bluuebunny/crossref_metadata_2025_split huggingface dataset:
Born small, die young: Intrinsic, size-selective mortality in marine larval fish
Authors: Garrido S. , Ben-Hamadou R. , Santos A.M.P. , Ferreira S. , Teodósio M.A. , Cotano U. , Irigoien X. , Peck M.A. , Saiz E. , Ré P. 
Published: November 2015

AbstractMortality during the early stages is a major cause of the natural variations in the size and recruitment strength of marine fish populations. In this study, the relation between the size-at-hatch and early survival was assessed using laboratory experiments and on field-caught larvae of the European sardine (Sardina pilchardus). Larval size-at-hatch was not related to the egg size but was significantly, positively related to the diameter of the otolith-at-hatch. Otolith diameter-at-hatch was also significantly correlated with survival-at-age in fed and unfed larvae in the laboratory. For sardine larvae collected in the Bay of Biscay during the spring of 2008, otolith radius-at-hatch was also significantly related to viability. Larval mortality has frequently been related to adverse environmental conditions and intrinsic factors affecting feeding ability and vulnerability to predators. Our study offers evidence indicating that a significant portion of fish mortality occurs during the endogenous (yolk) and mixed (yolk /prey) feeding period in the absence of predators, revealing that marine fish with high fecundity, such as small pelagics, can spawn a relatively large amount of eggs resulting in small larvae with no chances to survive. Our findings help to better understand the mass mortalities occurring at early stages of marine fish.
Intrinsic magnetic properties of single-phase Mn1+xGa (0 < x < 1) alloys
Authors: Lu Q. M. , Yue M. , Zhang H. G. , Wang M. L. , Yu F. , Huang Q. Z. , Ryan D. H. , Altounian Z. 
Published: November 2015

AbstractMagnetization measurements have been carried out on a series of carefully prepared single-phase Mn1 + xGa (0 < x < 1) alloys. The saturation magnetization Ms, measured at 5 K, has a value of 92.0 emu/g for x = 0.15. This is the highest value reported in these alloys and is close to the calculated value of 116 emu/g for the stoichiometric compound (x = 0). Ms decreases gradually with x and has a value of 60.7 emu/g for x = 0.86. This behavior is consistent with the extra Mn atoms occupying Ga sites and coupling antiferromagnetically with the rest of the Mn atoms. The intrinsic magnetic properties of the Mn-Ga alloys indicate their great potential as novel, rare-earth free permanent magnetic materials.
Meta-analysis of colistin for the treatment of Acinetobacter baumannii infection
Authors: Chen Zhijin , Chen Yu , Fang Yaogao , Wang Xiaotian , Chen Yanqing , Qi Qingsong , Huang Fang , Xiao Xungang 
Published: November 2015

AbstractMultidrug resistant among Acinetobacter baumannii infection is associated with a high mortality rate and limits the therapeutic options. The aim of this study was to assess the safety and efficacy of colistin monotherapy vs. other single antibiotic therapy AND colistin-based combination therapy (with other antibiotics) vs. colistin alone for the treatment of Acinetobacter baumannii infection. Online electronic database were searched for studies evaluating colistin with or without other antibiotics in treatment of patients with drug-resistant Acinetobacter baumannii infection. Totally, twelve studies met the inclusion criteria. For colistin-based combination therapy, six articles including 668 patients were included. Our results showed that the overall clinical response did not differ significantly between colistin-based combination therapy and monotherapy (OR = 1.37, 95% CI = 0.86–2.19, P = 0.18). This insignificance was also detected in ICU mortality, length of stay and nephrotoxicity (P > 0.05). However, the colistin-based combination therapy was shown increasing the microbiological response (OR = 2.14, 95% CI = 1.48–3.07, P < 0.0001). For colistin monotherapy, six studies involving 491 patients were analyzed. The results were in concordance with the findings of the colistin-based combination therapy group. Our results suggest that colistin may be a promising therapy as safe and efficacious as standard antibiotics for the treatment of drug-resistant Acinetobacter baumannii infection.
Improving vagal activity ameliorates cardiac fibrosis induced by angiotensin II: in vivo and in vitro
Authors: Liu Jin-Jun , Huang Ning , Lu Yi , Zhao Mei , Yu Xiao-Jiang , Yang Yang , Yang Yong-hua , Zang Wei-Jin 
Published: November 2015

AbstractCardiac remodeling is characterized by overactivity of the renin–angiotensin system (RAS) and withdrawal of vagal activity. We hypothesized that improving vagal activity could attenuate cardiac fibrosis induced by angiotensin II (Ang II) in vivo and in vitro. Rats were subjected to abdominal aorta constriction (AAC) with or without pyridostigmine (PYR) (31 mg/kg/d). After 8 weeks, PYR significantly decreased Ang II level, AT1 protein expression and collagen deposition in cardiac tissue and improved heart rate variability, baroreflex sensitivity and cardiac function, which were abolished by atropine. In vitro, treatment of cardiac fibroblasts (CFs) with Ang II (10−7 M) increased cell proliferation, migration, transformation and secretory properties, which were significantly diminished by acetylcholine (ACh, 10−6 M). Subsequently, Ang II significantly increased collagen type I expression as well as metalloproteinase (MMP)-2 expression and activity. Transforming growth factor (TGF)-β1 expression and Smad3 phosphorylation presented a similar trend. Notably, the knockdown of the acetylcholine M2 receptor by siRNA could abolish ACh anti-fibrotic action. These data implicated cholinesterase inhibitor can increase vagal activity and reduce local Ang II level and ACh inhibit Ang II pro-fibrotic effects. Our findings suggested that the parasympathetic nervous system can serve as a promising target for cardiac remodeling treatment.
Structures of the CDK12/CycK complex with AMP-PNP reveal a flexible C-terminal kinase extension important for ATP binding
Authors: Dixon-Clarke Sarah E. , Elkins Jonathan M. , Cheng S.-W. Grace , Morin Gregg B. , Bullock Alex N. 
Published: November 2015

AbstractCyclin-dependent kinase 12 (CDK12) promotes transcriptional elongation by phosphorylation of the RNA polymerase II C-terminal domain (CTD). Structure-function studies show that this activity is dependent on a C-terminal kinase extension, as well as the binding of cyclin K (CycK). To better define these interactions we determined the crystal structure of the human CDK12/CycK complex with and without the kinase extension in the presence of AMP-PNP. The structures revealed novel features for a CDK, including a large β4-β5 loop insertion that contributes to the N-lobe interaction with the cyclin. We also observed two different conformations of the C-terminal kinase extension that effectively open and close the ATP pocket. Most notably, bound AMP-PNP was only observed when trapped in the closed state. Truncation of this C-terminal structure also diminished AMP-PNP binding, as well as the catalytic activity of the CDK12/CycK complex. Further kinetic measurements showed that the full length CDK12/CycK complex was significantly more active than the two crystallised constructs suggesting a critical role for additional domains. Overall, these results demonstrate the intrinsic flexibility of the C-terminal extension in CDK12 and highlight its importance for both ATP binding and kinase activity.
Composition and Interactions of Hepatitis B Virus Quasispecies Defined the Virological Response During Telbivudine Therapy
Authors: Zhou Bin , Dong Hui , He Yungang , Sun Jian , Jin Weirong , Xie Qing , Fan Rong , Wang Minxian , Li Ran , Chen Yangyi , Xie Shaoqing , Shen Yan , Huang Xin , Wang Shengyue , Lu Fengming , Jia Jidong , Zhuang Hui , Locarnini Stephen , Zhao Guo-Ping , Jin Li , Hou Jinlin 
Published: November 2015

AbstractReverse transcriptase (RT) mutations contribute to hepatitis B virus resistance during antiviral therapy with nucleos(t)ide analogs. However, the composition of the RT quasispecies and their interactions during antiviral treatment have not yet been thoroughly defined. In this report, 10 patients from each of 3 different virological response groups, i.e., complete virological response, partial virological response and virological breakthrough, were selected from a multicenter trial of Telbivudine treatment. Variations in the drug resistance-related critical RT regions in 107 serial serum samples from the 30 patients were examined by ultra-deep sequencing. A total of 496,577 sequence reads were obtained, with an average sequencing coverage of 4,641X per sample. The phylogenies of the quasispecies revealed the independent origins of two critical quasispecies, i.e., the rtA181T and rtM204I mutants. Data analyses and theoretical modeling showed a cooperative-competitive interplay among the quasispecies. In particular, rtM204I mutants compete against other quasispecies, which eventually leads to virological breakthrough. However, in the absence of rtM204I mutants, synergistic growth of the drug-resistant rtA181T mutants with the wild-type quasispecies could drive the composition of the viral population into a state of partial virological response. Furthermore, we demonstrated that the frequency of drug-resistant mutations in the early phase of treatment is important for predicting the virological response to antiviral therapy.
Three-dimensional Reconstruction of Peripheral Nerve Internal Fascicular Groups
Authors: Zhong Yingchun , Wang Liping , Dong Jianghui , Zhang Yi , Luo Peng , Qi Jian , Liu Xiaolin , Xian Cory J. 
Published: November 2015

AbstractPeripheral nerves are important pathways for receiving afferent sensory impulses and sending out efferent motor instructions, as carried out by sensory nerve fibers and motor nerve fibers. It has remained a great challenge to functionally reconnect nerve internal fiber bundles (or fascicles) in nerve repair. One possible solution may be to establish a 3D nerve fascicle visualization system. This study described the key technology of 3D peripheral nerve fascicle reconstruction. Firstly, fixed nerve segments were embedded with position lines, cryostat-sectioned continuously, stained and imaged histologically. Position line cross-sections were identified using a trained support vector machine method and the coordinates of their central pixels were obtained. Then, nerve section images were registered using the bilinear method and edges of fascicles were extracted using an improved gradient vector flow snake method. Subsequently, fascicle types were identified automatically using the multi-directional gradient and second-order gradient method. Finally, a 3D virtual model of internal fascicles was obtained after section images were processed. This technique was successfully applied for 3D reconstruction for the median nerve of the hand-wrist and cubital fossa regions and the gastrocnemius nerve. This nerve internal fascicle 3D reconstruction technology would be helpful for aiding peripheral nerve repair and virtual surgery.
Competing Anisotropy-Tunneling Correlation of the CoFeB/MgO Perpendicular Magnetic Tunnel Junction: An Electronic Approach
Authors: Yang Chao-Yao , Chang Shu-Jui , Lee Min-Han , Shen Kuei-Hung , Yang Shan-Yi , Lin Horng-Ji , Tseng Yuan-Chieh 
Published: November 2015

AbstractWe intensively investigate the physical principles regulating the tunneling magneto-resistance (TMR) and perpendicular magnetic anisotropy (PMA) of the CoFeB/MgO magnetic tunnel junction (MTJ) by means of angle-resolved x-ray magnetic spectroscopy. The angle-resolved capability was easily achieved and it provided greater sensitivity to symmetry-related d-band occupation compared to traditional x-ray spectroscopy. This added degree of freedom successfully solved the unclear mechanism of this MTJ system renowned for controllable PMA and excellent TMR. As a surprising discovery, these two physical characteristics interact in a competing manner because of opposite band-filling preference in space-correlated symmetry of the 3d-orbital. An overlooked but harmful superparamagnetic phase resulting from magnetic inhomogeneity was also observed. This important finding reveals that simultaneously achieving fast switching and a high tunneling efficiency at an ultimate level is improbable for this MTJ system owing to its fundamental limit in physics. We suggest that the development of independent TMR and PMA mechanisms is critical towards a complementary relationship between the two physical characteristics, as well as the realization of superior performance, of this perpendicular MTJ. Furthermore, this study provides an easy approach to evaluate the futurity of any emerging spintronic candidates by electronically examining the relationship between their magnetic anisotropy and transport.
Mesoporous-silica nanofluidic channels for quick enrichment/extraction of trace pesticide molecules
Authors: Xu Pengcheng , Chen Chuanzhao , Li Xinxin 
Published: November 2015

AbstractAs nanofluidic channels, uniaxially oriented mesoporous-silica is, for the first time, in-situ self-assembled in a microfluidic chip for quick enrichment/extraction of ng L−1(ppt)-level organo-phosphorous (OP) pesticide residue from aqueous solution to ethanol. This micro/nano combined pre-treatment chip is essential for following gas chromatography-mass spectrometry (GC-MS) quantitative analysis. Featuring huge surface area and dense silanol groups at the inwall surface, the mesoporous-silica is uniaxially self-assembled in a micro-reservoir to form a pile of nanofluidic channels (diameter = 2.1 nm). The captured/enriched pesticide molecules in the nanochannels can be efficiently extracted by much smaller volume of ethanol due to its much higher solubility to OP. In our affirming experiment, three mixed OP pesticides of dichlorvos, paraoxon and chlorpyrifos (in water) are captured/enriched by the nano-channels and eluted/extracted by only 0.6 mL ethanol. The whole process only takes 16 min. The GC-MS quantitative results for the extracted three pesticides indicate that the extraction recovery achieves 80%. The achieved limit of quantification (LOQ) and the limit of detection (LOD) are 100 ng L−1 and 30 ng L−1, respectively. The nanofluidic-channel pre-treatment technique is promising in various application fields like agriculture and food safety security.
Coherent interaction with two-level fluctuators using near field scanning microwave microscopy
Authors: de Graaf S. E. , Danilov A. V. , Kubatkin S. E. 
Published: November 2015

AbstractNear field Scanning Microwave Microscopy (NSMM) is a scanning probe technique that non-invasively can obtain material properties on the nano-scale at microwave frequencies. While focus has been on developing room-temperature systems it was recently shown that this technique can potentially reach the quantum regime, opening up for applications in materials science and device characterization in solid state quantum information processing. In this paper we theoretically investigate this new regime of NSMM. Specifically we show that interaction between a resonant NSMM probe and certain types of two-level systems become possible when the NSMM probe operates in the (sub-) single photon regime and we expect a high signal-to-noise ratio if operated under the right conditions. This would allow to detect single atomic material defects with energy splittings in the GHz range with nano-scale resolution, provided that individual defects in the material under study are well enough separated. We estimate that this condition is fulfilled for materials with loss tangents below tan δ ∼ 10−3 which holds for materials used in today’s quantum circuits and devices where typically tan δ < 10−5. We also propose several extensions to a resonant NSMM that could improve sensitivity and functionality also for microscopes operating in a high power regime.
RNA-based, transient modulation of gene expression in human haematopoietic stem and progenitor cells
Authors: Diener Yvonne , Jurk Marion , Kandil Britta , Choi Yeong-Hoon , Wild Stefan , Bissels Ute , Bosio Andreas 
Published: November 2015

AbstractModulation of gene expression is a useful tool to study the biology of haematopoietic stem and progenitor cells (HSPCs) and might also be instrumental to expand these cells for therapeutic approaches. Most of the studies so far have employed stable gene modification by viral vectors that are burdensome when translating protocols into clinical settings. Our study aimed at exploring new ways to transiently modify HSPC gene expression using non-integrating, RNA-based molecules. First, we tested different methods to deliver these molecules into HSPCs. The delivery of siRNAs with chemical transfection methods such as lipofection or cationic polymers did not lead to target knockdown, although we observed more than 90% fluorescent cells using a fluorochrome-coupled siRNA. Confocal microscopic analysis revealed that despite extensive washing, siRNA stuck to or in the cell surface, thereby mimicking a transfection event. In contrast, electroporation resulted in efficient, siRNA-mediated protein knockdown. For transient overexpression of proteins, we used optimised mRNA molecules with modified 5′- and 3′-UTRs. Electroporation of mRNA encoding GFP resulted in fast, efficient and persistent protein expression for at least seven days. Our data provide a broad-ranging comparison of transfection methods for hard-to-transfect cells and offer new opportunities for DNA-free, non-integrating gene modulation in HSPCs.
Characterization of stem/progenitor cell cycle using murine circumvallate papilla taste bud organoid
Authors: Aihara Eitaro , Mahe Maxime M. , Schumacher Michael A. , Matthis Andrea L. , Feng Rui , Ren Wenwen , Noah Taeko K. , Matsu-ura Toru , Moore Sean R. , Hong Christian I. , Zavros Yana , Herness Scott , Shroyer Noah F. , Iwatsuki Ken , Jiang Peihua , Helmrath Michael A. , Montrose Marshall H. 
Published: November 2015

AbstractLeucine-rich repeat-containing G-protein coupled receptor 5-expressing (Lgr5+) cells have been identified as stem/progenitor cells in the circumvallate papillae and single cultured Lgr5+cells give rise to taste cells. Here we use circumvallate papilla tissue to establish a three-dimensional culture system (taste bud organoids) that develops phenotypic characteristics similar to native tissue, including a multilayered epithelium containing stem/progenitor in the outer layers and taste cells in the inner layers. Furthermore, characterization of the cell cycle of the taste bud progenitor niche reveals striking dynamics of taste bud development and regeneration. Using this taste bud organoid culture system and FUCCI2 transgenic mice, we identify the stem/progenitor cells have at least 5 distinct cell cycle populations by tracking within 24-hour synchronized oscillations of proliferation. Additionally, we demonstrate that stem/progenitor cells have motility to form taste bud organoids. Taste bud organoids provides a system for elucidating mechanisms of taste signaling, disease modeling and taste tissue regeneration.
Transgenic mouse model for imaging of interleukin-1β-related inflammation in vivo
Authors: Iwawaki Takao , Akai Ryoko , Oikawa Daisuke , Toyoshima Takae , Yoshino Mayuko , Suzuki Mitsumi , Takeda Naoki , Ishikawa Tomo-o , Kataoka Yosky , Yamamura Ken-ichi 
Published: November 2015

AbstractInflammation is a biological response associated with symptoms of various diseases and its study is important in gaining an understanding of the pathological conditions of such diseases and in making strategic plans for promoting healing. It is therefore essential to develop technologies for the detection of inflammatory conditions. Interleukin-1β (IL-1β) is a proinflammatory cytokine produced and secreted mainly by monocytes and macrophages in response to inflammatory stimulation. The activation of IL-1β is regulated through transcriptional induction by the promoter and post-translational processing by the inflammasome. Here we have developed a reporter gene to monitor the activation status of IL-1β by using a dual regulation system and, by using the reporter gene, we have established a mouse model that permits low-invasive visualization of the inflammatory status. Previous reporter systems dependent on the transcription or processing of IL-1β show problems in terms of background noise or signal specificity. Our reporter system overcomes these weaknesses by combining advantages from regulation by a promoter and processing of IL-1β. Our mouse model detected specific physiological inflammation in the liver and pancreas caused by hepatitis or pancreatitis models, respectively. Our reporter gene and mouse model are therefore expected to become useful bioresources for future medical science.
An accessory wall teichoic acid glycosyltransferase protects Staphylococcus aureus from the lytic activity of Podoviridae
Authors: Li Xuehua , Gerlach David , Du Xin , Larsen Jesper , Stegger Marc , Kühner Petra , Peschel Andreas , Xia Guoqing , Winstel Volker 
Published: November 2015

AbstractMany Staphylococcus aureus have lost a major genetic barrier against phage infection, termed clustered regularly interspaced palindromic repeats (CRISPR/cas). Hence, S. aureus strains frequently exchange genetic material via phage-mediated horizontal gene transfer events, but, in turn, are vulnerable in particular to lytic phages. Here, a novel strategy of S. aureus is described, which protects S. aureus against the lytic activity of Podoviridae, a unique family of staphylococcal lytic phages with short, non-contractile tails. Unlike most staphylococcal phages, Podoviridae require a precise wall teichoic acid (WTA) glycosylation pattern for infection. Notably, TarM-mediated WTA α-O-GlcNAcylation prevents infection of Podoviridae while TarS-mediated WTA β-O-GlcNAcylation is required for S. aureus susceptibility to podoviruses. Tracking the evolution of TarM revealed an ancient origin in other staphylococci and vertical inheritance during S. aureus evolution. However, certain phylogenetic branches have lost tarM during evolution, which rendered them podovirus-susceptible. Accordingly, lack of tarM correlates with podovirus susceptibility and can be converted into a podovirus-resistant phenotype upon ectopic expression of tarM indicating that a “glyco-switch” of WTA O-GlcNAcylation can prevent the infection by certain staphylococcal phages. Since lytic staphylococcal phages are considered as anti-S. aureus agents, these data may help to establish valuable strategies for treatment of infections.