bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pentacle gold–copper alloy nanocrystals: a new system for entering male germ cells in vitro and in vivo
Authors: Lin Yu , He Rong , Sun Liping , Yang Yushan , Li Wenqing , Sun Fei 
Published: December 2016

AbstractGold-based nanocrystals have attracted considerable attention for drug delivery and biological applications due to their distinct shapes. However, overcoming biological barriers is a hard and inevitable problem, which restricts medical applications of nanomaterials in vivo. Seeking for an efficient transportation to penetrate biological barriers is a common need. There are three barriers: blood-testis barrier, blood-placenta barrier, and blood-brain barrier. Here, we pay close attention to the blood-testis barrier. We found that the pentacle gold–copper alloy nanocrystals not only could enter GC-2 cells in vitro in a short time, but also could overcome the blood–testis barrier and enter male germ cells in vivo. Furthermore, we demonstrated that the entrance efficiency would become much higher in the development stages. The results also suggested that the pentacle gold–copper alloy nanocrystals could easier enter to germ cells in the pathological condition. This system could be a new method for theranostics in the reproductive system.
Genetically regulated hepatic transcripts and pathways orchestrate haematological, biochemical and body composition traits
Authors: Ponsuksili Siriluck , Trakooljul Nares , Hadlich Frieder , Haack Fiete , Murani Eduard , Wimmers Klaus 
Published: December 2016

AbstractThe liver is the central metabolic organ and exhibits fundamental functions in haematological traits. Hepatic expression, haematological, plasma biochemical, and body composition traits were assessed in a porcine model (n = 297) to establish tissue-specific genetic variations that influence the function of immune-metabolism-correlated expression networks. At FDR (false discovery rate) <1%, more than 3,600 transcripts were jointly correlated (r = |0.22–0.48|) with the traits. Functional enrichment analysis demonstrated common links of metabolic and immune traits. To understand how immune and metabolic traits are affected via genetic regulation of gene expression, eQTLs were assessed. 20517 significant (FDR < 5%) eQTLs for 1401 transcripts were identified, among which 443 transcripts were associated with at least one of the examined traits and had cis-eQTL (such as ACO1 (6.52 × 10−7) and SOD1 (6.41 × 10−30). The present study establishes a comprehensive view of hepatic gene activity which links together metabolic and immune traits in a porcine model for medical research.
BTeam, a Novel BRET-based Biosensor for the Accurate Quantification of ATP Concentration within Living Cells
Authors: Yoshida Tomoki , Kakizuka Akira , Imamura Hiromi 
Published: December 2016

AbstractATP levels may represent fundamental health conditions of cells. However, precise measurement of intracellular ATP levels in living cells is hindered by the lack of suitable methodologies. Here, we developed a novel ATP biosensor termed “BTeam”. BTeam comprises a yellow fluorescent protein (YFP), the ATP binding domain of the ε subunit of the bacterial ATP synthase, and an ATP-nonconsuming luciferase (NLuc). To attain emission, BTeam simply required NLuc substrate. BTeam showed elevated bioluminescence resonance energy transfer efficiency upon ATP binding, resulted in the emission spectra changes correlating with ATP concentrations. By using values of YFP/NLuc emission ratio to represent ATP levels, BTeam achieved steady signal outputs even though emission intensities were altered. With this biosensor, we succeeded in the accurate quantification of intracellular ATP concentrations of a population of living cells, as demonstrated by detecting the slight distribution in the cytosol (3.7–4.1 mM) and mitochondrial matrix (2.4–2.7 mM) within some cultured cell lines. Furthermore, BTeam allowed continuous tracing of cytosolic ATP levels of the same cells, as well as bioluminescent imaging of cytosolic ATP dynamics within individual cells. This simple and accurate technique should be an effective method for quantitative measurement of intracellular ATP concentrations.
Identification of DEP domain-containing proteins by a machine learning method and experimental analysis of their expression in human HCC tissues
Authors: Liao Zhijun , Wang Xinrui , Zeng Yeting , Zou Quan 
Published: December 2016

AbstractThe Dishevelled/EGL-10/Pleckstrin (DEP) domain-containing (DEPDC) proteins have seven members. However, whether this superfamily can be distinguished from other proteins based only on the amino acid sequences, remains unknown. Here, we describe a computational method to segregate DEPDCs and non-DEPDCs. First, we examined the Pfam numbers of the known DEPDCs and used the longest sequences for each Pfam to construct a phylogenetic tree. Subsequently, we extracted 188-dimensional (188D) and 20D features of DEPDCs and non-DEPDCs and classified them with random forest classifier. We also mined the motifs of human DEPDCs to find the related domains. Finally, we designed experimental verification methods of human DEPDC expression at the mRNA level in hepatocellular carcinoma (HCC) and adjacent normal tissues. The phylogenetic analysis showed that the DEPDCs superfamily can be divided into three clusters. Moreover, the 188D and 20D features can both be used to effectively distinguish the two protein types. Motif analysis revealed that the DEP and RhoGAP domain was common in human DEPDCs, human HCC and the adjacent tissues that widely expressed DEPDCs. However, their regulation was not identical. In conclusion, we successfully constructed a binary classifier for DEPDCs and experimentally verified their expression in human HCC tissues.
Bioorthogonal chemical imaging of metabolic activities in live mammalian hippocampal tissues with stimulated Raman scattering
Authors: Hu Fanghao , Lamprecht Michael R. , Wei Lu , Morrison Barclay , Min Wei 
Published: December 2016

AbstractBrain is an immensely complex system displaying dynamic and heterogeneous metabolic activities. Visualizing cellular metabolism of nucleic acids, proteins, and lipids in brain with chemical specificity has been a long-standing challenge. Recent development in metabolic labeling of small biomolecules allows the study of these metabolisms at the global level. However, these techniques generally require nonphysiological sample preparation for either destructive mass spectrometry imaging or secondary labeling with relatively bulky fluorescent labels. In this study, we have demonstrated bioorthogonal chemical imaging of DNA, RNA, protein and lipid metabolism in live rat brain hippocampal tissues by coupling stimulated Raman scattering microscopy with integrated deuterium and alkyne labeling. Heterogeneous metabolic incorporations for different molecular species and neurogenesis with newly-incorporated DNA were observed in the dentate gyrus of hippocampus at the single cell level. We further applied this platform to study metabolic responses to traumatic brain injury in hippocampal slice cultures, and observed marked upregulation of protein and lipid metabolism particularly in the hilus region of the hippocampus within days of mechanical injury. Thus, our method paves the way for the study of complex metabolic profiles in live brain tissue under both physiological and pathological conditions with single-cell resolution and minimal perturbation.
Structural basis of the substrate preference towards CMP for a thymidylate synthase MilA involved in mildiomycin biosynthesis
Authors: Zhao Gong , Chen Cheng , Xiong Wei , Gao Tuling , Deng Zixin , Wu Geng , He Xinyi 
Published: December 2016

AbstractModified pyrimidine monophosphates such as methyl dCMP (mdCMP), hydroxymethyl dUMP (hmdUMP) and hmdCMP in some phages are synthesized by a large group of enzymes termed as thymidylate synthases (TS). Thymidylate is a nucleotide required for DNA synthesis and thus TS is an important drug target. In the biosynthetic pathway of the nucleoside fungicide mildiomycin isolated from Streptomyces rimofaciens ZJU5119, a cytidylate (CMP) hydroxymethylase, MilA, catalyzes the conversion of CMP into 5′-hydroxymethyl CMP (hmCMP) with an efficiency (kcat/KM) of 5-fold faster than for deoxycytidylate (dCMP). MilA is thus the first enzyme of the TS superfamily preferring CMP to dCMP. Here, we determined the crystal structures of MilA and its complexes with various substrates including CMP, dCMP and hmCMP. Comparing these structures to those of dCMP hydroxymethylase (CH) from T4 phage and TS from Escherichia coli revealed that two residues in the active site of CH and TS, a serine and an arginine, are respectively replaced by an alanine and a lysine, Ala176 and Lys133, in MilA. Mutation of A176S/K133R of MilA resulted in a reversal of substrate preference from CMP to dCMP. This is the first study reporting the evolution of the conserved TS in substrate selection from DNA metabolism to secondary nucleoside biosynthesis.
New Potassium Sodium Niobate Single Crystal with Thickness-independent High-performance for Photoacoustic Angiography of Atherosclerotic Lesion
Authors: Zhu Benpeng , Zhu Yuhang , Yang Jie , Ou-Yang Jun , Yang Xiaofei , Li Yongxiang , Wei Wei 
Published: December 2016

AbstractThe synthesis of (K0.45Na0.55)0.96Li0.04NbO3 (KNLN) single crystals with a <100>-orientation, using a seed-free solid state crystal growth method, is described here. With the thickness of the crystals decreasing down to the order of tens of micrometers, this new lead-free single crystal exhibits thickness-independent electrical behavior, and maintains superior piezoelectric constant (d33 = 670 pC N−1) and electromechanical coupling factor (kt = 0.55). The successful fabrication of a tiny intravascular photoacoustic probe, with a 1 mm outside diameter, is achieved using a single crystal with a thickness of around 60 μm, in combination with a 200 μm core multimode fiber. Wire phantom photoacoustic images show that the axial resolution and lateral resolution of the single crystal based probe are 60 and 220 μm, respectively. In addition, intravascular photoacoustic imaging of the atherosclerotic lesion of a human artery is presented. In the time-domain and frequency-domain images, calcified regions are clearly distinguishable from surrounding tissue. These interesting results demonstrate that KNN-based lead-free piezoelectric single crystals are a promising candidate to substitute for lead-based piezoelectric materials for photoacoustic imaging in the future.
Cpf1 Is A Versatile Tool for CRISPR Genome Editing Across Diverse Species of Cyanobacteria
Authors: Ungerer Justin , Pakrasi Himadri B. 
Published: December 2016

AbstractCyanobacteria are the ideal organisms for the production of a wide range of bioproducts as they can convert CO2 directly into the desired end product using solar energy. Unfortunately, the engineering of cyanobacteria to create efficient cell factories has been impaired by the cumbersome genetic tools that are currently available for these organisms; especially when trying to accumulate multiple modifications. We sought to construct an efficient and precise tool for generating numerous markerless modifications in cyanobacteria using CRISPR technology and the alternative nuclease, Cpf1. In this study we demonstrate rapid engineering of markerless knock-ins, knock-outs and point mutations in each of three model cyanobacteria; Synechococcus, Synechocystis and Anabaena. The markerless nature of cpf1 genome editing will allow for complex genome modification that was not possible with previously existing technology while facilitating the development of cyanobacteria as highly modified biofactories.
Angle- and Polarization-Insensitive Metamaterial Absorber using Via Array
Authors: Lim Daecheon , Lee Dongju , Lim Sungjoon 
Published: December 2016

AbstractIn this paper, we propose an angle- and polarization-insensitive metamaterial absorber. We design a metamaterial unit cell that is based on a split ring cross resonator (SRCR). We observe that the absorption frequency and absorption ratio are insensitive to incident angles when a via array surrounds the SRR. We demonstrate the effect of the via array using full-wave simulations by comparing the absorptivity of the SRCR with and without the via array. Because of the symmetric geometry, we also realize polarization insensitivity. We build the proposed absorber on a printed-circuit-board with 30 × 30 unit cells, and we demonstrate its performance experimentally in free space. Under normal incidence, the fabricated absorber shows 99.6% absorptivity at 11.3 GHz for all polarization angles, while for oblique incidence, the fabricated absorber maintains an absorptivity higher than 90% for incident angles up to 70° and 60° for transverse magnetic (TM) and transverse electric (TE) modes, respectively.
Solid-state NMR Study of Ion Adsorption and Charge Storage in Graphene Film Supercapacitor Electrodes
Authors: Li Kecheng , Bo Zheng , Yan Jianhua , Cen Kefa 
Published: December 2016

AbstractGraphene film has been demonstrated as promising active materials for electric double layer capacitors (EDLCs), mainly due to its excellent mechanical flexibility and freestanding morphology. In this work, the distribution and variation pattern of electrolyte ions in graphene-film based EDLC electrodes are investigated with a 11B magic-angle spinning nuclear magnetic resonance (MAS-NMR) spectroscopy. For neutral graphene films soaked with different amounts of electrolytes (1 M TEABF4/ACN), weakly and strongly adsorbed anions are identified based on the resonances at different 11B chemical shifts. Unlike other porous carbonaceous materials, the strongly adsorbed anions are found as the major electrolyte anions components in graphene films. Further measurements on the ion population upon charging are carried out with applying different charging voltages on the graphene films. Results indicate that the charging process of graphene-film based EDLCs can be divided into two distinct charge storage stages (i.e., ejection of co-ions and adsorption of counter-ions) for different voltages. The as-obtained results will be useful for the design and fabrication of high performance graphene-film based EDLCs.
The levels of the sex hormones are not different between type 1 and type 2 endometrial cancer
Authors: Wan Jiayi , Gao Yifei , Zeng Ke , Yin Yongxiang , Zhao Min , Wei Jia , Chen Qi 
Published: December 2016

AbstractThe involvement of hormonal factors in developing endometrial cancer is well documented. In particular, excess or unopposed estrogen is a major risk factor. Endometrial cancer is divided into estrogen-dependent and estrogen-independent types. Studies suggested that the subtypes of endometrial cancer share many common risk factors. Whether the levels of sex hormones differ between types 1 and 2 endometrial cancer has not been investigated. In this study, levels of estrogen, progesterone, testosterone, follicle stimulating hormone (FSH) and luteinizing hormone (LH) were investigated between type 1 and type 2 endometrial cancer taking into account menopausal status and parity. The sex hormones levels and estrogen and progesterone receptors were measured in 187 women with endometrial cancer. The levels of estradiol (E2), progesterone, testosterone, FSH and LH were not different between the subtypes of endometrial cancer regardless of menopausal status. In addition, the sex hormones were not different between patients of different party regardless of the menopausal status. The majority of type 1 (96%) and type 2 (82%) endometrial cancers were estrogen and progesterone receptor positive. Our data suggest that type 2 endometrial cancer is not completely estrogen independent, and type 1 and type 2 endometrial cancers may have a similar pathogenesis.
Mumbling: Macho or Morphology?
Authors: Weirich Melanie , Fuchs Susanne , Simpson Adrian , Winkler Ralf , Perrier Pascal 
Published: December 2016

Purpose
Mumbling as opposed to clear speech is a typical male characteristic in speech and can be the consequence of a small jaw opening. Whereas behavioral reasons have often been offered to explain sex-specific differences with respect to clear speech, the purpose of this study is to investigate a potential anatomical reason for smaller jaw openings in male than in female speakers.

Method
Articulatory data from 2 data sets (American English and German) were analyzed with respect to jaw opening in low vowels during speech. Particular focus was placed on sex-specific differences, also incorporating potential interactions with different accent conditions in 1 of the data sets. In addition, a modeling study compared the articulatory consequences of similar jaw-opening settings in a typical male and a typical female articulatory model.

Results
Greater jaw openings were found for the female speakers, in particular in the accented condition, where jaw opening was found to be larger. In line with this finding, the modeling study showed that similar jaw-opening settings in male and female speakers led to differences in pharyngeal constriction, resulting in complete radico-pharyngeal closure in the male model.

Conclusion
The empirical and modeling findings suggest a possible physiological component in sex-specific differences in speech clarity for low vowels.
Effect of Domain Initial Strengthening on Vowel Height and Backness Contrasts in French: Acoustic and Ultrasound Data
Authors: Georgeton Laurianne , Antolík Tanja Kocjančič , Fougeron Cécile 
Published: December 2016

Purpose
Phonetic variation due to domain initial strengthening was investigated with respect to the acoustic and articulatory distinctiveness of vowels within a subset of the French oral vowel system /i, e, ɛ, a, o, u/, organized along 4 degrees of height for the front vowels and 2 degrees of backness at the close and midclose height levels.

Method
Acoustic and lingual ultrasound data were examined to characterize the production of vowels in intonational phrase initial position, compared with intonational phrase medial position, for 4 speakers.

Results
Formant values and estimates of lingual constriction location and degree differed according to the prosodic position independent of vowel duration, with a higher F1 for /a/, a higher F2 for /ɛ/, a backer constriction for /o/ and /a/ but a fronter constriction for /ɛ/, and a narrower constriction for /e, ɛ, u, o/ but a wider constriction for /a/. For most speakers, these variations enlarge the acoustic and/or articulatory distance between members of the pairs /e-ɛ/, /ɛ-a/, /u-o/, /i-u/, and /e-o/ but reduce the distinction within the pair /i-e/.

Conclusions
These changes in intonational phrase initial position are vowel dependent and frequently contribute to augmenting the phonetic distinctiveness between vowels contrasting along the height and backness dimensions.
Statistical Catch-Free Age-Structured Assessment to Estimate Year-Class Strength for Inland Recreational Fisheries: A Largemouth Bass Example
Authors: Feltz Nicholas G. , Catalano Matthew J. 
Published: December 2016

Abstract
Statistical catch-at-age analysis (SCAA) is commonly used to estimate recruitment and mortality for large-scale, economically important fish stocks, but fishery-dependent catch-at-age data are often unavailable for smaller-scale inland fisheries, thus limiting the use of SCAA. In these systems, a catch-free approach to age-structure modeling may be useful for estimating recruitment and mortality rates solely from a time series of survey age composition and catch rate data by estimating recruitment as a relative index of year-class strength (Rt). Here, we demonstrate a statistical catch-free age-structured assessment (SCFASA) model for small-scale inland fish stocks as an alternative to traditional catch curve approaches by using Largemouth Bass Micropterus salmoides as an example. We fitted the SCFASA to fishery-independent survey age composition and catch-per-effort data from Largemouth Bass stocks in three Alabama reservoirs to estimate Rt, annual fishing mortality rates, and age-specific electrofishing survey vulnerability; we compared Rt to catch curve residual estimates and performed a sensitivity analysis under a variety of model assumptions. Model estimates of Rt and temporal trends in fishing mortality were robust to changes in assumptions about the effective sample size of multinomial age samples, natural mortality rate, and temporal variability in fishing mortality. However, the magnitude of instantaneous fishing mortality rates at two of the three reservoirs was somewhat higher than empirical estimates for similar stocks and was sensitive to model assumptions. Our application of the SCFASA to survey data sets routinely collected by management agencies for Largemouth Bass potentially provides a comprehensive approach to estimating Rt, mortality, and sampling vulnerability for these stocks without increasing sampling effort. Future investigations of SCFASA's utility for small-scale inland stocks should address the potential for bias in the magnitude of fishing mortality estimates due to incorrectly specified vulnerability schedules.
Received October 5, 2015; accepted September 19, 2016 Published online December 21, 2016
Oviposition-site mimicry
Authors: Johnson Steven D. , Schiestl Florian P. 
Published: December 2016

AbstractOf all the floral mimicry systems covered in this book, oviposition-site mimicry is probably the most widespread (in terms of geography and the number of plant species and lineages represented) and the most diverse (in terms of floral signals). It is also the most under-appreciated system of floral mimicry and is certainly less well known than floral sexual mimicry. The widespread phenomenon of floral oviposition-site mimicry includes mimicry of fruit, carrion, feces and fungal substrates that are used by insects as brood sites. Chemical signals are key in all of these systems, but there is also evidence for combined effects of chemical and visual signals (in other words multimodal signals).
Special cases
Authors: Johnson Steven D. , Schiestl Florian P. 
Published: December 2016

AbstractThis chapter deals with topics that are contentious, difficult to categorize, or fall somewhat outside the mainstream of floral mimicry research. The concept of Müllerian mimicry has been applied to resemblance among rewarding flowers, but this chapter shows that the evidence that this reflects a process of mimicry remains tenuous. Intersexual resemblance of flowers of dioecious plants is clearly not mimicry in the classical sense, but selection does appear to maintain similarity, particularly in cases where only one sex offers a reward. These special cases illustrate the potentially ubiquitous nature of mimicry phenomena and also the fact that many mimicry systems involve more species than just a single mimic, model, and operator.
Future directions in floral mimicry research
Authors: Johnson Steven D. , Schiestl Florian P. 
Published: December 2016

AbstractMore than 200 years after the discovery of floral mimicry by Sprengel many questions about this fascinating natural phenomenon remain unanswered. Floral mimicry has traditionally been a relatively small field of research compared with animal mimicry; however, floral mimicry studies now account for almost a third of all studies dealing with mimicry among organisms. This chapter looks to the future of mimicry research and focuses on molecular approaches and their potential to answer unresolved questions about speciation. The inclusion of this chapter does not mean that the future of mimicry research is purely molecular rather than ecological. However, it can be considered that molecular approaches are not specific to a particular type of mimicry system, and it therefore makes more sense to deal with this topic in a single chapter and to discuss ecological approaches in the chapters that focus on each type of floral mimicry.