bluuebunny/crossref_metadata_2025_split huggingface dataset:
3D tracking of single nanoparticles and quantum dots in living cells by out-of-focus imaging with diffraction pattern recognition
Authors: Gardini Lucia , Capitanio Marco , Pavone Francesco S. 
Published: November 2015

AbstractLive cells are three-dimensional environments where biological molecules move to find their targets and accomplish their functions. However, up to now, most single molecule investigations have been limited to bi-dimensional studies owing to the complexity of 3d-tracking techniques. Here, we present a novel method for three-dimensional localization of single nano-emitters based on automatic recognition of out-of-focus diffraction patterns. Our technique can be applied to track the movements of single molecules in living cells using a conventional epifluorescence microscope. We first demonstrate three-dimensional localization of fluorescent nanobeads over 4 microns depth with accuracy below 2 nm in vitro. Remarkably, we also establish three-dimensional tracking of Quantum Dots, overcoming their anisotropic emission, by adopting a ligation strategy that allows rotational freedom of the emitter combined with proper pattern recognition. We localize commercially available Quantum Dots in living cells with accuracy better than 7 nm over 2 microns depth. We validate our technique by tracking the three-dimensional movements of single protein-conjugated Quantum Dots in living cell. Moreover, we find that important localization errors can occur in off-focus imaging when improperly calibrated and we give indications to avoid them. Finally, we share a Matlab script that allows readily application of our technique by other laboratories.
Comparison between Ultrasound Guided Transperineal and Transrectal Prostate Biopsy: A Prospective, Randomized and Controlled Trial
Authors: Guo Le-Hang , Wu Rong , Xu Hui-Xiong , Xu Jun-Mei , Wu Jian , Wang Shuai , Bo Xiao-Wan , Liu Bo-Ji 
Published: November 2015

AbstractThis prospective study of comparing transperineal prostate biopsy (TPBx) with transrectal prostate biopsy (TRBx) was aimed to provide evidence for clinicians to select the appropriate biopsy approach under different conditions. TPBx (n = 173) and TRBx (n = 166) were performed randomly for 339 patients who were suspicious of prostate cancer (PCa). The cancer detection rate (CDR), complication rate, visual analogue scale (VAS) score, most painful procedure, number of repeated biopsy and additional anesthesia and operating time (starting from lying down on the operating table to getting up) were recorded. The results showed that TPBx and TRBx were equivalent in CDR (35.3% vs. 31.9%) and minor complication rate (44.9% vs. 41.0%) (both P > 0.05). The major complication rate was lower in TPBx than in TRBx (0.6% vs. 4.3%, P < 0.05). TPBx was more time-consuming (17.51 ± 3.33 min vs. 14.73 ± 3.25 min) and painful (VAS score: 4.0 vs. 2.0); and it had higher rates of repeated biopsy (3.2% vs. 1.1%) and additional anesthesia (15.0% vs. 1.2%) (all P < 0.05). In summary, both TPBx and TRBx are effective to detect PCa. The major complication rate for TRBx is higher, whereas TPBx procedure is more complex and painful.
Characterising the bacterial microbiota across the gastrointestinal tracts of dairy cattle: membership and potential function
Authors: Mao Shengyong , Zhang Mengling , Liu Junhua , Zhu Weiyun 
Published: November 2015

AbstractThe bacterial community composition and function in the gastrointestinal tracts (GITs) of dairy cattle is very important, since it can influence milk production and host health. However, our understanding of bacterial communities in the GITs of dairy cattle is still very limited. This study analysed bacterial communities in ten distinct GIT sites (the digesta and mucosa of the rumen, reticulum, omasum, abomasum, duodenum, jejunum, ileum, cecum, colon and rectum) in six dairy cattle. The study observed 542 genera belonging to 23 phyla distributed throughout the cattle GITs, with the Firmicutes, Bacteroidetes and Proteobacteria predominating. In addition, data revealed significant spatial heterogeneity in composition, diversity and species abundance distributions of GIT microbiota. Furthermore, the study inferred significant differences in the predicted metagenomic profiles among GIT regions. In particular, the relative abundances of the genes involved in carbohydrate metabolism were overrepresented in the digesta samples of forestomaches and the genes related to amino acid metabolism were mainly enriched in the mucosal samples. In general, this study provides the first deep insights into the composition of GIT microbiota in dairy cattle and it may serve as a foundation for future studies in this area.
Dual subcellular compartment delivery of doxorubicin to overcome drug resistant and enhance antitumor activity
Authors: Song Yan-feng , Liu Dao-zhou , Cheng Ying , Liu Miao , Ye Wei-liang , Zhang Bang-le , Liu Xin-you , Zhou Si-yuan 
Published: November 2015

AbstractIn order to overcome drug resistant and enhance antitumor activity of DOX, a new pH-sensitive micelle (DOX/DQA-DOX@DSPE-hyd-PEG-AA) was prepared to simultaneously deliver DOX to nucleus and mitochondria. Drug released from DOX/DQA-DOX@DSPE-hyd-PEG-AA showed a pH-dependent manner. DOX/DQA-DOX@DSPE-hyd-PEG-AA induced the depolarization of mitochondria and apoptosis in MDA-MB-231/ADR cells and A549 cells, which resulted in the high cytotoxicity of DOX/DQA-DOX@DSPE-hyd-PEG-AA against MDA-MB-231/ADR cells and A549 cells. Confocal microscopy confirmed that DOX/DQA-DOX@DSPE-hyd-PEG-AA simultaneously delivered DQA-DOX and DOX to the mitochondria and nucleus of tumor cell. After DOX/DQA-DOX@DSPE-hyd-PEG-AA was injected to the tumor-bearing nude mice by the tail vein, DOX was mainly found in tumor tissue. But DOX was widely distributed in the whole body after the administration of free DOX. Compared with free DOX, the same dose of DOX/DQA-DOX@DSPE-hyd-PEG-AA significantly inhibited the growth of DOX-resistant tumor in tumor-bearing mice without obvious systemic toxicity. Therefore, dual subcellular compartment delivery of DOX greatly enhanced the antitumor activity of DOX on DOX-resistant tumor. DOX/DQA-DOX@DSPE-hyd-PEG-AA has the potential in target therapy for DOX-resistant tumor.
Double-twist cylinders in liquid crystalline cholesteric blue phases observed by transmission electron microscopy
Authors: Tanaka Shu , Yoshida Hiroyuki , Kawata Yuto , Kuwahara Ryusuke , Nishi Ryuji , Ozaki Masanori 
Published: November 2015

AbstractCholesteric blue phases are liquid crystalline phases in which the constituent rod-like molecules spontaneously form three-dimensional, helical structures. Despite theoretical predictions that they are composed of cylindrical substructures within which the liquid crystal molecules are doubly twisted, real space observation of the arrangement of such structures had not been performed. Through transmission electron microscopy of photopolymerized blue phases with controlled lattice plane orientations, we report real space observation and comparison of the lattice structures of blue phases I and II. The two systems show distinctly different contrasts, reflecting the theoretically predicted, body centred and simple cubic arrangement of the double-twist cylinders. Transmission electron microscopy also reveals different tendencies of the two blue phases to align on unidirectionally rubbed surfaces. We thus show that TEM observation of alignment-controlled, photopolymerized liquid crystals can be a powerful tool to investigate complex liquid crystalline order.
Human corneal stromal stem cells support limbal epithelial cells cultured on RAFT tissue equivalents
Authors: Kureshi Alvena K , Dziasko Marc , Funderburgh James L , Daniels Julie T 
Published: November 2015

AbstractHuman limbal epithelial cells (HLE) and corneal stromal stem cells (CSSC) reside in close proximity in vivo in the corneal limbal stem cell niche. However, HLE are typically cultured in vitro without supporting niche cells. Here, we re-create the cell-cell juxtaposition of the native environment in vitro, to provide a tool for investigation of epithelial-stromal cell interactions and to optimize HLE culture conditions for potential therapeutic application. RAFT (Real Architecture For 3D Tissue) tissue equivalents (TEs) were used as a 3-dimensional substrate for co-culturing HLE and CSSC. Our results demonstrate that a monolayer of HLE that maintained expression of p63α, ABCB5, CK8 and CK15 (HLE markers), formed on the surface of RAFT TEs within 13 days of culture. CSSC remained in close proximity to HLE and maintained expression of mesenchymal stem cell markers. This simple technique has a short preparation time of only 15 days with the onset of HLE layering and differentiation observed. Furthermore, co-cultivation of HLE with another niche cell type (CSSC) directly on RAFT TEs, eliminates the requirement for animal-derived feeder cells. RAFT TEs may be useful for future therapeutic delivery of multiple cell types to restore the limbal niche following ocular surface injury or disease.
Motivation and value influences in the relative balance of goal-directed and habitual behaviours in obsessive-compulsive disorder
Authors: Voon V , Baek K , Enander J , Worbe Y , Morris L S , Harrison N A , Robbins T W , Rück C , Daw N 
Published: November 2015

AbstractOur decisions are based on parallel and competing systems of goal-directed and habitual learning, systems which can be impaired in pathological behaviours. Here we focus on the influence of motivation and compare reward and loss outcomes in subjects with obsessive-compulsive disorder (OCD) on model-based goal-directed and model-free habitual behaviours using the two-step task. We further investigate the relationship with acquisition learning using a one-step probabilistic learning task. Forty-eight OCD subjects and 96 healthy volunteers were tested on a reward and 30 OCD subjects and 53 healthy volunteers on the loss version of the two-step task. Thirty-six OCD subjects and 72 healthy volunteers were also tested on a one-step reversal task. OCD subjects compared with healthy volunteers were less goal oriented (model-based) and more habitual (model-free) to reward outcomes with a shift towards greater model-based and lower habitual choices to loss outcomes. OCD subjects also had enhanced acquisition learning to loss outcomes on the one-step task, which correlated with goal-directed learning in the two-step task. OCD subjects had greater stay behaviours or perseveration in the one-step task irrespective of outcome. Compulsion severity was correlated with habitual learning in the reward condition. Obsession severity was correlated with greater switching after loss outcomes. In healthy volunteers, we further show that greater reward magnitudes are associated with a shift towards greater goal-directed learning further emphasizing the role of outcome salience. Our results highlight an important influence of motivation on learning processes in OCD and suggest that distinct clinical strategies based on valence may be warranted.
Neuroplasticity-dependent and -independent mechanisms of chronic deep brain stimulation in stressed rats
Authors: Bambico F R , Bregman T , Diwan M , Li J , Darvish-Ghane S , Li Z , Laver B , Amorim B O , Covolan L , Nobrega J N , Hamani C 
Published: November 2015

AbstractChronic ventromedial prefrontal cortex (vmPFC) deep brain stimulation (DBS) improves depressive-like behaviour in rats via serotonergic and neurotrophic-related mechanisms. We hypothesise that, in addition to these substrates, DBS-induced increases in hippocampal neurogenesis may also be involved. Our results show that stress-induced behavioural deficits in the sucrose preference test, forced swim test, novelty-suppressed feeding test (NSFT) and elevated plus maze were countered by chronic vmPFC DBS. In addition, stressed rats receiving stimulation had significant increases in hippocampal neurogenesis, PFC and hippocampal brain-derived neurotrophic factor levels. To block neurogenesis, stressed animals given DBS were injected with temozolomide. Such treatment reversed the anxiolytic-like effect of stimulation in the NSFT without significantly affecting performance in other behavioural tests. Taken together, our findings suggest that neuroplastic changes, including neurogenesis, may be involved in specific anxiolytic effects of DBS without affecting its general antidepressant-like response.
A requirement of serotonergic p38α mitogen-activated protein kinase for peripheral immune system activation of CNS serotonin uptake and serotonin-linked behaviors
Authors: Baganz N L , Lindler K M , Zhu C B , Smith J T , Robson M J , Iwamoto H , Deneris E S , Hewlett W A , Blakely R D 
Published: November 2015

AbstractAlterations in central serotonin (5-hydroxytryptamine, 5-HT) neurotransmission and peripheral immune activation have been linked to multiple neuropsychiatric disorders, including depression, schizophrenia and autism. The antidepressant-sensitive 5-HT transporter (SERT, SLC6A4), a critical determinant of synaptic 5-HT inactivation, can be regulated by pro-inflammatory cytokine signaling. Systemic innate immune system activation via intraperitoneal lipopolysaccharide (LPS) injection rapidly elevates brain SERT activity and 5-HT clearance. Moreover, the pro-inflammatory cytokine interleukin (IL)-1β rapidly stimulates SERT activity in raphe nerve terminal preparations ex vivo, effects that are attenuated by pharmacological p38 MAPK inhibition. To establish a role of serotonergic p38α MAPK signaling in LPS/IL-1β-induced SERT regulation and attendant behavioral responses, we pursued studies in mice that afford conditional elimination of p38α MAPK in 5-HT neurons (p38α5HT−). We found p38α5HT− and control (p38α5HT+) littermates to be indistinguishable in viability and growth and to express equivalent levels of SERT protein and synaptosomal 5-HT transport activity. Consistent with pharmacological studies, however, IL-1β fails to increase SERT activity in midbrain synaptosomes prepared from p38α5HT− animals. Moreover, although LPS elevated plasma corticosterone and central/peripheral pro-inflammatory cytokines in p38α5HT− animals, elevations in midbrain SERT activity were absent nor were changes in depressive and anxiety-like behaviors observed. Our studies support an obligate role of p38α MAPK signaling in 5-HT neurons for the translation of immune activation to SERT regulation and 5-HT-modulated behaviors.
Exercise Training Improves Whole Body Insulin Resistance via Adiponectin Receptor 1
Authors: Cho J.-K. , Kim S.-U. , Hong H.-R. , Yoon J.-H. , Kang H.-S. 
Published: November 2015

AbstractLittle is known regarding whether adiponectin receptors mediate high-intensity interval training (HIT)-induced improvement of insulin resistance associated with obesity. This study investigated the effect of HIT on whole body insulin resistance in high-fat diet-induced obese mice. 5-week-old male mice (N=30) were randomly assigned to standard chow (SC) (n=10) or HFD (n=20) for 23 weeks. After 15 weeks of dietary treatment, the HFD mice were further assigned to HFD (n=10) or HFD plus HIT (HFD+HIT, n=10). The HFD+HIT mice were subjected to HIT during the last 8 weeks of the 23-week HFD course. HFD resulted in whole body insulin resistance, hypoadiponectinemia, suppressed expression of adiponectin receptor 1(AdipoR1) and 2 (AdipoR2), suppressed expression of phosphorylated AMP-activated protein kinase (p-AMPK) and NAD-dependent deacetylase sirtuin-1 (SIRT1), and decreased mRNAs of peroxisome proliferator-activated receptor-α (PPARα), carnitine palmitoyltransferase I (CPT1), and acyl CoA oxidase (ACO) in skeletal muscle. In contrast, HIT alleviated whole body insulin resistance and prevented decreased levels of total adiponectin in both serum and adipose tissue. HIT also prevented the down-regulation of AdipoR1 and AMPK/SIRT1 proteins and the down-regulation of PPARα, CPT1, and ACO mRNAs. The current findings show that HIT alleviates whole body insulin resistance due to HFD-induced obesity via the AdipoR1 and AMPK/SIRT1 mediated-signaling pathway in skeletal muscle, implying the potential role of HIT to combat this metabolic condition.
Adrenal Incidentaloma and Subclinical Cushing’s Syndrome: A Longitudinal Follow-Up Study by Endoscopic Ultrasound
Authors: Collienne Maike , Timmesfeld Nina , Bergmann Simona , Goebel Joachim , Kann Peter 
Published: November 2015

Abstract
Purpose Adrenal incidentaloma (AI) and adrenal masses in cases of subclinical Cushing’s syndrome (SCS) initially require follow-up imaging. In this study we used endoscopic ultrasound (EUS) as a method for high-resolution imaging. The aim was to evaluate the growth rate of AI and SCS by EUS.
Materials and Methods This retrospective analysis included 93 out of 229 patients with AI or SCS who were investigated longitudinally by EUS in our university hospital between 1997 and 2013. The longitudinal follow-up required at least two investigations by EUS and evaluation of endocrine function. Plasma renin, serum aldosterone, 24 h urinary catecholamines and 2 mg dexamethasone suppression test were performed. EUS was performed at baseline and during follow-up. Each time, the maximum diameter was measured. Three groups were defined: non-functioning adenomas (NFA), non-functioning nodular hyperplasias (NFH) and SCS.
Results 86 patients had non-functioning masses [NFM] (59 NFA, 48 NFH) and 7 patients had SCS (10 masses). At baseline the mean diameter was 19.4 (± 9.3) mm (NFM) and 19.6 (± 9.2) mm (SCS). The mean follow-up period was 31.6 ± 28.7 months. The estimated mean growth rates per year were low: They were 0.35 mm/yr [NFA], 0.02 mm/yr [NFH] and 0.53 mm/yr [SCS]. Furthermore, there was no malignant progression of any mass.
Conclusion The growth rate as determined by EUS was low for all tumor entities observed in this study. There was no difference in tumor growth between the groups.
Registration of Supine MR Mammography with Breast Ultrasound for Surgical Planning of Breast Conserving Surgery: A Feasibility Study
Authors: Pickles Martin , Gibbs Peter , Hubbard Anne , Rahman Ayesha , Wieczorek Joanna , Roychaudhury Ronjabati , Bradley Caroline , Turnbull Lindsay 
Published: November 2015

Abstract
Purpose To report the feasibility, accuracy and initial clinical experience of the use of real-time magnetic resonance navigated ultrasound (rtMRnUS) in the surgical planning of breast-conserving surgery (BCS) via guide wire insertion.
Materials and Methods 29 participants were recruited into this prospective ethics committee approved study. The first 4 cases were utilized as a training set. Participants underwent a supine contrast-enhanced breast MR examination with external fiducials and corresponding ink marks placed on the skin of the affected breast to act as co-registration pairs. MR examinations included both functional and morphological images. A LOGIQ E9 ultrasound system (GE Healthcare, Milwaukee, WI, USA) equipped with a 6 – 15 MHz transducer was utilized for rtMRnUS. To facilitate point co-registration of the previously acquired MR dataset with the real-time ultrasound, co-registration pairs were identified on both imaging modalities. The following co-registration quality metrics were recorded: root mean square deviation (RMSD), lesion and global accuracies. Post co-registration guide wire insertion was performed.
Results Co-registration was successfully undertaken in all participants. Results from 25 participants are presented. The median (min, max) RMSD was 3.3 mm (0.6 mm, 8.8 mm). The global accuracy was assessed as very good (8), good (12), moderate (3) and poor (2) while the median (min, max) lesion accuracy was recorded at 8.9 mm (2.1 mm, 33.2 mm).
Conclusion The use of rtMRnUS to facilitate guide wire insertion is a feasible technique. Generally, very good or good global registration can be expected. Lesion accuracy results indicate that a median difference, in 3 D space, of 9 mm can be expected between imaging modalities.
3.2.2 Oxidation Other Than with Cytochrome P450s
Authors: Herter S. , Turner N. J. 
Published: November 2015

AbstractThe laccase- or tyrosinase-catalyzed oxidation of phenolic compounds leads to the generation of radical cations which subsequently produce quinoid derivatives. Acting as electrophilic Michael acceptors, quinones can undergo successive reactions amongst themselves yielding homomolecular products. In the presence of nucleophiles acting as coupling partners, enzymatically generated quinones undergo hetero-cross-coupling reactions to give novel hybrid molecules. In contrast to laccases, tyrosinase enzymes also catalyze the ortho-hydroxylation of monophenols, giving rise to catechols and benzo-1,2-quinones. Unspecific peroxygenases (UPOs) catalyze the hydroxylation of a broad range of C—H containing substrates, including small aromatic compounds, larger polycyclic aromatic hydrocarbons, heteroaromatics, alkanes, and cycloalkanes. A common feature of UPOs and chloroperoxidases (CPOs) is found in the asymmetric epoxidation of alkenes to yield the corresponding epoxides, often with high enantiomeric excess.
3.5.2 Oxidation at Sulfur
Authors: Grogan G. 
Published: November 2015

AbstractThe asymmetric biocatalytic oxidation of sulfides can be performed with high enantioselectivity by a number of different enzymes, allowing access to biologically active compounds including flavors and pharmaceuticals, and also chiral auxiliaries for organic synthesis. The application of biocatalysts in asymmetric sulfoxidation has benefited recently from advances in molecular biology that allow the study and application of individual enzymes, either purified or expressed in recombinant strains of E. coli. In this chapter, the major contemporary approaches to biocatalytic sulfoxidation, including enzymes such as peroxidases, flavin-dependent monooxygenases, and dioxygenases, are reviewed. In addition, the most user-friendly examples of enzyme-catalyzed sulfoxidation are illustrated using practical exemplar procedures from the relevant literature.
3.8.2 Merging of Metal, Organic, and Enzyme Catalysis
Authors: Gröger H. , Hummel W. 
Published: November 2015

AbstractThis chapter reviews multistep, one-pot processes through a combination of the catalytic disciplines of enzyme catalysis and chemocatalysis (metal catalysis, organocatalysis), demonstrating that enzymes as catalysts can be compatible with a broad range of man-made chemocatalysts, spanning the range from heterogeneous to homogeneous catalysts and metal catalysts to organocatalysts. Such chemoenzymatic one-pot syntheses, which combine reactions without the need to work-up intermediates, are attractive, for example, with respect to both process efficiency and sustainability.