bluuebunny/crossref_metadata_2025 huggingface dataset:
Capturing 3D Water Flow in Rooted Soil by Ultra-fast Neutron Tomography
Authors: Tötzke Christian , Kardjilov Nikolay , Manke Ingo , Oswald Sascha E.
Published: July 2017

Water infiltration in soil is not only affected by the inherent heterogeneities of soil, but even more by the interaction with plant roots and their water uptake. Neutron tomography is a unique non-invasive 3D tool to visualize plant root systems together with the soil water distribution in situ. So far, acquisition times in the range of hours have been the major limitation for imaging 3D water dynamics. Implementing an alternative acquisition procedure we boosted the speed of acquisition capturing an entire tomogram within 10 s. This allows, for the first time, tracking of a water front ascending in a rooted soil column upon infiltration of deuterated water time-resolved in 3D. Image quality and resolution could be sustained to a level allowing for capturing the root system in high detail. Good signal-to-noise ratio and contrast were the key to visualize dynamic changes in water content and to localize the root uptake. We demonstrated the ability of ultra-fast tomography to quantitatively image quick changes of water content in the rhizosphere and outlined the value of such imaging data for 3D water uptake modelling. The presented method paves the way for time-resolved studies of various 3D flow and transport phenomena in porous systems.
Neurogenesis from Sox2 expressing cells in the adult cerebellar cortex
Authors: Ahlfeld Julia , Filser Severin , Schmidt Felix , Wefers Annika K. , Merk Daniel J. , Glaß Rainer , Herms Jochen , Schüller Ulrich
Published: July 2017

We identified a rare undifferentiated cell population that is intermingled with the Bergmann glia of the adult murine cerebellar cortex, expresses the stem cell markers Sox2 and Nestin, and lacks markers of glial or neuronal differentiation. Interestingly, such Sox2+ S100− cells of the adult cerebellum expanded after adequate physiological stimuli in mice (exercise), and Sox2+ precursors acquired positivity for the neuronal marker NeuN over time and integrated into cellular networks. In human patients, SOX2+ S100− cells similarly increased in number after relevant pathological insults (infarcts), suggesting a similar expansion of cells that lack terminal glial differentiation.
Machine Learning Model Analysis of Breeding Habitats for the Black-necked Crane in Central Asian Uplands under Anthropogenic Pressures
Authors: Han Xuesong , Guo Yumin , Mi Chunrong , Huettmann Falk , Wen Lijia
Published: July 2017

The black-necked crane (Grus nigricollis) is the only alpine crane species and is endemic to the Tibetan Plateau. The breeding habitats of this species are poorly understood, which greatly hampers practical research and conservation work. Using machine learning methods and the best-available data from our 7,000-kilometer mega-transect survey and open access data, we built the first species distribution model (SDM) to analyze the black-necked crane’s breeding habitats. Our model showed that current conservation gaps account for 26.7% of its predicted breeding habitats. Specifically, the northern parts of the Hengduan Mountains and the southeastern Tibet Valley, the northern side of the middle Kunlun Mountains, parts of the Pamir Plateau, the northern Pakistan Highlands and the western Hindu Kush should be considered as its main potential breeding areas. Additionally, our model suggested that the crane prefers to breed in alpine meadows at an elevation over 2,800 m, a maximum temperature of the warmest month below 20.5 °C, and a temperature seasonality above 7,800 units. The identified conservation gaps and potential breeding areas can aid in clearly prioritizing future conservation and research, but more attention and study should be directed to the unassessed Western Development of China to secure this endangered crane lineage and other wildlife on the Tibetan Plateau.
Discontinuous boundaries of slow slip events beneath the Bungo Channel, southwest Japan
Authors: Nakata Ryoko , Hino Hideitsu , Kuwatani Tatsu , Yoshioka Shoichi , Okada Masato , Hori Takane
Published: July 2017

The down-dip limit of the seismogenic zone and up-dip and down-dip limits of the deep low-frequency tremors in southwest Japan are clearly imaged by the hypocentre distribution. Previous studies using smooth constraints in inversion analyses estimated that long-term slow slip events (L-SSEs) beneath the Bungo Channel are distributed smoothly from the down-dip part of the seismogenic zone to the up-dip part of the tremors. Here, we use fused regularisation, a type of sparse modelling suitable for detecting discontinuous changes in the model parameters to estimate the slip distribution of L-SSEs. The largest slip abruptly becomes zero at the down-dip limit of the seismogenic zone, is immediately reduced to half at the up-dip limit of the tremors, and becomes zero near its down-dip limit. Such correspondences imply that some thresholds exist in the generation processes for both tremors and SSEs. Hence, geodetic data inversion with sparse modelling can detect such high resolution in the slip distribution.
Particle Adsorption on Hydrogel Surfaces in Aqueous Media due to van der Waals Attraction
Authors: Sato Naoko , Aoyama Yurina , Yamanaka Junpei , Toyotama Akiko , Okuzono Tohru
Published: July 2017

Particle adhesion onto hydrogels has recently attracted considerable attention because of the potential biomedical applications of the resultant materials. A variety of interactions have been taken advantage of for adsorption, including electrostatic forces, hydrophobic interactions and hydrogen bonding. In this study, we report significant adsorption of submicron-sized silica particles onto hydrogel surfaces in water, purely by van der Waals (vdW) attraction. The vdW forces enabled strong adhesions between dielectric materials in air. However, because the Hamaker constant decreases in water typically by a factor of approximately 1/100, it is not clear whether vdW attraction is the major driving force in aqueous settings. We investigated the adsorption of silica particles (diameter = 25–600 nm) on poly(acrylamide) and poly(dimethylacrylamide) gels using optical microscopy, under conditions where chemical and electrostatic adsorption is negligible. The quantity of adsorbed particles decreased on decreasing the Hamaker constant by varying the refractive indices of the particles and medium (ethyleneglycol/water), indicating that the adsorption is because of the vdW forces. The adsorption isotherm was discussed based on the adhesive contact model in consideration of the deformation of the gel surface. The present findings will advance the elucidation and development of adsorption in various types of soft materials.
3D anatomical and perfusion MRI for longitudinal evaluation of biomaterials for bone regeneration of femoral bone defect in rats
Authors: Ribot Emeline J. , Tournier Clement , Aid-Launais Rachida , Koonjoo Neha , Oliveira Hugo , Trotier Aurelien J. , Rey Sylvie , Wecker Didier , Letourneur Didier , Amedee Vilamitjana Joelle , Miraux Sylvain
Published: July 2017

Magnetic Resonance Imaging (MRI) appears as a good surrogate to Computed Tomography (CT) scan as it does not involve radiation. In this context, a 3D anatomical and perfusion MR imaging protocol was developed to follow the evolution of bone regeneration and the neo-vascularization in femoral bone defects in rats. For this, three different biomaterials based on Pullulan-Dextran and containing either Fucoidan or HydroxyApatite or both were implanted. In vivo MRI, ex vivo micro-CT and histology were performed 1, 3 and 5 weeks after implantation. The high spatially resolved (156 × 182 × 195 µm) anatomical images showed a high contrast from the defects filled with biomaterials that decreased over time due to bone formation. The 3D Dynamic Contrast Enhanced (DCE) imaging with high temporal resolution (1 image/19 s) enabled to detect a modification in the Area-Under-The-Gadolinium-Curve over the weeks post implantation. The high sensitivity of MRI enabled to distinguish which biomaterial was the least efficient for bone regeneration, which was confirmed by micro-CT images and by a lower vessel density observed by histology. In conclusion, the methodology developed here highlights the efficiency of longitudinal MRI for tissue engineering as a routine small animal exam.
The N-terminal dimerization is required for TDP-43 splicing activity
Authors: Jiang Lei-Lei , Xue Wei , Hong Jun-Ye , Zhang Jun-Ting , Li Min-Jun , Yu Shao-Ning , He Jian-Hua , Hu Hong-Yu
Published: July 2017

TDP-43 is a nuclear factor that functions in promoting pre-mRNA splicing. Deletion of the N-terminal domain (NTD) and nuclear localization signal (NLS) (i.e., TDP-35) results in mislocalization to cytoplasm and formation of inclusions. However, how the NTD functions in TDP-43 activity and proteinopathy remains largely unknown. Here, we studied the structure and function of the NTD in inclusion formation and pre-mRNA splicing of TDP-43 by using biochemical and biophysical approaches. We found that TDP-43 NTD forms a homodimer in solution in a concentration-dependent manner, and formation of intermolecular disulfide results in further tetramerization. Based on the NMR structure of TDP-43 NTD, the dimerization interface centered on Leu71 and Val72 around the β7-strand was defined by mutagenesis and size-exclusion chromatography. Cell experiments revealed that the N-terminal dimerization plays roles in protecting TDP-43 against formation of cytoplasmic inclusions and enhancing pre-mRNA splicing activity of TDP-43 in nucleus. This study may provide mechanistic insights into the physiological function of TDP-43 and its related proteinopathies.
Emergence of hysteresis loop in social contagions on complex networks
Authors: Su Zhen , Wang Wei , Li Lixiang , Xiao Jinghua , Stanley H. Eugene
Published: July 2017

Understanding the spreading mechanisms of social contagions in complex network systems has attracted much attention in the physics community. Here we propose a generalized threshold model to describe social contagions. Using extensive numerical simulations and theoretical analyses, we find that a hysteresis loop emerges in the system. Specifically, the steady state of the system is sensitive to the initial conditions of the dynamics of the system. In the steady state, the adoption size increases discontinuously with the transmission probability of information about social contagions, and trial size exhibits a non-monotonic pattern, i.e., it first increases discontinuously then decreases continuously. Finally we study social contagions on heterogeneous networks and find that network topology does not qualitatively affect our results.
After infection with Leishmania infantum, Golden Hamsters (Mesocricetus auratus) become more attractive to female sand flies (Lutzomyia longipalpis)
Authors: Nevatte T. M. , Ward R. D. , Sedda L. , Hamilton J. G. C.
Published: July 2017

In Brazil, human and canine visceral leishmaniasis is caused by infection with Leishmania infantum, a Protist parasite transmitted by blood-feeding female Lutzomyia longipalpis sand flies. The objective of this study was to determine if the odour of hamsters, infected with Le. infantum, was more attractive than the odour of the same hamsters, before they were infected. The attractiveness of odour collected from individual hamsters (n = 13), before they were infected, was compared in a longitudinal study, with the attractiveness of the odour of the same hamster in a Y-tube olfactometer bioassay, at a late stage of infection. The odour of six of the golden hamsters was significantly more attractive to 50% of the female sand flies at the end of infection compared to before infection and the odour of four of the golden hamsters was significantly more attractive to 75% of the female sand flies at the end of infection. These results strongly indicate that hamsters infected with Le. infantum become significantly more attractive to a greater proportion of female sand flies as the infection progresses.
Solute carriers affect Anopheles stephensi survival and Plasmodium berghei infection in the salivary glands
Authors: Couto J. , Antunes S. , Pinheiro-Silva R. , do Rosário V. , de la Fuente J. , Domingos A.
Published: July 2017

Malaria is caused by mosquito-bornePlasmodiumspp. parasites that must infect and survive within mosquito salivary glands (SGs) prior to host transmission. Recent advances in transcriptomics and the complete genome sequencing of mosquito vectors have increased our knowledge of the SG genes and proteins involved in pathogen infection and transmission. Membrane solute carriers are key proteins involved in drug transport and are useful in the development of new interventions for transmission blocking. Herein, we applied transcriptomics analysis to compare SGs mRNA levels inAnopheles stephensifed on non-infected andP. berghei-infected mice. TheA. stephensisolute carriersprestinAandNDAE1were up-regulated in response to infection. These molecules are predicted to interact with each other, and are reportedly involved in the maintenance of cell homeostasis. To further evaluate their functions in mosquito survival and parasite infection, these genes were knocked down by RNA interference. Knockdown ofprestinAandNDAE1resulted in reduction of the number of sporozoites in mosquito SGs. Moreover,NDAE1knockdown strongly impacted mosquito survival, resulting in the death of half of the treated mosquitoes. Overall, our findings indicate the importance of prestinA and NDAE1 in interactions between mosquito SGs andPlasmodium, and suggest the need for further research.
Integrin α6β4 Upregulates Amphiregulin and Epiregulin through Base Excision Repair-Mediated DNA Demethylation and Promotes Genome-wide DNA Hypomethylation
Authors: Carpenter Brittany L. , Liu Jinpeng , Qi Lei , Wang Chi , O’Connor Kathleen L.
Published: July 2017

Aberrant DNA methylation patterns are a common theme across all cancer types. Specific DNA demethylation of regulatory sequences can result in upregulation of genes that are critical for tumor development and progression. Integrin α6β4 is highly expressed in pancreatic carcinoma and contributes to cancer progression, in part, through the specific DNA demethylation and upregulation of epidermal growth factor receptor (EGFR) ligands amphiregulin (AREG) and epiregulin (EREG). Whole genome bisulfite sequencing (WGBS) revealed that integrin α6β4 signaling promotes an overall hypomethylated state and site specific DNA demethylation of enhancer elements within the proximal promoters of AREG and EREG. Additionally, we find that the base excision repair (BER) pathway is required to maintain expression of AREG and EREG, as blocking DNA repair molecules, TET1 GADD45A, TDG, or PARP-1 decreased gene expression. Likewise, we provide the novel finding that integrin α6β4 confers an enhanced ability on cells to repair DNA lesions and survive insult. Therefore, while many known signaling functions mediated by integrin α6β4 that promote invasive properties have been established, this study demonstrates that integrin α6β4 can dramatically impact the epigenome of cancer cells, direct global DNA methylation levels toward a hypomethylated state, and impact DNA repair and subsequent cell survival.
Human intrahepatic CD69 + CD8+ T cells have a tissue resident memory T cell phenotype with reduced cytolytic capacity
Authors: Stelma Femke , de Niet Annikki , Sinnige Marjan J. , van Dort Karel A. , van Gisbergen Klaas P. J. M. , Verheij Joanne , van Leeuwen Ester M. M. , Kootstra Neeltje A. , Reesink Hendrik W.
Published: July 2017

Tissue resident memory T cells (TRM) have been identified in various tissues, however human liver TRM to date remain unidentified. TRM can be recognized by CD69 and/or CD103 expression and may play a role in the pathology of chronic hepatitis B (CHB) and hepatitis C virus infection (CHC). Liver and paired blood mononuclear cells from 17 patients (including 4 CHB and 6 CHC patients) were isolated and CD8+ T cells were comprehensively analysed by flowcytometry, immunohistochemistry and qPCR. The majority of intrahepatic CD8+ T cells expressed CD69, a marker used to identify TRM, of which a subset co-expressed CD103. CD69 + CD8+ T cells expressed low levels of S1PR1 and KLF2 and a large proportion (>90%) was CXCR6+, resembling liver TRM in mice and liver resident NK cells in human. Cytotoxic proteins were only expressed in a small fraction of liver CD69 + CD8+ T cells in patients without viral hepatitis, however, in livers from CHB patients more CD69 + CD8+ T cells were granzyme B+. In CHC patients, less intrahepatic CD69 + CD8+ T cells were Hobit+ as compared to CHB and control patients. Intrahepatic CD69 + CD8+ T cells likely TRM which have a reduced cytolytic potential. In patients with chronic viral hepatitis TRM have a distinct phenotype.
An In Vitro Model for the Ocular Surface and Tear Film System
Authors: Lu Qiaozhi , Yin Hongbo , Grant Michael P. , Elisseeff Jennifer H.
Published: July 2017

Dry eye is a complicated ocular surface disease whose exact pathogenesis is not yet fully understood. For the therapeutic evaluation and pathogenesis study of dry eye, we established an in vitro three-dimensional (3D) coculture model for the ocular surface. It is composed of rabbit conjunctival epithelium and lacrimal gland cell spheroids, and recapitulates the aqueous and mucin layers of the tear film. We first investigated the culture conditions for both cell types to optimize their secretory functions, by employing goblet cell enrichment, air-lifting culture, and 3D spheroid formation techniques. The coculture of the two cell components leads to elevated secretion and higher expression of tear secretory markers. We also compared several coculture systems, and found that direct cell contact between the two cell types significantly increased tear secretion. Inflammation was induced to mimic dry eye disease in the coculture model system. Our results showed that the coculture system provides a more physiologically relevant therapeutic response compared to monocultures. Our work provides a complex 3D model as a recapitulation of the ocular surface and tear film system, which can be further developed as a model for dry eye disease and therapeutic evaluation.
Tumor-targeted delivery of siRNA using fatty acyl-CGKRK peptide conjugates
Authors: Sharma Meenakshi , El-Sayed Naglaa Salem , Do Hung , Parang Keykavous , Tiwari Rakesh Kumar , Aliabadi Hamidreza Montazeri
Published: July 2017

Tumor-targeted carriers provide efficient delivery of chemotherapeutic agents to tumor tissue. CGKRK is one of the well-known tumor targeting peptides with significant specificity for angiogenic blood vessels and tumor cells. Here, we designed fatty acyl conjugated CGKRK peptides, based on the hypothesis that hydrophobically-modified CGKRK peptide could enhance cellular permeation and delivery of siRNA targeted to tumor cells for effective silencing of selected proteins. We synthesized six fatty acyl-peptide conjugates, using a diverse chain of saturated and unsaturated fatty acids to study the efficiency of this approach. At peptide:siRNA weight/weight ratio of 10:1 (N/P ≈ 13.6), almost all the peptides showed complete binding with siRNA, and at a w/w ratio of 20:1 (N/P ≈ 27.3), complete protection of siRNA from early enzymatic degradation was observed. Conjugated peptides and peptide/siRNA complexes did not show significant cytotoxicity in selected cell lines. The oleic acid-conjugated peptide showed the highest efficiency in siRNA uptake and silencing of kinesin spindle protein at peptide:siRNA w/w ratio of 80:1 (N/P ≈ 109). The siRNA internalization into non-tumorigenic kidney cells was negligible with all fatty acyl-peptide conjugates. These results indicate that conjugation of fatty acids to CGKRK could create an efficient delivery system for siRNA silencing specifically in tumor cells.
Anti-tubercular Activity of Pyrazinamide is Independent of trans-Translation and RpsA
Authors: Dillon Nicholas A. , Peterson Nicholas D. , Feaga Heather A. , Keiler Kenneth C. , Baughn Anthony D.
Published: July 2017

Pyrazinamide (PZA) is a first line anti-tubercular drug for which the mechanism of action remains unresolved. Recently, it was proposed that the active form of PZA, pyrazinoic acid (POA), disrupts the ribosome rescue process of trans-translation in Mycobacterium tuberculosis. This model suggested that POA binds within the carboxy-terminal domain of ribosomal protein S1 (RpsA) and inhibits trans-translation leading to accumulation of stalled ribosomes. Here, we demonstrate that M. tuberculosis RpsA interacts with single stranded RNA, but not with POA. Further, we show that an rpsA polymorphism previously identified in a PZA resistant strain does not confer PZA resistance when reconstructed in a laboratory strain. Finally, by utilizing an in vitro trans-translation assay with purified M. tuberculosis ribosomes we find that an interfering oligonucleotide can inhibit trans-translation, yet POA does not inhibit trans-translation. Based on these findings, we conclude that the action of PZA is entirely independent of RpsA and trans-translation in M. tuberculosis.
Helical Phase Structure of Radiation from an Electron in Circular Motion
Authors: Katoh M. , Fujimoto M. , Mirian N. S. , Konomi T. , Taira Y. , Kaneyasu T. , Hosaka M. , Yamamoto N. , Mochihashi A. , Takashima Y. , Kuroda K. , Miyamoto A. , Miyamoto K. , Sasaki S.
Published: July 2017

We theoretically show that a single free electron in circular motion radiates an electromagnetic wave possessing helical phase structure, which is closely related to orbital angular momentum carried by it. We experimentally demonstrate it by interference and double-slit diffraction experiments on radiation from relativistic electrons in spiral motion. Our results indicate that photons carrying orbital angular momentum should be created naturally by cyclotron/synchrotron radiations or Compton scatterings in various situations in cosmic space. We propose promising laboratory vortex photon sources in various wavelengths ranging from radio wave to gamma-rays.
A novel proton transfer mechanism in the SLC11 family of divalent metal ion transporters
Authors: Pujol-Giménez Jonai , Hediger Matthias A. , Gyimesi Gergely
Published: July 2017

In humans, the H+-coupled Fe2+ transporter DMT1 (SLC11A2) is essential for proper maintenance of iron homeostasis. While X-ray diffraction has recently unveiled the structure of the bacterial homologue ScaDMT as a LeuT-fold transporter, the exact mechanism of H+-cotransport has remained elusive. Here, we used a combination of molecular dynamics simulations, in silico pK
a
calculations and site-directed mutagenesis, followed by rigorous functional analysis, to discover two previously uncharacterized functionally relevant residues in hDMT1 that contribute to H+-coupling. E193 plays a central role in proton binding, thereby affecting transport properties and electrogenicity, while N472 likely coordinates the metal ion, securing an optimally “closed” state of the protein. Our molecular dynamics simulations provide insight into how H+-translocation through E193 is allosterically linked to intracellular gating, establishing a novel transport mechanism distinct from that of other H+-coupled transporters.
Radiation loss of planar surface plasmon polaritons transmission lines at microwave frequencies
Authors: Xu Zhixia , Li Shunli , Yin Xiaoxing , Zhao Hongxin , Liu Leilei
Published: July 2017

Radiation loss of a typical spoof surface plasmon polaritons (SSPPs) transmission line (TL) is investigated in this paper. A 325 mm-long SSPPs TL is designed and fabricated. Simulated results show that radiation loss contributes more to transmission loss than dielectric loss and conductor loss from 2 GHz to 10 GHz. Radiation loss of the SSPPs TL could be divided into two parts, one is caused by the input mode converter, and the other is caused by the corrugated metallic strip. This paper explains mechanisms of radiation loss from different parts, designs a loaded SSPPs TL with a series of resistors to absorb electromagnetic energy on corrugated metallic strip, and then discriminates radiation loss from the input mode converter, proposes the concept of average radiation length (ARL) to evaluate radiation loss from SSPPs of finite length, and concludes that radiation loss is mainly caused by corrugated structure of finite length at low frequency band and by the input mode converter at high frequency band. To suppress radiation loss, a mixed slow wave TL based on the combination of coplanar waveguides (CPWs) and SSPPs is presented. The designed structure, sample fabrication and experimental verification are discussed.
PI3K p85α Subunit-deficient Macrophages Protect Mice from Acute Colitis due to the Enhancement of IL-10 Production
Authors: Hayashi Shusaku , Hamada Takayuki , Zinsou Donald G. A. , Oshiro Momoe , Itoi Kana , Yamamoto Takeshi , Kadowaki Makoto
Published: July 2017

We investigated the role of the PI3K p85α subunit in the development of acute colitis with a focus on intestinal macrophages. Experimental acute colitis was induced using 3% dextran sulfate sodium (DSS) in drinking water for 7 days. The severity of DSS-induced acute colitis was significantly attenuated in p85α hetero-deficient (p85α+/−) mice compared with WT mice. The expression of proinflammatory mediators in intestinal macrophages isolated from the inflamed colonic mucosa was significantly suppressed in p85α+/− colitis mice compared with WT colitis mice. Interestingly, we found that bone marrow-derived macrophages (BMDMs) from p85α+/− mice produced a significantly higher amount of IL-10 than BMDMs from WT mice. The adoptive transfer of p85α+/− BMDMs, but not WT BMDMs, significantly improved the severity in WT colitis mice, and this effect was reversed by anti-IL-10 antibody. Furthermore, the expression of IL-10 in the intestinal macrophages of p85α+/− normal colonic mucosa was significantly higher than that in the intestinal macrophages of WT normal colonic mucosa. The present results demonstrate that p85α+/− mice exhibit a reduced susceptibility to DSS-induced acute colitis. Our study suggests that a deficiency of PI3K p85α enhances the production of IL-10 in intestinal macrophages, thereby suppressing the development of DSS-induced acute colitis.
Prognostic role of Glasgow prognostic score in patients with colorectal cancer: evidence from population studies
Authors: Liu Yangyang , He Xingkang , Pan Jie , Chen Shujie , Wang Liangjing
Published: July 2017

Glasgow prognostic score (GPS) has been reported to be an indicator of prognosis for various cancers. However, the relationship between GPS and colorectal cancers (CRC) remains unclear. A comprehensive search of Pubmed, Embase, Cochrane library, Web of Science, ChinaInfo and Chinese National Knowledge Infrastructure was performed to identify eligible studies, from which the risk of overall survival (OS) and cancer-specific survival (CSS) were extracted. A random-effect model was adopted to combine hazard ratio (HR) and 95% confidence interval (CI). 25 articles with a total of 5660 participants were included. The pooled results indicated that elevated GPS was associated with poor OS (HR = 2.83, 95%CI: 2.00–4.00, P < 0.01) and CSS (HR = 1.94, 95%CI: 1.51–2.49, P < 0.01). This correlation was confirmed both in primary operable and advanced inoperable patients. Increased GPS was also closely related to advanced tumour-node-metastasis (TNM) stage (odds ratio [OR] = 1.44, 95% CI: 1.010–2.065, P < 0.05) and elevated level of serum carcinoembryonic antigen (OR = 2.252, 95% CI: 1.508–3.362, P < 0.01). Subgroup analysis revealed a significant association between high GPS and poor survival outcome according to the factors of sample size, study of region and cut-off value of GPS level. These findings suggest that GPS may serve as a reliable predictive index for patients with CRC.
C26-Ceramide as highly sensitive biomarker for the diagnosis of Farber Disease
Authors: Cozma Claudia , Iurașcu Marius-Ionuț , Eichler Sabrina , Hovakimyan Marina , Brandau Oliver , Zielke Susanne , Böttcher Tobias , Giese Anne-Katrin , Lukas Jan , Rolfs Arndt
Published: July 2017

Farber disease (FD) is a rare autosomal recessive disease caused by mutations in the acid ceramidase gene (ASAH1). Low ceramidase activity results in the accumulation of fatty substances, mainly ceramides. Hallmark symptoms at clinical level are periarticular nodules, lipogranulomas, swollen and painful joints and a hoarse voice. FD phenotypes are heterogeneous varying from mild to very severe cases, with the patients not surviving past their first year of life. The diagnostic aspects of FD are poorly developed due to the rarity of the disease. In the present study, the screening for ceramides and related molecules was performed in Farber affected patients (n = 10), carriers (n = 11) and control individuals (n = 192). This study has the highest number of enrolled Farber patients and carriers reported to present. Liquid chromatography multiple reaction mass spectrometry (LC/MRM-MS) studies revealed that the ceramide C26:0 and especially its isoform 1 is a highly sensitive and specific biomarker for FD (p < 0.0001). The new biomarker can be determined directly in the dried blood spot extracts with low sample consumption. This allows for easy sample preparation, high reproducibility and use in high throughput screenings.
Critical behavior of the van der Waals bonded high T

C
ferromagnet Fe3GeTe2
Authors: Liu Bingjie , Zou Youming , Zhou Shiming , Zhang Lei , Wang Zhe , Li Hexuan , Qu Zhe , Zhang Yuheng
Published: July 2017

Fe3GeTe2 is a promising candidate for van der Waals bonded ferromagnet because of its high Curie temperature and the prediction that its ferromagnetism can maintain upon exfoliating down to single layer. Here, we have reported the critical behavior to understand its ferromagnetic exchange. Based on various techniques including modified Arrott plot, Kouvel-Fisher plot, and critical isotherm analysis, a set of reliable critical exponents (β = 0.327 ± 0.003, γ = 1.079 ± 0.005, and δ = 4.261 ± 0.009) has been obtained. The critical behavior suggests a three-dimensional long-range magnetic coupling with the exchange distance decaying as J(r) ≈ r−4.6 in Fe3GeTe2. The possible origin of three-dimensional magnetic characteristics in van der Waals bonded magnets is discussed.
Surface molecular imprinted polymers based on Mn-doped ZnS quantum dots by atom transfer radical polymerization for a room-temperature phosphorescence probe of bifenthrin
Authors: Wu Xuelian , Lv Xiaodong , Wang Jixiang , Sun Lin , Yan Yongsheng
Published: July 2017

Based on the room-temperature phosphorescence (RTP) peculiarity of Mn-doped ZnS quantum dots (QDs), a bifenthrin sensor was fabricated by coupling molecular imprinted polymers (MIPs) on the surface of silane modified QDs via atom transfer radical polymerization (ATRP).
A fluorescent aptasensor with product-triggered amplification by exonuclease III digestion for highly sensitive ATP detection
Authors: He Shengnan , Qu Long , Tan Ying , Liu Feng , Wang Yu , Zhang Wei , Cai Zhiming , Mou Lisha , Jiang Yuyang
Published: July 2017

An improved sensitivity of an ATP detection assay was achieved by using an allosteric probe and exonuclease III digestion product-triggered signal amplification.
Quantification of the contents in biojet fuel blends using near infrared spectroscopy and multivariate calibration
Authors: Terra Luciana A. , Filgueiras Paulo R. , Alves Julio Cesar L. , Poppi Ronei J.
Published: July 2017

A methodology was developed for quantification of blends of HEFA, farnesane and petroleum-derived jet fuel using near infrared spectroscopy and multivariate calibration.
Orthogonal thiol–ene ‘click’ reactions: a powerful combination for fabrication and functionalization of patterned hydrogels
Authors: Cengiz N. , Gevrek T. N. , Sanyal R. , Sanyal A.
Published: July 2017

The fabrication of ‘thiol–ene’ functionalizable hydrogel micropatterns using an ‘orthogonally’ functionalizable polymeric system is disclosed.
Copper-catalyzed trifluoromethylazidation and rearrangement of aniline-linked 1,7-enynes: access to CF3-substituted azaspirocyclic dihydroquinolin-2-ones and furoindolines
Authors: Yu Liu-Zhu , Wei Yin , Shi Min
Published: July 2017

A set of reactions involving copper-catalyzed trifluoromethylazidation and then rearrangement of aniline-linked 1,7-enynes was developed, and provided facile access to azaspirocyclic dihydroquinolin-2-ones, furoindolines and functionalized aziridines.
A bioorthogonal fluorescent probe for mitochondrial hydrogen sulfide: new strategy for cancer cell labeling
Authors: Velusamy Nithya , Binoy Anupama , Bobba Kondapa Naidu , Nedungadi Divya , Mishra Nandita , Bhuniya Sankarprasad
Published: July 2017

A chemodosimeter fluorescent probeMito-HSdiscriminates cancer cells from healthy cells based on the endogenous H2S formation in mitochondria.
Structural and dynamic properties of the C-terminal region of the Escherichia coli RNA chaperone Hfq: integrative experimental and computational studies
Authors: Wen Bin , Wang Weiwei , Zhang Jiahai , Gong Qingguo , Shi Yunyu , Wu Jihui , Zhang Zhiyong
Published: July 2017

The structural dynamics of the C-terminal region of Hfq and its functional role were investigated by integrative experimental and computational studies.
Computational studies on the Rh-catalyzed carboxylation of a C(sp2)–H bond using CO2
Authors: Lv Xiangying , Zhang Linhui , Sun Beibei , Li Zhi , Wu Yan-Bo , Lu Gang
Published: July 2017

CO2 insertion is facilitated by the critical effects of a Lewis acid and an agostic interaction.
Self-assembled colloidal complexes of polyphenol–gelatin and their stabilizing effects on emulsions
Authors: Huang Yu , Li Aijun , Qiu Chaoying , Teng YingLai , Wang Yong
Published: July 2017

We studied the in-depth characteristics including the binding interactions and morphological structure of tannic acid (TA)/grape seed proanthocyanidins (GSP) and gelatin (GLT) colloidal complexes, and evaluated the lipid oxidation of emulsions formed by the colloidal complexes.
Organic matrix-induced formation of a discrete cyclic [Cl2(H2O)2]2− cluster
Authors: Safin Damir A. , Babashkina Maria G. , Robeyns Koen , Garcia Yann
Published: July 2017

Reaction of 6-NH2-Py-2-NHC(S)NHP(S)(OiPr)2 with DMFA·2HCl leads to the co-crystallization product of 2,6-di(4H-1,2,4-triazol-4-yl)pyridine and 2,6-diaminopyridinium chloride monohydrate (1) and N-(diisopropoxythiophosphoryl)-N′-(6-(4H-1,2,4-triazol-4-yl))pyridin-2-ylthiocarbamide (2).
Organocatalytic enantioselective construction of isatin-derived N-alkoxycarbonyl 1,3-aminonaphthols via sterically encumbered hydrocarbon-substituted quinine-based squaramide
Authors: Karahan Seda , Tanyeli Cihangir
Published: July 2017

2-Adamantyl substituted quinine-squaramide catalyzed aza-Friedel–Crafts reaction of N-carbamate isatin ketimines with naphthol afforded chiral isatin-derived 1,3-aminonaphthols with excellent enantioselectivity up to greater than 99% and quantitative yield.
Synthesis, the electronic properties and efficient photoinduced electron transfer of new pyrrolidine[60]fullerene- and isoxazoline[60]fullerene-BODIPY dyads: nitrile oxide cycloaddition under mild conditions using PIFA
Authors: Cabrera-Espinoza Andrea , Insuasty Braulio , Ortiz Alejandro
Published: July 2017

The first synthesis of fulleroisoxazoline-BODIPY whose electron-accepting ability of the C60 cage is better than its fulleropyrrolidine-BODIPY counterpart.
Pickering high internal phase emulsions stabilized by worm-like polymeric nanoaggregates
Authors: Zhang Qi , Wang Chengjian , Fu Milin , Wang Jianli , Zhu Shiping
Published: July 2017

The first worm-stabilized Pickering high internal phase emulsion (HIPE) system was developed to prepare ultra-light porous monoliths.
The origin of bisignate circularly polarized luminescence (CPL) spectra from chiral polymer aggregates and molecular camphor: anti-Kasha's rule revealed by CPL excitation (CPLE) spectra
Authors: Duong Sang Thi , Fujiki Michiya
Published: July 2017

The first CPL excitation measurements of poly(fluorene-alt-bithiophene) aggregates and for comparison, camphor led to an idea of broken Kasha's rule.
Lightweight, interconnected VO2 nanoflowers hydrothermally grown on 3D graphene networks for wide-voltage-window supercapacitors
Authors: Wang Junya , Zhang Xuetao , Zhang Yue , Abas Asim , Zhao Xiaohua , Yang Zhiwei , Su Qing , Lan Wei , Xie Erqing
Published: July 2017

Highly stable and interconnected VO2 nanoflowers were uniformly grown on flexible three dimensional graphene networks, which directly served as a lightweight and high conductivity supercapacitor electrode (VO2 NF@3DG).
Molecular dynamics simulations of nanoscale engravings on an alkanethiol monolayer
Authors: Zhang Zhengqing , Ahn Yoonho , Jang Joonkyung
Published: July 2017

Thermal stability of nanoscale engravings on alkanethiol monolayer.
Dynamics of an amorphous pharmacologically active compound – diazepam: a QENS study combined with molecular dynamics simulations
Authors: Pajzderska Aleksandra , Gonzalez Miguel A. , Embs Jan P. , Mielcarek Jadwiga , Wąsicki Jan W.
Published: July 2017

Understanding the origin of the distribution of correlation times of methyl groups reorientation by experimental and theoretical studies.
Activity profiles of analog series containing pan assay interference compounds
Authors: Gilberg Erik , Stumpfe Dagmar , Bajorath Jürgen
Published: July 2017

Shown is the distribution of activity profiles (color-coded bars) of analog series containing PAINS substructures in a heatmap.
Perhydrohelicenes and other diamond-lattice based hydrocarbons: the choreography of inversion
Authors: Alder Roger W. , Butts Craig P. , Sessions Richard B.
Published: July 2017

Overall inversion in fused cyclohexane oligomers 2, 3, and 4 (all based on cis-decalin 1) occurs by a rolling process involving no more than two adjacent rings in twist-boat conformations at any time.
Graphene-hollow-cubes with network-faces assembled a 3D micro-structured transparent and free-standing film for high performance supercapacitors
Authors: Li Na , Huang Xuankai , Zhang Haiyan , Shi Zhicong , Wang Chengxin
Published: July 2017

A kind of 3D micro-structured transparent and free-standing film assembled by graphene-hollow-cubes with network-faces was developed using a micro-structured NaCl template.
Facile and one-step synthesis of a free-standing 3D MoS2–rGO/Mo binder-free electrode for efficient hydrogen evolution reaction
Authors: Barman Barun Kumar , Das Debanjan , Nanda Karuna Kar
Published: July 2017

Free-standing 3D MoS2/Mo and MoS2–rGO/Mo electrodes were prepared via a facile, one-step hydrothermal method for enhanced hydrogen evolution reaction (HER) performance.
Stacking modular DNA circuitry in cascading self-assembly of spherical nucleic acids
Authors: Yao Dongbao , Xiao Shiyan , Zhou Xiang , Li Hui , Wang Bei , Wei Bing , Liang Haojun
Published: July 2017

Integrated circuitries are successfully built through using the cascaded modular strategy with the assistance of stochastic simulations.
Dy3+@Mn4+co-doped Ca14Ga10−mAlmZn6O35far-red emitting phosphors with high brightness and improved luminescence and energy transfer properties for plant growth LED lights
Authors: Zhou Zhi , Xia Mao , Zhong Yuan , Gai Shujie , Huang Shengxiong , Tian Yun , Lu Xiangyang , Zhou Nan
Published: July 2017

A novel deep red phosphor Ca14Ga10−mAlmZn6O35:Dy3+,Mn4+(CGAZO:Dy3+,Mn4+) for plant growth LED lighting was successfully synthesizedviahigh-temperature solid-state reaction method and an effective energy transfer from Dy3+to Mn4+in the CGAZO host had been verified.
Engineering biology: a key driver of the bio‐economy
Authors: Kitney Richard I. , Freemont Paul S.
Published: July 2017

This study provides a relatively brief overview of the field of synthetic biology/engineering biology for the non‐specialist reader. This is in line with one of the basic aims of the new journal Engineering Biology – which is to open up the field to a much wider audience than those currently engaged and, particularly, to people working in companies and disciplines whose technology may be relevant to the field. Consequently, the study contains some didactic material.
The reactants equation of state for the tri-amino-tri-nitro-benzene (TATB) based explosive PBX 9502
Authors: Aslam Tariq D.
Published: July 2017

The response of high explosives (HEs), due to mechanical and/or thermal insults, is of great importance for both safety and performance. A major component of how an HE responds to these stimuli stems from its reactant equation of state (EOS). Here, the tri-amino-tri-nitro-benzene based explosive PBX 9502 is investigated by examining recent experiments. Furthermore, a complete thermal EOS is calibrated based on the functional form devised by Wescott, Stewart, and Davis [J. Appl. Phys. 98, 053514 (2005)]. It is found, by comparing to earlier calibrations, that a variety of thermodynamic data are needed to sufficiently constrain the EOS response over a wide range of thermodynamic state space. Included in the calibration presented here is the specific heat as a function of temperature, isobaric thermal expansion, and shock Hugoniot response. As validation of the resulting model, isothermal compression and isentropic compression are compared with recent experiments.
The standard mean-field treatment of inter-particle attraction in classical DFT is better than one might expect
Authors: Archer Andrew J. , Chacko Blesson , Evans Robert
Published: July 2017

In classical density functional theory (DFT), the part of the Helmholtz free energy functional arising from attractive inter-particle interactions is often treated in a mean-field or van der Waals approximation. On the face of it, this is a somewhat crude treatment as the resulting functional generates the simple random phase approximation (RPA) for the bulk fluid pair direct correlation function. We explain why using standard mean-field DFT to describe inhomogeneous fluid structure and thermodynamics is more accurate than one might expect based on this observation. By considering the pair correlation function g(x) and structure factor S(k) of a one-dimensional model fluid, for which exact results are available, we show that the mean-field DFT, employed within the test-particle procedure, yields results much superior to those from the RPA closure of the bulk Ornstein-Zernike equation. We argue that one should not judge the quality of a DFT based solely on the approximation it generates for the bulk pair direct correlation function.
Selected configuration interaction method using sampled first-order corrections to wave functions
Authors: Ohtsuka Yuhki , Hasegawa Jun-ya
Published: July 2017

A new selected configuration interaction (CI) method was proposed for the potential energy surfaces of quasi-degenerate and excited states. Slater determinants are generated by sampling the first-order corrections to the target-state wave functions using the quantum Monte Carlo method in determinant space. As in the Monte Carlo (MC) CI method, the wave function is improved at each iteration by generating new determinants and applying a pruning step. Compared to the random generation in the MCCI calculations, the number of iterations before convergence is significantly reduced. Regarding the potential energy curves of the ground and excited states of C2, the non-parallelity errors were sufficiently small, thus indicating the method’s applicability to the calculations of potential energy surfaces.
Characterization of hypervelocity metal fragments for explosive initiation
Authors: Yeager John D. , Bowden Patrick R. , Guildenbecher Daniel R. , Olles Joseph D.
Published: July 2017

The fragment impact response of two plastic-bonded explosive (PBX) formulations was studied using explosively driven aluminum fragments. A generic aluminum-capped detonator generated sub-mm aluminum particles moving at hypersonic velocities. The ability of these fragments to initiate reaction or otherwise damage two PBX materials was assessed using go/no-go experiments at standoff distances of up to 160 mm. Lower density PBX 9407 (RDX-based) was initiable at up to 115 mm, while higher density PBX 9501 (HMX-based) was only initiable at up to 6 mm. Several techniques were used to characterize the size, distribution, and velocity of the particles. Witness plate materials, including copper and polycarbonate, and backlit high speed video were used to characterize the distribution of particles, finding that the aluminum cap did not fragment homogeneously but rather with larger particles in a ring surrounding finer particles. Finally, precise digital holography experiments were conducted to measure the three-dimensional shape and size of the fastest-moving fragments, which ranged between 100 and 700 μm and traveled between 2.2 and 3.2 km/s. Crucially, these experiments showed variability in the fragmentation in terms of the number of fragments at the leading edge of the fragment field, indicating that both single and multiple shock impacts could be imparted to the target material. These types of data are critical for safety experiments and hydrocode simulations to quantify shock-to-detonation transition mechanisms and the associated risk-margins for these materials.
The constant force continuous molecular dynamics for potentials with multiple discontinuities
Authors: Padilla L. A. , Benavides A. L.
Published: July 2017

In this work, we present an extension of the constant force approach [P. Orea and G. Odriozola, J. Chem. Phys. 138, 214105 (2013)] to the case of potentials with multiple discontinuities. To illustrate the method, we selected the square well potential of range λ=1.5 that exhibits two discontinuities. Square well single phase properties, vapor-liquid phase diagram, and surface tension were calculated and compared with available simulation data. Besides, we analyzed the internal energies of a square well plus a square shoulder potential having three discontinuities. For both potentials, a good agreement has been found when compared with results of other simulation techniques (discontinuous molecular dynamics and Monte Carlo methods). This extension can be easily implemented to more general and efficient continuous molecular dynamics packages (HOOMD, GROMACS, NAMD, etc.).
Evidence of nanodiamond-self-assembly in a liquid crystal, and the consequent impacts on the liquid crystal properties
Authors: Basu Rajratan , Skaggs Nicole , Shalov Samuel , Brereton Peter
Published: July 2017

A small quantity of nanodiamonds (NDs) was dispersed in a nematic liquid crystal (LC), and the NDs were found to exhibit an anisotropic self-assembly along the nematic director. The anisotropic assembly of the NDs in the LC matrix was probed by measuring the dielectric anisotropy, Δε, of the LC+ND system, which showed a significant increase in Δε. Additional studies revealed that the presence of NDs reduced the rotational viscosity and the pretilt angle of the LC. The studies were carried out with several ND concentrations in the LC and the experimental results coherently suggest that there exists an optimal concentration of ND. Above this optimal ND concentration, the anisotropic assembly of the NDs was found to be not effective anymore. The rotational viscosity and the pretilt angle of the LC were found to increase above the optimal concentration of ND.