bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fast revascularization of the injured area is essential to support zebrafish heart regeneration
Authors: Marín-Juez Rubén , Marass Michele , Gauvrit Sebastien , Rossi Andrea , Lai Shih-Lei , Materna Stefan C. , Black Brian L. , Stainier Didier Y. R. 
Published: September 2016

Significance
A heart attack occurs when blood flow to part of the heart is blocked, and oxygen and nutrients are unable to reach that tissue, irreversibly damaging cardiac muscle cells. Dead muscle cells are replaced by a noncontractile scar that affects cardiac function. Unlike humans, zebrafish can regenerate their heart after injury, replacing the scarred tissue with new cardiomyocytes. Understanding the mechanisms zebrafish deploy to regenerate their heart may help us design more efficient therapies for human heart disease. In this study, we show that to regenerate their heart, zebrafish quickly revascularize the damaged area, and that this ability to revascularize is temporally restricted.
Ab initio structure determination from prion nanocrystals at atomic resolution by MicroED
Authors: Sawaya Michael R. , Rodriguez Jose , Cascio Duilio , Collazo Michael J. , Shi Dan , Reyes Francis E. , Hattne Johan , Gonen Tamir , Eisenberg David S. 
Published: September 2016

Significance
Microelectron diffraction (MicroED) is a cryo-EM method capable of determining atomic resolution macromolecular structures from nanocrystals of dose-sensitive biological macromolecules. To date, MicroED requires a reasonably accurate guess of the positions of atoms in a structure to solve it, a technique known as molecular replacement. We now show that this need for prior knowledge about a structure is eliminated in cases when crystals diffract to atomic resolution, relying only on the accuracy of the MicroED intensity measurements. Our findings provide a basis for solving structures from tiny crystals that diffract to high resolution, but are presently disregarded because of their small size.
Binding of phosphatidic acid by NsD7 mediates the formation of helical defensin–lipid oligomeric assemblies and membrane permeabilization
Authors: Kvansakul Marc , Lay Fung T. , Adda Christopher G. , Veneer Prem K. , Baxter Amy A. , Phan Thanh Kha , Poon Ivan K. H. , Hulett Mark D. 
Published: September 2016

Significance
Direct attack of target cell membranes by protein oligomerization is a powerful innate defense mechanism used widely throughout nature. Defensins are ubiquitous innate immunity mediators that are able to recognize certain phospholipids, and subsequently oligomerize to attack target cell membranes. We now show that the plant defensin NsD7 is able to bind the cellular phospholipid, phosphatidic acid (PA), which triggers defensin oligomerization in a unique manner. Our crystal structure of the NsD7–PA oligomer revealed a striking double-helical defensin–lipid oligomer that features a novel phospholipid-binding site mediating PA binding and membrane permeabilization. This demonstrates that defensins use their conserved small fold in a remarkably flexible way to specifically recognize a range of phospholipids during innate defense using different binding sites.
Biophysical comparison of ATP synthesis mechanisms shows a kinetic advantage for the rotary process
Authors: Anandakrishnan Ramu , Zhang Zining , Donovan-Maiye Rory , Zuckerman Daniel M. 
Published: September 2016

Significance
All living organisms—archaea, bacteria, and eukarya—use an intricate rotary molecular machine to synthesize ATP, the energy currency of the cell. Why did evolution select such an elaborate machine when a simpler alternating-access mechanism, already present in cells, could be used for ATP synthesis? Our analysis shows that the rotary mechanism is faster than other possible mechanisms, particularly under challenging conditions, suggesting a possible evolutionary advantage.
Vascular smooth muscle cell durotaxis depends on extracellular matrix composition
Authors: Hartman Christopher D. , Isenberg Brett C. , Chua Samantha G. , Wong Joyce Y. 
Published: September 2016

Significance
Many cell types have been observed to migrate toward stiffer regions of mechanical gradients in a process termed durotaxis. Tissue stiffness gradients are being discovered in an increasing number of diseases, including cancer and fibrotic diseases. However, the role of ECM composition, which often changes in diseased tissues with stiffness, in directing this behavior has not previously been investigated. To understand how stiffness gradients and changing matrix composition may affect cell migration in disease, we have designed a mechanical gradient platform that allows for independent control of absolute stiffness, gradient steepness, and ECM coating. We demonstrate that smooth muscle cells will undergo durotaxis on mechanical gradients coated with fibronectin but not laminin.
Cell cycle progression inCaulobacterrequires a nucleoid-associated protein with high AT sequence recognition
Authors: Ricci Dante P. , Melfi Michael D. , Lasker Keren , Dill David L. , McAdams Harley H. , Shapiro Lucy 
Published: September 2016

SignificanceIn all organisms, morphological and functional diversity is the product of cell type-specific genetic programs. Asymmetric cell division inCaulobacteryields daughter cells that differ functionally due to the differential read-out of their genomes. Here, we report the discovery of GapR, a conserved DNA-binding protein required for cell cycle progression. We show that GapR only associates with DNA sequences of high adenine and thymine (AT) content, colocating with cell cycle master regulators that control genes mediating swarmer cell development. GapR protein distributes asymmetrically, accumulating on the compacted chromosome of the daughter swarmer cell compartment prior to division. We argue thatCaulobacterhas co-opted a protein that associates with AT-rich DNA to provide spatial control during an asymmetric cell division.
Fluorescent metallacycle-cored polymers via covalent linkage and their use as contrast agents for cell imaging
Authors: Zhang Mingming , Li Shuya , Yan Xuzhou , Zhou Zhixuan , Saha Manik Lal , Wang Yu-Cai , Stang Peter J. 
Published: September 2016

Significance
Fluorescent polymers play an important role in bioimaging due to their improved brightness, inertness to microenvironment, and good biocompatibility. In this article, we used tetraphenylene (TPE) derivatives that give strong fluorescence emission in an aggregated state as fluorophores and synthesized fluorescent polymers via the covalent linkage of TPE-based rhomboidal Pt(II) metallacycles. Due to the integration of covalent linkage-induced aggregation of the monomers, the aggregation-induced emission character of TPE derivatives together with Pt(II)-based metal−ligand interactions, these polymers exhibit enhanced emission compared with their corresponding precursors, making them applicable as excellent cell imaging agents. Considering the potential anticancer activity of rhomboidal Pt(II) metallacycles, these polymers may serve as theranostic agents for both bioimaging and cancer therapy.
Cellulose synthase complexes act in a concerted fashion to synthesize highly aggregated cellulose in secondary cell walls of plants
Authors: Li Shundai , Bashline Logan , Zheng Yunzhen , Xin Xiaoran , Huang Shixin , Kong Zhaosheng , Kim Seong H. , Cosgrove Daniel J. , Gu Ying 
Published: September 2016

Significance
Plant cell walls are important in plant development and for textiles, wood products, and bioenergy. Cellulose, the microfibrillar component of primary cell walls (PCWs) and secondary cell walls (SCWs), is formed by cellulose synthase complexes (CSCs) at the plasma membrane. Here, we show that CSCs behave differently during PCW and SCW synthesis and form microfibrils with different organization. During PCW synthesis, dispersed CSCs synthesize cellulose microfibrils with low aggregation, whereas during SCW synthesis, densely arranged groups of CSCs move coherently to synthesize highly aggregated microfibrils. Our study suggests that controlled alterations in CSC distribution and orchestrated movements contribute to the high density and bundling of cellulose microfibrils in SCWs.
Structure of the unliganded form of the proprotein convertase furin suggests activation by a substrate-induced mechanism
Authors: Dahms Sven O. , Arciniega Marcelino , Steinmetzer Torsten , Huber Robert , Than Manuel E. 
Published: September 2016

Significance
The prototypical proprotein convertase furin proteolytically activates many precursor proteins and is essential for cellular homeostasis of the cell. Furin and other proprotein convertase are also associated with a number of diseases, including cancer, atherosclerosis, hypercholesterolaemia, and infectious diseases. A hallmark of furin and its physiologic function is its stringent specificity for polybasic substrates. Here we describe several structural states of the protein by X-ray crystallography and further characterize them by molecular dynamics simulations. The transition between these conformers is triggered by substrate binding and calcium ligation, respectively, and helps explain the stringent specificity of furin and its functional features. These studies may pave the way for novel strategies of structure-guided inhibitor development.
Risk and Protective Factors Associated with Adolescent Girls’ Substance Use: Data from a Nationwide Facebook Sample
Authors: Schwinn Traci M. , Schinke Steven P. , Hopkins Jessica , Thom Bridgette 
Published: September 2016

Background: Despite overall reductions in teenage substance use, adolescent girls’ rates of substance use remain unacceptably high. This article examines whether girls’ substance use is associated with general risk and protective factors (goal setting, problem solving, refusal skills, peer use, and self-efficacy) and gender-specific risk and protective factors (communication style, coping skills, self-esteem, body image, perceived stress, anxiety, and depression). Methods: Cross-sectional data were collected in 2013 via online surveys from a nationwide sample of adolescent girls ( N = 788), aged 13 and 14 years, who were recruited through Facebook. Results: In multivariate analyses, controlling for correlates of adolescent substance use, 11 of the 13 general and gender-specific risk and protective factors were consistently associated with past-month alcohol, cigarette, and other drug use in the expected direction; past-month marijuana use was associated with 8 of the 13 factors. Refusal skills, peer use, coping, and depressive mood were most consistently and strongly associated with substance use. Conclusions: Substance abuse prevention programs targeting adolescent girls should focus on such general risk and protective factors as problem solving, refusal skills, peer influences, and self-efficacy, as well as such gender-specific risk and protective factors as communication style, coping, self-esteem, body image, perceived stress, and mood management.
The Prevalence of Binge Drinking among Primary Care Residents
Authors: Greene Magdalena , Johnson J. Aaron , Seale J. Paul , Tindol Allen , Le Kristy B. , Clemow Diana D. , Barham Ann H. , Miller David P. 
Published: September 2016

Background Over one quarter of American adults binge drink, resulting in significant alcohol-related morbidity and mortality. Although brief interventions can decrease patients’ alcohol use, many physicians in training do not provide this service. This study examines the prevalence of binge drinking among primary care residents, and the association of resident drinking behaviors with addressing patients’ hazardous alcohol use. Methods Between July 2013 and August 2014, the authors surveyed all trainees in 6 primary care residency programs. The survey assessed self-reported frequency of binge drinking, confidence working with hazardous drinkers, and the performance of brief interventions when hazardous drinking was detected in patients. Results 221 of 246 residents completed the survey (response rate 89.8%). Half of residents (109/221) reported at least one episode of binge drinking in the prior year, and 18% (39/221) reported binge drinking at least once a month. In multivariable analysis, monthly binge drinking was associated with male gender (OR 2.5, 95% CI 1.1–5.4) and year of training (OR 0.25 for Year 3 vs. Year 1, 95% CI 0.07–0.90). Few residents felt confident they could help patients cut down or quit alcohol, regardless of personal binge drinking history (19% for those who binged monthly, 24% for those who binged 1–11 times a year, and 27% for those who never binged, p for trend = 0.31). Performance of brief interventions did not vary by personal binge drinking history. Conclusions Binge drinking is common among primary care residents. In addition to training residents to effectively intervene with hazardous drinkers, residency programs should address the high prevalence of binge drinking by their physicians in training.
Comparative study on stabilization mechanism of monomeric cytochrome c5 from deep-sea piezophilic Shewanella violacea
Authors: Masanari Misa , Fujii Sotaro , Kawahara Kazuki , Oki Hiroya , Tsujino Hirofumi , Maruno Takahiro , Kobayashi Yuji , Ohkubo Tadayasu , Wakai Satoshi , Sambongi Yoshihiro 
Published: September 2016

Abstract
Monomeric cytochrome c5 from deep-sea piezophilic Shewanella violacea (SVcytc5) was stable against heat and denaturant compared with the homologous protein from shallow-sea piezo-sensitive Shewanella livingstonensis (SLcytc5). Here, the SVcytc5 crystal structure revealed that the Lys-50 side chain on the flexible loop formed a hydrogen bond with heme whereas that of corresponding hydrophobic Leu-50 could not form such a bond in SLcytc5, which appeared to be one of possible factors responsible for the difference in stability between the two proteins. This structural insight was confirmed by a reciprocal mutagenesis study on the thermal stability of these two proteins. As SVcytc5 was isolated from a deep-sea piezophilic bacterium, the present comparative study indicates that adaptation of monomeric SVcytc5 to high pressure environments results in stabilization against heat.
Plasma rotation from momentum transport by neutrals in tokamaks
Authors: Omotani J. , Pusztai I. , Newton S. , Fülöp T. 
Published: September 2016

Abstract
Neutral atoms can strongly influence the intrinsic rotation and radial electric field at the tokamak edge. Here, we present a framework to investigate these effects when the neutrals dominate the momentum transport. We explore the parameter space numerically, using highly flexible model geometries and a state of the art kinetic solver. We find that the most important parameters controlling the toroidal rotation and electric field are the major radius where the neutrals are localized and the plasma collisionality. This offers a means to influence the rotation and electric field by, for example, varying the radial position of the X-point to change the major radius of the neutral peak.
Influence of energetic ions on neoclassical tearing modes
Authors: Cai Huishan 
Published: September 2016

Abstract
In addition to their effect on the linear stability of tearing modes, energetic particles can influence the nonlinear evolution of a magnetic island through an uncompensated cross field current due to the effect of charge separation when the orbit width of an energetic particle is much larger than the island width. The corresponding return parallel current may compensate the loss of bootstrap current in the magnetic island. This nonlinear effect depends on the island’s propagation frequency (the rotation frequency of the island relative to the plasma), the density gradient of energetic ions and magnetic shear. If the island’s propagation frequency is positive, the effect of the uncompensated current plays a stable role on neoclassical tearing modes. When the magnetic shear is sufficiently small, this effect becomes significant and can partially cancel or even overcome the destabilizing effect of the perturbed bootstrap current. In ITER this provides a possibility of using energetic ions to suppress the neoclassical tearing mode for the steady state and hybrid scenarios with weak magnetic shear.
Numerical modeling of tokamak breakdown phase driven by pure Ohmic heating under ideal conditions
Authors: Jiang Wei , Peng Yanli , Zhang Ya , Lapenta Giovanni 
Published: September 2016

Abstract
We have simulated tokamak breakdown phase driven by pure Ohmic heating with implicit particle in cell/Monte Carlo collision (PIC/MCC) method. We have found two modes can be differentiated. When performing breakdown at low initial gas pressure, we find that it works at lower density and current, but higher temperature, and requires lower heating power, compared to when having a high initial pressure. Further, two stages can be distinguished during the avalanche process. One is the fast avalanche stage, in which the plasma is heated by induced toroidal electric field. The other is the slow avalanche stage, which begins when the plasma density reaches 1015 m−3. It has been shown that ions are mainly heated by ambipolar field and become stochastic in the velocity distribution. However, when the induced electric field is low, there exists a transition phase between the two stages. Our model simulates the breakdown and early hydrogen burn-through under ideal conditions during tokamak start-up. It adopted fewer assumptions, and can give an idealized range of operative parameters for Ohmic start-up. Qualitatively, the results agree well with certain experimental observations.
Tomographic reconstruction of the beam emissivity profile in the negative ion source NIO1
Authors: Fonnesu N. , Agostini M. , Pasqualotto R. , Serianni G. , Veltri P. 
Published: September 2016

Abstract
A versatile negative hydrogen ion source named NIO1 of a moderate size (130 mA total extracted H− current, 9 apertures, 60 kV total acceleration) has been developed and installed at Consorzio RFX. It will allow great experimental flexibility, very beneficial for studying several important issues related to beam extraction, optics and performance optimization, in view of SPIDER and MITICA, the two full-scale experiments for the ITER neutral beam injector under construction at RFX. The main target of emission tomography applied to an ion beam is the reconstruction of the emissivity profile, from which the ion density distribution can be obtained. The measurement of the beam density profile and of its uniformity throughout the pulse duration with a non-invasive diagnostic, such as tomography, would represent an effective method for monitoring the ion source operation and for malfunction detection. The application of this diagnostic to the NIO1 beam will represent the experimental verification of the possibility to reconstruct a multi-beamlet profile, in the interest of the next tomography systems for SPIDER and MITICA. In this paper, a feasibility study of the tomographic diagnostic for NIO1 is presented. A tomography code based on algebraic reconstruction techniques has been developed for this purpose and the transport of the nine H− beamlets is simulated with a Monte Carlo particle tracking code from the ion source to the tomography plane, where the beam emissivity profile to be reconstructed is calculated. The reference emissivity profile is reconstructed by the tomography code considering different possible layouts of the detection system, in order to find the best compromise between the quality of reconstructions and the complexity of the diagnostic. Results show that a tomography system based on six linear CCD cameras should be capable of reconstructing the NIO1 emissivity profile with an rms error lower than 10%. How instrumental noise in the integrated signals affects the reconstructed beam emissivity profiles is also studied. A simple low-pass filter is found effective if the noise level is less than 10%; otherwise a more sophisticated filtering technique must be considered.
A substellar companion to Pleiades HII 3441
Authors: Konishi Mihoko , Matsuo Taro , Yamamoto Kodai , Samland Matthias , Sudo Jun , Shibai Hiroshi , Itoh Yoichi , Fukagawa Misato , Sumi Takahiro , Kudo Tomoyuki , Hashimoto Jun , Kuzuhara Masayuki , Kusakabe Nobuhiko , Abe Lyu , Akiyama Eiji , Brandner Wolfgang , Brandt Timothy D. , Carson Joseph C. , Feldt Markus , Goto Miwa , Grady Carol A. , Guyon Olivier , Hayano Yutaka , Hayashi Masahiko , Hayashi Saeko S. , Henning Thomas , Hodapp Klaus W. , Ishii Miki , Iye Masanori , Janson Markus , Kandori Ryo , Knapp Gillian R. , Kwon Jungmi , McElwain Michael W. , Mede Kyle , Miyama Shoken , Morino Jun-Ichi , Moro-Martín Amaya , Nishimura Tetsuo , Oh Daehyeon , Pyo Tae-Soo , Serabyn Eugene , Schlieder Joshua E. , Suenaga Takuya , Suto Hiroshi , Suzuki Ryuji , Takahashi Yasuhiro H. , Takami Michihiro , Takato Naruhisa , Terada Hiroshi , Thalmann Christian , Turner Edwin L. , Watanabe Makoto , Wisniewski John P. , Yamada Toru , Takami Hideki , Usuda Tomonori , Tamura Motohide 
Published: September 2016

Abstract
We find a new substellar companion to the Pleiades member star, Pleiades HII 3441, using the Subaru telescope with adaptive optics. The discovery is made as part of the high-contrast imaging survey to search for planetary-mass and substellar companions in the Pleiades and young moving groups. The companion has a projected separation of 0${^{\prime\prime}_{.}}$49 ± 0${^{\prime\prime}_{.}}$02 (66 ± 2 au) and a mass of 68 ± 5 MJ based on three observations in the J-, H-, and Ks-bands. The spectral type is estimated to be M7 (∼2700 K), and thus no methane absorption is detected in the H band. Our Pleiades observations result in the detection of two substellar companions including one previously reported among 20 observed Pleiades stars, and indicate that the fraction of substellar companions in the Pleiades is about $10.0^{+26.1}_{-8.8}$%. This is consistent with multiplicity studies of both the Pleiades stars and other open clusters.
Medication Adherence in Patients Undergoing Methadone Maintenance Treatment in Xi’an, China
Authors: Zhou Kaina , Li Hengxin , Wei Xiaoli , Li Xiaomei , Zhuang Guihua 
Published: September 2016

Objectives:
To identify medication adherence and its influencing factors among patients of 14 methadone maintenance treatment (MMT) clinics in Xi’an, China.

Methods:
Data were obtained from the National AIDS Information System-Community Methadone Maintenance Treatment. All patients registered in the system were not permitted to take methadone at home without professionals’ supervision. Medication adherence was assessed using categorical (ie, dropout or retained) and continuous (ie, treatment time, methadone use time, and percentage of methadone use days) variables. Percentages of methadone use days of >90%, 50% to 90%, or <50% indicated good, moderate, and poor adherence, respectively. Multivariate Cox stepwise regression analysis was used to identify the influencing factors.

Results:
Of the 10,398 patients, 52.2% had dropped out of MMT by December 31, 2013, whereas only 11.8% regularly visited the clinic for daily methadone (ie, >90% methadone use days) during a certain period. Protective factors were older age (>30 years); female sex; having no contact with peer drug users over the past month; no needle-sharing experience; a negative initial morphine urine test; and a higher average daily methadone dose (>20 mg) (P < 0.05). Risk factors were answering “others” for marital status; being employed; having a lack of stable income; not living with family; answering “others” for drug use type; frequently engaging in unauthorized drug use during MMT; no readmission; long travel times to the MMT clinic (>30 minutes); having no convenient MMT service time; and being dissatisfied with MMT service (P < 0.05).

Conclusions:
Based on our findings, multimodal intervention and management programs can be developed to improve poor medication adherence among the MMT patient population.