bluuebunny/crossref_metadata_2025_split huggingface dataset:
Two-Layer Elastographic 3-D Traction Force Microscopy
Authors: Álvarez-González Begoña , Zhang Shun , Gómez-González Manuel , Meili Ruedi , Firtel Richard A. , Lasheras Juan C. , del Álamo Juan C. 
Published: January 2017

AbstractCellular traction force microscopy (TFM) requires knowledge of the mechanical properties of the substratum where the cells adhere to calculate cell-generated forces from measurements of substratum deformation. Polymer-based hydrogels are broadly used for TFM due to their linearly elastic behavior in the range of measured deformations. However, the calculated stresses, particularly their spatial patterns, can be highly sensitive to the substratum’s Poisson’s ratio. We present two-layer elastographic TFM (2LETFM), a method that allows for simultaneously measuring the Poisson’s ratio of the substratum while also determining the cell-generated forces. The new method exploits the analytical solution of the elastostatic equation and deformation measurements from two layers of the substratum. We perform an in silico analysis of 2LETFM concluding that this technique is robust with respect to TFM experimental parameters, and remains accurate even for noisy measurement data. We also provide experimental proof of principle of 2LETFM by simultaneously measuring the stresses exerted by migrating Physarum amoeboae on the surface of polyacrylamide substrata, and the Poisson’s ratio of the substrata. The 2LETFM method could be generalized to concurrently determine the mechanical properties and cell-generated forces in more physiologically relevant extracellular environments, opening new possibilities to study cell-matrix interactions.
Soybean cyclophilin GmCYP1 interacts with an isoflavonoid regulator GmMYB176
Authors: Mainali Hemanta Raj , Vadivel Arun Kumaran Anguraj , Li Xuyan , Gijzen Mark , Dhaubhadel Sangeeta 
Published: January 2017

AbstractCyclophilins (CYPs) belong to the immunophilin superfamily with peptidyl-prolyl cis-trans isomerase (PPIase) activity. They catalyze the interconversion of the cis- and trans-rotamers of the peptidyl-prolyl amide bond of peptides. A yeast-two-hybrid screening using the isoflavonoid regulator GmMYB176 as bait identified GmCYP1 as one of the interacting proteins in soybean embryos. GmCYP1 localizes both in the nucleus and cytoplasm, and interacts in planta with GmMYB176, in the nucleus, and with SGF14l (a soybean 14-3-3 protein) in the nucleus and the cytoplasm. GmCYP1 contains a single cyclophilin-like domain and displays a high sequence identity with other plant CYPs that are known to have stress-specific function. Tissue-specific expression of GmCYP1 revealed higher expression in developing seeds compared to other vegetative tissues, suggesting their seed-specific role. Furthermore, GmCYP1 transcript level was reduced in response to stress. Since isoflavonoids are involved in plant stress resistance against biotic and abiotic factors, the interaction of GmCYP1 with the isoflavonoid regulators GmMYB176 and 14-3-3 protein suggests its role in defense in soybean.
Heat-Related Hospitalizations in Older Adults: An Amplified Effect of the First Seasonal Heatwave
Authors: Liss Alexander , Wu Ruiruo , Chui Kenneth Kwan Ho , Naumova Elena N. 
Published: January 2017

AbstractOlder adults are highly vulnerable to the detriment of extreme weather. The rapid non-linear increase in heat-related morbidity is difficult to quantify, hindering the attribution of direct effects of exposure on severe health outcomes. We examine the effects of ambient temperatures on heat-related hospitalizations (HH) among the elderly in presence of strong seasonality and by assessing the effects caused by the first and subsequent seasonal heatwaves. We empirically derived the thresholds for a heatwave episode in Boston MSA based on 16 years of daily observations. We compared the health risks of heatwaves using the proposed and four alternative definitions. 701 cases of HH in older residents of Boston area were examined using harmonic regression models, designed to capture the non-linear effects of ambient temperatures and heatwave episodes when the night-time temperature is above 65.5 °F for 3 consecutive nights. The overall relative risk of HH associated with a heatwave episode was 6.9 [95%CI:4.8–9.8]. The relative risk of HH associated with the first heatwave increases up to 13.3 [95%CI:7.4–24.0]. The risk declined to 3.7 [95%CI:2.4–5.8] for the subsequent heatwave. Four other commonly used heatwave definitions confirmed these findings. Public health actions have to target the first heatwave to maximize the impact of preventive measures.
Regulation of plasma histamine levels by the mast cell clock and its modulation by stress
Authors: Nakamura Yuki , Ishimaru Kayoko , Shibata Shigenobu , Nakao Atsuhito 
Published: January 2017

AbstractAt steady state, plasma histamine levels exhibit circadian variations with nocturnal peaks, which is implicated in the nighttime exacerbation of allergic symptoms. However, the regulatory mechanisms are largely unexplored. This study determined how steady-state plasma histamine levels are regulated and affected by environmental factors. We found that plasma histamine levels decreased in mast cell–deficient mice and their circadian variations were lost in mast cell–deficient mice reconstituted with bone marrow–derived mast cells (BMMCs) harboring a mutation in the circadian gene Clock. Clock temporally regulates expression of organic cation transporter 3 (OCT3), which is involved in histamine transport, in mast cells; OCT inhibition abolished circadian variations in plasma histamine levels. Mice housed under aberrant light/dark conditions or suffering from restraint stress exhibited de-synchronization of the mast cell clockwork, concomitant with the loss of circadian variations in OCT3 expression and plasma histamine levels. The degree of compound 48/80–induced plasma extravasation in mice was correlated with plasma histamine levels. Collectively, the mast cell clock mediates circadian regulation of plasma histamine levels at steady state, in part by controlling OCT3 expression, which can be modulated by stress. Additionally, we propose that plasma histamine levels potentiate mast cell–mediated allergic reactions.
Live visualization of genomic loci with BiFC-TALE
Authors: Hu Huan , Zhang Hongmin , Wang Sheng , Ding Miao , An Hui , Hou Yingping , Yang Xiaojing , Wei Wensheng , Sun Yujie , Tang Chao 
Published: January 2017

AbstractTracking the dynamics of genomic loci is important for understanding the mechanisms of fundamental intracellular processes. However, fluorescent labeling and imaging of such loci in live cells have been challenging. One of the major reasons is the low signal-to-background ratio (SBR) of images mainly caused by the background fluorescence from diffuse full-length fluorescent proteins (FPs) in the living nucleus, hampering the application of live cell genomic labeling methods. Here, combining bimolecular fluorescence complementation (BiFC) and transcription activator-like effector (TALE) technologies, we developed a novel method for labeling genomic loci (BiFC-TALE), which largely reduces the background fluorescence level. Using BiFC-TALE, we demonstrated a significantly improved SBR by imaging telomeres and centromeres in living cells in comparison with the methods using full-length FP.
Herb pair Danggui-Honghua: mechanisms underlying blood stasis syndrome by system pharmacology approach
Authors: Yue Shi-Jun , Xin Lan-Ting , Fan Ya-Chu , Li Shu-Jiao , Tang Yu-Ping , Duan Jin-Ao , Guan Hua-Shi , Wang Chang-Yun 
Published: January 2017

AbstractHerb pair Danggui-Honghua has been frequently used for treatment of blood stasis syndrome (BSS) in China, one of the most common clinical pathological syndromes in traditional Chinese medicine (TCM). However, its therapeutic mechanism has not been clearly elucidated. In the present study, a feasible system pharmacology model based on chemical, pharmacokinetic and pharmacological data was developed via network construction approach to clarify the mechanisms of this herb pair. Thirty-one active ingredients of Danggui-Honghua possessing favorable pharmacokinetic profiles and biological activities were selected, interacting with 42 BSS-related targets to provide potential synergistic therapeutic actions. Systematic analysis of the constructed networks revealed that these targets such as HMOX1, NOS2, NOS3, HIF1A and PTGS2 were mainly involved in TNF signaling pathway, HIF-1 signaling pathway, estrogen signaling pathway and neurotrophin signaling pathway. The contribution index of every active ingredient also indicated six compounds, including hydroxysafflor yellow A, safflor yellow A, safflor yellow B, Z-ligustilide, ferulic acid, and Z-butylidenephthalide, as the principal components of this herb pair. These results successfully explained the polypharmcological mechanisms underlying the efficiency of Danggui-Honghua for BSS treatment, and also probed into the potential novel therapeutic strategies for BSS in TCM.
A novel monoclonal antibody targeting coxsackie virus and adenovirus receptor inhibits tumor growth in vivo
Authors: Kawada Manabu , Inoue Hiroyuki , Kajikawa Masunori , Sugiura Masahito , Sakamoto Shuichi , Urano Sakiko , Karasawa Chigusa , Usami Ihomi , Futakuchi Mitsuru , Masuda Tohru 
Published: January 2017

AbstractTo create a new anti-tumor antibody, we conducted signal sequence trap by retrovirus-meditated expression method and identified coxsackie virus and adenovirus receptor (CXADR) as an appropriate target. We developed monoclonal antibodies against human CXADR and found that one antibody (6G10A) significantly inhibited the growth of subcutaneous as well as orthotopic xenografts of human prostate cancer cells in vivo. Furthermore, 6G10A also inhibited other cancer xenografts expressing CXADR, such as pancreatic and colorectal cancer cells. Knockdown and overexpression of CXADR confirmed the dependence of its anti-tumor activity on CXADR expression. Our studies of its action demonstrated that 6G10A exerted its anti-tumor activity primarily through both antibody-dependent cellular cytotoxicity and complement-dependent cytotoxicity. Moreover, 6G10A reacted with human tumor tissues, such as prostate, lung, and brain, each of which express CXADR. Although we need further evaluation of its reactivity and safety in human tissues, our results show that a novel anti-CXADR antibody may be a feasible candidate for cancer immunotherapy.
From an indirect response pharmacodynamic model towards a secondary signal model of dose-response relationship between exercise training and physical performance
Authors: Busso Thierry 
Published: January 2017

AbstractThe aim of this study was to test the suitability of using indirect responses for modeling the effects of physical training on performance. We formulated four different models assuming that increase in performance results of the transformation of a signal secondary to the primary stimulus which is the training dose. The models were designed to be used with experimental data with daily training amounts ascribed to input and performance measured at several dates ascribed to output. The models were tested using data obtained from six subjects who trained on a cycle ergometer over a 15-week period. The data fit for each subject was good for all of the models. Goodness-of-fit and consistency of parameter estimates favored the model that took into account the inhibition of production of training effect. This model produced an inverted-U shape graphic when plotting daily training dose against performance because of the effect of one training session on the cumulated effects of previous sessions. In conclusion, using secondary signal-dependent response provided a framework helpful for modeling training effect which could enhance the quantitative methods used to analyze how best to dose physical activity for athletic performance or healthy living.
“Mycobacterium massilipolynesiensis” sp. nov., a rapidly-growing mycobacterium of medical interest related to Mycobacterium phlei
Authors: Phelippeau M. , Asmar S. , Osman D. Aboubaker , Sassi M. , Robert C. , Michelle C. , Musso D. , Drancourt M. 
Published: January 2017

AbstractIn French Polynesia, respiratory tract clinical isolate M26, displayed unusual phenotype and contradictory phylogenetic affiliations, suggesting a hitherto unidentified rapidly-growing Mycobacterium species. The phenotype of strain M26 was further characterized and its genome sequenced. Strain M26 genome consists in a 5,732,017-bp circular chromosome with a G + C% of 67.54%, comprising 5,500 protein-coding genes and 52 RNA genes (including two copies of the 16 S rRNA gene). One region coding for a putative prophage was also predicted. An intriguing characteristic of strain M26’s genome is the large number of genes encoding polyketide synthases and nonribosomal peptide synthases. Phylogenomic analysis showed that strain M26’s genome is closest to the Mycobacterium phlei genome with a 76.6% average nucleotide identity. Comparative genomics of 33 Mycobacterium genomes yielded 361 genes unique to M26 strain which functional annotation revealed 84.21% of unknown function and 3.88% encoding lipid transport and metabolism; while 48.87% of genes absent in M26 strain have unknown function, 9.5% are implicated in transcription and 19% are implicated in transport and metabolism. Strain M26’s unique phenotypic and genomic characteristics indicate it is representative of a new species named “Mycobacterium massilipolynesiensis”. Looking for mycobacteria in remote areas allows for the discovery of new Mycobacterium species.
The influence of tip shape on bending force during needle insertion
Authors: van de Berg Nick J. , de Jong Tonke L. , van Gerwen Dennis J. , Dankelman Jenny , van den Dobbelsteen John J. 
Published: January 2017

AbstractSteering of needles involves the planning and timely modifying of instrument-tissue force interactions to allow for controlled deflections during the insertion in tissue. In this work, the effect of tip shape on these forces was studied using 10 mm diameter needle tips. Six different tips were selected, including beveled and conical versions, with or without pre-bend or pre-curve. A six-degree-of-freedom force/torque sensor measured the loads during indentations in tissue simulants. The increased insertion (axial) and bending (radial) forces with insertion depth — the force-displacement slopes — were analyzed. Results showed that the ratio between radial and axial forces was not always proportional. This means that the tip load does not have a constant orientation, as is often assumed in mechanics-based steering models. For all tip types, the tip-load assumed a more radial orientation with increased axial load. This effect was larger for straight tips than for pre-bent or pre-curved tips. In addition, the force-displacement slopes were consistently higher for (1) increased tip angles, and for (2) beveled tips compared to conical tips. Needles with a bent or curved tip allow for an increased bending force and a decreased variability of the tip load vector orientation.
Ultrafast carrier dynamics in Ge by ultra-broadband mid-infrared probe spectroscopy
Authors: Yeh Tien-Tien , Shirai Hideto , Tu Chien-Ming , Fuji Takao , Kobayashi Takayoshi , Luo Chih-Wei 
Published: January 2017

AbstractIn this study, we carried out 800-nm pump and ultra-broadband mid-infrared (MIR) probe spectroscopy with high time-resolution (70 fs) in bulk Ge. By fitting the time-resolved difference reflection spectra [ΔR(ω)/R(ω)] with the Drude model in the 200–5000 cm−1 region, the time-dependent plasma frequency and scattering rate have been obtained. Through the calculation, we can further get the time-dependent photoexcited carrier concentration and carrier mobility. The Auger recombination essentially dominates the fast relaxation of photoexcited carriers within 100 ps followed by slow relaxation due to diffusion. Additionally, a novel oscillation feature is clearly found in time-resolved difference reflection spectra around 2000 cm−1 especially for high pump fluence, which is the Lorentz oscillation lasting for about 20 ps due to the Coulomb force exerted just after the excitation.
Understanding the molecular mechanism for the differential inhibitory activities of compounds against MTH1
Authors: Wang Mian , Zhou Shuilian , Chen Qing , Wang Lisheng , Liang Zhiqun , Wang Jianyi 
Published: January 2017

AbstractMTH1 can hydrolyze oxidized nucleotides and is required for cancer survival. The IC50 values were 0.8 nM for TH287 with a methyl substitution, 5.0 nM for TH588 with a cyclopropyl substitution, and 2.1 μM for TH650 with an oxetanyl substitution. Thus, it is very significant to understand inhibitory mechanisms of these structurally similar compounds against MTH1 and influences of the substituent on the bioactivities. Our MD researches indicate that TH287 maintains significant hydrogen bonds with Asn33 and Asp119, stabilizes the binding site, and induces MTH1 adopt a closed motion, leading to a high inhibitory activity. When bound with TH588, the binding site can be partially stabilized and take a semi-closed state, which is because the cyclopropyl group in TH588 has larger steric hindrance than a methyl group in TH287. So TH588 has a slightly reduced inhibitory activity compared to TH287. TH650 induces greater conformation fluctuations than TH588 and the binding site adopts an opening state, which is caused by the large bulk of oxetanyl group and the interference of solvent on the oxetanyl substituent, leading to the lowest inhibitory activity. Thus, the inhibitory activity follows a TH287 > TH588 > TH650 trend, which well matches with the experimental finding.
Microscopic Evolution of Laboratory Volcanic Hybrid Earthquakes
Authors: Ghaffari H. O. , Griffith W. A. , Benson P. M. 
Published: January 2017

AbstractCharacterizing the interaction between fluids and microscopic defects is one of the long-standing challenges in understanding a broad range of cracking processes, in part because they are so difficult to study experimentally. We address this issue by reexamining records of emitted acoustic phonon events during rock mechanics experiments under wet and dry conditions. The frequency spectrum of these events provides direct information regarding the state of the system. Such events are typically subdivided into high frequency (HF) and low frequency (LF) events, whereas intermediate “Hybrid” events, have HF onsets followed by LF ringing. At a larger scale in volcanic terranes, hybrid events are used empirically to predict eruptions, but their ambiguous physical origin limits their diagnostic use. By studying acoustic phonon emissions from individual microcracking events we show that the onset of a secondary instability–related to the transition from HF to LF–occurs during the fast equilibration phase of the system, leading to sudden increase of fluid pressure in the process zone. As a result of this squeezing process, a secondary instability akin to the LF event occurs. This mechanism is consistent with observations of hybrid earthquakes.
The NAC-type transcription factor OsNAC2 regulates ABA-dependent genes and abiotic stress tolerance in rice
Authors: Shen Jiabin , Lv Bo , Luo Liqiong , He Jianmei , Mao Chanjuan , Xi Dandan , Ming Feng 
Published: January 2017

AbstractPlants can perceive environmental changes and respond to external stressors. Here, we show thatOsNAC2, a member of the NAC transcription factor family, was strongly induced by ABA and osmotic stressors such as drought and high salt. With reduced yields under drought conditions at the flowering stage,OsNAC2overexpression lines had lower resistance to high salt and drought conditions. RNAi plants showed enhanced tolerance to high salinity and drought stress at both the vegetative and flowering stages. Furthermore, RNAi plants had improved yields after drought stress. A microarray assay indicated that many ABA-dependent stress-related genes were down-regulated inOsNAC2overexpression lines. We further confirmed thatOsNAC2directly binds the promoters ofLATE EMBRYOGENESIS ABUNDANT 3 (OsLEA3) andStress-Activated Protein Kinases 1 (OsSAPK1), two marker genes in the abiotic stress and ABA response pathways, respectively. Our results suggest that in riceOsNAC2regulates both abiotic stress responses and ABA-mediated responses, and acts at the junction between the ABA and abiotic stress pathways.
Characteristics of unilateral tibial plateau fractures among adult patients hospitalized at an orthopaedic trauma centre in China
Authors: Liu Yong , Liao Zhengwen , Shang Lei , Huang Wenhua , Zhang Dawei , Pei Guoxian 
Published: January 2017

AbstractThe aim of this study was to investigate the characteristics of unilateral tibial plateau fractures among hospitalized adult patients in Xijing Hospital, to evaluate the accuracy of Schatzker classification system and AO/OTA classification system to tibial plateau fractures. We retrospectively analysed clinical data on 274 patients admitted to Xijing Hospital between September 2006 and August 2015. The patients’ demographic characteristics, admission periods and seasons, external causes and fracture types were recorded and summarized. Then the characteristics of tibial plateau fractures and the accuracy rate of these two classification systems were analysed. Schatzker type II fractures and AO/OTA type 41-B3 fractures were the most common types. The external causes differed between genders, types of employment, urban-rural residents and both two systems. In addition, some fractures were difficult to classify using Schatzker or AO/OTA classification system. Rural male physical labourers aged between 30–59 years-old were most likely to suffer from unilateral tibial plateau fractures, due to traffic accidents, falls and indoor activity injuries, or falls from height. We should pay more attention to the related people and professions, which contributed to the high occurrence of tibial plateau fractures. Besides that, further improvements are required for both Schatzker and AO/OTA classification systems.
Transcriptome and Gene Expression Analysis of Cylas formicarius (Coleoptera: Brentidae) During Different Development Stages
Authors: Ma Juan , Wang Rongyan , Li Xiuhua , Gao Bo , Chen Shulong 
Published: January 2017

AbstractThe sweet potato weevil, Cylas formicarius (F.) (Coleoptera: Brentidae), is an important pest of sweet potato worldwide. However, there is limited knowledge on the molecular mechanisms underlying growth and differentiation of C. formicarius. The transcriptomes of the eggs, second instar larvae, third instar larvae (L3), pupae, females, and males of C. formicarius were sequenced using Illumina sequencing technology for obtaining global insights into developing transcriptome characteristics and elucidating the relative functional genes. A total of 54,255,544 high-quality reads were produced, trimmed, and de novo assembled into 115,281 contigs. 61,686 unigenes were obtained, with an average length of 1,009 nt. Among these unigenes, 17,348 were annotated into 59 Gene Ontology (GO) terms and 12,660 were assigned to 25 Cluster of Orthologous Groups classes, whereas 24,796 unigenes were mapped to 258 pathways. Differentially expressed unigenes between various developmental stages of C. formicarius were detected. Higher numbers of differentially expressed genes (DEGs) were recorded in the eggs versus L3 and eggs versus male samples (2,141 and 2,058 unigenes, respectively) than the others. Genes preferentially expressed in each stage were also identified. GO and pathway-based enrichment analysis were used to further investigate the functions of the DEGs. In addition, the expression profiles of ten DEGs were validated by quantitative real-time PCR. The transcriptome profiles presented in this study and these DEGs detected by comparative analysis of different developed stages of C. formicarius will facilitate the understanding of the molecular mechanism of various living process and will contribute to further genome-wide research.