bluuebunny/crossref_metadata_2025 huggingface dataset:
Scaling photonic lanterns for space-division multiplexing
Authors: Velázquez-Benítez Amado M. , Antonio-López J. Enrique , Alvarado-Zacarías Juan C. , Fontaine Nicolas K. , Ryf Roland , Chen Haoshuo , Hernández-Cordero Juan , Sillard Pierre , Okonkwo Chigo , Leon-Saval Sergio G. , Amezcua-Correa Rodrigo
Published: June 2018

We present a new technique allowing the fabrication of large modal count photonic lanterns for space-division multiplexing applications. We demonstrate mode-selective photonic lanterns supporting 10 and 15 spatial channels by using graded-index fibres and microstructured templates. These templates are a versatile approach to position the graded-index fibres in the required geometry for efficient mode sampling and conversion. Thus, providing an effective scalable method for large number of spatial modes in a repeatable manner. Further, we demonstrate the efficiency and functionality of our photonic lanterns for optical communications. Our results show low insertion and mode dependent losses, as well as enhanced mode selectivity when spliced to few mode transmission fibres. These photonic lantern mode multiplexers are an enabling technology for future ultra-high capacity optical transmission systems.
The guanine nucleotide exchange factor Arhgef7/βPix promotes axon formation upstream of TC10
Authors: López Tobón Alejandro , Suresh Megalakshmi , Jin Jing , Vitriolo Alessandro , Pietralla Thorben , Tedford Kerry , Bossenz Michael , Mahnken Kristina , Kiefer Friedemann , Testa Giuseppe , Fischer Klaus-Dieter , Püschel Andreas W.
Published: June 2018

The characteristic six layers of the mammalian neocortex develop sequentially as neurons are generated by neural progenitors and subsequently migrate past older neurons to their final position in the cortical plate. One of the earliest steps of neuronal differentiation is the formation of an axon. Small GTPases play essential roles during this process by regulating cytoskeletal dynamics and intracellular trafficking. While the function of GTPases has been studied extensively in cultured neurons andin vivomuch less is known about their upstream regulators. Here we show that Arhgef7 (also called βPix or Cool1) is essential for axon formation during cortical development. The loss of Arhgef7 results in an extensive loss of axons in cultured neurons and in the developing cortex. Arhgef7 is a guanine-nucleotide exchange factor (GEF) for Cdc42, a GTPase that has a central role in directing the formation of axons during brain development. However, active Cdc42 was not able to rescue the knockdown of Arhgef7. We show that Arhgef7 interacts with the GTPase TC10 that is closely related to Cdc42. Expression of active TC10 can restore the ability to extend axons in Arhgef7-deficient neurons. Our results identify an essential role of Arhgef7 during neuronal development that promotes axon formation upstream of TC10.
Cadmium-induced apoptosis in neuronal cells is mediated by Fas/FasL-mediated mitochondrial apoptotic signaling pathway
Authors: Yuan Yan , Zhang Yajing , Zhao Shiwen , Chen Jie , Yang Jinlong , Wang Tao , Zou Hui , Wang Yi , Gu Jianhong , Liu Xuezhong , Bian Jianchun , Liu Zongping
Published: June 2018

Cadmium (Cd) is a toxic metal capable of damaging brain. Studies have demonstrated that Cd can induce apoptosis in neuronal cells. The CD95/APO-1 (Fas)/Fas Ligand (FasL) signaling pathway is one of the primary apoptosis pathways, but the role and regulatory mechanism of this pathway in neuronal cells remain unclear. Here, we demonstrated the underlying mechanism of the Fas/FasL system involving the mitochondrial apoptotic pathway in neuronal cells. Primary rat cerebral cortical neurons and PC12 cells were exposed to Cd, which significantly activated expression of Fas, FasL, Fas-associated death domain (FADD) and cleaved caspase-8. However, expression of cleaved caspase-8 decreased at 20 µM Cd in primary cerebral cortical neurons. Importantly, Cd-induced apoptotic morphological changes and increase in the apoptosis rate were partially blocked by Z-IETD-FMK, which is a specific inhibitor of caspase-8. Cd-mediated increase of apoptosis rate was inhibited by anti-FasL antibody. Furthermore, our data revealed that Z-IETD-FMK also blocked increase of truncated BH3 interacting domain death agonist (tBID)/BID, decrease of the B-cell lymphoma 2 (Bcl-2)/Bcl-2 associate X protein (Bax) ratio and mitochondrial membrane potential (MMP), release of cytochrome c, as well as cleavage of caspase-9/3 and poly (ADP-ribose) polymerase (PARP) induced by Cd. Taken together, our results demonstrate that the Fas/FasL-mediated mitochondrial apoptotic pathway plays an important role in Cd-induced neuronal apoptosis.
Amino Acid Chiral Selection Via Weak Interactions in Stellar Environments: Implications for the Origin of Life
Authors: Famiano Michael A. , Boyd Richard N. , Kajino Toshitaka , Onaka Takashi , Mo Yirong
Published: June 2018

Magnetochiral phenomena may be responsible for the selection of chiral states of biomolecules in meteoric environments. For example, the Supernova Amino Acid Processing (SNAAP) Model was proposed previously as a possible mode of magnetochiral selection of amino acids by way of the weak interaction in strong magnetic fields. In earlier work, this model was shown to produce an enantiomeric excess (ee) as high as 0.014% for alanine. In this paper we present the results of molecular quantum chemistry calculations from which ees are determined for the α-amino acids plus isovaline and norvaline, which were found to have positive ees in meteorites. Calculations are performed for both isolated and aqueous states. In some cases, the aqueous state was found to produce larger ees reaching values as high as a few percent under plausible conditions.
Dying cells expose a nuclear antigen cross-reacting with anti-PD-1 monoclonal antibodies
Authors: Metzger Philipp , Kirchleitner Sabrina V. , Koenig Lars M. , Hörth Christine , Kobold Sebastian , Endres Stefan , Schnurr Max , Duewell Peter
Published: June 2018

Checkpoint molecules such as programmed death 1 (PD-1) dampen excessive T cell activation to preserve immune homeostasis. PD-1-specific monoclonal antibodies have revolutionized cancer therapy, as they reverse tumour-induced T cell exhaustion and restore CTL activity. Based on this success, deciphering underlying mechanisms of PD-1-mediated immune functions has become an important field of immunological research. Initially described for T cells, there is emerging evidence of unconventional PD-1 expression by myeloid as well as tumor cells, yet, with cell-intrinsic functions in various animal tumor models. Here, we describe positive PD-1 antibody staining of various murine immune and tumour cells that is, unlike for T cells, not the PD-1 receptor and restricted to cells with low forward scatter characteristics. Based on flow cytometry and various approaches, including two established murine anti-PD-1 antibody clones, CRISPR/Cas9 genome editing and confocal imaging, we describe a staining pattern assigned to a nuclear antigen cross-reacting with anti-PD-1 monoclonal antibodies. Lack of PD-1 expression was further underlined by the analysis of PD-1 expression from B16-F10-derived 3D cultures and ex vivo tumours. Thus, our data provide multiple lines of evidence that PD-1 expression by non-T cells is unlikely to be the case and, taking recent data of PD-1 tumour cell-intrinsic functions into account, suggest that other antibody-mediated pathways might apply.
Notochordal cell matrix as a bioactive lubricant for the osteoarthritic joint
Authors: de Vries S. A. H. , van Doeselaar M. , Kaper H. J. , Sharma P. K. , Ito K.
Published: June 2018

Notochordal cell derived matrix (NCM) can induce regenerative effects on nucleus pulposus cells and may exert such effects on chondrocytes as well. Furthermore, when dissolved at low concentrations, NCM forms a viscous fluid with potential lubricating properties. Therefore, this study tests the feasibility of the use of NCM as a regenerative lubricant for the osteoarthritic joint. Chondrocyte-seeded alginate beads were cultured in base medium (BM), BM with NCM (NCM), or BM with TGF-β1 (TGF), as well as BM and NCM treated with IL-1β. NCM increased GAG deposition and cell proliferation (stronger than TGF), and GAG/DNA ratio and hydroxyproline content (similar to TGF). These effects were maintained in the presence of IL-1β. Moreover, NCM mitigated expression of IL-1β-induced IL-6, IL-8, ADAMTS-5 and MMP-13. Reciprocating sliding friction tests of cartilage on glass were performed to test NCM’s lubricating properties relative to hyaluronic acid (HA), and showed a dose-dependent reduction in coefficient of friction with NCM, similar to HA. NCM has anabolic and anti-inflammatory effects on chondrocytes, as well as lubricating properties. Therefore, intra-articular NCM injection may have potential as a treatment to minimize pain while restoring the affected cartilage tissue in the osteoarthritic joint.
Microstructural Design for Improving Ductility of An Initially Brittle Refractory High Entropy Alloy
Authors: Soni V. , Senkov O. N. , Gwalani B. , Miracle D. B. , Banerjee R.
Published: June 2018

Typically, refractory high-entropy alloys (RHEAs), comprising a two-phase ordered B2 + BCC microstructure, exhibit extraordinarily high yield strengths, but poor ductility at room temperature, limiting their engineering application. The poor ductility is attributed to the continuous matrix being the ordered B2 phase in these alloys. This paper presents a novel approach to microstructural engineering of RHEAs to form an “inverted” BCC + B2 microstructure with discrete B2 precipitates dispersed within a continuous BCC matrix, resulting in improved room temperature compressive ductility, while maintaining high yield strength at both room and elevated temperature.
Vortex lattice in the crossover of a Bose gas from weak coupling to unitarity
Authors: Adhikari S. K. , Salasnich L.
Published: June 2018

The formation of a regular lattice of quantized vortices in a fluid under rotation is a smoking-gun signature of its superfluid nature. Here we study the vortex lattice in a dilute superfluid gas of bosonic atoms at zero temperature along the crossover from the weak-coupling regime, where the inter-atomic scattering length is very small compared to the average distance between atoms, to the unitarity regime, where the inter-atomic scattering length diverges. This study is based on high-performance numerical simulations of the time-dependent nonlinear Schrödinger equation for the superfluid order parameter in three spatial dimensions, using a realistic analytical expression for the bulk equation of state of the system along the crossover from weak-coupling to unitarity. This equation of state has the correct weak-coupling and unitarity limits and faithfully reproduces the results of an accurate multi-orbital microscopic calculation. Our numerical predictions of the number of vortices and root-mean-square sizes are important benchmarks for future experiments.
Limitation of Optical Enhancement in Ultra-thin Solar Cells Imposed by Contact Selectivity
Authors: Islam Raisul , Saraswat Krishna
Published: June 2018

Ultra-thin crystalline silicon (c-Si) solar cell suffers both from poor light absorption and minority carrier recombination at the contacts resulting in low contact selectivity. Yet most of the research focuses on improving the light absorption by introducing novel light trapping technique. Our work shows that for ultra-thin absorber, the benefit of optical enhancement is limited by low contact selectivity. Using simulation we observe that performance enhancement from light trapping starts to saturate as the absorber scales down because of the increase in probability of the photo-generated carriers to recombine at the metal contact. Therefore, improving the carrier selectivity of the contacts, which reduces the recombination at contacts, is important to improve the performance of the solar cell beyond what is possible by enhancing light absorption only. The impact of improving contact selectivity increases as the absorber thickness scales below 20 micrometer (μm). Light trapping provides better light management and improving contact selectivity provides better photo-generated carrier management. When better light management increases the number of photo-generated carriers, better carrier management is a useful optimization knob to achieve the efficiency close to the thermodynamic limit. Our work explores a design trade-off in detail which is often overlooked by the research community.
Model of the adaptive immune response system against HCV infection reveals potential immunomodulatory agents for combination therapy
Authors: Obaid Ayesha , Naz Anam , Ikram Aqsa , Awan Faryal Mehwish , Raza Abida , Ahmad Jamil , Ali Amjad
Published: June 2018

A regulated immune system employs multiple cell types, diverse variety of cytokines and interacting signalling networks against infections. Systems biology offers a promising solution to model and simulate such large populations of interacting components of immune systems holistically. This study focuses on the distinct components of the adaptive immune system and analysis, both individually and in association with HCV infection. The effective and failed adaptive immune response models have been developed followed by interventions/perturbations of various treatment strategies to get better assessment of the treatment responses under varying stimuli. Based on the model predictions, the NK cells, T regulatory cells, IL-10, IL-21, IL-12, IL-2 entities are found to be the most critical determinants of treatment response. The proposed potential immunomodulatory therapeutic interventions include IL-21 treatment, blocking of inhibitory receptors on T-cells and exogenous anti-IL-10 antibody treatment. The relative results showed that these interventions have differential effect on the expression levels of cellular and cytokines entities of the immune response. Notably, IL-21 enhances the expression of NK cells, Cytotoxic T lymphocytes and CD4+ T cells and hence restore the host immune potential. The models presented here provide a starting point for cost-effective analysis and more comprehensive modeling of biological phenomenon.
One-step synthesis of Nickle Iron-layered double hydroxide/reduced graphene oxide/carbon nanofibres composite as electrode materials for asymmetric supercapacitor
Authors: Wang Feifei , Wang Ting , Sun Shiguo , Xu Yongqian , Yu Ruijin , Li Hongjuan
Published: June 2018

A novel NiFe-LDH/RGO/CNFs composite was produced by using a facile one-step hydrothermal method as electrode for supercapacitor. Compared with NiFe-LDH/CNFs, NiFe-LDH/CNTs and NiFe-LDH/RGO, NiFe-LDH/RGO/CNFs demonstrated a high specific capacitance of 1330.2 F g−1 at 1 A g−1 and a super rate capability of 64.2% from 1 to 20 A g−1, indicating great potential for supercapacitor application. Additionally, an asymmetric supercapacitor using NiFe-LDH/RGO/CNFs composite as positive electrode material and activated carbon as negative electrode material was assembled. The asymmetric supercapacitor can work in the voltage range of 0–1.57 V. It displayed high energy density of 33.7 W h kg−1 at power density of 785.8 W kg−1 and excellent cycling stability with 97.1% of the initial capacitance after 2500 cycles at 8 A g−1. Two flexible AC//LDH-RGO-CNFs ASC devices connected in series were able to light up a red LED indicator after being fully charged. The results demonstrate that the AC//LDH-RGO-CNFs ASC has a promising potential in commercial application.
Extracellular vesicles with altered tetraspanin CD9 and CD151 levels confer increased prostate cell motility and invasion
Authors: Brzozowski Joshua S. , Bond Danielle R. , Jankowski Helen , Goldie Belinda J. , Burchell Rachel , Naudin Crystal , Smith Nathan D. , Scarlett Christopher J. , Larsen Martin R. , Dun Matthew D. , Skelding Kathryn A. , Weidenhofer Judith
Published: June 2018

To facilitate intercellular communication, cells release nano-sized, extracellular vesicles (EVs) to transfer biological cargo to both local and distant sites. EVs are enriched in tetraspanins, two of which (CD9 and CD151) have altered expression patterns in many solid tumours, including prostate cancer, as they advance toward metastasis. We aimed to determine whether EVs from prostate cells with altered CD9 and CD151 expression could influence cellular behaviour and increase the metastatic capabilities of non-tumourigenic prostate cells. EVs were isolated by ultrafiltration and characterised for their tetraspanin expression and size distribution. iTRAQ was used to identify differences between RWPE1 and tetraspanin-modified RWPE1 EV proteomes, showing an enrichment in protein degradation pathways. Addition of EVs from RWPE1 cells with reduced CD9 or increased CD151 abundance resulted in increased invasion of RWPE1 cells, and increased migration in the case of high CD151 abundance. We have been able to show that alteration of CD9 and CD151 on prostate cells alters the proteome of their resultant EVs, and that these EVs can enhance the migratory and invasive capabilities of a non-tumourigenic prostate cellular population. This work suggests that cellular tetraspanin levels can alter EVs, potentially acting as a driver of metastasis in prostate cancer.
Decorrelation Signal of Diabetic Hyperreflective Foci on Optical Coherence Tomography Angiography
Authors: Murakami Tomoaki , Suzuma Kiyoshi , Dodo Yoko , Yoshitake Tatsuya , Yasukura Shota , Nakanishi Hideo , Fujimoto Masahiro , Oishi Maho , Tsujikawa Akitaka
Published: June 2018

Diabetic hyperreflective foci in the outer retinal layers are a clinically relevant finding on optical coherence tomography (OCT) images, although their characteristics remain to be elucidated. Here we investigated the decorrelation signal around hyperreflective foci on OCT angiography (OCTA) images in diabetic retinopathy (DR). We retrospectively reviewed sufficient quality OCTA images from 102 eyes of 66 patients that were obtained using split-spectrum amplitude-decorrelation angiography algorithm. Most confluent hyperreflective foci were randomly deposited or appeared in a radiating array on the en-face structural OCT images in the inner nuclear layer (INL) or Henle’s fiber layer (HFL), respectively. Within the INL, hyperreflective foci were not accompanied by decorrelation signals and attached to capillaries on OCTA images. Decorrelation signals were sometimes delineated in hyperreflective foci in the HFL and other times appeared to be pseudopod-like or wrapping around hyperreflective foci, referred to as reflectance-decorrelated foci. The decorrelation signal intensity of hyperreflective foci in the HFL was associated with logMAR VA (R = 0.553, P < 0.001) and central subfield thickness (R = 0.408, P < 0.001) but not with DR severity. These data suggest that reflectance-decorrelated foci on OCTA images are clinically relevant as well as shed lights on the properties in diabetic hyperreflective foci.
D5 dopamine receptors control glutamatergic AMPA transmission between the motor cortex and subthalamic nucleus
Authors: Froux Lionel , Le Bon-Jego Morgane , Miguelez Cristina , Normand Elisabeth , Morin Stephanie , Fioramonti Stéphanie , Barresi Massimo , Frick Andreas , Baufreton Jerome , Taupignon Anne
Published: June 2018

Corticofugal fibers target the subthalamic nucleus (STN), a component nucleus of the basal ganglia, in addition to the striatum, their main input. The cortico-subthalamic, or hyperdirect, pathway, is thought to supplement the cortico-striatal pathways in order to interrupt/change planned actions. To explore the previously unknown properties of the neurons that project to the STN, retrograde and anterograde tools were used to specifically identify them in the motor cortex and selectively stimulate their synapses in the STN. The cortico-subthalamic neurons exhibited very little sag and fired an initial doublet followed by non-adapting action potentials. In the STN, AMPA/kainate synaptic currents had a voltage-dependent conductance, indicative of GluA2-lacking receptors and were partly inhibited by Naspm. AMPA transmission displayed short-term depression, with the exception of a limited bandpass in the 5 to 15 Hz range. AMPA synaptic currents were negatively controlled by dopamine D5 receptors. The reduction in synaptic strength was due to postsynaptic D5 receptors, mediated by a PKA-dependent pathway, but did not involve a modified rectification index. Our data indicated that dopamine, through post-synaptic D5 receptors, limited the cortical drive onto STN neurons in the normal brain.
Fibrinogen – A Practical and Cost Efficient Biomarker for Detecting Periprosthetic Joint Infection
Authors: Klim S. M. , Amerstorfer F. , Gruber G. , Bernhardt G. A. , Radl R. , Leitner L. , Leithner A. , Glehr M.
Published: June 2018

The early and accurate diagnosis of periprosthetic joint infection (PJI) can be challenging. Fibrinogen plays an important role in mediating inflammation of bacterial infections and therefore could be a valuable biomarker for PJI. The purpose of this study was to investigate the sensitivity and specificity of serum levels of fibrinogen in detecting PJI, and to compare the results with the established PJI biomarkers C-reactive protein (CRP) and leukocyte count. Eighty-four patients (124 surgeries) were prospectively included. The preoperatively analyzed parameters were fibrinogen, CRP and leukocyte count. The sensitivity and specificity of the biomarkers were calculated and compared. Fibrinogen (p < 0.001), CRP (p < 0.001) and leukocyte count (p < 0.001) had a statistically significant correlation with the criteria defining the presence of PJI. For fibrinogen, the value of 519 mg/dl had a sensitivity of 0.90 and a specificity of 0.66. The CRP cut-off point of 11.00 mg/dl had a sensitivity of 0.90 and a specificity of 0.74. The leukocyte count of 5.68 G/l had a sensitivity of 0.90 and a specificity of 0.39. Our results indicated that fibrinogen is a significant biomarker for detecting a bacterial PJI. It has shown to be a cost-efficient diagnostic support with high sensitivity and specificity.
Chemokine CXCL16 mediates acinar cell necrosis in cerulein induced acute pancreatitis in mice
Authors: Sakuma Yojiro , Kodama Yuzo , Eguchi Takaaki , Uza Norimitsu , Tsuji Yoshihisa , Shiokawa Masahiro , Maruno Takahisa , Kuriyama Katsutoshi , Nishikawa Yoshihiro , Yamauchi Yuki , Tsuda Motoyuki , Ueda Tatsuki , Matsumori Tomoaki , Morita Toshihiro , Tomono Teruko , Kakiuchi Nobuyuki , Mima Atsushi , Sogabe Yuko , Marui Saiko , Kuwada Takeshi , Okada Akihiko , Watanabe Tomohiro , Nakase Hiroshi , Chiba Tsutomu , Seno Hiroshi
Published: June 2018

Severe acute pancreatitis is a lethal inflammatory disease frequently accompanied by pancreatic necrosis. We aimed to identify a key regulator in the development of pancreatic necrosis. A cytokine/chemokine array using sera from patients with acute pancreatitis (AP) revealed that serum CXCL16 levels were elevated according to the severity of pancreatitis. In a mouse model of AP, Cxcl16 expression was induced in pancreatic acini in the late phase with the development of pancreatic necrosis. Cxcl16−/− mice revealed similar sensitivity as wild-type (WT) mice to the onset of pancreatitis, but better resisted development of acinar cell necrosis with attenuated neutrophil infiltration. A cytokine array and immunohistochemistry revealed lower expression of Ccl9, a neutrophil chemoattractant, in the pancreatic acini of Cxcl16−/− mice than WT mice. Ccl9 mRNA expression was induced by stimulation with Cxcl16 protein in pancreatic acinar cells in vitro, suggesting a Cxcl16/Ccl9 cascade. Neutralizing antibody against Cxcl16 ameliorated pancreatic injury in the mouse AP model with decreased Ccl9 expression and less neutrophil accumulation. In conclusion, Cxcl16 expressed in pancreatic acini contributes to the development of acinar cell necrosis through the induction of Ccl9 and subsequent neutrophil infiltration. CXCL16 could be a new therapeutic target in AP.
Six-Year Incidence and Risk Factors of Age-Related Macular Degeneration in Singaporean Indians: The Singapore Indian Eye Study
Authors: Foo Valencia Hui Xian , Yanagi Yasuo , Nguyen Quang Duc , Sabanayagam Charumathi , Lim Sing Hui , Neelam Kumari , Wang Jie Jin , Mitchell Paul , Cheng Ching-Yu , Wong Tien Yin , Cheung Chui Ming Gemmy
Published: June 2018

We aimed to determine the 6-year incidence and risk factors of age-related macular degeneration (AMD) in first and second generations of Singaporean Indians. Baseline examination was conducted in 2007–9 and 6-year propsective follow-up examination of this Indian population in 2013–5. All participants underwent interviews with questionnaires and comprehensive medical and eye examinations. Incidence was age-standardized to Singaporean 2010 census. Risk factors associated with AMD incidence were assessed and compared between first and second generations of immigrants. Among 2200 persons who participated in the follow-up examination (75.5% response rate), gradable fundus photographs were available in 2105. The 6-year age-standardized incidences of early and late AMD were 5.26% and 0.51% respectively. Incident early AMD was associated with cardiovascular disease history (HR 1.59, 95% CI 1.04–2.45), underweight body mass index (BMI) (HR 3.12, 95% CI 1.37–7.14) (BMI of <18.5 vs 18.51–25 kg/m2), heavy alcohol drinking (HR 3.14 95% CI 1.25–7.89) and ARMS2 rs3750847 homozygous genetic loci carrier (HR 2.52, 95% CI 1.59–3.99). We found a relatively low incidence of early AMD in this Singaporean Indian population compared to Caucasian populations. Both first and second-generation Indian immigrants have similar incidence and risk factor patterns for early AMD.
UV radiation enhanced oxygen vacancy formation caused by the PLD plasma plume
Authors: Hensling F. V. E. , Keeble D. J. , Zhu J. , Brose S. , Xu C. , Gunkel F. , Danylyuk S. , Nonnenmann S. S. , Egger W. , Dittmann R.
Published: June 2018

Pulsed Laser Deposition is a commonly used non-equilibrium physical deposition technique for the growth of complex oxide thin films. A wide range of parameters is known to influence the properties of the used samples and thin films, especially the oxygen-vacancy concentration. One parameter has up to this point been neglected due to the challenges of separating its influence from the influence of the impinging species during growth: the UV-radiation of the plasma plume. We here present experiments enabled by a specially designed holder to allow a separation of these two influences. The influence of the UV-irradiation during pulsed laser deposition on the formation of oxygen-vacancies is investigated for the perovskite model material SrTiO3. The carrier concentration of UV-irradiated samples is nearly constant with depth and time. By contrast samples not exposed to the radiation of the plume show a depth dependence and a decrease in concentration over time. We reveal an increase in Ti-vacancy–oxygen-vacancy-complexes for UV irradiated samples, consistent with the different carrier concentrations. We find a UV enhanced oxygen-vacancy incorporation rate as responsible mechanism. We provide a complete picture of another influence parameter to be considered during pulsed laser depositions and unravel the mechanism behind persistent-photo-conductivity in SrTiO3.
Anti-inflammatory role of 15-lipoxygenase contributes to the maintenance of skin integrity in mice
Authors: Kim Sang-Nam , Akindehin Seun , Kwon Hyun-Jung , Son Yeon-Ho , Saha Abhirup , Jung Young-Suk , Seong Je-Kyung , Lim Kyung-Min , Sung Jong-Hyuk , Maddipati Krishna Rao , Lee Yun-Hee
Published: June 2018

15-lipoxygenase is involved in the generation of specialized pro-resolving lipid mediators that play essential roles in resolution and inflammatory responses. Here, we investigated anti-inflammatory role of Alox15 in skin homeostasis. We demonstrated that knockout (KO) of Alox15 led to hair loss and disrupted the structural integrity of the dorsal skin. Alox15 KO resulted in loss of hair follicle stem cells and abnormal transition of dermal adipocytes into fibroblasts. Alox15 deficiency increased infiltration of proinflammatory macrophages and upregulated proinflammatory and necroptotic signaling in dermal adipose tissue in the dorsal skin. Lipidomic analysis revealed severe loss of resolvin D2 in the dorsal skin of Alox15 KO mice compared to wild type controls. Treatment with resolvin D2 reduced skin inflammation in Alox15 KO mice. Collectively, these results indicate that Alox15-mediated production of resolvin D2 is required to maintain skin integrity by suppressing dermal inflammation.
The intrinsically disordered E-domains regulate the IGF-1 prohormones stability, subcellular localisation and secretion
Authors: Annibalini Giosuè , Contarelli Serena , De Santi Mauro , Saltarelli Roberta , Di Patria Laura , Guescini Michele , Villarini Anna , Brandi Giorgio , Stocchi Vilberto , Barbieri Elena
Published: June 2018

Insulin-like growth factor-1 (IGF-1) is synthesised as a prohormone (proIGF-1) requiring enzymatic activity to yield the mature IGF-1. Three proIGF-1s are encoded by alternatively spliced IGF-1 mRNAs: proIGF-1Ea, proIGF-1Eb and proIGF-1Ec. These proIGF-1s have a common IGF-1 mature sequence but different E-domains. The structure of the E-domains has not been resolved, and their molecular functions are still unclear. Here, we show that E-domains are Intrinsically Disordered Regions that have distinct regulatory functions on proIGF-1s production. In particular, we identified a highly conserved N-glycosylation site in the Ea-domain, which regulated intracellular proIGF-1Ea level preventing its proteasome-mediated degradation. The inhibition of N-glycosylation by tunicamycin or glucose starvation markedly reduced proIGF-1Ea and mature IGF-1 production. Interestingly, 2-deoxyglucose, a glucose and mannose analogue, increased proIGF-1Ea and mature IGF-1 levels, probably leading to an accumulation of an under-glycosylated proIGF-1Ea that was still stable and efficiently secreted. The proIGF-1Eb and proIGF-1Ec were devoid of N-glycosylation sites, and hence their production was unaffected by N-glycosylation inhibitors. Moreover, we demonstrated that alternative Eb- and Ec-domains controlled the subcellular localisation of proIGF-1s, leading to the nuclear accumulation of both proIGF-1Eb and proIGF-1Ec. Our results demonstrated that E-domains are regulatory elements that control IGF-1 production and secretion.
Super-resolution CT Image Reconstruction Based on Dictionary Learning and Sparse Representation
Authors: Jiang Changhui , Zhang Qiyang , Fan Rui , Hu Zhanli
Published: June 2018

In this paper, a single-computed tomography (CT) image super-resolution (SR) reconstruction scheme is proposed. This SR reconstruction scheme is based on sparse representation theory and dictionary learning of low- and high-resolution image patch pairs to improve the poor quality of low-resolution CT images obtained in clinical practice using low-dose CT technology. The proposed strategy is based on the idea that image patches can be well represented by sparse coding of elements from an overcomplete dictionary. To obtain similarity of the sparse representations, two dictionaries of low- and high-resolution image patches are jointly trained. Then, sparse representation coefficients extracted from the low-resolution input patches are used to reconstruct the high-resolution output. Sparse representation is used such that the trained dictionary pair can reduce computational costs. Combined with several appropriate iteration operations, the reconstructed high-resolution image can attain better image quality. The effectiveness of the proposed method is demonstrated using both clinical CT data and simulation image data. Image quality evaluation indexes (root mean squared error (RMSE) and peak signal-to-noise ratio (PSNR)) indicate that the proposed method can effectively improve the resolution of a single CT image.
NtLTP4, a lipid transfer protein that enhances salt and drought stresses tolerance in Nicotiana tabacum
Authors: Xu Yang , Zheng Xinxin , Song Yunzhi , Zhu Lifei , Yu Zipeng , Gan Liming , Zhou Shumei , Liu Hongmei , Wen Fujiang , Zhu Changxiang
Published: June 2018

Lipid transfer proteins (LTPs), a class of small, ubiquitous proteins, play critical roles in various environmental stresses. However, their precise biological functions remain unknown. Here we isolated an extracellular matrix-localised LTP, NtLTP4, from Nicotiana tabacum. The overexpression of NtLTP4 in N. tabacum enhanced resistance to salt and drought stresses. Upon exposure to high salinity, NtLTP4-overexpressing lines (OE lines) accumulated low Na+ levels. Salt-responsive genes, including Na+/H+ exchangers (NHX1) and high-affinity K+ transporter1 (HKT1), were dramatically higher in OE lines than in wild-type lines. NtLTP4 might regulate transcription levels of NHX1 and HKT1 to alleviate the toxicity of Na+. Interestingly, OE lines enhanced the tolerance of N. tabacum to drought stress by reducing the transpiration rate. Moreover, NtLTP4 could increase reactive oxygen species (ROS)-scavenging enzyme activity and expression levels to scavenge excess ROS under drought and high salinity conditions. We used a two-hybrid yeast system and screened seven putative proteins that interact with NtLTP4 in tobacco. An MAPK member, wound-induced protein kinase, was confirmed to interact with NtLTP4 via co-immunoprecipitation and a firefly luciferase complementation imaging assay. Taken together, this is the first functional analysis of NtLTP4, and proves that NtLTP4 positively regulates salt and drought stresses in N. tabacum.
Brain Cell Type Specific Gene Expression and Co-expression Network Architectures
Authors: McKenzie Andrew T. , Wang Minghui , Hauberg Mads E. , Fullard John F. , Kozlenkov Alexey , Keenan Alexandra , Hurd Yasmin L. , Dracheva Stella , Casaccia Patrizia , Roussos Panos , Zhang Bin
Published: June 2018

Elucidating brain cell type specific gene expression patterns is critical towards a better understanding of how cell-cell communications may influence brain functions and dysfunctions. We set out to compare and contrast five human and murine cell type-specific transcriptome-wide RNA expression data sets that were generated within the past several years. We defined three measures of brain cell type-relative expression including specificity, enrichment, and absolute expression and identified corresponding consensus brain cell “signatures,” which were well conserved across data sets. We validated that the relative expression of top cell type markers are associated with proxies for cell type proportions in bulk RNA expression data from postmortem human brain samples. We further validated novel marker genes using an orthogonal ATAC-seq dataset. We performed multiscale coexpression network analysis of the single cell data sets and identified robust cell-specific gene modules. To facilitate the use of the cell type-specific genes for cell type proportion estimation and deconvolution from bulk brain gene expression data, we developed an R package, BRETIGEA. In summary, we identified a set of novel brain cell consensus signatures and robust networks from the integration of multiple datasets and therefore transcend limitations related to technical issues characteristic of each individual study.
Optimization of Assembly Pipeline may Improve the Sequence of the Chloroplast Genome in Quercus spinosa
Authors: Zhang Xiangzhou , Hu Yong , Liu Mei , Lang Tiange
Published: June 2018

Obtaining chloroplast (cp) genome sequence is necessary for studying physiological roles in plants. However, it is difficult to use traditional sequencing methods to get cp genome sequences because of the complex procedures of preparing templates. With the advent of next-generation sequencing technology, massive genome sequences can be produced. Thus, a good pipeline to assemble next-generation sequence reads with optimized k-mer length is essential to get whole cp genome sequences. Moreover, adjustment of other parameters is also very important, especially for the assembly of the cp genome. In this study, we developed a pipeline to generate the cp genome for Quercus spinosa. When Quercus rubra was used as a reference, we achieved coverage of 97.75% after optimizing k-mer length as well as other parameters. The efficiency of the pipeline makes it a useful method for cp genome construction in plants. It also provides great perspective on the analysis of cp genome characteristics and evolution.
NF-кB increases LPS-mediated procalcitonin production in human hepatocytes
Authors: Bai Yongfeng , Lu Jun , Cheng Ying , Zhang Feng , Fan Xueyu , Weng Yuanyuan , Zhu Jin
Published: June 2018

For years, procalcitonin (PCT) has been employed as a diagnostic biomarker for the severity of sepsis and septic shock, as well as for guiding the application of antibiotics. However, the molecular/cellular basis for the regulation of PCT production is not fully understood. In this study, we identified the signalling pathway by which the expression of PCT was induced by lipopolysaccharide in human hepatocytes at the mRNA and protein levels. This expression was dependent on nuclear transcription factor κB (NF-κB), as indicated by a NF-κB binding site (nt −53 to −44) found in the PCT promoter region. We also showed that microRNA-513b (miR-513b) was also able to bind to the 3′-untranslated region (UTR) of the PCT promoter sequence. Meanwhile, the activation of NF-κB down-regulated the expression of miR-513b. In conclusion, we suggest that NF-κB is capable of enhancing the expression of PCT by either directly activating the transcription of the PCT gene or indirectly modulating the expression of its regulatory component, miR-513b. Our results indicate a molecular mechanism responsible for the regulation of PCT production.
Mathematical Modeling of the Function of Warburg Effect in Tumor Microenvironment
Authors: Shamsi Milad , Saghafian Mohsen , Dejam Morteza , Sanati-Nezhad Amir
Published: June 2018

Tumor cells are known for their increased glucose uptake rates even in the presence of abundant oxygen. This altered metabolic shift towards aerobic glycolysis is known as the Warburg effect. Despite an enormous number of studies conducted on the causes and consequences of this phenomenon, little is known about how the Warburg effect affects tumor growth and progression. We developed a multi-scale computational model to explore the detailed effects of glucose metabolism of cancer cells on tumorigenesis behavior in a tumor microenvironment. Despite glycolytic tumors, the growth of non-glycolytic tumor is dependent on a congruous morphology without markedly interfering with glucose and acid concentrations of the tumor microenvironment. Upregulated glucose metabolism helped to retain oxygen levels above the hypoxic limit during early tumor growth, and thus obviated the need for neo-vasculature recruitment. Importantly, simulating growth of tumors within a range of glucose uptake rates showed that there exists a spectrum of glucose uptake rates within which the tumor is most aggressive, i.e. it can exert maximal acidic stress on its microenvironment and most efficiently compete for glucose supplies. Moreover, within the same spectrum, the tumor could grow to invasive morphologies while its size did not markedly shrink.
Optimization of Culture Conditions for Enhanced Growth, Lipid and Docosahexaenoic Acid (DHA) Production of Aurantiochytrium SW1 by Response Surface Methodology
Authors: Nazir Yusuf , Shuib Shuwahida , Kalil Mohd Sahaid , Song Yuanda , Hamid Aidil Abdul
Published: June 2018

In this study, optimization of growth, lipid and DHA production of Aurantiochytrium SW1 was carried out using response surface methodology (RSM) in optimizing initial fructose concentration, agitation speed and monosodium glutamate (MSG) concentration. Central composite design was applied as the experimental design and analysis of variance (ANOVA) was used to analyze the data. ANOVA analysis revealed that the process which adequately represented by quadratic model was significant (p < 0.0001) for all the response. All the three factors were significant (p < 0.005) in influencing the biomass and lipid data while only two factors (agitation speed and MSG) gave significant effect on DHA production (p < 0.005). The estimated optimal conditions for enhanced growth, lipid and DHA production were 70 g/L fructose, 250 rpm agitation speed and 10 g/L MSG. Consequently, the quadratic model was validated by applying the estimated optimum conditions, which confirmed the model validity where 19.0 g/L biomass, 9.13 g/L lipid and 4.75 g/L of DHA were produced. The growth, lipid and DHA were 28, 36 and 35% respectively higher than that produced in the original medium prior to optimization.
Aptamer immobilization on amino-functionalized metal–organic frameworks: an ultrasensitive platform for the electrochemical diagnostic of Escherichia coli O157:H7
Authors: Shahrokhian Saeed , Ranjbar Saba
Published: June 2018

Herein, we report the development of an electrochemical biosensor for Escherichia coli O157:H7 diagnostic based on amino-functionalized metal–organic frameworks (MOFs) as a new generation of organic–inorganic hybrid nanocomposites.
A novel “signal-on” photoelectrochemical sensor for ultrasensitive detection of alkaline phosphatase activity based on a TiO2/g-C3N4heterojunction
Authors: Wang Feng Xia , Ye Cui , Mo Shi , Liao Liu Li , Zhang Xiao Fang , Ling Yu , Lu Lu , Luo Hong Qun , Li Nian Bing
Published: June 2018

A novel “signal-on” photoelectrochemical sensor for ultrasensitive detection of alkaline phosphatase activity was developed using TiO2/g-C3N4heterojunction.
Monoclonal antibody sequence assessment using a hybrid quadrupole-Orbitrap mass spectrometer
Authors: Farrell Amy , Carillo Sara , Scheffler Kai , Cook Ken , Bones Jonathan
Published: June 2018

A multi-faceted method to verify anti-IL8 monoclonal antibody protein sequence using hybrid Orbitrap mass spectrometer.
Photo-triggered release of 5-fluorouracil from a MOF drug delivery vehicle
Authors: Roth Stefaniak Kristina , Epley Charity C. , Novak Joshua J. , McAndrew Margaret L. , Cornell Hannah D. , Zhu Jie , McDaniel Dylan K. , Davis Jennifer L. , Allen Irving C. , Morris Amanda J. , Grove Tijana Z.
Published: June 2018

A nano metal–organic-framework (nanoMOF) was employed as a first-of-its kind drug delivery vehicle (DDV) for the photo-controlled release of therapeutics with simultaneous breakdown of the carrier into small molecules.
Formation mechanism of rectangular-ambulatory-plane TiO2 plates: an insight into the role of hydrofluoric acid
Authors: Zou Yajun , Gao Ge , Wang Zhenyu , Shi Jian-Wen , Wang Hongkang , Ma Dandan , Fan Zhaoyang , Chen Xin , Wang Zeyan , Niu Chunming
Published: June 2018

A novel rectangular-ambulatory-plane TiO2 plate with exposed {001} facets was developed for the first time, and its formation mechanism was well revealed.
Access to small molecule semiconductors via C–H activation for photovoltaic applications
Authors: Shome Sanchari , Singh Surya Prakhash
Published: June 2018

Reporting ruthenium carboxylate-catalysed single step oxidative cross coupling that challenges the conventional Stille and Suzuki coupling reactions, to afford BT and MFBT derivatives.
Fast, low-cost preparation of hackmanite minerals with reversible photochromic behavior using a microwave-assisted structure-conversion method
Authors: Carvalho José M. , Norrbo Isabella , Ando Rômulo A. , Brito Hermi F. , Fantini Márcia C. A. , Lastusaari Mika
Published: June 2018

A microwave-assisted structure-conversion (MASC) method was used to obtain photochromic hackmanites (M,Na)8Al6Si6O24(Cl,S)2 (M: Li, Na, and K) in a fast (12 to 20 min) one-step process.
A quantitative topological descriptor for linear co-oligomer fusion
Authors: Koskin Igor P. , Mostovich Evgeny A. , Benassi Enrico , Kazantsev Maxim S.
Published: June 2018

A purely topological descriptor allows quantitative correlation of the fusion degree with optoelectronic performance.
Direct synthesis of N-terminal thiazolidine-containing peptide thioesters from peptide hydrazides
Authors: Sato Kohei , Tanaka Shoko , Yamamoto Kazuki , Tashiro Yosuke , Narumi Tetsuo , Mase Nobuyuki
Published: June 2018

We report a simple and promising synthetic method to oxidize peptide hydrazides containing N-terminal thiazolidine as a protected cysteine.
A noncanonical amino acid-based relay system for site-specific protein labeling
Authors: Chen Yuda , Loredo Axel , Gordon Aviva , Tang Juan , Yu Chenfei , Ordonez Janett , Xiao Han
Published: June 2018

A noncanonical amino acid-based relay system spanning the biosynthesis, incorporation, and bioconjugation of p-aminophenylalanine was developed for site-specific protein labeling.
DNA-mediated anisotropic silica coating of upconversion nanoparticles
Authors: Ren Wei , Zhou Yingzhu , Wen Shihui , He Hao , Lin Gungun , Liu Deming , Jin Dayong
Published: June 2018

We report a facile approach of using DNA molecules as switches to selectively activate silica coating onto specific facets of upconversion nanoparticles.
Temperature-dependent insertion and adsorption of lithium on spinel Li4Ti5O12(111) thin films – an angle-resolved XPS study
Authors: Kim Jihyun , Buchner Florian , Behm R. Jürgen
Published: June 2018

Aiming at a detailed understanding of the Li adsorption and insertion behavior on/into lithium titanate (Li4Ti5O12, LTO), which is a promising anode material in Li-ion batteries, we have investigated the interaction of vapor deposited Li with LTO in the temperature range between 80 K and room temperature by ARXPS.
How low-resolution structural data predict the conformational changes of a protein: a study on data-driven molecular dynamics simulations
Authors: Harada Ryuhei , Shigeta Yasuteru
Published: June 2018

Parallel cascade selection molecular dynamics (PaCS-MD) is a conformational sampling method for generating transition pathways between a given reactant and a product.
Oxyhydroxide of metallic nanowires in a molecular H2O and H2O2 environment and their effects on mechanical properties
Authors: Aral Gurcan , Islam Md Mahbubul , Wang Yun-Jiang , Ogata Shigenobu , Duin Adri C. T. van
Published: June 2018

To avoid unexpected environmental mechanical failure, there is a strong need to fully understand the details of the oxidation process and intrinsic mechanical properties of reactive metallic iron (Fe) nanowires (NWs) under various aqueous reactive environmental conditions.
Superaerophobic P-doped Ni(OH)2/NiMoO4 hierarchical nanosheet arrays grown on Ni foam for electrocatalytic overall water splitting
Authors: Xi Wenguang , Yan Gang , Tan Huaqiao , Xiao Liguang , Cheng Sihang , Khan Shifa Ullah , Wang Yonghui , Li Yangguang
Published: June 2018

Low-cost and durable P-doped Ni(OH)2/NiMoO4 hierarchical nanosheet arrays grown on Ni foam have been explored as an integrated electrocatalyst towards overall water splitting with high efficiencies.
A vapochromic strategy for ammonia sensing based on a bipyridinium constructed porous framework
Authors: Chen Cheng , Rao Huizhen , Lin Shen , Zhang Jie
Published: June 2018

A vapochromic strategy has been developed for ammonia sensing through the competitive complexation of ammonia and an enhanced charge transfer effect.
Reversible Fe(ii) uptake/release by magnetite nanoparticles
Authors: Peng Huan , Pearce Carolyn I. , Huang Weifeng , Zhu Zhenli , N'Diaye Alpha T. , Rosso Kevin M. , Liu Juan
Published: June 2018

The reversible flow of Fe(ii) across the magnetite–solution interface impacts the stoichiometry and reactivity of magnetite nanoparticles.
Bifidobacteria attenuate the development of metabolic disorders, with inter- and intra-species differences
Authors: Zhu Guangsu , Ma Fangli , Wang Gang , Wang Yuanyuan , Zhao Jianxin , Zhang Hao , Chen Wei
Published: June 2018

Supplementation with specific Bifidobacterium strains will attenuate some hallmark parameters of metabolic syndrome in high-fat–high-sucrose treated rats, elevate the levels of SCFAs in gut and change the gut microbiota composition beneficially.