bluuebunny/crossref_metadata_2025_split huggingface dataset:
Resting-state brain alteration after a single dose of SSRI administration predicts 8-week remission of patients with major depressive disorder
Authors: Cheng Y. , Xu J. , Arnone D. , Nie B. , Yu H. , Jiang H. , Bai Y. , Luo C. , Campbell R. A. A. , Shan B. , Xu L. , Xu X. 
Published: October 2016

BackgroundThe present study investigated alteration of brain resting-state activity induced by antidepressant treatment and attempted to investigate whether treatment efficacy can be predicted at an early stage of pharmacological treatment.MethodForty-eight first-episode medication-free patients diagnosed with major depression received treatment with escitalopram. Resting-state functional magnetic resonance imaging was administered prior to treatment, 5 h after the first dose, during the course of pharmacological treatment (week 4) and at endpoint (week 8). Resting-state activity was evaluated in the course of the 8-week treatment and in relation to clinical improvement.ResultsEscitalopram dynamically modified resting-state activity in depression during the treatment. After 5 h the antidepressant induced a significant decrease in the signal in the occipital cortex and an increase in the dorsolateral and dorsomedial prefrontal cortices and middle cingulate cortex. Furthermore, while remitters demonstrated more obvious changes following treatment, these were more modest in non-responders suggesting possible tonic and dynamic differences in the serotonergic system. Changes after 5 h in the caudate, occipital and temporal cortices were the best predictor of clinical remission at endpoint.ConclusionsThis study revealed the possibility of using the measurement of resting-state neural changes a few hours after acute administration of antidepressant to identify individuals likely to remit after a few weeks of treatment.
Comparative and parallel genome-wide association studies for metabolic and agronomic traits in cereals
Authors: Chen Wei , Wang Wensheng , Peng Meng , Gong Liang , Gao Yanqiang , Wan Jian , Wang Shouchuang , Shi Lei , Zhou Bin , Li Zongmei , Peng Xiaoxi , Yang Chenkun , Qu Lianghuan , Liu Xianqing , Luo Jie 
Published: October 2016

AbstractThe plant metabolome is characterized by extensive diversity and is often regarded as a bridge between genome and phenome. Here we report metabolic and phenotypic genome-wide studies (mGWAS and pGWAS) in rice grain that, in addition to previous metabolic GWAS in rice leaf and maize kernel, show both distinct and overlapping aspects of genetic control of metabolism within and between species. We identify new candidate genes potentially influencing important metabolic and/or morphological traits. We show that the differential genetic architecture of rice metabolism between different tissues is in part determined by tissue specific expression. Using parallel mGWAS and pGWAS we identify new candidate genes potentially responsible for variation in traits such as grain colour and size, and provide evidence of metabotype-phenotype linkage. Our study demonstrates a powerful strategy for interactive functional genomics and metabolomics in plants, especially the cloning of minor QTLs for complex phenotypic traits.
Comparative survey of the relative impact of mRNA features on local ribosome profiling read density
Authors: O’Connor Patrick B. F. , Andreev Dmitry E. , Baranov Pavel V. 
Published: October 2016

AbstractRibosome profiling (Ribo-seq), a promising technology for exploring ribosome decoding rates, is characterized by the presence of infrequent high peaks in ribosome footprint density and by long alignment gaps. Here, to reduce the impact of data heterogeneity we introduce a simple normalization method, Ribo-seq Unit Step Transformation (RUST). RUST is robust and outperforms other normalization techniques in the presence of heterogeneous noise. We illustrate how RUST can be used for identifying mRNA sequence features that affect ribosome footprint densities globally. We show that a few parameters extracted with RUST are sufficient for predicting experimental densities with high accuracy. Importantly the application of RUST to 30 publicly available Ribo-seq data sets revealed a substantial variation in sequence determinants of ribosome footprint frequencies, questioning the reliability of Ribo-seq as an accurate representation of local ribosome densities without prior quality control. This emphasizes our incomplete understanding of how protocol parameters affect ribosome footprint densities.
Microfluidic cantilever detects bacteria and measures their susceptibility to antibiotics in small confined volumes
Authors: Etayash Hashem , Khan M. F. , Kaur Kamaljit , Thundat Thomas 
Published: October 2016

AbstractIn the fight against drug-resistant bacteria, accurate and high-throughput detection is essential. Here, a bimaterial microcantilever with an embedded microfluidic channel with internal surfaces chemically or physically functionalized with receptors selectively captures the bacteria passing through the channel. Bacterial adsorption inside the cantilever results in changes in the resonance frequency (mass) and cantilever deflection (adsorption stress). The excitation of trapped bacteria using infrared radiation (IR) causes the cantilever to deflect in proportion to the infrared absorption of the bacteria, providing a nanomechanical infrared spectrum for selective identification. We demonstrate the in situ detection and discrimination of Listeria monocytogenes at a concentration of single cell per μl. Trapped Escherichia coli in the microchannel shows a distinct nanomechanical response when exposed to antibiotics. This approach, which combines enrichment with three different modes of detection, can serve as a platform for the development of a portable, high-throughput device for use in the real-time detection of bacteria and their response to antibiotics.
Neofunctionalization of zona pellucida proteins enhances freeze-prevention in the eggs of Antarctic notothenioids
Authors: Cao Lixue , Huang Qiao , Wu Zhichao , Cao Dong-dong , Ma Zhanling , Xu Qianghua , Hu Peng , Fu Yanxia , Shen Yu , Chan Jiulin , Zhou Cong-zhao , Zhai Wanying , Chen Liangbiao 
Published: October 2016

AbstractThe mechanisms by which the eggs of the Antarctic notothenioid fishes avoid freezing are not fully understood. Zona pellucida proteins (ZPs) are constituents of the chorion which forms a protective matrix surrounding the egg. Here we report occurrence of freezing temperature-related gene expansion and acquisition of unusual ice melting-promoting (IMP) activity in a family of Antarctic notothenioid ZPs (AnnotoZPs). Members of AnnotoZPs are shown to bind with ice and non-colligatively depress the melting point of a solution in a range of 0.26 to 0.65 °C at a moderate concentration. Eggs of zebrafishes expressing an AnnotoZP transgene show improved melting point depression and enhanced survival in freezing conditions. Mutational analyses in a representative AnnotoZP indicate the ZP domain and patches of acidic residues are essential structures for the IMP activity. AnnotoZPs, therefore, represent a group of macromolecules that prevent freezing by a unique ZP–ice interaction mechanism distinct from the known antifreeze proteins.
Retinal transplantation of photoreceptors results in donor–host cytoplasmic exchange
Authors: Santos-Ferreira Tiago , Llonch Sílvia , Borsch Oliver , Postel Kai , Haas Jochen , Ader Marius 
Published: October 2016

AbstractPre-clinical studies provided evidence for successful photoreceptor cell replacement therapy. Migration and integration of donor photoreceptors into the retina has been proposed as the underlying mechanism for restored visual function. Here we reveal that donor photoreceptors do not structurally integrate into the retinal tissue but instead reside between the photoreceptor layer and the retinal pigment epithelium, the so-called sub-retinal space, and exchange intracellular material with host photoreceptors. By combining single-cell analysis, Cre/lox technology and independent labelling of the cytoplasm and nucleus, we reliably track allogeneic transplants demonstrating cellular content transfer between graft and host photoreceptors without nuclear translocation. Our results contradict the common view that transplanted photoreceptors migrate and integrate into the photoreceptor layer of recipients and therefore imply a re-interpretation of previous photoreceptor transplantation studies. Furthermore, the observed interaction of donor with host photoreceptors may represent an unexpected mechanism for the treatment of blinding diseases in future cell therapy approaches.
Magnetodielectric detection of magnetic quadrupole order in Ba(TiO)Cu4(PO4)4 with Cu4O12 square cupolas
Authors: Kimura K. , Babkevich P. , Sera M. , Toyoda M. , Yamauchi K. , Tucker G. S. , Martius J. , Fennell T. , Manuel P. , Khalyavin D. D. , Johnson R. D. , Nakano T. , Nozue Y. , Rønnow H. M. , Kimura T. 
Published: October 2016

AbstractIn vortex-like spin arrangements, multiple spins can combine into emergent multipole moments. Such multipole moments have broken space-inversion and time-reversal symmetries, and can therefore exhibit linear magnetoelectric (ME) activity. Three types of such multipole moments are known: toroidal; monopole; and quadrupole moments. So far, however, the ME activity of these multipole moments has only been established experimentally for the toroidal moment. Here we propose a magnetic square cupola cluster, in which four corner-sharing square-coordinated metal-ligand fragments form a noncoplanar buckled structure, as a promising structural unit that carries an ME-active multipole moment. We substantiate this idea by observing clear magnetodielectric signals associated with an antiferroic ME-active magnetic quadrupole order in the real material Ba(TiO)Cu4(PO4)4. The present result serves as a useful guide for exploring and designing new ME-active materials based on vortex-like spin arrangements.
Non-Hermitian engineering of single mode two dimensional laser arrays
Authors: Teimourpour Mohammad H. , Ge Li , Christodoulides Demetrios N. , El-Ganainy Ramy 
Published: October 2016

AbstractA new scheme for building two dimensional laser arrays that operate in the single supermode regime is proposed. This is done by introducing an optical coupling between the laser array and lossy pseudo-isospectral chains of photonic resonators. The spectrum of this discrete reservoir is tailored to suppress all the supermodes of the main array except the fundamental one. This spectral engineering is facilitated by employing the Householder transformation in conjunction with discrete supersymmetry. The proposed scheme is general and can in principle be used in different platforms such as VCSEL arrays and photonic crystal laser arrays.
ProQ3: Improved model quality assessments using Rosetta energy terms
Authors: Uziela Karolis , Shu Nanjiang , Wallner Björn , Elofsson Arne 
Published: October 2016

AbstractQuality assessment of protein models using no other information than the structure of the model itself has been shown to be useful for structure prediction. Here, we introduce two novel methods, ProQRosFA and ProQRosCen, inspired by the state-of-art method ProQ2, but using a completely different description of a protein model. ProQ2 uses contacts and other features calculated from a model, while the new predictors are based on Rosetta energies: ProQRosFA uses the full-atom energy function that takes into account all atoms, while ProQRosCen uses the coarse-grained centroid energy function. The two new predictors also include residue conservation and terms corresponding to the agreement of a model with predicted secondary structure and surface area, as in ProQ2. We show that the performance of these predictors is on par with ProQ2 and significantly better than all other model quality assessment programs. Furthermore, we show that combining the input features from all three predictors, the resulting predictor ProQ3 performs better than any of the individual methods. ProQ3, ProQRosFA and ProQRosCen are freely available both as a webserver and stand-alone programs at http://proq3.bioinfo.se/.
Short-term Effects of Risperidone Monotherapy on Spontaneous Brain Activity in First-episode Treatment-naïve Schizophrenia Patients: A Longitudinal fMRI Study
Authors: Hu Mao-Lin , Zong Xiao-Fen , Zheng Jun-Jie , Pantazatos Spiro P. , Miller Jeffrey M. , Li Zong-Chang , Liao Yan-Hui , He Ying , Zhou Jun , Sang De-En , Zhao Hong-Zeng , Lv Lu-Xian , Tang Jin-Song , Mann J. John , Chen Xiao-Gang 
Published: October 2016

AbstractIt is unclear whether abnormal spontaneous neural activation patterns found in chronic schizophrenia patients (CSP) are part of the pathogenesis of disease, consequences of chronic illness, or effects of antipsychotic treatment. We performed a longitudinal resting-state functional magnetic resonance imaging (fMRI) study in 42 treatment-naïve first-episode schizophrenia patients (FESP) at baseline and then after 8-weeks of risperidone monotherapy and compared the findings to 38 healthy volunteers. Spontaneous brain activity was quantified using the fractional amplitude of low-frequency fluctuations (fALFF) and regional homogeneity (ReHo) and compared between patients and controls. Pretreatment, patients exhibited higher fALFF in left caudate compared with controls. After treatment, patients had elevated fALFF in bilateral putamen and right caudate and increased ReHo in right caudate and left putamen. Greater increase of fALFF in the left putamen correlated with less improvement in positive symptoms. Thus, abnormalities of spontaneous neural activity in chronic schizophrenia is at least partly due to a medication effect. The observed post-treatment increase in striatal intrinsic activity may reflect counter-therapeutic functional adaptation to dopamine D2 receptor occupancy required for medication effects on psychosis.
A novel injectable BRET-based in vivo imaging probe for detecting the activity of hypoxia-inducible factor regulated by the ubiquitin-proteasome system
Authors: Kuchimaru Takahiro , Suka Tomoya , Hirota Keisuke , Kadonosono Tetsuya , Kizaka-Kondoh Shinae 
Published: October 2016

AbstractThe ubiquitin-proteasome system (UPS) is a selective protein degradation system that plays a critical role in many essential biological processes by regulating the existence of various cellular proteins. The target proteins of UPS are recognized and tagged with polyubiquitin chains by E3 ubiquitin ligases, which have high substrate-specific activities. Here we present a novel injectable imaging probe POL-N that can detect the UPS-regulated hypoxia-inducible factor (HIF) activity in vivo. Because the luciferase is fused to the E3 ligase-recognition domain of the HIF-1α, POL-N is intact only in the HIFα-overexpressing cells, that is, HIF-active cells, generating signals via an intramolecular bioluminescence resonance energy transfer (BRET) between luciferase and a near-infrared (NIR) fluorescent dye at the C-terminal end of the probe. Off-target signals of the NIR-BRET were so low that we could achieve highly sensitive and fast detection of intratumoral HIF-activity. Notably, we successfully detected hypoxic liver metastasis, which is extremely difficult to detect by injectable imaging probes due to strong off-target signals, as early as 1 h after systemic injection of POL-N. Our probe design can be widely adapted to UPS-target proteins and may contribute to the exploration of their roles in animal disease models.
Efficiency Enhancement of Hybrid Perovskite Solar Cells with MEH-PPV Hole-Transporting Layers
Authors: Chen Hsin-Wei , Huang Tzu-Yen , Chang Ting-Hsiang , Sanehira Yoshitaka , Kung Chung-Wei , Chu Chih-Wei , Ikegami Masashi , Miyasaka Tsutomu , Ho Kuo-Chuan 
Published: October 2016

AbstractIn this study, hybrid perovskite solar cells are fabricated using poly[2-methoxy-5-(2-ethylhexyloxy)-1,4-phenylenevinylene] (MEH-PPV) and poly(3-hexylthiophene-2,5-diyl) (P3HT) as dopant-free hole-transporting materials (HTMs) and two solution processes (one- and two-step methods, respectively) for preparing methylammonium lead iodide perovskite. By optimizing the concentrations and solvents of MEH-PPV solutions, a power conversion efficiency of 9.65% with hysteresis-less performance is achieved, while the device with 2,2′,7,7′-tetrakis(N,N-di-p-methoxyphenylamine)-9,9′spirobifluorene (Spiro-OMeTAD) doped with lithium salts and tert-butylpyridine (TBP) exhibits an efficiency of 13.38%. This result shows that non-doped MEH-PPV is a suitable, low-cost HTM for efficient polymer-based perovskite solar cells. The effect of different morphologies of methylammonium lead iodide perovskite on conversion efficiency is also investigated by incident photon-to-electron conversion efficiency (IPCE) curves and electrochemical impedance spectroscopy (EIS).
Relationship between neuroticism, childhood trauma and cognitive-affective responses to auditory verbal hallucinations
Authors: So Suzanne Ho-wai , Begemann Marieke J. H. , Gong Xianmin , Sommer Iris E. 
Published: October 2016

AbstractNeuroticism has been shown to adversely influence the development and outcome of psychosis. However, how this personality trait associates with the individual’s responses to psychotic symptoms is less well known. Auditory verbal hallucinations (AVHs) have been reported by patients with psychosis and non-clinical individuals. There is evidence that voice-hearers who are more distressed by and resistant against the voices, as well as those who appraise the voices as malevolent and powerful, have poorer outcome. This study aimed to examine the mechanistic association of neuroticism with the cognitive-affective reactions to AVH. We assessed 40 psychotic patients experiencing frequent AVHs, 135 non-clinical participants experiencing frequent AVHs and 126 healthy individuals. In both clinical and non-clinical voice-hearers alike, a higher level of neuroticism was associated with more distress and behavioral resistance in response to AVHs, as well as a stronger tendency to perceive voices as malevolent and powerful. Neuroticism fully mediated the found associations between childhood trauma and the individuals’ cognitive-affective reactions to voices. Our results supported the role of neurotic personality in shaping maladaptive reactions to voices. Neuroticism may also serve as a putative mechanism linking childhood trauma and psychological reactions to voices. Implications for psychological models of hallucinations are discussed.
Bimodal Control of Heat Transport at Graphene–Metal Interfaces Using Disorder in Graphene
Authors: Kim Jaehyeon , Khan Muhammad Ejaz , Ko Jae-Hyeon , Kim Jong Hun , Lee Eui-Sup , Suh Joonki , Wu Junqiao , Kim Yong-Hyun , Park Jeong Young , Lyeo Ho-Ki 
Published: October 2016

AbstractThermal energy transport across the interfaces of physically and chemically modified graphene with two metals, Al and Cu, was investigated by measuring thermal conductance using the time-domain thermoreflectance method. Graphene was processed using a He2+ ion-beam with a Gaussian distribution or by exposure to ultraviolet/O3, which generates structural or chemical disorder, respectively. Hereby, we could monitor changes in the thermal conductance in response to varying degrees of disorder. We find that the measured conductance increases as the density of the physical disorder increases, but undergoes an abrupt modulation with increasing degrees of chemical modification, which decreases at first and then increases considerably. Moreover, we find that the conductance varies inverse proportionally to the average distance between the structural defects in the graphene, implying a strong in-plane influence of phonon kinetics on interfacial heat flow. We attribute the bimodal results to an interplay between the distinct effects on graphene’s vibrational modes exerted by graphene modification and by the scattering of modes.
Multiphoton imaging reveals that nanosecond pulsed electric fields collapse tumor and normal vascular perfusion in human glioblastoma xenografts
Authors: Bardet Sylvia M. , Carr Lynn , Soueid Malak , Arnaud-Cormos Delia , Leveque Philippe , O’Connor Rodney P. 
Published: October 2016

AbstractDespite the biomedical advances of the last century, many cancers including glioblastoma are still resistant to existing therapies leaving patients with poor prognoses. Nanosecond pulsed electric fields (nsPEF) are a promising technology for the treatment of cancer that have thus far been evaluated in vitro and in superficial malignancies. In this paper, we develop a tumor organoid model of glioblastoma and apply intravital multiphoton microscopy to assess their response to nsPEFs. We demonstrate for the first time that a single 10 ns, high voltage electric pulse (35–45 kV/cm), collapses the perfusion of neovasculature and also alters the diameter of capillaries and larger vessels in normal tissue. These results contribute to the fundamental understanding of nsPEF effects in complex tissue environments and confirm the potential of nsPEFs to disrupt the microenvironment of solid tumors such as glioblastoma.
Non-invasive modulation of somatosensory evoked potentials by the application of static magnetic fields over the primary and supplementary motor cortices
Authors: Kirimoto Hikari , Asao Akihiko , Tamaki Hiroyuki , Onishi Hideaki 
Published: October 2016

AbstractThis study was performed to investigate the possibility of non-invasive modulation of SEPs by the application of transcranial static magnetic field stimulation (tSMS) over the primary motor cortex (M1) and supplementary motor cortex (SMA) and to measure the strength of the NdFeB magnetic field by using a gaussmeter. An NdFeB magnet or a non-magnetic stainless steel cylinder (for sham stimulation) was settled on the scalp over M1 and SMA of 14 subjects for periods of 15 min. SEPs following right median nerve stimulation were recorded before and immediately after, 5 min after and 10 min after tSMS from sites C3′ and F3. Amplitudes of the N33 component of SEPs at C3′ significantly decreased immediately after tSMS over M1 by up to 20%. However, tSMS over the SMA did not affect the amplitude of any of the SEP components. At a distance of 2–3 cm (rough depth of the cortex), magnetic field strength was in the range of 110–190 mT. Our results that tSMS over M1 can reduce the amplitude of SEPs are consistent with those of low-frequency repeated TMS and cathodal tDCS studies. Therefore, tSMS could be a useful tool for modulating cortical somatosensory processing.
“RaMassays”: Synergistic Enhancement of Plasmon-Free Raman Scattering and Mass Spectrometry for Multimodal Analysis of Small Molecules
Authors: Alessandri Ivano , Vassalini Irene , Bertuzzi Michela , Bontempi Nicolò , Memo Maurizio , Gianoncelli Alessandra 
Published: October 2016

AbstractSiO2/TiO2core/shell (T-rex) beads were exploited as “all-in-one” building-block materials to create analytical assays that combine plasmon-free surface enhanced Raman scattering (SERS) and surface assisted laser desorption/ionization (SALDI) mass spectrometry (RaMassays). Such a multi-modal approach relies on the unique optical properties of T-rex beads, which are able to harvest and manage light in both UV and Vis range, making ionization and Raman scattering more efficient. RaMassays were successfully applied to the detection of small (molecular weight, M.W. <400 Da) molecules with a key relevance in biochemistry and pharmaceutical analysis. Caffeine and cocaine were utilized as molecular probes to test the combined SERS/SALDI response of RaMassays, showing excellent sensitivity and reproducibility. The differentiation between amphetamine/ephedrine and theophylline/theobromine couples demonstrated the synergistic reciprocal reinforcement of SERS and SALDI. Finally, the conversion of L-tyrosine in L-DOPA was utilized to probe RaMassays as analytical tools for characterizing reaction intermediates without introducing any spurious effects. RaMassays exhibit important advantages over plasmonic nanoparticles in terms of reproducibility, absence of interference and potential integration in multiplexed devices.