visell Yon 
Published: March 2016

Significance
In animals and machines, our understanding of tactile function has hitherto been based primarily on information collected at, or near to, the region of contact of a tactile probe with an object. Using the human hand as a case in point, we show that during natural interactions with ordinary objects, mechanical energy originating at finger contact propagates through the whole hand, and that vibration signals that are captured remotely contain sufficient information to discriminate between gestures and between the touched objects. Our results shed light on possible tactile processes in humans and animals and may yield advances in tactile sensing for robotic manipulation or lead to novel paradigms for wearable computing.
Measuring and modeling diffuse scattering in protein X-ray crystallography
Authors: Van Benschoten Andrew H. , Liu Lin , Gonzalez Ana , Brewster Aaron S. , Sauter Nicholas K. , Fraser James S. , Wall Michael E. 
Published: March 2016

Significance
The structural details of protein motions are critical to understanding many biological processes, but they are often hidden to conventional biophysical techniques. Diffuse X-ray scattering can reveal details of the correlated movements between atoms; however, the data collection historically has required extra effort and dedicated experimental protocols. We have measured 3D diffuse intensities in X-ray diffraction from CypA and trypsin crystals using standard crystallographic data collection techniques. Analysis of the resulting data is consistent with the protein motions resembling diffusion in a liquid or vibrations of a soft solid. Our results show that using diffuse scattering to model protein motions can become a component of routine crystallographic analysis through the extension of commonplace methods.
Predation risk drives social complexity in cooperative breeders
Authors: Groenewoud Frank , Frommen Joachim Gerhard , Josi Dario , Tanaka Hirokazu , Jungwirth Arne , Taborsky Michael 
Published: March 2016

SignificanceIt is widely accepted that high predation risk may select for group living, but predation is not regarded as a primary driver of social complexity. This view neglects the important effect of predation on dispersal and offspring survival, which may require cooperation among group members. The significance of predation for the evolution of social complexity can be well illustrated by behavioral and morphological adaptations of highly social animals showing division of labor, such as eusocial insects and cooperatively breeding fishes. By examining the diversity of social organization in a cooperative cichlid in relation to ecological variation, we show that predation risk has the greatest explanatory power of social complexity. This stresses the significance of predation for social evolution.
Simultaneous single-molecule epigenetic imaging of DNA methylation and hydroxymethylation
Authors: Song Chun-Xiao , Diao Jiajie , Brunger Axel T. , Quake Stephen R. 
Published: March 2016

Significance
DNA epigenetic modifications in the forms of 5-methylcytosine (5mC) and 5-hydroxylmethylcytosine (5hmC) play crucial regulatory functions in the mammalian genome. Here we developed an ultrasensitive single-molecule epigenetic imaging technology for detecting and quantifying 5hmC and 5mC. By conducting single-molecule fluorescence resonance energy transfer experiments, we discovered high levels of adjacent and opposing methylated and hydroxymethylated CpG sites in the mouse genome, a previously unappreciated structure which may play an important role in gene regulation.
Endocrine vasculatures are preferable targets of an antitumor ineffective low dose of anti-VEGF therapy
Authors: Zhang Yin , Yang Yunlong , Hosaka Kayoko , Huang Guichun , Zang Jingwu , Chen Fang , Zhang Yun , Samani Nilesh J. , Cao Yihai 
Published: March 2016

Significance
Defining targets and functional impacts of systemic treatment with antiangiogenic drugs on tumors and healthy tissues are crucial for understanding their therapeutic efficacy, drug resistance, adverse effects, and timeline of therapy. In the present study, we used both mouse and human tumor models to recapitulate clinical situations in which antiangiogenic drugs were systemically delivered to mice. Antiangiogenic drugs at low dosages produced broad effects on vessel regression in several endocrine organs. Prolonged treatment with the nonantitumor low dose of antiangiogenic drugs causes endocrine dysfunction in thyroid and adrenal gland. In fact, clinically manifested adverse effects, including hypertension, hypothyroidism, and glucocorticoid dysfunction, have been reproduced in our preclinical models by a low dose of an anti-VEGF drug.
Engineering a long-acting, potent GLP-1 analog for microstructure-based transdermal delivery
Authors: Yang Peng-Yu , Zou Huafei , Chao Elizabeth , Sherwood Lance , Nunez Vanessa , Keeney Michael , Ghartey-Tagoe Esi , Ding Zhongli , Quirino Herlinda , Luo Xiaozhou , Welzel Gus , Chen Guohua , Singh Parminder , Woods Ashley K. , Schultz Peter G. , Shen Weijun 
Published: March 2016

Significance
Many therapeutic peptides suffer from short plasma half-lives and, as a consequence, require frequent injections to be therapeutically effective; this in turn can adversely affect patient compliance. Here, we describe the development of a novel peptide engineering strategy that incorporates a serum protein binding motif into a covalent side-chain staple. This approach was used to generate stapled long-acting glucagon-like peptide-1 analogs with potency comparable to exendin-4 and significantly enhanced pharmacokinetic properties. Administration by a dissolvable microstructure-based transdermal system resulted in sustained therapeutic blood concentrations with glucose lowering activity in guinea pigs. This approach likely provides a general, straightforward platform for generating stapled long-acting peptide hormones for a range of therapeutic applications.
Land-use policies and corporate investments in agriculture in the Gran Chaco and Chiquitano
Authors: le Polain de Waroux Yann , Garrett Rachael D. , Heilmayr Robert , Lambin Eric F. 
Published: March 2016

Significance
A growing global demand for agricultural products such as soybeans and beef is causing agriculture to expand into forest ecosystems. Many countries are tightening environmental regulations as a response. Because agricultural companies can move, there is a risk that stringent land-use regulations might just displace land conversion geographically. A better understanding of how these regulations affect companies’ movements is therefore crucial for designing effective conservation policies. Here we analyze the determinants of siting choices by agricultural companies. We find that companies that tend to clear more forest prefer areas with lower deforestation restrictions, and that all companies prefer areas with low enforcement. However, these effects are less important than the availability of forestland or the proximity to current investments.
Rise, stagnation, and rise of Danish women’s life expectancy
Authors: Lindahl-Jacobsen Rune , Rau Roland , Jeune Bernard , Canudas-Romo Vladimir , Lenart Adam , Christensen Kaare , Vaupel James W. 
Published: March 2016

SignificanceLife expectancy is the most commonly used measure of health status in a population. Life expectancy has increased rapidly in most western populations over the past two centuries. There has been an ongoing debate about the relative contribution of cohort and period effects on a nation’s life expectancy, but few concrete examples of strong cohort effects exist. In this study, we use demographic approaches to study cohort effects on the life expectancy of Danish women. We identify a clear-cut and strong cohort effect: the case of the interwar generations of Danish women.
Genome-wide kinetics of DNA excision repair in relation to chromatin state and mutagenesis
Authors: Adar Sheera , Hu Jinchuan , Lieb Jason D. , Sancar Aziz 
Published: March 2016

Significance
Nucleotide excision repair is the sole mechanism for removing bulky adducts from the human genome, including those formed by UV radiation and chemotherapeutic drugs. We used eXcision Repair-sequencing, a genomic assay for measuring DNA repair, to map the kinetics of repair after UV treatment. These genome-wide repair maps, in turn, allowed us to infer how excision repair is influenced by DNA packaging. Active and open chromatin regions were repaired more rapidly than other genomic regions. Repair in repressed and heterochromatic regions is slower and persists for up to 2 d. Furthermore, late-repaired regions are associated with a higher level of cancer-linked somatic mutations, highlighting the importance of efficient DNA repair and linking chromatin organization to cancer mutagenesis.