bluuebunny/crossref_metadata_2025_split huggingface dataset:
A microfluidic device to study neuronal and motor responses to acute chemical stimuli in zebrafish
Authors: Candelier Raphaël , Sriti Murmu Meena , Alejo Romano Sebastián , Jouary Adrien , Debrégeas Georges , Sumbre Germán 
Published: July 2015

AbstractZebrafish larva is a unique model for whole-brain functional imaging and to study sensory-motor integration in the vertebrate brain. To take full advantage of this system, one needs to design sensory environments that can mimic the complex spatiotemporal stimulus patterns experienced by the animal in natural conditions. We report on a novel open-ended microfluidic device that delivers pulses of chemical stimuli to agarose-restrained larvae with near-millisecond switching rate and unprecedented spatial and concentration accuracy and reproducibility. In combination with two-photon calcium imaging and recordings of tail movements, we found that stimuli of opposite hedonic values induced different circuit activity patterns. Moreover, by precisely controlling the duration of the stimulus (50–500 ms), we found that the probability of generating a gustatory-induced behavior is encoded by the number of neurons activated. This device may open new ways to dissect the neural-circuit principles underlying chemosensory perception.
An Efficient Genome-Wide Fusion Partner Screening System for Secretion of Recombinant Proteins in Yeast
Authors: Bae Jung-Hoon , Hyun Sung Bong , Kim Hyun-Jin , Park Soon-Ho , Lim Kwang-Mook , Kim Mi-Jin , Lee Cho-Ryong , Sohn Jung-Hoon 
Published: July 2015

AbstractTo produce rarely secreted recombinant proteins in the yeast Saccharomyces cerevisiae, we developed a novel genome-wide optimal translational fusion partner (TFP) screening system that involves recruitment of an optimal secretion signal and fusion partner. A TFP library was constructed from a genomic and truncated cDNA library by using the invertase-based signal sequence trap technique. The efficiency of the system was demonstrated using two rarely secreted proteins, human interleukin (hIL)-2 and hIL-32. Optimal TFPs for secretion of hIL-2 and hIL-32 were easily selected, yielding secretion of these proteins up to hundreds of mg/L. Moreover, numerous uncovered yeast secretion signals and fusion partners were identified, leading to efficient secretion of various recombinant proteins. Selected TFPs were found to be useful for the hypersecretion of other recombinant proteins at yields of up to several g/L. This screening technique could provide new methods for the production of various types of difficult-to-express proteins.
Identification of PblB mediating galactose-specific adhesion in a successful Streptococcus pneumoniae clone
Authors: Hsieh Yu-Chia , Lin Tzu-Lung , Lin Che-Ming , Wang Jin-Town 
Published: July 2015

AbstractThe pneumococcal genome is variable and there are minimal data on the influence of the accessory genome on phenotype. Pneumococcal serotype 14 sequence type (ST) 46 had been the most prevalent clone causing pneumonia in children in Taiwan. A microarray was constructed using the genomic DNA of a clinical strain (NTUH-P15) of serotype 14 ST46. Using DNA hybridization, genomic variations in NTUH-P15 were compared to those of 3 control strains. Microarray analysis identified 7 genomic regions that had significant increases in hybridization signals in the NTUH-P15 strain compared to control strains. One of these regions encoded PblB, a phage-encoded virulence factor implicated (in Streptococcus mitis) in infective endocarditis. The isogenic pblB mutant decreased adherence to A549 human lung epithelial cell compared to wild-type NTUH-P15 strain (P = 0.01). Complementation with pblB restored the adherence. PblB is predicted to contain a galactose-binding domain-like region. Preincubation of NTUH-P15 with D-galactose resulted in decreases of adherence to A549 cell in a dose-dependent manner. Challenge of mice with NTUH-P15, isogenic pblB mutant and pblB complementation strains determined that PblB was required for bacterial persistence in the nasopharynx and lung. PblB, as an adhesin mediating the galactose-specific adhesion activity of pneumococci, promote pneumococcal clonal success.
Dosimetric Comparison and Evaluation of Three Radiotherapy Techniques for Use after Modified Radical Mastectomy for Locally Advanced Left-sided Breast Cancer
Authors: Ma Changchun , Zhang Wuzhe , Lu Jiayang , Wu Lili , Wu Fangcai , Huang Baotian , Lin Yan , Li Dongsheng 
Published: July 2015

AbstractThis study aimed to compare the post-modified radical mastectomy radiotherapy (PMRMRT) for left-sided breast cancer utilizing 3-dimensional conformal radiotherapy with field-in-field technique (3DCRT-FinF), 5-field intensity-modulated radiation therapy (5F-IMRT) and 2- partial arc volumetric modulated arc therapy (2P-VMAT). We created the 3 different PMRMRT plans for each of the ten consecutive patients. We performed Kruskal-Wallis analysis of variance (ANOVA) followed by the Dunn’s-type multiple comparisons to establish a hierarchy in terms of plan quality and dosimetric benefits. P < 0.05 was considered statistically significant. Both 5F-IMRT and 2P-VMAT plans exhibited similar PTV coverage (V95%), hotspot areas (V110%) and conformity (all p > 0.05) and significantly higher PTV coverage compared with 3DCRT-FinF (both p < 0.001). In addition, 5F-IMRT plans provided significantly less heart and left lung radiation exposure than 2P-VMAT (all p < 0.05). The 3DCRT-FinF plans with accurately estimated CTV displacement exhibited enhanced target coverage but worse organs at risk (OARs) sparing compared with those plans with underestimated displacements. Our results indicate that 5F-IMRT has dosimetrical advantages compared with the other two techniques in PMRMRT for left-sided breast cancer given its optimal balance between PTV coverage and OAR sparing (especially heart sparing). Individually quantifying and minimizing CTV displacement can significantly improve dosage distribution.
Surmounting intrinsic quantum-measurement uncertainties in Gaussian-state tomography with quadrature squeezing
Authors: Řeháček Jaroslav , Teo Yong Siah , Hradil Zdeněk , Wallentowitz Sascha 
Published: July 2015

AbstractWe reveal that quadrature squeezing can result in significantly better quantum-estimation performance with quantum heterodyne detection (of H. P. Yuen and J. H. Shapiro) as compared to quantum homodyne detection for Gaussian states, which touches an important aspect in the foundational understanding of these two schemes. Taking single-mode Gaussian states as examples, we show analytically that the competition between the errors incurred during tomogram processing in homodyne detection and the Arthurs-Kelly uncertainties arising from simultaneous incompatible quadrature measurements in heterodyne detection can often lead to the latter giving more accurate estimates. This observation is also partly a manifestation of a fundamental relationship between the respective data uncertainties for the two schemes. In this sense, quadrature squeezing can be used to overcome intrinsic quantum-measurement uncertainties in heterodyne detection.
Nonfunctional ingestion of plant miRNAs in silkworm revealed by digital droplet PCR and transcriptome analysis
Authors: Jia Ling , Zhang Dayan , Xiang Zhonghuai , He Ningjia 
Published: July 2015

AbstractSince a plant miRNA (miR168) cross-regulating a mammalian transcript was reported, miRNA-mediated cross-kingdom communication has become one of the most compelling but controversial topics. In the present study, we used silkworm and mulberry, which is a model for studies on the interactions between the insect and its host plant, to address whether miRNA-mediated cross-kingdom communication is a common phenomenon. The results of TA clone, Sanger sequencing and droplet digital PCR demonstrated that several mulberry-derived miRNAs could enter to silkworm hemolymph and multiple tested tissues. Synthetic miR166b was also detected in hemolymph and fat body. However, the ingestion of synthetic miR166b did not play roles in silkworm physiological progress, which was revealed by RNA-seq analyses, RT-PCR and phenotypic investigations. Mulberry miRNAs are convincingly transferred to the silkworm orally and no physiological process associated with the miRNAs was demonstrable. The results provided a new aspect of cross-kingdom miRNA transfer.
Circadian and ultradian rhythms of clock gene expression in the suprachiasmatic nucleus of freely moving mice
Authors: Ono Daisuke , Honma Ken-ichi , Honma Sato 
Published: July 2015

AbstractIn mammals, the temporal order of physiology and behavior is primarily regulated by the circadian pacemaker located in the hypothalamic suprachiasmatic nucleus (SCN). Rhythms are generated in cells by an auto-regulatory transcription/translation feedback loop, composed of several clock genes and their protein products. Taking advantage of bioluminescence reporters, we have succeeded in continuously monitoring the expression of clock gene reporters Per1-luc, PER2::LUC and Bmal1-ELuc in the SCN of freely moving mice for up to 3 weeks in constant darkness. Bioluminescence emitted from the SCN was collected with an implanted plastic optical fiber which was connected to a cooled photomultiplier tube. We found robust circadian rhythms in the clock gene expression, the phase-relation of which were the same as those observed ex vivo. The circadian rhythms were superimposed by episodic bursts which had ultradian periods of approximately 3.0 h. Episodic bursts often accompanied activity bouts, but stoichiometric as well as temporal analyses revealed no causality between them. Clock gene expression in the SCN in vivo is regulated by the circadian pacemaker and ultradian rhythms of unknown origin.
Autophagy confers DNA damage repair pathways to protect the hematopoietic system from nuclear radiation injury
Authors: Lin Weiwei , Yuan Na , Wang Zhen , Cao Yan , Fang Yixuan , Li Xin , Xu Fei , Song Lin , Wang Jian , Zhang Han , Yan Lili , Xu Li , Zhang Xiaoying , Zhang Suping , Wang Jianrong 
Published: July 2015

AbstractAutophagy is essentially a metabolic process, but its in vivo role in nuclear radioprotection remains unexplored. We observed that ex vivo autophagy activation reversed the proliferation inhibition, apoptosis and DNA damage in irradiated hematopoietic cells. In vivo autophagy activation improved bone marrow cellularity following nuclear radiation exposure. In contrast, defective autophagy in the hematopoietic conditional mouse model worsened the hematopoietic injury, reactive oxygen species (ROS) accumulation and DNA damage caused by nuclear radiation exposure. Strikingly, in vivo defective autophagy caused an absence or reduction in regulatory proteins critical to both homologous recombination (HR) and non-homologous end joining (NHEJ) DNA damage repair pathways, as well as a failure to induce these proteins in response to nuclear radiation. In contrast, in vivo autophagy activation increased most of these proteins in hematopoietic cells. DNA damage assays confirmed the role of in vivo autophagy in the resolution of double-stranded DNA breaks in total bone marrow cells as well as bone marrow stem and progenitor cells upon whole body irradiation. Hence, autophagy protects the hematopoietic system against nuclear radiation injury by conferring and intensifying the HR and NHEJ DNA damage repair pathways and by removing ROS and inhibiting apoptosis.
A new functional classification system (FGA/B) with prognostic value for glioma patients
Authors: Friedlein Katharina , Bozhkov Yavor , Hore Nirjhar , Merkel Andreas , Sommer Björn , Brandner Sebastian , Buchfelder Michael , Savaskan Nicolai E. , Eyüpoglu Ilker Y. 
Published: July 2015

AbstractDespite advances in multimodal treatments, malignant gliomas remain characterized by a short survival time. Surgical treatment is accepted to be the first line of therapy, with recent studies revealing that maximal possible tumor reduction exerts significant impact on patient outcome. Consideration of tumor localization in relation to functionally eloquent brain areas has been gaining increasing importance. Despite existing assessment methods, the availability of a simple but reliable preoperative grading based on functional data would therefore prove to be indispensable for the prediction of postoperative outcome and hence for overall survival in glioma patients. We performed a clinical investigation comprising 322 patients with gliomas and developed a novel classification system of preoperative tumor status, which considers tumor operability based on two graduations (Friedlein Grading - FG): FGA with lesions at safe distance to eloquent regions which can be completely resected and FGB referring to tumors which can only be partially resected or biopsied. Investigation of outcome revealed that FGA were characterized by a significantly longer overall survival time compared to FGB. We offer the opportunity to classify brain tumors in a dependable and reproducible manner. The FGA/B grading method provides high prognostic value with respect to overall survival time in relation to the extent of location-dependent tumor resection.
The oxytocin system promotes resilience to the effects of neonatal isolation on adult social attachment in female prairie voles
Authors: Barrett C E , Arambula S E , Young L J 
Published: July 2015

AbstractGenes and social experiences interact to create variation in social behavior and vulnerability to develop disorders of the social domain. Socially monogamous prairie voles display remarkable diversity in neuropeptide receptor systems and social behavior. Here, we examine the interaction of early-life adversity and brain oxytocin receptor (OTR) density on adult social attachment in female prairie voles. First, pups were isolated for 3 h per day, or unmanipulated, from postnatal day 1–14. Adult subjects were tested on the partner preference (PP) test to assess social attachment and OTR density in the brain was quantified. Neonatal social isolation impaired female PP formation, without affecting OTR density. Accumbal OTR density was, however, positively correlated with the percent of time spent huddling with the partner in neonatally isolated females. Females with high accumbal OTR binding were resilient to neonatal isolation. These results are consistent with the hypothesis that parental nurturing shapes neural systems underlying social relationships by enhancing striatal OTR signaling. Thus, we next determined whether early touch, mimicking parental licking and grooming, stimulates hypothalamic OT neuron activity. Tactile stimulation induced immediate-early gene activity in OT neurons in neonates. Finally, we investigated whether pharmacologically potentiating OT release using a melanocortin 3/4 agonist, melanotan-II (10 mg kg−1 subcutaneously), would mitigate the social isolation-induced impairments in attachment behavior. Neonatal melanotan-II administration buffered against the effects of early isolation on partner preference formation. Thus, variation in accumbal OTR density and early OT release induced by parental nurturing may moderate susceptibility to early adverse experiences, including neglect.
ATP stimulates pannexin 1 internalization to endosomal compartments
Authors: Boyce Andrew K.J. , Kim Michelle S. , Wicki-Stordeur Leigh E. , Swayne Leigh Anne 
Published: July 2015

The ubiquitous pannexin 1 (Panx1) ion- and metabolite-permeable channel mediates the release of ATP, a potent signalling molecule. In the present study, we provide striking evidence that ATP, in turn, stimulates internalization of Panx1 to intracellular membranes. These findings hold important implications for understanding the regulation of Panx1 when extracellular ATP is elevated. In the nervous system, this includes phenomena such as synaptic plasticity, pain, precursor cell development and stroke; outside of the nervous system, this includes things like skeletal and smooth muscle activity and inflammation. Within 15 min, ATP led to significant Panx1–EGFP internalization. In a series of experiments, we determined that hydrolysable ATP is the most potent stimulator of Panx1 internalization. We identified two possible mechanisms for Panx1 internalization, including activation of ionotropic purinergic (P2X) receptors and involvement of a putative ATP-sensitive residue in the first extracellular loop of Panx1 (Trp74). Internalization was cholesterol-dependent, but clathrin, caveolin and dynamin independent. Detailed analysis of Panx1 at specific endosome sub-compartments confirmed that Panx1 is expressed in endosome membranes of the classical degradation pathway under basal conditions and that elevation of ATP levels diverts a sub-population to recycling endosomes. This is the first report detailing endosome localization of Panx1 under basal conditions and the potential for ATP regulation of its surface expression. Given the ubiquitous expression profile of Panx1 and the importance of ATP signalling, these findings are of critical importance for understanding the role of Panx1 in health and disease.
Fully pipelined CORDIC‐based inverse kinematic FPGA design for biped robots
Authors: Chung Rih‐Lung , Zhang Yi‐Qin , Chen Shih‐Lun 
Published: July 2015

A high‐speed field‐programmable gate array (FPGA) design is proposed to calculate angles and distances for biped robots in real time. A low‐complexity and high‐accuracy hardware‐oriented algorithm based on CORDIC was developed. To reduce hardware cost, a hardware sharing technique was used to realise a CORDIC scaling factor generator and three hardware sharing machines. Moreover, the multipliers and dividers were replaced by cost‐efficiency components, such as adders and shifters to further reduce hardware cost. In addition, the proposed design was implemented with a fully pipelined architecture, which achieved improved operating frequency and throughput efficiency. The proposed design was realised and verified by an FPGA device with a maximum operating frequency of 127 MHz, which achieved the calculation of angles and distances for biped robots in real time. Compared with the previous design, this work not only reduced hardware cost by at least 49.6% and average errors by at least 67.2%, but also improved the average executing performance by 62.7% when calculating ten angles for the biped robots.
Study of the instability of the Poiseuille flow using a thermodynamic formalism
Authors: Wang Jianchun , Li Qianxiao , E Weinan 
Published: July 2015

Significance
The stability of Poiseuille flow is among the most classical problems in fluid mechanics going back to the pioneering work of Reynolds. Despite a huge amount of effort, particularly recent advances in experimental studies, we still lack a suitable theoretical framework. In this paper, we develop a thermodynamic formalism for studying this problem. We show that this formalism allows us to identify a unique critical Reynolds number at which the laminar flow loses stability. We also study the free energy, action, and other thermodynamic relations for the macroscopic quantities associated with the flow. The formalism developed here should be applicable to a large class of problems exhibiting subcritical instabilities.
Activity-dependent mismatch between axo-axonic synapses and the axon initial segment controls neuronal output
Authors: Wefelmeyer Winnie , Cattaert Daniel , Burrone Juan 
Published: July 2015

Significance
Neurons integrate synaptic inputs at the axon initial segment (AIS), where the action potential is initiated. Recent findings have shown this structure to be highly plastic. Here, we focus on the axo-axonic synapses formed onto the AIS and show that although chronic increases in neuronal activity result in a distal relocation of the AIS, the synapses do not change position. Computational modeling suggests this spatial mismatch has critical functional consequences on neuronal output, allowing the cell to downregulate its own excitability and thus respond homeostatically to chronic stimulation.
Earliest economic exploitation of chicken outside East Asia: Evidence from the Hellenistic Southern Levant
Authors: Perry-Gal Lee , Erlich Adi , Gilboa Ayelet , Bar-Oz Guy 
Published: July 2015

SignificanceThis study offers new evidence on the cultural history of the chicken, a species that until recently received limited attention compared with other domesticated animals. We provide evidence for the earliest known economic exploitation of the chicken outside its original distribution. This intensified use is first documented in the Southern Levant during the Hellenistic period (fourth–second centuries B.C.E.), at least 100 y before chickens spread widely across Europe. We explore the mechanisms for the spread of chickens as an important species in livestock economies from Asian to Mediterranean and European economies in antiquity to become one of the most widespread and dominant domesticates in the world today.
Impact of fossil fuel emissions on atmospheric radiocarbon and various applications of radiocarbon over this century
Authors: Graven Heather D. 
Published: July 2015

SignificanceA wide array of scientific disciplines and industries use radiocarbon analyses; for example, it is used in dating of archaeological specimens and in forensic identification of human and wildlife tissues, including traded ivory. Over the next century, fossil fuel emissions will produce a large amount of CO2with no14C because fossil fuels have lost all14C over millions of years of radioactive decay. Atmospheric CO2, and therefore newly produced organic material, will appear as though it has “aged,” or lost14C by decay. By 2050, fresh organic material could have the same14C/C ratio as samples from 1050, and thus be indistinguishable by radiocarbon dating. Some current applications for14C may cease to be viable, and other applications will be strongly affected.
Regulation of ribosomal DNA amplification by the TOR pathway
Authors: Jack Carmen V. , Cruz Cristina , Hull Ryan M. , Keller Markus A. , Ralser Markus , Houseley Jonathan 
Published: July 2015

Significance
We tend to think of our genome as an unchanging store of information; however, recent evidence suggests that genomes vary between different cells in the same organism. How these differences arise and what effects they have remain unknown, but clearly our genome can change. In a single-celled organism, genome changes occur at random, and advantageous changes slowly propagate by natural selection. However, it is known that the DNA encoding ribosomes can change simultaneously in a whole population. Here we show that signaling pathways that sense environmental nutrients control genome change at the ribosomal DNA. This demonstrates that not all genome changes occur at random and that cells possess specific mechanisms to optimize their genome in response to the environment.
Music training alters the course of adolescent auditory development
Authors: Tierney Adam T. , Krizman Jennifer , Kraus Nina 
Published: July 2015

Significance
We show that in-school music training changes the course of adolescent brain development. Relative to an active control group that shows the expected wane in subcortical response consistency, adolescents undertaking in-school music training maintained heightened neural consistency throughout high school. The music training group also exhibited earlier emergence of the adult cortical response, suggesting that in-school music accelerates neurodevelopment. These changes seem to benefit literacy skills: both groups improved in phonological awareness relative to the general population, but the music training group improved more compared with the active controls. Our results support the notion that the adolescent brain remains receptive to training, underscoring the importance of enrichment during teenage years.