bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ecobody technology: rapid monoclonal antibody screening method from single B cells using cell-free protein synthesis for antigen-binding fragment formation
Authors: Ojima-Kato Teruyo , Nagai Satomi , Nakano Hideo 
Published: October 2017

AbstractWe report a rapid and cost-effective monoclonal antibody screening method from single animal B cells using reverse transcription (RT)-PCR and Escherichia coli cell-free protein synthesis (CFPS), which allows evaluation of antibodies within 2 working days. This process is named “Ecobody technology”. The method includes strategies to isolate B cells that specifically bind an antigen from the peripheral blood of immunised animals, and single-cell RT-PCR to generate DNA fragments of the VH and VL genes, followed by CFPS for production of fragments of antigen binding (Fab). In the CFPS step, we employed our techniques: 1) ‘Zipbody’ as a method for producing Fab, in which the association of heavy and light chains is facilitated by adhesive leucine zipper peptides fused at the C-termini of the Fab; and 2) an N-terminal SKIK peptide tag that can increase protein expression levels. Using Ecobody technology, we obtained highly-specific monoclonal antibodies for the antigens Vibrio parahaemolyticus and E. coli O26. The anti-V. parahaemolyticus Zipbody mAb was further produced in E. coli strain SHuffle T7 Express in inclusion bodies and refolded by a conventional method, resulting in significant antigen-binding activity (KD = 469 pM) and productivity of 8.5 mg purified antibody/L-culture.
Active Immunization Against hIAPP Oligomers Ameliorates the Diabetes- Associated Phenotype in a Transgenic Mice Model
Authors: Bram Yaron , Peled Sivan , Brahmachari Sayanti , Harlev Michael , Gazit Ehud 
Published: October 2017

AbstractType 2 diabetes is characterized by insulin tolerance in target cells followed by a reduction of pancreatic β-cell mass. Islet amyloid polypeptide oligomeric assemblies were shown to contribute to β-cell apoptosis by forming discrete pores that destabilize the cellular membrane. We previously characterized α-helical cytotoxic islet amyloid polypeptide oligomers which interact with cell membranes, following a complete internalization that leads to cellular apoptosis. Moreover, antibodies which bind the oligomers and neutralize the cytotoxicity were exclusively identified in the serum of type 2 diabetes patients. Here, we examined the usage of the newly characterized oligomers as an active immunization agent targeting amyloid self- assembly in a diabetes-associated phenotype transgenic mice model. Immunized transgenic mice showed an increase in hIAPP-antibody serum titer as well as improvement in diabetes-associated parameters. Lower fasting blood glucose levels, higher insulin, and lower islet amyloid polypeptide accumulation were observed. Furthermore, antibodies derived from the immunized mice reduced hIAPP oligomers cytotoxicity towards β-cells in a dose-dependent manner. This study highlights the significance of targeting the early amyloid self-assembly events for potential disease management. Furthermore, it demonstrates that α-helical oligomers conformers are valid epitope for the development of future immunization therapy.
Remodeling of the Streptococcus mutans proteome in response to LrgAB and external stresses
Authors: Ahn Sang-Joon , Gu Tongjun , Koh Jin , Rice Kelly C. 
Published: October 2017

AbstractThe Streptococcus mutans Cid/Lrg system represents an ideal model to study how this organism withstands various stressors encountered in the oral cavity. Mutation of lrgAB renders S. mutans more sensitive to oxidative, heat, and vancomycin stresses. Here, we have performed a comprehensive proteomics experiment using label-free quantitative mass spectrometry to compare the proteome changes of wild type UA159 and lrgAB mutant strains in response to these same stresses. Importantly, many of identified proteins showed either a strikingly large fold-change, or were completely suppressed or newly induced in response to a particular stress condition. Notable stress proteome changes occurred in a variety of functional categories, including amino acid biosynthesis, energy metabolism, protein synthesis, transport/binding, and transcriptional/response regulators. In the non-stressed growth condition, mutation of lrgAB significantly altered the abundance of 76 proteins (a fold change >1.4, or <0.6, p-value <0.05) and several of these matched the stress proteome of the wild type strain. Interestingly, the statistical correlation between the proteome changes and corresponding RNA-seq transcriptomic studies was relatively low (rho(ρ) <0.16), suggesting that adaptation to a new environment may require radical proteome turnover or metabolic remodeling. Collectively, this study reinforces the importance of LrgAB to the S. mutans stress response.
Controlled Self-assembly of Stem Cell Aggregates Instructs Pluripotency and Lineage Bias
Authors: Xie Angela W. , Binder Bernard Y. K. , Khalil Andrew S. , Schmitt Samantha K. , Johnson Hunter J. , Zacharias Nicholas A. , Murphy William L. 
Published: October 2017

AbstractStem cell-derived organoids and other 3D microtissues offer enormous potential as models for drug screening, disease modeling, and regenerative medicine. Formation of stem/progenitor cell aggregates is common in biomanufacturing processes and critical to many organoid approaches. However, reproducibility of current protocols is limited by reliance on poorly controlled processes (e.g., spontaneous aggregation). Little is known about the effects of aggregation parameters on cell behavior, which may have implications for the production of cell aggregates and organoids. Here we introduce a bioengineered platform of labile substrate arrays that enable simple, scalable generation of cell aggregates via a controllable 2D-to-3D “self-assembly”. As a proof-of-concept, we show that labile substrates generate size- and shape-controlled embryoid bodies (EBs) and can be easily modified to control EB self-assembly kinetics. We show that aggregation method instructs EB lineage bias, with faster aggregation promoting pluripotency loss and ectoderm, and slower aggregation favoring mesoderm and endoderm. We also find that aggregation kinetics of EBs markedly influence EB structure, with slower kinetics resulting in increased EB porosity and growth factor signaling. Our findings suggest that controlling internal structure of cell aggregates by modifying aggregation kinetics is a potential strategy for improving 3D microtissue models for research and translational applications.
Baf53a is involved in survival of mouse ES cells, which can be compensated by Baf53b
Authors: Zhu Bo , Ueda Atsushi , Song Xiaohong , Horike Shin-ichi , Yokota Takashi , Akagi Tadayuki 
Published: October 2017

AbstractThe human Baf (Brg1/Brm associated factor) complex, also known as the mammalian SWI/SNF chromatin-remodeling complex, is involved in a variety of cellular processes. The pluripotency and self-renewal abilities are major characteristics of embryonic stem (ES) cells and are regulated by the ES cell-specific BAF (esBAF) complex. Baf53a is one of the subunits of the esBAF complex. Here, we found that Baf53a was expressed in undifferentiated ES cells and that it interacted with Oct3/4. Analyses of tetracycline-inducible Baf53a conditional knockout ES cells revealed that the undifferentiated markers, including Nanog and Oct3/4, were expressed in Baf53a-deficient ES cells; however, growth of the cells was repressed, and expression of p53, p21, and cleaved Caspase 3 was increased. Cell death of Baf53a-deficient ES cells was rescued by overexpression of Baf53a, but not by the Baf53a M3 mutant (E388A/R389A/R390A). Interestingly, Baf53b, a homologue of Baf53a, rescued cell death of Baf53a-deficient ES cells. Baf53a-deficient ES cells overexpressing exogenous Baf53a or Baf53b remained in the undifferentiated state, proliferated, and repressed expression of p21. In summary, our findings suggest that Baf53a is involved in the survival of ES cells by regulating p53 and Caspase3, and that Baf53b is able to compensate for this functional aspect of Baf53a.
Plasmonic nanohole array for enhancing the SERS signal of a single layer of graphene in water
Authors: Mahigir Amirreza , Chang Te-Wei , Behnam Ashkan , Liu Gang Logan , Gartia Manas Ranjan , Veronis Georgios 
Published: October 2017

AbstractWe numerically design and experimentally test a SERS-active substrate for enhancing the SERS signal of a single layer of graphene (SLG) in water. The SLG is placed on top of an array of silver-covered nanoholes in a polymer and is covered with water. Here we report a large enhancement of up to 2 × 105 in the SERS signal of the SLG on the patterned plasmonic nanostructure for a 532 nm excitation laser wavelength. We provide a detailed study of the light-graphene interactions by investigating the optical absorption in the SLG, the density of optical states at the location of the SLG, and the extraction efficiency of the SERS signal of the SLG. Our numerical calculations of both the excitation field and the emission rate enhancements support the experimental results. We find that the enhancement is due to the increase in the confinement of electromagnetic fields on the location of the SLG that results in enhanced light absorption in the graphene at the excitation wavelength. We also find that water droplets increase the density of optical radiative states at the location of the SLG, leading to enhanced spontaneous emission rate of graphene at its Raman emission wavelengths.
Optical properties, spectral, and lifetime measurements of central nervous system tumors in humans
Authors: Poulon F. , Mehidine H. , Juchaux M. , Varlet P. , Devaux B. , Pallud J. , Abi Haidar D. 
Published: October 2017

AbstractA key challenge of central nervous system tumor surgery is to discriminate between brain regions infiltrated by tumor cells and surrounding healthy tissue. Although monitoring of autofluorescence could potentially be an efficient way to provide reliable information for these regions, we found little information on this subject, and thus we conducted studies of brain tissue optical properties. This particular study focuses on the different optical quantitative responses of human central nervous system tumors and their corresponding controls. Measurements were performed on different fixed human tumoral and healthy brain samples. Four groups of central nervous system tumors (glioblastoma, diffuse glioma, meningioma and metastasis) were discriminated from healthy brain and meninx control tissues. A threshold value was found for the scattering and absorption coefficient between tumoral and healthy groups. Emission Spectra of healthy tissue had a significant higher intensity than tumoral groups. The redox and optical index ratio were thenn calculated and these also showed significant discrimination. Two fluorescent molecules, NADH and porphyrins, showed distinct lifetim values among the different groups of samples. This study defines several optical indexes that can act as combinated indicators to discriminate healthy from tumoral tissues.
A numerical analysis of a magnetocaloric refrigerator with a 16-layer regenerator
Authors: Zhang Mingkan , Abdelaziz Omar , Momen Ayyoub M. , Abu-Heiba Ahmad 
Published: October 2017

AbstractA numerical analysis was conducted to study a room temperature magnetocaloric refrigerator with a 16-layer parallel plates active magnetic regenerator (AMR). Sixteen layers of LaFeMnSiH having different Curie temperatures were employed as magnetocaloric material (MCM) in the regenerator. Measured properties data was used. A transient one dimensional (1D) model was employed, in which a unique numerical method was developed to significantly accelerate the simulation speed of the multi-layer AMR system. As a result, the computation speed of a multi-layer AMR case was very close to the single-layer configuration. The performance of the 16-layer AMR system in different frequencies and utilizations has been investigated using this model. To optimize the layer length distribution of the 16-layer MCMs in the regenerator, a set of 137 simulations with different MCM distributions based on the Design of Experiments (DoE) method was conducted and the results were analyzed. The results show that the 16-layer AMR system can operate up to 84% of Carnot cycle COP at a temperature span of 41 K, which cannot be obtained using an AMR with fewer layers. The DoE results indicate that for a 16-layer AMR system, the uniform distribution is very close to the optimized design.
Implementation of cascade logic gates and majority logic gate on a simple and universal molecular platform
Authors: Gao Jinting , Liu Yaqing , Lin Xiaodong , Deng Jiankang , Yin Jinjin , Wang Shuo 
Published: October 2017

AbstractWiring a series of simple logic gates to process complex data is significantly important and a large challenge for untraditional molecular computing systems. The programmable property of DNA endows its powerful application in molecular computing. In our investigation, it was found that DNA exhibits excellent peroxidase-like activity in a colorimetric system of TMB/H2O2/Hemin (TMB, 3,3′, 5,5′-Tetramethylbenzidine) in the presence of K+ and Cu2+, which is significantly inhibited by the addition of an antioxidant. According to the modulated catalytic activity of this DNA-based catalyst, three cascade logic gates including AND-OR-INH (INHIBIT), AND-INH and OR-INH were successfully constructed. Interestingly, by only modulating the concentration of Cu2+, a majority logic gate with a single-vote veto function was realized following the same threshold value as that of the cascade logic gates. The strategy is quite straightforward and versatile and provides an instructive method for constructing multiple logic gates on a simple platform to implement complex molecular computing.
Realization of Rectangular Artificial Spin Ice and Direct Observation of High Energy Topology
Authors: Ribeiro I. R. B. , Nascimento F. S. , Ferreira S. O. , Moura-Melo W. A. , Costa C. A. R. , Borme J. , Freitas P. P. , Wysin G. M. , de Araujo C. I. L. , Pereira A. R. 
Published: October 2017

AbstractIn this work, we have constructed and experimentally investigated frustrated arrays of dipoles forming two-dimensional artificial spin ices with different lattice parameters (rectangular arrays with horizontal and vertical lattice spacings denoted by a and b respectively). Arrays with three different aspect ratios γ = a/b = $$\sqrt{{\bf{2}}}$$

2

, $$\sqrt{{\bf{3}}}$$

3

and $$\sqrt{{\bf{4}}}$$

4

are studied. Theoretical calculations of low-energy demagnetized configurations for these same parameters are also presented. Experimental data for demagnetized samples confirm most of the theoretical results. However, the highest energy topology (doubly-charged monopoles) does not emerge in our theoretical model, while they are seen in experiments for large enough γ. Our results also insinuate that the string tension connecting two magnetic monopoles in a pair vanishes in rectangular lattices with a critical ratio γ = γ
c
= $$\sqrt{{\bf{3}}}$$

3

, supporting previous theoretical predictions.
The neural representation of human versus nonhuman bipeds and quadrupeds
Authors: Papeo Liuba , Wurm Moritz F. , Oosterhof Nikolaas N. , Caramazza Alfonso 
Published: October 2017

AbstractHow do humans recognize humans among other creatures? Recent studies suggest that a preference for conspecifics may emerge already in perceptual processing, in regions such as the right posterior superior temporal sulcus (pSTS), implicated in visual perception of biological motion. In the current functional MRI study, participants viewed point-light displays of human and nonhuman creatures moving in their typical bipedal (man and chicken) or quadrupedal mode (crawling-baby and cat). Stronger activity for man and chicken versus baby and cat was found in the right pSTS responsive to biological motion. The novel effect of pedalism suggests that, if right pSTS contributes to recognizing of conspecifics, it does so by detecting perceptual features (e.g. bipedal motion) that reliably correlate with their appearance. A searchlight multivariate pattern analysis could decode humans and nonhumans across pedalism in the left pSTS and bilateral posterior cingulate cortex. This result implies a categorical human-nonhuman distinction, independent from within-category physical/perceptual variation. Thus, recognizing conspecifics involves visual classification based on perceptual features that most frequently co-occur with humans, such as bipedalism, and retrieval of information that determines category membership above and beyond visual appearance. The current findings show that these processes are at work in separate brain networks.
Species composition and seasonal dynamics of aphid parasitoids and hyperparasitoids in wheat fields in northern China
Authors: Yang Fan , Xu Lei , Wu Yue-Kun , Wang Qian , Yao Zhi-Wen , Žikić Vladimir , Tomanović Željko , Ferrer-Suay Mar , Selfa Jesús , Pujade-Villar Juli , Traugott Michael , Desneux Nicolas , Lu Yan-Hui , Guo Yu-Yuan 
Published: October 2017

AbstractParasitoids are important natural enemies of aphids in wheat fields of northern China, and interest in them has increased in recent years. However, little is known regarding parasitoids of wheat aphids, which has hindered the study and understanding of aphid-parasitoid interactions. In the present study, three primary parasitoids and 15 hyperparasitoids were collected in wheat fields during a 2-year survey in northern China (2014, 2015) and a 2-year investigation at Langfang, Hebei Province (2015, 2016). Among them, Aphidius uzbekistanicus Luzhetski was found most frequently among the primary parasitoids, while Pachyneuron aphidis (Bouché) dominated the hyperparasitoid community. Investigation of the dynamics of wheat aphids and parasitoids revealed that the primary parasitoids appeared early in the growing period and that the hyperparasitoids appeared later. Analysis of the seasonal dynamics revealed that growth of the parasitoid population followed that of the aphid population and that the parasitism rates were highest in the late growing period.
Complement receptors C5aR1 and C5aR2 act differentially during the early immune response after bone fracture but are similarly involved in bone repair
Authors: Kovtun Anna , Bergdolt Stephanie , Hägele Yvonne , Matthes Rebekka , Lambris John D. , Huber-Lang Markus , Ignatius Anita 
Published: October 2017

AbstractSeverely injured patients frequently suffer compromised fracture healing because of systemic post-traumatic inflammation. An important trigger of the posttraumatic immune response is the complement anaphylatoxin C5a, which acts via two receptors, C5aR1 and C5aR2, expressed on immune and bone cells. The blockade of C5a-mediated inflammation during the early inflammatory phase was demonstrated to improve fracture healing after severe injury. However, the distinct roles of the two complement receptors C5aR1 and C5aR2 in bone has to date not been studied. Here, we investigated bone turnover and regeneration in mice lacking either C5aR1 or C5aR2 in a model of isolated fracture and after severe injury, combining the fracture with an additional thoracic trauma. Both C5aR1−/− and C5aR2−/− mice displayed an increased bone mass compared to wild-type controls due to reduced osteoclast formation and increased osteoblast numbers, respectively. Following fracture, the inflammatory response was differently affected in these strains: It was decreased in C5aR1−/− mice but enhanced in C5aR2−/− mice. Both strains exhibited impaired fracture healing, disturbed osteoclastogenesis and delayed cartilage-to-bone transformation. Thus, our data suggest that C5aR1 and C5aR2 differentially regulate the immune response after fracture and are required for effective cartilage-to-bone transformation in the fracture callus and for undisturbed bone healing.
Minocycline modulates microglia polarization in ischemia-reperfusion model of retinal degeneration and induces neuroprotection
Authors: Ahmed Amel , Wang Lei-Lei , Abdelmaksoud Safaa , Aboelgheit Amal , Saeed Safaa , Zhang Chun-Li 
Published: October 2017

AbstractRetinal ischemia-reperfusion (IR) injury causes irreversible loss of neurons and ultimately leads to permanent visual impairment and blindness. The cellular response under this pathological retinal condition is less clear. Using genetically modified mice, we systematically examined the behavior of microglia/macrophages after injury. We show that IR leads to activation of microglia/macrophages indicated by migration and proliferation of resident microglia and recruitment of circulating monocytes. IR-induced microglia/macrophages associate with apoptotic retinal neurons. Very interestingly, neuron loss can be mitigated by minocycline treatment. Minocycline induces Il4 expression and M2 polarization of microglia/macrophages. IL4 neutralization dampens minocycline-induced M2 polarization and neuroprotection. Given a well-established safety profile as an antibiotic, our results provide a rationale for using minocycline as a therapeutic agent for treating ischemic retinal degeneration.
Expression and regulation of long noncoding RNAs during the osteogenic differentiation of periodontal ligament stem cells in the inflammatory microenvironment
Authors: Zhang Qingbin , Chen Li , Cui Shiman , Li Yan , Zhao Qi , Cao Wei , Lai Shixiang , Yin Sanjun , Zuo Zhixiang , Ren Jian 
Published: October 2017

AbstractAlthough long noncoding RNAs (lncRNAs) have been emerging as critical regulators in various tissues and biological processes, little is known about their expression and regulation during the osteogenic differentiation of periodontal ligament stem cells (PDLSCs) in inflammatory microenvironment. In this study, we have identified 63 lncRNAs that are not annotated in previous database. These novel lncRNAs were not randomly located in the genome but preferentially located near protein-coding genes related to particular functions and diseases, such as stem cell maintenance and differentiation, development disorders and inflammatory diseases. Moreover, we have identified 650 differentially expressed lncRNAs among different subsets of PDLSCs. Pathway enrichment analysis for neighboring protein-coding genes of these differentially expressed lncRNAs revealed stem cell differentiation related functions. Many of these differentially expressed lncRNAs function as competing endogenous RNAs that regulate protein-coding transcripts through competing shared miRNAs.