bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating the Distributional Approach to Inferring Marketplace Exchange: A Test Case from the Mexican Gulf Lowlands
Authors: Garraty Christopher P. 
Published: February 2017

AbstractOver a decade ago Kenneth Hirth (1998, 2000) developed a “distributional approach” for archaeologically inferring the existence of marketplace exchange based on analyses of domestic artifact collections. Domestic collections, he reasoned, will be relatively homogeneous in areas where most or all households rely on marketplace exchange to acquire domestic provisions. The present study evaluates Hirth’s distributional approach using a statistical measure of diversity (heterogeneity) to quantify variability among domestic collection units over a large area. The data for this study come from the Middle Postclassic lower Blanco region of Veracruz (A.D. 1200–A.D. 1350), an unknown context of marketplace exchange. A comparison of diversity scores calculated on surface sherd collections from the lower Blanco region with scores from Late Postclassic Teotihuacan (A.D. 1350–A.D. 1520)—a known context of marketplace exchange—suggests the existence of a marketplace exchange system in the lower Blanco region, likely centered at the town of El Sauce. In addition, changes in intercollection diversity (sherds) and obsidian concentrations with increasing distance from the center suggest El Sauce’s market service area encompassed a radius of approximately six to nine kilometers.
Specialized Production of San Martín Orange Ware at Teotihuacan, Mexico
Authors: Sullivan Kristin S. 
Published: February 2017

AbstractSpecialized production forms an important component of the socioeconomic organization of ancient complex societies. Excavation provides critical information on the internal organization of production within a particular workshop and permits the recovery of features not preserved on the surface. In large settlements like Teotihuacan where modern occupation covers much of the ancient city, it is not feasible to fully excavate every suspected craft production locale. At Teotihuacan and in other complex societies, the use of surface indications to generate thematic maps permits discussion of the spatial relationships between economic and social units within the settlement. I use the surface collections made by the Teotihuacan Mapping Project and the partial excavation of one apartment compound and ceramic workshop in the Tlajinga district to consider the organization of specialized production in this neighborhood. I rely on the co-occurrence of ceramic production indicators to define likely workshops, using the surface collections from the excavated workshop as a reasonable indicator of production. Considering the evidence for vessel form specialization and dimensional standardization and previous ethnoarchaeological analyses of the excavated materials, Tlajinga district pottery production appears to have been maximally organized at the community level, with individual apartment compounds forming the basic production units.
City and Reciprocity: The Role of Cultural Beliefs in the Roman Economy
Authors: Verboven Koenraad 
Published: February 2017

Over the past decade, the New Institutional Economics have become a popular model for analyzing ancient economic history. However, the notion of cultural beliefs, which plays a central role in Douglass North’s recent work and Avner Greif’s analysis of institutional change, has been largely ignored. This article argues that a neo-institutional approach taking this notion into account offers a better means of understanding how ideology and moral values influenced the ancient economy than the Finleyan model. Rather than acting as a deterministic constraint on human behavior, cultural beliefs help to orient decision making and allow one to anticipate the (re)actions of others.
This article explores two key sets of norms and values in Roman culture that profoundly marked the economy’s institutional framework. The first focused on reciprocity, which supported social networks beyond the confines of the familia-freedmen group and underlay the development of contract and agency law. The second was based on citizenship, which shaped political culture by creating individual rights and obligations that the political elite was given the authority to enforce in order to secure and stimulate both private and common interests. This resulted in Roman law and the distribution of justice. Ideologically, the Roman Empire presented itself as a meta-city that incorporated local communities, which were in turn gradually transformed to fit the civitas model.
Both sets of beliefs lowered transaction costs without threatening the preeminent position of local and imperial aristocracies. Toward the end of the second century CE, local communities weakened as the imperial administration grew stronger, causing local and regional aristocracies to turn to the imperial court and army for status, influence, and power. The ideology of citizenship as the guiding principle of political culture gave way to that of the sacred emperor, who guaranteed divine justice and order.
Hotspots of aberrant enhancer activity punctuate the colorectal cancer epigenome
Authors: Cohen Andrea J. , Saiakhova Alina , Corradin Olivia , Luppino Jennifer M. , Lovrenert Katreya , Bartels Cynthia F. , Morrow James J. , Mack Stephen C. , Dhillon Gursimran , Beard Lydia , Myeroff Lois , Kalady Matthew F. , Willis Joseph , Bradner James E. , Keri Ruth A. , Berger Nathan A. , Pruett-Miller Shondra M. , Markowitz Sanford D. , Scacheri Peter C. 
Published: February 2017

AbstractIn addition to mutations in genes, aberrant enhancer element activity at non-coding regions of the genome is a key driver of tumorigenesis. Here, we perform epigenomic enhancer profiling of a cohort of more than forty genetically diverse human colorectal cancer (CRC) specimens. Using normal colonic crypt epithelium as a comparator, we identify enhancers with recurrently gained or lost activity across CRC specimens. Of the enhancers highly recurrently activated in CRC, most are constituents of super enhancers, are occupied by AP-1 and cohesin complex members, and originate from primed chromatin. Many activate known oncogenes, and CRC growth can be mitigated through pharmacologic inhibition or genome editing of these loci. Nearly half of all GWAS CRC risk loci co-localize to recurrently activated enhancers. These findings indicate that the CRC epigenome is defined by highly recurrent epigenetic alterations at enhancers which activate a common, aberrant transcriptional programme critical for CRC growth and survival.
Molecular determinant of the effects of hydrostatic pressure on protein folding stability
Authors: Chen Calvin R. , Makhatadze George I. 
Published: February 2017

AbstractHydrostatic pressure is an important environmental variable that plays an essential role in biological adaptation for many extremophilic organisms (for example, piezophiles). Increase in hydrostatic pressure, much like increase in temperature, perturbs the thermodynamic equilibrium between native and unfolded states of proteins. Experimentally, it has been observed that increase in hydrostatic pressure can both increase and decrease protein stability. These observations suggest that volume changes upon protein unfolding can be both positive and negative. The molecular details of this difference in sign of volume changes have been puzzling the field for the past 50 years. Here we present a comprehensive thermodynamic model that provides in-depth analysis of the contribution of various molecular determinants to the volume changes upon protein unfolding. Comparison with experimental data shows that the model allows quantitative predictions of volume changes upon protein unfolding, thus paving the way to proteome-wide computational comparison of proteins from different extremophilic organisms.
Implementation of concurrent electrolytic generation of two homogeneous mediators under widened potential conditions to facilitate removal of air-pollutants
Authors: Govindan Muthuraman , Bond Alan M. , Moon Il-Shik 
Published: February 2017

AbstractElectro-scrubbing is being developed as a futuristic technology for the removal of air-pollutants. To date, only one homogeneous mediator for the removal of air pollutants has been generated in each experiment using a divided electrolytic flow cell in an acidic medium. This paper reports the concurrent generation of two homogenous mediators, one at the anodic half-cell containing an acidic solution and the other at the cathodic half-cell containing a basic solution. The concept was inspired by the change in pH that occurs during water electrolysis in a divided cell. A 10 M KOH electrolyte medium assisted in the electrochemical generation of low valent 14% Co1+ ([CoI(CN)5]4−) mediator formed from reduction of [CoII(CN)5]3− which was accompanied by a change in the solution 'oxidation reduction potential' (ORP) of −1.05 V Simultaneously, 41% of Co3+ was generated from oxidation of CoIISO4 in the anodic half-cell. No change in the solution ORP was observed at the cathodic half-cell when both half-cells contain 5 M H2SO4, and Co3+ was formed in the anodic half-cell. An electro-scrubbing approach based on the above principles was developed and tested on gaseous-pollutants, CH3CHO and CCl4, by Co3+ and Co1+, respectively, with 90 and 96% removal achieved, respectively.
Tai Chi Chuan and Baduanjin practice modulates functional connectivity of the cognitive control network in older adults
Authors: Tao Jing , Chen Xiangli , Egorova Natalia , Liu Jiao , Xue Xiehua , Wang Qin , Zheng Guohua , Li Moyi , Hong Wenjun , Sun Sharon , Chen Lidian , Kong Jian 
Published: February 2017

AbstractCognitive impairment is one of the most common problem saffecting older adults. In this study, we investigated whether Tai Chi Chuan and Baduanjin practice can modulate mental control functionand the resting state functional connectivity (rsFC) of the cognitive control network in older adults. Participants in the two exercise groups practiced either Tai Chi Chuan or Baduanjin for 12 weeks, and those in the control group received basic health education. Memory tests and fMRI scans were conducted at baseline and at the end of the study. Seed-based (bilateral dorsolateral prefrontal cortex, DLPFC) rsFC analysis was performed. We found that compared to the controls, 1) both Tai Chi Chuan and Baduanjin groups demonstrated significant improvements in mental control function; 2) the Tai Chi Chuan group showed a significant decrease in rsFC between the DLPFC and the left superior frontal gyrus (SFG) and anterior cingulate cortex; and 3) the Baduanjin group showed a significant decrease in rsFC between the DLPFC and the left putamen and insula. Mental control improvement was negatively associated with rsFC DLPFC-putamen changes across all subjects. These findings demonstrate the potential of Tai Chi Chuan and Baduanjin exercises in preventing cognitive decline.
Novel peptides for deciphering structural and signalling functions of E-cadherin in mouse embryonic stem cells
Authors: Segal Joe M. , Ward Christopher M. 
Published: February 2017

AbstractWe have previously shown that E-cadherin regulates the naive pluripotent state of mouse embryonic stem cells (mESCs) by enabling LIF-dependent STAT3 phosphorylation, with E-cadherin null mESCs exhibiting over 3000 gene transcript alterations and a switch to Activin/Nodal-dependent pluripotency. However, elucidation of the exact mechanisms associated with E-cadherin function in mESCs is compounded by the difficulty in delineating the structural and signalling functions of this protein. Here we show that mESCs treated with the E-cadherin neutralising antibody DECMA-1 or the E-cadherin binding peptide H-SWELYYPLRANL-NH2 (Epep) exhibit discrete profiles for pluripotent transcripts and NANOG protein expression, demonstrating that the type of E-cadherin inhibitor employed dictates the cellular phenotype of mESCs. Alanine scanning mutation of Epep revealed residues critical for Tbx3, Klf4 and Esrrb transcript repression, cell-cell contact abrogation, cell survival in suspension, STAT3 phosphorylation and water solubility. STAT3 phosphorylation was found to be independent of loss of cell-cell contact and Activin/Nodal-dependent pluripotency and a peptide is described that enhances STAT3 phosphorylation and Nanog transcript and protein expression in mESCs. These peptides represent a useful resource for deciphering the structural and signalling functions of E-cadherin and demonstrate that complete absence of E-cadherin protein is likely required for hierarchical signalling pathway alterations in mESCs.
Growth-inducing effects of argon plasma on soybean sprouts via the regulation of demethylation levels of energy metabolism-related genes
Authors: Zhang Jiao Jiao , Jo Jin Oh , Huynh Do Luong , Mongre Raj Kumar , Ghosh Mrinmoy , Singh Amit Kumar , Lee Sang Baek , Mok Young Sun , Hyuk Park , Jeong Dong Kee 
Published: February 2017

AbstractThis study was conducted to determine the effects of argon plasma on the growth of soybean [Glycine max (L.) Merr.] sprouts and investigate the regulation mechanism of energy metabolism. The germination and growth characteristics were modified by argon plasma at different potentials and exposure durations. Upon investigation, plasma treatment at 22.1 kV for 12 s maximized the germination and seedling growth of soybean, increasing the concentrations of soluble protein, antioxidant enzymes, and adenosine triphosphate (ATP) as well as up-regulating ATP a1, ATP a2, ATP b1, ATP b2, ATP b3, target of rapamycin (TOR), growth-regulating factor (GRF) 1–6, down-regulating ATP MI25 mRNA expression, and increasing the demethylation levels of the sequenced region of ATP a1, ATP b1, TOR, GRF 5, and GRF 6 of 6-day-old soybean sprouts. These observations indicate that argon plasma promotes soybean seed germination and sprout growth by regulating the demethylation levels of ATP, TOR, and GRF.
New murine Niemann-Pick type C models bearing a pseudoexon-generating mutation recapitulate the main neurobehavioural and molecular features of the disease
Authors: Gómez-Grau Marta , Albaigès Júlia , Casas Josefina , Auladell Carme , Dierssen Mara , Vilageliu Lluïsa , Grinberg Daniel 
Published: February 2017

AbstractNiemann-Pick disease type C (NPC) is a rare neurovisceral disease caused mainly by mutations in the NPC1 gene. This autosomal recessive lysosomal disorder is characterised by the defective lysosomal secretion of cholesterol and sphingolipids. No effective therapy exists for the disease. We previously described a deep intronic point mutation (c.1554-1009 G > A) in NPC1 that generated a pseudoexon, which could be corrected at the cellular level using antisense oligonucleotides. Here, we describe the generation of two mouse models bearing this mutation, one in homozygosity and the other in compound heterozygosity with the c.1920delG mutation. Both the homozygotes for the c.1554-1009 G > A mutation and the compound heterozygotes recapitulated the hallmarks of NPC. Lipid analysis revealed accumulation of cholesterol in the liver and sphingolipids in the brain, with both types of transgenic mice displaying tremor and ataxia at 7–8 weeks of age. Behavioural tests showed motor impairment, hyperactivity, reduced anxiety-like behaviour and impaired learning and memory performances, features consistent with those reported previously in NPC animal models and human patients. These mutant mice, the first NPC models bearing a pseudoexon-generating mutation, could be suitable for assessing the efficacy of specific splicing-targeted therapeutic strategies against NPC.
Magnetoresistive sensors for measurements of DNA hybridization kinetics – effect of TINA modifications
Authors: Rizzi G. , Dufva M. , Hansen M. F. 
Published: February 2017

AbstractWe present the use of magnetoresistive sensors integrated in a microfluidic system for real-time studies of the hybridization kinetics of DNA labeled with magnetic nanoparticles to an array of surface-tethered probes. The nanoparticles were magnetized by the magnetic field from the sensor current. A local negative reference ensured that only the specific binding signal was measured. Analysis of the real-time hybridization using a two-compartment model yielded both the association and dissociation constants kon, and koff. The effect of probe modifications with ortho-Twisted Intercalating Nucleic Acid (TINA) was studied. Such modifications have been demonstrated to increase the melting temperature of DNA hybrids in solution and are also relevant for surface-based DNA sensing. Kinetic data for DNA probes with no TINA modification or with TINA modifications at the 5′ end (1 × TINA) or at both the 5′ and 3′ ends (2 × TINA) were compared. TINA modifications were found to provide a relative decrease of koff by a factor of 6-20 at temperatures from 57.5 °C to 60 °C. The values of kon were generally in the range between 0.5-2 × 105 M−1s−1 and showed lower values for the unmodified probe than for the TINA modified probes. The observations correlated well with measured melting temperatures of the DNA hybrids.
Loss of HSulf-1: The Missing Link between Autophagy and Lipid Droplets in Ovarian Cancer
Authors: Roy Debarshi , Mondal Susmita , Khurana Ashwani , Jung Deok-Beom , Hoffmann Robert , He Xiaoping , Kalogera Eleftheria , Dierks Thomas , Hammond Edward , Dredge Keith , Shridhar Viji 
Published: February 2017

AbstractDefective autophagy and deranged metabolic pathways are common in cancer; pharmacologic targeting of these two pathways could provide a viable therapeutic option. However, how these pathways are regulated by limited availability of growth factors is still unknown. Our study shows that HSulf-1 (endosulfatase), a known tumor suppressor which attenuates heparin sulfate binding growth factor signaling, also regulates interplay between autophagy and lipogenesis. Silencing of HSulf-1 in OV202 and TOV2223 cells (ovarian cancer cell lines) resulted in increased lipid droplets (LDs), reduced autophagic vacuoles (AVs) and less LC3B puncta. In contrast, HSulf-1 proficient cells exhibit more AVs and reduced LDs. Increased LDs in HSulf-1 depleted cells was associated with increased ERK mediated cPLA2S505 phosphorylation. Conversely, HSulf-1 expression in SKOV3 cells reduced the number of LDs and increased the number of AVs compared to vector controls. Furthermore, pharmacological (AACOCF3) and ShRNA mediated downregulation of cPLA2 resulted in reduced LDs, and increased autophagy. Finally, in vivo experiment using OV202 Sh1 derived xenograft show that AACOCF3 treatment effectively attenuated tumor growth and LD biogenesis. Collectively, these results show a reciprocal regulation of autophagy and lipid biogenesis by HSulf-1 in ovarian cancer.
Metabolomic profiling of reactive persulfides and polysulfides in the aqueous and vitreous humors
Authors: Kunikata Hiroshi , Ida Tomoaki , Sato Kota , Aizawa Naoko , Sawa Tomohiro , Tawarayama Hiroshi , Murayama Namie , Fujii Shigemoto , Akaike Takaaki , Nakazawa Toru 
Published: February 2017

AbstractWe investigate the metabolomic profile of reactive persulfides and polysulfides in the aqueous and vitreous humors. Eighteen eyes of 18 consecutive patients with diabetes mellitus (DM) and diabetic retinopathy underwent microincision vitrectomy combined with cataract surgery. Samples of the aqueous and vitreous humors were collected and underwent mass spectrometry-based metabolomic profiling of reactive persulfides and polysulfides (polysulfidomics). The effect of reactive polysulfide species on the viability of immortalized retinal cells (the RGC-5 cell line) under oxidative stress (induced with H2O2) was also evaluated with an Alamar Blue assay. The experiments showed that cysteine persulfides (CysSSH), oxidized glutathione trisulfide (GSSSG) and cystine were elevated in the aqueous humor, and CysSSH, Cys, and cystine were elevated in the vitreous. Furthermore, GSSSG, cystine, and CysSSH levels were correlated in the aqueous and vitreous humors. A comparison, in DM and control subjects, of plasma levels of reactive persulfides and polysulfides showed that they did not differ. In vitro findings revealed that reactive polysulfide species increased cell viability under oxidative stress. Thus, various reactive persulfides and polysulfides appear to be present in the eye, and some reactive sulfide species, which have a protective effect against oxidative stress, are upregulated in the aqueous and vitreous humors of DM eyes.
Searching for new loci and candidate genes for economically important traits through gene-based association analysis of Simmental cattle
Authors: Xia Jiangwei , Fan Huizhong , Chang Tianpeng , Xu Lingyang , Zhang Wengang , Song Yuxin , Zhu Bo , Zhang Lupei , Gao Xue , Chen Yan , Li Junya , Gao Huijiang 
Published: February 2017

AbstractSingle-marker genome-wide association study (GWAS) is a convenient strategy of genetic analysis that has been successful in detecting the association of a number of single-nucleotide polymorphisms (SNPs) with quantitative traits. However, analysis of individual SNPs can only account for a small proportion of genetic variation and offers only limited knowledge of complex traits. This inadequacy may be overcome by employing a gene-based GWAS analytic approach, which can be considered complementary to the single-SNP association analysis. Here we performed an initial single-SNP GWAS for bone weight (BW) and meat pH value with a total of 770,000 SNPs in 1141 Simmental cattle. Additionally, 21836 cattle genes collected from the Ensembl Genes 83 database were analyzed to find supplementary evidence to support the importance of gene-based association study. Results of the single SNP-based association study showed that there were 11 SNPs significantly associated with bone weight (BW) and two SNPs associated with meat pH value. Interestingly, all of these SNPs were located in genes detected by the gene-based association study.
Collagen scaffold microenvironments modulate cell lineage commitment for differentiation of bone marrow cells into regulatory dendritic cells
Authors: Fang Yongxiang , Wang Bin , Zhao Yannan , Xiao Zhifeng , Li Jing , Cui Yi , Han Sufang , Wei Jianshu , Chen Bing , Han Jin , Meng Qingyuan , Hou Xianglin , Luo Jianxun , Dai Jianwu , Jing Zhizhong 
Published: February 2017

AbstractThe microenvironment plays a pivotal role for cell survival and functional regulation, and directs the cell fate determination. The biological functions of DCs have been extensively investigated to date. However, the influences of the microenvironment on the differentiation of bone marrow cells (BMCs) into dendritic cells (DCs) are not well defined. Here, we established a 3D collagen scaffold microenvironment to investigate whether such 3D collagen scaffolds could provide a favourable niche for BMCs to differentiate into specialised DCs. We found that BMCs embedded in the 3D collagen scaffold differentiated into a distinct subset of DC, exhibiting high expression of CD11b and low expression of CD11c, co-stimulator (CD40, CD80, CD83, and CD86) and MHC-II molecules compared to those grown in 2D culture. DCs cultured in the 3D collagen scaffold possessed weak antigen uptake ability and inhibited T-cell proliferation in vitro; in addition, they exhibited potent immunoregulatory function to alleviate allo-delay type hypersensitivity when transferred in vivo. Thus, DCs differentiated in the 3D collagen scaffold were defined as regulatory DCs, indicating that collagen scaffold microenvironments probably play an important role in modulating the lineage commitment of DCs and therefore might be applied as a promising tool for generation of specialised DCs.