bluuebunny/crossref_metadata_2025_split huggingface dataset:
THE PREHISTORY OF THE SUBSYSTEMS OF SECOND-ORDER ARITHMETIC
Authors: DEAN WALTER , WALSH SEAN 
Published: February 2017

AbstractThis paper presents a systematic study of the prehistory of the traditional subsystems of second-order arithmetic that feature prominently in the reverse mathematics program promoted by Friedman and Simpson. We look in particular at: (i) the long arc from Poincaré to Feferman as concerns arithmetic definability and provability, (ii) the interplay between finitism and the formalization of analysis in the lecture notes and publications of Hilbert and Bernays, (iii) the uncertainty as to the constructive status of principles equivalent to Weak König’s Lemma, and (iv) the large-scale intellectual backdrop to arithmetical transfinite recursion in descriptive set theory and its effectivization by Borel, Lusin, Addison, and others.
Dislocation mechanisms and 3D twin architectures generate exceptional strength-ductility-toughness combination in CrCoNi medium-entropy alloy
Authors: Zhang Zijiao , Sheng Hongwei , Wang Zhangjie , Gludovatz Bernd , Zhang Ze , George Easo P. , Yu Qian , Mao Scott X. , Ritchie Robert O. 
Published: February 2017

AbstractCombinations of high strength and ductility are hard to attain in metals. Exceptions include materials exhibiting twinning-induced plasticity. To understand how the strength-ductility trade-off can be defeated, we apply in situ, and aberration-corrected scanning, transmission electron microscopy to examine deformation mechanisms in the medium-entropy alloy CrCoNi that exhibits one of the highest combinations of strength, ductility and toughness on record. Ab initio modelling suggests that it has negative stacking-fault energy at 0K and high propensity for twinning. With deformation we find that a three-dimensional (3D) hierarchical twin network forms from the activation of three twinning systems. This serves a dual function: conventional twin-boundary (TB) strengthening from blockage of dislocations impinging on TBs, coupled with the 3D twin network which offers pathways for dislocation glide along, and cross-slip between, intersecting TB-matrix interfaces. The stable twin architecture is not disrupted by interfacial dislocation glide, serving as a continuous source of strength, ductility and toughness.
Gate-controlled conductance switching in DNA
Authors: Xiang Limin , Palma Julio L. , Li Yueqi , Mujica Vladimiro , Ratner Mark A. , Tao Nongjian 
Published: February 2017

AbstractExtensive evidence has shown that long-range charge transport can occur along double helical DNA, but active control (switching) of single-DNA conductance with an external field has not yet been demonstrated. Here we demonstrate conductance switching in DNA by replacing a DNA base with a redox group. By applying an electrochemical (EC) gate voltage to the molecule, we switch the redox group between the oxidized and reduced states, leading to reversible switching of the DNA conductance between two discrete levels. We further show that monitoring the individual conductance switching allows the study of redox reaction kinetics and thermodynamics at single molecular level using DNA as a probe. Our theoretical calculations suggest that the switch is due to the change in the energy level alignment of the redox states relative to the Fermi level of the electrodes.
Scaffolding and completing genome assemblies in real-time with nanopore sequencing
Authors: Cao Minh Duc , Nguyen Son Hoang , Ganesamoorthy Devika , Elliott Alysha G. , Cooper Matthew A. , Coin Lachlan J. M. 
Published: February 2017

AbstractThird generation sequencing technologies provide the opportunity to improve genome assemblies by generating long reads spanning most repeat sequences. However, current analysis methods require substantial amounts of sequence data and computational resources to overcome the high error rates. Furthermore, they can only perform analysis after sequencing has completed, resulting in either over-sequencing, or in a low quality assembly due to under-sequencing. Here we present npScarf, which can scaffold and complete short read assemblies while the long read sequencing run is in progress. It reports assembly metrics in real-time so the sequencing run can be terminated once an assembly of sufficient quality is obtained. In assembling four bacterial and one eukaryotic genomes, we show that npScarf can construct more complete and accurate assemblies while requiring less sequencing data and computational resources than existing methods. Our approach offers a time- and resource-effective strategy for completing short read assemblies.
Dissecting the molecular organization of the translocon-associated protein complex
Authors: Pfeffer Stefan , Dudek Johanna , Schaffer Miroslava , Ng Bobby G. , Albert Sahradha , Plitzko Jürgen M. , Baumeister Wolfgang , Zimmermann Richard , Freeze Hudson H. , Engel Benjamin D. , Förster Friedrich 
Published: February 2017

AbstractIn eukaryotic cells, one-third of all proteins must be transported across or inserted into the endoplasmic reticulum (ER) membrane by the ER protein translocon. The translocon-associated protein (TRAP) complex is an integral component of the translocon, assisting the Sec61 protein-conducting channel by regulating signal sequence and transmembrane helix insertion in a substrate-dependent manner. Here we use cryo-electron tomography (CET) to study the structure of the native translocon in evolutionarily divergent organisms and disease-linked TRAP mutant fibroblasts from human patients. The structural differences detected by subtomogram analysis form a basis for dissecting the molecular organization of the TRAP complex. We assign positions to the four TRAP subunits within the complex, providing insights into their individual functions. The revealed molecular architecture of a central translocon component advances our understanding of membrane protein biogenesis and sheds light on the role of TRAP in human congenital disorders of glycosylation.
Strong electronic interaction and multiple quantum Hall ferromagnetic phases in trilayer graphene
Authors: Datta Biswajit , Dey Santanu , Samanta Abhisek , Agarwal Hitesh , Borah Abhinandan , Watanabe Kenji , Taniguchi Takashi , Sensarma Rajdeep , Deshmukh Mandar M. 
Published: February 2017

AbstractQuantum Hall effect provides a simple way to study the competition between single particle physics and electronic interaction. However, electronic interaction becomes important only in very clean graphene samples and so far the trilayer graphene experiments are understood within non-interacting electron picture. Here, we report evidence of strong electronic interactions and quantum Hall ferromagnetism seen in Bernal-stacked trilayer graphene. Due to high mobility ∼500,000 cm2V−1s−1 in our device compared to previous studies, we find all symmetry broken states and that Landau-level gaps are enhanced by interactions; an aspect explained by our self-consistent Hartree–Fock calculations. Moreover, we observe hysteresis as a function of filling factor and spikes in the longitudinal resistance which, together, signal the formation of quantum Hall ferromagnetic states at low magnetic field.
Chromatin remodeller Fun30Fft3 induces nucleosome disassembly to facilitate RNA polymerase II elongation
Authors: Lee Junwoo , Shik Choi Eun , David Seo Hogyu , Kang Keunsoo , Gilmore Joshua M. , Florens Laurence , Washburn Michael P. , Choe Joonho , Workman Jerry L. , Lee Daeyoup 
Published: February 2017

AbstractPrevious studies have revealed that nucleosomes impede elongation of RNA polymerase II (RNAPII). Recent observations suggest a role for ATP-dependent chromatin remodellers in modulating this process, but direct in vivo evidence for this is unknown. Here using fission yeast, we identify Fun30Fft3 as a chromatin remodeller, which localizes at transcribing regions to promote RNAPII transcription. Fun30Fft3 associates with RNAPII and collaborates with the histone chaperone, FACT, which facilitates RNAPII elongation through chromatin, to induce nucleosome disassembly at transcribing regions during RNAPII transcription. Mutants, resulting in reduced nucleosome-barrier, such as deletion mutants of histones H3/H4 themselves and the genes encoding components of histone deacetylase Clr6 complex II suppress the defects in growth and RNAPII occupancy of cells lacking Fun30Fft3. These data suggest that RNAPII utilizes the chromatin remodeller, Fun30Fft3, to overcome the nucleosome barrier to transcription elongation.
Portraying entanglement between molecular qubits with four-dimensional inelastic neutron scattering
Authors: Garlatti E. , Guidi T. , Ansbro S. , Santini P. , Amoretti G. , Ollivier J. , Mutka H. , Timco G. , Vitorica-Yrezabal I. J. , Whitehead G. F. S. , Winpenny R. E. P. , Carretta S. 
Published: February 2017

AbstractEntanglement is a crucial resource for quantum information processing and its detection and quantification is of paramount importance in many areas of current research. Weakly coupled molecular nanomagnets provide an ideal test bed for investigating entanglement between complex spin systems. However, entanglement in these systems has only been experimentally demonstrated rather indirectly by macroscopic techniques or by fitting trial model Hamiltonians to experimental data. Here we show that four-dimensional inelastic neutron scattering enables us to portray entanglement in weakly coupled molecular qubits and to quantify it. We exploit a prototype (Cr7Ni)2 supramolecular dimer as a benchmark to demonstrate the potential of this approach, which allows one to extract the concurrence in eigenstates of a dimer of molecular qubits without diagonalizing its full Hamiltonian.
Layer-specific optogenetic activation of pyramidal neurons causes beta–gamma entrainment of neonatal networks
Authors: Bitzenhofer Sebastian H , Ahlbeck Joachim , Wolff Amy , Wiegert J. Simon , Gee Christine E. , Oertner Thomas G. , Hanganu-Opatz Ileana L. 
Published: February 2017

AbstractCoordinated activity patterns in the developing brain may contribute to the wiring of neuronal circuits underlying future behavioural requirements. However, causal evidence for this hypothesis has been difficult to obtain owing to the absence of tools for selective manipulation of oscillations during early development. We established a protocol that combines optogenetics with electrophysiological recordings from neonatal mice in vivo to elucidate the substrate of early network oscillations in the prefrontal cortex. We show that light-induced activation of layer II/III pyramidal neurons that are transfected by in utero electroporation with a high-efficiency channelrhodopsin drives frequency-specific spiking and boosts network oscillations within beta–gamma frequency range. By contrast, activation of layer V/VI pyramidal neurons causes nonspecific network activation. Thus, entrainment of neonatal prefrontal networks in fast rhythms relies on the activation of layer II/III pyramidal neurons. This approach used here may be useful for further interrogation of developing circuits, and their behavioural readout.
Effect of hydrogen on the integrity of aluminium–oxide interface at elevated temperatures
Authors: Li Meng , Xie De-Gang , Ma Evan , Li Ju , Zhang Xi-Xiang , Shan Zhi-Wei 
Published: February 2017

AbstractHydrogen can facilitate the detachment of protective oxide layer off metals and alloys. The degradation is usually exacerbated at elevated temperatures in many industrial applications; however, its origin remains poorly understood. Here by heating hydrogenated aluminium inside an environmental transmission electron microscope, we show that hydrogen exposure of just a few minutes can greatly degrade the high temperature integrity of metal–oxide interface. Moreover, there exists a critical temperature of ∼150 °C, above which the growth of cavities at the metal–oxide interface reverses to shrinkage, followed by the formation of a few giant cavities. Vacancy supersaturation, activation of a long-range diffusion pathway along the detached interface and the dissociation of hydrogen-vacancy complexes are critical factors affecting this behaviour. These results enrich the understanding of hydrogen-induced interfacial failure at elevated temperatures.
Both overlapping and independent mechanisms determine how diet and insulin-ligand knockouts extend lifespan of Drosophila melanogaster
Authors: Zandveld Jelle , van den Heuvel Joost , Zwaan Bastiaan J. , Piper Matthew D.W. 
Published: February 2017

AbstractLifespan in many organisms, including Drosophila melanogaster, can be increased by reduced insulin-IGF-like signaling (IIS) or by changes in diet. Most studies testing whether IIS is involved in diet-mediated lifespan extension employ only a few diets, but recent data shows that a broad range of nutritional environments is required. Here, we present lifespan data of long-lived Drosophila, lacking three of the eight insulin-like peptides [Drosophila insulin-like peptides 2,3,5 (dilp2-3,5)] on nine different diets that surround the optimum for lifespan. Their nutritional content was varied by manipulating sugar and yeast concentrations independently, and thus incorporated changes in both diet restriction and nutrient balance. The mutants were substantially longer-lived than controls on every diet, but the effects on the lifespan response to sugar and yeast differed. Our data illustrates how a greater coverage of diet balance (DB) and restriction can unify differing interpretations of how IIS might be involved in the response of lifespan to diet.
Spatial dynamics of TB within a highly urbanised Asian metropolis using point patterns
Authors: Das Sourav , Cook Alex R. , Wah Win , Win Khin Mar Kyi , Chee Cynthia Bin Eng , Wang Yee Tang , Yang Hsu Li 
Published: February 2017

AbstractSingapore is a high-income country in a region with a high prevalence of tuberculosis. The Singapore Tuberculosis (TB) Elimination Program (STEP) was set up in 1997, and the better surveillance and clinical management practices initiated under STEP led to a decade-long decline in the incidence levels. However, incidence rates started to rise again since 2008. The reasons for this rise are unclear. This study involved a spatial analysis of the epidemiology of TB among Singapore residents. More than 30 000 cases reported during 1995–2011 and their residential addresses were analysed for spatial risk and spatial clustering, using spatial point pattern methodology. The principal factor responsible for the increasing resident TB incidence in Singapore is the changing age profile of the population. In particular the burgeoning population aged above 65 years accounts for the increase in reported cases. Singapore’s population has one of the world’s lowest fertility and mortality rates, and the elderly population is projected to grow substantially over the next few decades. Tuberculosis rates may therefore continue to rise even with static or improving case management and surveillance.
Accelerated disease progression and robust innate host response in aged SIVmac239-infected Chinese rhesus macaques is associated with enhanced immunosenescence
Authors: Zheng Hong-Yi , Zhang Ming-Xu , Chen Min , Jiang Jin , Song Jia-Hao , Lian Xiao-Dong , Tian Ren-Rong , Zhang Xiao-Liang , Zhang Lin-Tao , Pang Wei , Zhang Gao-Hong , Zheng Yong-Tang 
Published: February 2017

AbstractThe elderly population infected with HIV-1 is often characterized by the rapid AIDS progression and poor treatment outcome, possibly because of immunosenescence resulting from both HIV infection and aging. However, this hypothesis remains to be fully tested. Here, we studied 6 young and 12 old Chinese rhesus macaques (ChRM) over the course of three months after simian immunodeficiency virus (SIV) SIVmac239 infection. Old ChRM showed a higher risk of accelerated AIDS development than did young macaques, owing to rapidly elevated plasma viral loads and decreased levels of CD4+ T cells. The low frequency of naïve CD4+ T cells before infection was strongly predictive of an increased disease progression, whereas the severe depletion of CD4+ T cells and the rapid proliferation of naïve lymphocytes accelerated the exhaustion of naïve lymphocytes in old ChRM. Moreover, in old ChRM, a robust innate host response with defective regulation was associated with a compensation for naïve T cell depletion and a high level of immune activation. Therefore, we suggest that immunosenescence plays an important role in the accelerated AIDS progression in elderly individuals and that SIV-infected old ChRM may be a favorable model for studying AIDS pathogenesis and researching therapies for elderly AIDS patients.
Hydrolysis of Hyaluronic Acid in Lymphedematous Tissue Alleviates Fibrogenesis via TH1 Cell-Mediated Cytokine Expression
Authors: Cho Sungrae , Roh Kangsan , Park Jaehyun , Park Yong Seok , Lee Minji , Cho Seungchan , Kil Eui-Joon , Cho Mun-Ju , Oh Jeong Su , Byun Hee-Seong , Cho Sang-Ho , Park Kyewon , Kang Hee , Koo Jinmo , Yeom Chang-Hwan , Lee Sukchan 
Published: February 2017

AbstractAlthough surgery and radiation are beneficial for treating cancer, they can also lead to malfunctions of the lymphatic system such as secondary lymphedema. This abnormality of the lymphatic system is characterized by severe swelling, adipogenesis, inflammation, and fibrosis in the lymphedematous region. Moreover, the proliferation of fibrotic tissue in the lymphedematous region generates edema that is no longer spontaneously reversible. No treatment for fibrosis has been validated in patients with lymphedema. In our efforts to develop a therapeutic agent for lymphedema fibrosis, we used a newly established mouse hind limb model. Previous studies have demonstrated that hyaluronic acid accumulates in the lymphedematous region. Thus, we challenged mice with of hyaluronidase (HYAL), with the aim of reducing fibrogenesis. After subcutaneous injections in the lymphedematous mouse leg every two days, the volume of lymphedema had reduced significantly by 7 days post-operation. Histochemical analysis indicated that collagen accumulation and myofibroblast differentiation were decreased in epidermal tissues after HYAL injection. Moreover, it was associated with upregulation of interferon-gamma, increased numbers of Th1 cells, and downregulation of interleukin-4 and interleukin-6 in the lymphedematous region and spleen. These results indicate that hydrolysis of hyaluronic acid can boost an anti-fibrotic immune response in the mouse lymphedema model.
Context-independent essential regulatory interactions for apoptosis and hypertrophy in the cardiac signaling network
Authors: Kang Jun Hyuk , Lee Ho-Sung , Park Daebeom , Kang Yun-Won , Kim Seon Myeong , Gong Jeong-Ryeol , Cho Kwang-Hyun 
Published: February 2017

AbstractApoptosis and hypertrophy of cardiomyocytes are the primary causes of heart failure and are known to be regulated by complex interactions in the underlying intracellular signaling network. Previous experimental studies were successful in identifying some key signaling components, but most of the findings were confined to particular experimental conditions corresponding to specific cellular contexts. A question then arises as to whether there might be essential regulatory interactions that prevail across diverse cellular contexts. To address this question, we have constructed a large-scale cardiac signaling network by integrating previous experimental results and developed a mathematical model using normalized ordinary differential equations. Specific cellular contexts were reflected to different kinetic parameters sampled from random distributions. Through extensive computer simulations with various parameter distributions, we revealed the five most essential context-independent regulatory interactions (between: (1) αAR and Gαq, (2) IP3 and calcium, (3) epac and CaMK, (4) JNK and NFAT, and (5) p38 and NFAT) for hypertrophy and apoptosis that were consistently found over all our perturbation analyses. These essential interactions are expected to be the most promising therapeutic targets across a broad spectrum of individual conditions of heart failure patients.
A Novel High-Density Phase and Amorphization of Nitrogen-Rich 1H-Tetrazole (CH2N4) under High Pressure
Authors: Li Wenbo , Huang Xiaoli , Bao Kuo , Zhao Zhonglong , Huang Yanping , Wang Lu , Wu Gang , Zhou Bo , Duan Defang , Li Fangfei , Zhou Qiang , Liu Bingbing , Cui Tian 
Published: February 2017

AbstractThe high-pressure behaviors of nitrogen-rich 1H-tetrazole (CH2N4) have been investigated by in situ synchrotron X-ray diffraction (XRD) and Raman scattering up to 75 GPa. A first crystalline-to-crystalline phase transition is observed and identified above ~3 GPa with a large volume collapse (∼18% at 4.4 GPa) from phase I to phase II. The new phase II forms a dimer-like structure, belonging to P1 space group. Then, a crystalline-to-amorphous phase transition takes place over a large pressure range of 13.8 to 50 GPa, which is accompanied by an interphase region approaching paracrystalline state. When decompression from 75 GPa to ambient conditions, the final product keeps an irreversible amorphous state. Our ultraviolet (UV) absorption spectrum suggests the final product exhibits an increase in molecular conjugation.
Performance, kinetic, and biodegradation pathway evaluation of anaerobic fixed film fixed bed reactor in removing phthalic acid esters from wastewater
Authors: Ahmadi Ehsan , Yousefzadeh Samira , Ansari Mohsen , Ghaffari Hamid Reza , Azari Ali , Miri Mohammad , Mesdaghinia Alireza , Nabizadeh Ramin , Kakavandi Babak , Ahmadi Peyman , Badi Mojtaba Yegane , Gholami Mitra , Sharafi Kiomars , Karimaei Mostafa , Ghoochani Mahboobeh , Brahmand Masoud Binesh , Mohseni Seyed Mohsen , Sarkhosh Maryam , Rezaei Soheila , Asgharnia Hosseinali , Dehghanifard Emad , Jafari Behdad , Mortezapour Alireza , Moghaddam Vahid Kazemi , Mahmoudi Mohammad Molla , Taghipour Nader 
Published: February 2017

AbstractEmerging and hazardous environmental pollutants like phthalic acid esters (PAEs) are one of the recent concerns worldwide. PAEs are considered to have diverse endocrine disrupting effects on human health. Industrial wastewater has been reported as an important environment with high concentrations of PAEs. In the present study, four short-chain PAEs including diallyl phthalate (DAP), diethyl phthalate (DEP), dimethyl phthalate (DMP), and phthalic acid (PA) were selected as a substrate for anaerobic fixed film fixed bed reactor (AnFFFBR). The process performances of AnFFFBR, and also its kinetic behavior, were evaluated to find the best eco-friendly phthalate from the biodegradability point of view. According to the results and kinetic coefficients, removing and mineralizing of DMP occurred at a higher rate than other phthalates. In optimum conditions 92.5, 84.41, and 80.39% of DMP, COD, and TOC were removed. DAP was found as the most bio-refractory phthalate. The second-order (Grau) model was selected as the best model for describing phthalates removal.