bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Robust Method for Inferring Network Structures
Authors: Yang Yang , Luo Tingjin , Li Zhoujun , Zhang Xiaoming , Yu Philip S. 
Published: July 2017

AbstractInferring the network structure from limited observable data is significant in molecular biology, communication and many other areas. It is challenging, primarily because the observable data are sparse, finite and noisy. The development of machine learning and network structure study provides a great chance to solve the problem. In this paper, we propose an iterative smoothing algorithm with structure sparsity (ISSS) method. The elastic penalty in the model is introduced for the sparse solution, identifying group features and avoiding over-fitting, and the total variation (TV) penalty in the model can effectively utilize the structure information to identify the neighborhood of the vertices. Due to the non-smoothness of the elastic and structural TV penalties, an efficient algorithm with the Nesterov’s smoothing optimization technique is proposed to solve the non-smooth problem. The experimental results on both synthetic and real-world networks show that the proposed model is robust against insufficient data and high noise. In addition, we investigate many factors that play important roles in identifying the performance of ISSS.
A New Paradigm for Understanding and Enhancing the Critical Heat Flux (CHF) Limit
Authors: Fazeli Abdolreza , Moghaddam Saeed 
Published: July 2017

AbstractNearly a century of research on enhancing critical heat flux (CHF) has focused on altering the boiling surface properties such as its nucleation site density, wettability, wickability and heat transfer area. But, a mechanism to manipulate dynamics of the vapor and liquid interactions above the boiling surface as a means of enhancing CHF has not been proposed. Here, a new approach is implemented to limit the vapor phase lateral expansion over the heat transfer surface and actively control the surface wetted area fraction, known to decline monotonically with increasing heat flux. This new degree of freedom has enabled reaching unprecedented CHF levels and revealed new details about the physics of CHF. The impact of wickability, effective heat transfer area, and liquid pressure on CHF is precisely quantified. Test results show that, when rewetting is facilitated, the CHF increases linearly with the effective surface heat transfer area. A maximum CHF of 1.8 kW/cm2 was achieved on a copper structure with the highest surface area among all tested surfaces. A model developed based on the experimental data suggests that the thermal conductivity of the surface structures ultimately limits the CHF; and a maximum CHF of 7–8 kW/cm2 may be achieved using diamond surface structures.
Lybatides from Lycium barbarum Contain An Unusual Cystine-stapled Helical Peptide Scaffold
Authors: Tan Wei Liang , Wong Ka H. , Lei Jian , Sakai Naoki , Tan Hong Wei , Hilgenfeld Rolf , Tam James P. 
Published: July 2017

AbstractCysteine-rich peptides (CRPs) of 2–6 kDa are generally thermally and proteolytically stable because of their multiple cross-bracing disulfide bonds. Here, we report the discovery and characterization of two novel cystine-stapled CRPs, designated lybatide 1 and 2 (lyba1 and lyba2), from the cortex of Lycium barbarum root. Lybatides, 32 to 33 amino acids in length, are hyperstable and display a novel disulfide connectivity with a cysteine motif of C-C-C-C-CC-CC which contains two pairs of adjacent cysteines (-CC-CC). X-ray structure analysis revealed the presence of a single cystine-stabilized (α + π)-helix in lyba2, a rare feature of CRPs. Together, our results suggest that lybatides, one of the smallest four-disulfide-constrained plant CRPs, is a new family of CRPs. Additionally, this study provides new insights into the molecular diversity of plant cysteine-rich peptides and the unusual lybatide scaffold could be developed as a useful template for peptide engineering and therapeutic development.
The lncRNA MALAT1 acts as a competing endogenous RNA to regulate KRAS expression by sponging miR-217 in pancreatic ductal adenocarcinoma
Authors: Liu Pingping , Yang Haiyan , Zhang Jing , Peng Xiaozhong , Lu Zhaohui , Tong Weimin , Chen Jie 
Published: July 2017

AbstractThe long noncoding RNA (lncRNA) metastasis-associated lung adenocarcinoma transcript-1 (MALAT1) has been shown to play an important role in tumourigenesis. The aim of this study was to investigate the role of MALAT1 in pancreatic ductal adenocarcinoma. MALAT1 is expressed at higher levels in pancreatic ductal adenocarcinoma (PDAC) tissues than in nontumour tissues and in metastatic PDAC than in localized tumours. Patients with PDAC and high MALAT1 expression levels have shorter overall survival than patients with PDAC and low MALAT1 expression levels. Knocking down MALAT1 reduces pancreatic tumour cell growth and proliferation both in vitro and in vivo. Moreover, MALAT1 knockdown inhibits cell cycle progression and impairs tumour cell migration and invasion. We found that miR-217 can bind MALAT1 and regulate its expression in PDAC cell lines. We also found MALAT1 knockdown attenuates the protein expression of KRAS, a known target of miR-217. After MALAT1 knockdown, KRAS protein expression levels can be rescued through inhibition of miR-217 expression. More importantly, MALAT1 knockdown does not directly affect cellular miR-217 expression but decreases the miR-217 nucleus/cytoplasm ratio, suggesting that MALAT1 inhibits the translocation of miR-217 from the nucleus to the cytoplasm.
The behavioral and neural basis of empathic blame
Authors: Patil Indrajeet , Calò Marta , Fornasier Federico , Cushman Fiery , Silani Giorgia 
Published: July 2017

AbstractMature moral judgments rely both on a perpetrator’s intent to cause harm, and also on the actual harm caused–even when unintended. Much prior research asks how intent information is represented neurally, but little asks how even unintended harms influence judgment. We interrogate the psychological and neural basis of this process, focusing especially on the role of empathy for the victim of a harmful act. Using fMRI, we found that the ‘empathy for pain’ network was involved in encoding harmful outcomes and integrating harmfulness information for different types of moral judgments, and individual differences in the extent to which this network was active during encoding and integration of harmfulness information determined severity of moral judgments. Additionally, activity in the network was down-regulated for acceptability, but not blame, judgments for accidental harm condition, suggesting that these two types of moral evaluations are neurobiologically dissociable. These results support a model of “empathic blame”, whereby the perceived suffering of a victim colors moral judgment of an accidental harmdoer.
Inhibition of β-Glucocerebrosidase Activity Preserves Motor Unit Integrity in a Mouse Model of Amyotrophic Lateral Sclerosis
Authors: Henriques Alexandre , Huebecker Mylene , Blasco Hélène , Keime Céline , Andres Christian R. , Corcia Philippe , Priestman David A. , Platt Frances M. , Spedding Michael , Loeffler Jean-Philippe 
Published: July 2017

AbstractRecent metabolomic reports connect dysregulation of glycosphingolipids, particularly ceramide and glucosylceramide, to neurodegeneration and to motor unit dismantling in amyotrophic lateral sclerosis at late disease stage. We report here altered levels of gangliosides in the cerebrospinal fluid of amyotrophic lateral sclerosis patients in early disease stage. Conduritol B epoxide is an inhibitor of acid beta-glucosidase, and lowers glucosylceramide degradation. Glucosylceramide is the precursor for all of the more complex glycosphingolipids. In SOD1G86R mice, an animal model of amyotrophic lateral sclerosis, conduritol B epoxide preserved ganglioside distribution at the neuromuscular junction, delayed disease onset, improved motor function and preserved motor neurons as well as neuromuscular junctions from degeneration. Conduritol B epoxide mitigated gene dysregulation in the spinal cord and restored the expression of genes involved in signal transduction and axonal elongation. Inhibition of acid beta-glucosidase promoted faster axonal elongation in an in vitro model of neuromuscular junctions and hastened recovery after peripheral nerve injury in wild type mice. Here, we provide evidence that glycosphingolipids play an important role in muscle innervation, which degenerates in amyotrophic lateral sclerosis from the early disease stage. This is a first proof of concept study showing that modulating the catabolism of glucosylceramide may be a therapeutic target for this devastating disease.
Membrane progesterone receptor beta (mPRβ/Paqr8) promotes progesterone-dependent neurite outgrowth in PC12 neuronal cells via non-G protein-coupled receptor (GPCR) signaling
Authors: Kasubuchi Mayu , Watanabe Keita , Hirano Kanako , Inoue Daisuke , Li Xuan , Terasawa Kazuya , Konishi Morichika , Itoh Nobuyuki , Kimura Ikuo 
Published: July 2017

AbstractRecently, sex steroid membrane receptors garnered world-wide attention because they may be related to sex hormone-mediated unknown rapid non-genomic action that cannot be currently explained by their genomic action via nuclear receptors. Progesterone affects cell proliferation and survival via non-genomic effects. In this process, membrane progesterone receptors (mPRα, mPRβ, mPRγ, mPRδ, and mPRε) were identified as putative G protein-coupled receptors (GPCRs) for progesterone. However, the structure, intracellular signaling, and physiological functions of these progesterone receptors are still unclear. Here, we identify a molecular mechanism by which progesterone promotes neurite outgrowth through mPRβ (Paqr8) activation. Mouse mPRβ mRNA was specifically expressed in the central nervous system. It has an incomplete GPCR topology, presenting 6 transmembrane domains and did not exhibit typical GPCR signaling. Progesterone-dependent neurite outgrowth was exhibited by the promotion of ERK phosphorylation via mPRβ, but not via other progesterone receptors such as progesterone membrane receptor 1 (PGRMC-1) and nuclear progesterone receptor in nerve growth factor-induced neuronal PC12 cells. These findings provide new insights of regarding the non-genomic action of progesterone in the central nervous system.
Microbiota composition of the koala (Phascolarctos cinereus) ocular and urogenital sites, and their association with Chlamydia infection and disease
Authors: Vidgen Miranda E. , Hanger Jonathan , Timms Peter 
Published: July 2017

AbstractDisease caused by Chlamydia pecorum is characterised by ocular and urogenital infections that can lead to blindness and infertility in koalas. However, koalas that are infected with C. pecorum do not always progress to disease. In other host systems, the influence of the microbiota has been implicated in either accelerating or preventing infections progressing to disease. This study investigates the contribution of koala urogenital and ocular microbiota to Chlamydia infection and disease in a free ranging koala population. Using univariate and multivariate analysis, it was found that reproductive status in females and sexual maturation in males, were defining features in the koala urogenital microbiota. Changes in the urogenital microbiota of koalas is correlated with infection by the common pathogen, C. pecorum. The correlation of microbiota composition and C. pecorum infection is suggestive of members of the microbiota being involved in the acceleration or prevention of infections progressing to disease. The analysis also suggests that multiple microbes are likely to be associated with this process of disease progression, rather than a single organism. While other Chlamydia-like organisms were also detected, they are unlikely to contribute to chlamydial disease as they are rare members of the urogenital and ocular microbiota communities.
Anti-cancerous effect of albumin coated silver nanoparticles on MDA-MB 231 human breast cancer cell line
Authors: Azizi Marzieh , Ghourchian Hedayatoallah , Yazdian Fatemeh , Bagherifam Shahla , Bekhradnia Sara , Nyström Bo 
Published: July 2017

AbstractWith the aim of making specific targeting of silver nanoparticles as a drug for tumor cells and developing new anticancer agents, a novel nano-composite was developed. Albumin coated silver nanoparticles (ASNPs) were synthesized, and their anti-cancerous effects were evaluated against MDA-MB 231, a human breast cancer cell line. The synthesized ASNPs were characterized by spectroscopic methods. The morphological changes of the cells were observed by inverted, florescent microscopy and also by DNA ladder pattern on gel electrophoresis; the results revealed that the cell death process occurred through the apoptosis mechanism. It was found that ASNPs with a size of 90 nm and negatively charged with a zeta-potential of about −20 mV could be specifically taken up by tumor cells. The LD50 of ASNPs against MDA-MB 231 (5 μM), was found to be 30 times higher than that for white normal blood cells (152 μM). The characteristics of the synthesized ASNPs included; intact structure of coated albumin, higher cytotoxicity against cancer cells than over normal cells, and cell death based on apoptosis and reduction of gland tumor sizes in mice. This work indicates that ASNPs could be a good candidate for chemotherapeutic drug.
Costly neighbours: Heterospecific competitive interactions increase metabolic rates in dominant species
Authors: Janča Matouš , Gvoždík Lumír 
Published: July 2017

AbstractThe energy costs of self-maintenance (standard metabolic rate, SMR) vary substantially among individuals within a population. Despite the importance of SMR for understanding life history strategies, ecological sources of SMR variation remain only partially understood. Stress-mediated increases in SMR are common in subordinate individuals within a population, while the direction and magnitude of the SMR shift induced by interspecific competitive interactions is largely unknown. Using laboratory experiments, we examined the influence of con- and heterospecific pairing on SMR, spontaneous activity, and somatic growth rates in the sympatrically living juvenile newts Ichthyosaura alpestris and Lissotriton vulgaris. The experimental pairing had little influence on SMR and growth rates in the smaller species, L. vulgaris. Individuals exposed to con- and heterospecific interactions were more active than individually reared newts. In the larger species, I. alpestris, heterospecific interactions induced SMR to increase beyond values of individually reared counterparts. Individuals from heterospecific pairs and larger conspecifics grew faster than did newts in other groups. The plastic shift in SMR was independent of the variation in growth rate and activity level. These results reveal a new source of individual SMR variation and potential costs of co-occurrence in ecologically similar taxa.
The cancer-associated cell migration protein TSPAN1 is under control of androgens and its upregulation increases prostate cancer cell migration
Authors: Munkley Jennifer , McClurg Urszula L. , Livermore Karen E. , Ehrmann Ingrid , Knight Bridget , Mccullagh Paul , Mcgrath John , Crundwell Malcolm , Harries Lorna W. , Leung Hing Y. , Mills Ian G. , Robson Craig N. , Rajan Prabhakar , Elliott David J. 
Published: July 2017

AbstractCell migration drives cell invasion and metastatic progression in prostate cancer and is a major cause of mortality and morbidity. However the mechanisms driving cell migration in prostate cancer patients are not fully understood. We previously identified the cancer-associated cell migration protein Tetraspanin 1 (TSPAN1) as a clinically relevant androgen regulated target in prostate cancer. Here we find that TSPAN1 is acutely induced by androgens, and is significantly upregulated in prostate cancer relative to both normal prostate tissue and benign prostate hyperplasia (BPH). We also show for the first time, that TSPAN1 expression in prostate cancer cells controls the expression of key proteins involved in cell migration. Stable upregulation of TSPAN1 in both DU145 and PC3 cells significantly increased cell migration and induced the expression of the mesenchymal markers SLUG and ARF6. Our data suggest TSPAN1 is an androgen-driven contributor to cell survival and motility in prostate cancer.
Circulating primitive erythroblasts establish a functional, protein 4.1R-dependent cytoskeletal network prior to enucleating
Authors: Huang Yu-Shan , Delgadillo Luis F. , Cyr Kathryn H. , Kingsley Paul D. , An Xiuli , McGrath Kathleen E. , Mohandas Narla , Conboy John G. , Waugh Richard E. , Wan Jiandi , Palis James 
Published: July 2017

AbstractHematopoietic ontogeny is characterized by distinct primitive and definitive erythroid lineages. Definitive erythroblasts mature and enucleate extravascularly and form a unique membrane skeleton, composed of spectrin, 4.1R-complex, and ankyrinR-complex components, to survive the vicissitudes of the adult circulation. However, little is known about the formation and composition of the membrane skeleton in primitive erythroblasts, which progressively mature while circulating in the embryonic bloodstream. We found that primary primitive erythroblasts express the major membrane skeleton genes present in similarly staged definitive erythroblasts, suggesting that the composition and formation of this membrane network is conserved in maturing primitive and definitive erythroblasts despite their respective intravascular and extravascular locations. Membrane deformability and stability of primitive erythroblasts, assayed by microfluidic studies and fluorescence imaged microdeformation, respectively, significantly increase prior to enucleation. These functional changes coincide with protein 4.1 R isoform switching and protein 4.1R-null primitive erythroblasts fail to establish normal membrane stability and deformability. We conclude that maturing primitive erythroblasts initially navigate the embryonic vasculature prior to establishing a deformable cytoskeleton, which is ultimately formed prior to enucleation. Formation of an erythroid-specific, protein 4.1R-dependent membrane skeleton is an important feature not only of definitive, but also of primitive, erythropoiesis in mammals.
Secretome of in vitro cultured human embryos contains extracellular vesicles that are uptaken by the maternal side
Authors: Giacomini Elisa , Vago Riccardo , Sanchez Ana Maria , Podini Paola , Zarovni Natasa , Murdica Valentina , Rizzo Roberta , Bortolotti Daria , Candiani Massimo , Viganò Paola 
Published: July 2017

AbstractCommunication between embryo and maternal endometrium occurs during a specific time frame in which implantation is possible. Here we demonstrate for the first time that conditioned media from non-manipulated human embryos cultured in vitro for 3 days or up to the blastocyst stage contain extracellular vesicles (EVs) with a diameter of 50 to 200 nm and bearing the traditional microvesicle and exosome marker proteins CD63, CD9 and ALIX. The embryonic origin of these EVs has been confirmed by the presence of stemness gene transcripts and their enrichment in the non-classical HLA-G protein. NANOG and POU5F1 transcripts were shown to be contained in vesicles deriving from embryos at different stages of development. In line with a higher detection rate of the HLA-G protein in blastocysts compared to cleavage stage embryos, a significantly higher amount of HLA-G was found in vesicles accumulated in spent media from day 3 to day 5 of development compared to those isolated from the earlier stage. Uptake of dye-labeled embryo-derived EVs by human primary endometrial epithelial and stromal cells was also demonstrated with a fluorescence intensity signal significantly higher for cells treated with vesicles derived from blastocysts. Based on these findings, EV exchange may be suggested as an emerging way of communication at the maternal-fetal interface.
Prospective Study on Association of Prostatic Calcifications with Clinical Symptoms and Results of Treatment in Men with type III prostatitis
Authors: Fei Xiang , Jin Wei , Hua Shengyu , Song Yan 
Published: July 2017

AbstractThe purpose is to investigate the clinical significance of prostatic calculi in patients with chronic prostatitis and to discuss the possible treatment.The data from 277 young males with CP/CPPS were analyzed prospectively. Symptom severity was measured using the National Institutes of Health Chronic Prostatitis Symptom Index (NIH-CPSI) and the International Prostatic Symptoms Score (IPSS). Sexual function was assessed by the International Index of Erectile Function (IIEF-5) questionnaire. After four weeks of therapy, the NIH-CPSI, IPSS, and IIEF-5 tests were repeated. The variables were compared between patients with and without prostatic calcifications using the Students t-test or chi-square test. No significant differences were found between CP/CPPS patients with and without prostatic calcifications regarding age, body mass index, prostate volume, CPSI, IPSS and IIEF-5. Men with calcifications endured symptoms significantly longer (37.9 ± 25.2 versus 19.0 ± 16.4 months, P < 0.01), and had significantly higher white blood cell counts per high power field in expressed prostatic secretions (7.7 ± 12.8 versus 3.9 ± 4.7; P < 0.01), than patients without prostatic calcifications, who responded better to medication compared with patients with prostatic calcifications. In conclusion, patients with calcifications were more likely to have category IIIA disease and they required a longer medication period.
Different Repeat Annual Influenza Vaccinations Improve the Antibody Response to Drifted Influenza Strains
Authors: Plant Ewan P. , Fredell Lucy J. , Hatcher Blake A. , Li Xing , Chiang Meng-Jung , Kosikova Martina , Xie Hang , Zoueva Olga , Cost Angelia A. , Ye Zhiping , Cooper Michael J. 
Published: July 2017

AbstractSeasonal influenza vaccine formulas change almost every year yet information about how this affects the antibody repertoire of vaccine recipients is inadequate. New vaccine virus strains are selected, replacing older strains to better match the currently circulating strains. But even while the vaccine is being manufactured the circulating strains can evolve. The ideal response to a seasonal vaccine would maintain antibodies toward existing strains that might continue to circulate, and to generate cross-reactive antibodies, particularly towards conserved influenza epitopes, potentially limiting infections caused by newly evolving strains. Here we use the hemagglutination inhibition assay to analyze the antibody repertoire in subjects vaccinated two years in a row with either identical vaccine virus strains or with differing vaccine virus strains. The data indicates that changing the vaccine formulation results in an antibody repertoire that is better able to react with strains emerging after the vaccine virus strains are selected. The effect is observed for both influenza A and B strains in groups of subjects vaccinated in three different seasons. Analyses include stratification by age and sex.
Recycling and Self-Healing of Polybenzoxazines with Dynamic Sulfide Linkages
Authors: Arslan Mustafa , Kiskan Baris , Yagci Yusuf 
Published: July 2017

AbstractIn this work, a recycling and self-healing strategy for polybenzoxazines through both S–S bond cleavage-reformation reaction and supramolecular attractions is described. Both recyclable and self-healable polybenzoxazines can be prepared from low cost chemicals with a simple procedure in only 30 minutes. For this purpose, inverse vulcanization of poly(propylene oxide)benzoxazine (PPOB) and diallybenzoxazine (B-al) with elemental sulfur was performed at 185 °C. The obtained cross-linked polymer films exhibited thermally driven recycling ability up to 5 cycles. Moreover, the self-healing ability of a test specimen was shown. Spectral characterizations, thermal stability and fracture toughness of the films were investigated after each recycling.