bluuebunny/crossref_metadata_2025_split huggingface dataset:
PreMosa: extracting 2D surfaces from 3D microscopy mosaics
Authors: Blasse Corinna , Saalfeld Stephan , Etournay Raphaël , Sagner Andreas , Eaton Suzanne , Myers Eugene W 
Published: April 2017

Abstract

Motivation
A significant focus of biological research is to understand the development, organization and function of tissues. A particularly productive area of study is on single layer epithelial tissues in which the adherence junctions of cells form a 2D manifold that is fluorescently labeled. Given the size of the tissue, a microscope must collect a mosaic of overlapping 3D stacks encompassing the stained surface. Downstream interpretation is greatly simplified by preprocessing such a dataset as follows: (i) extracting and mapping the stained manifold in each stack into a single 2D projection plane, (ii) correcting uneven illumination artifacts, (iii) stitching the mosaic planes into a single, large 2D image and (iv) adjusting the contrast.

Results
We have developed PreMosa, an efficient, fully automatic pipeline to perform the four preprocessing tasks above resulting in a single 2D image of the stained manifold across which contrast is optimized and illumination is even. Notable features are as follows. First, the 2D projection step employs a specially developed algorithm that actually finds the manifold in the stack based on maximizing contrast, intensity and smoothness. Second, the projection step comes first, implying all subsequent tasks are more rapidly solved in 2D. And last, the mosaic melding employs an algorithm that globally adjusts contrasts amongst the 2D tiles so as to produce a seamless, high-contrast image. We conclude with an evaluation using ground-truth datasets and present results on datasets from Drosophila melanogaster wings and Schmidtae mediterranea ciliary components.

Availability and Implementation
PreMosa is available under https://cblasse.github.io/premosa

Supplementary information
Supplementary data are available at Bioinformatics online.
Radicalisation, Community and the Politics of Protest in the Spanish Second Republic: Asturias, 1931–34
Authors: Kerry Matthew 
Published: April 2017

Abstract
In October 1934 thousands of leftists took up arms in a two-week revolutionary insurrection in the northern Spanish region of Asturias which shook the Second Republic (1931–1936) and formed part of a critical European juncture of protest in 1934. This article rethinks the process of radicalisation—a key process for understanding both the insurrection and the wider polarisation of Spanish society prior to the Civil War—in the context of the Asturian coalfields. I argue that radicalisation, understood as a more militant, confrontational mode of politics, rather than as having any particular ideological content, needs to be located in the struggles, divisions and anxieties at a local level, shaped by understandings of community, within the wider national and international context. Increased tension and confrontation was due to a combination of factors, including competition amongst different leftist groups to present themselves as the most anticlerical, alienation from the main mining union, anxieties over the perceived emergence of fascism, and a spiral of protest and repression shaped by a more heavy-handed state policing strategy in 1934. The interplay of social and political factors provided the energy behind the revolutionary insurrection. This serves to re-evaluate the process of radicalisation in the Second Republic, and the politics and struggles of the working class in a dark and tumultuous decade for the European left.
Enhanced biological activities of gamma-irradiated persimmon leaf extract
Authors: Cho Byoung-Ok , Nchang Che Denis , Yin Hong-Hua , Jang Seon-Il 
Published: April 2017

Abstract
The aim of this study was to compare the anti-oxidative and anti-inflammatory activities of gamma-irradiated persimmon leaf extract (GPLE) with those of non-irradiated persimmon leaf extract (PLE). Ethanolic extract of persimmon leaf was exposed to gamma irradiation at a dose of 10 kGy. After gamma irradiation, the color of the extract changed from dark brown to light brown. The anti-oxidative and anti-inflammatory activities of GPLE and PLE were assessed from: total polyphenol and total flavonoid contents; 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay; 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) assay, and levels of pro-inflammatory mediators such as nitric oxide (NO), prostaglandin E2 (PGE2), tumor necrosis factor alpha (TNF-α) and interleukin-6 (IL-6). The total polyphenol contents of GPLE and PLE were determined to be 224.44 ± 1.54 and 197.33 ± 5.81 mg gallic acid equivalents (GAE)/g, respectively, and the total flavonoid contents of GPLE and PLE were 206.27 ± 1.15 and 167.60 ± 2.00 mg quercetin equivalents (QUE)/g, respectively. The anti-oxidant activities of GPLE and PLE as measured by DPPH assays were 338.33 ± 30.19 μg/ml (IC50) and 388.68 ± 8.45 μg/ml (IC50), respectively, and those measured by ABTS assays were 510.49 ± 15.12 μg/ml (IC50) and 731.30 ± 10.63 μg/ml (IC50), respectively. IC50 is the inhibitor concentration that reduces the response by 50%. GPLE strongly inhibited the production of NO, PGE2 and IL-6 compared with PLE in lipopolysaccharide-stimulated RAW264.7 macrophages. Furthermore, GPLE significantly inhibited the production of TNF-α and IL-6 cytokines compared with PLE in phorbol 12-myristate 13-acetate (PMA) plus A23187-stimulated HMC-1 human mast cells. These results indicate that gamma irradiation of PLE can enhance its anti-oxidative and anti-inflammatory activities through elevation of the phenolic contents. Therefore, gamma-irradiated PLE has potential for use in the food and cosmetic industries.
Characterization of relative biological effectiveness for conventional radiation therapy: a comparison of clinical 6 MV X-rays and 137Cs
Authors: Howard Michelle , Beltran Chris , Sarkaria Jann , Herman Michael G 
Published: April 2017

ABSTRACT
Various types of radiation are utilized in the treatment of cancer. Equal physical doses of different radiation types do not always result in the same amount of biological damage. In order to account for these differences, a scaling factor known as the relative biological effectiveness (RBE) can be used. 137Cesium (137Cs) has been used as a source of radiation in a significant body of radiation therapy research. However, high-energy X-rays, such as 6 MV X-rays, are currently used clinically to treat patients. To date, there is a gap in the literature regarding the RBE comparison of these two types of radiation. Therefore, the purpose of this study was to investigate the RBE of 137Cs relative to that of 6 MV X-rays. To determine the RBE, five cell lines were irradiated [Chinese hamster ovary (CHO); human lung adenocarcinoma (A549); human glioma (U251); human glioma (T98); and human osteosarcoma (U2OS)] by both types of radiation and assessed for cell survival using a clonogenic assay. Three of the five cell lines resulted in RBE values of ~1.00 to within 11% for all survival fractions, showing the physical and biological dose for these two types of radiation were equivalent. The other two cell lines gave RBE values differing from 1.00 by up to 36%. In conclusion, the results show the range in biological effect seen between cell lines, and therefore cell type must be considered when characterizing RBE.
Discovery of a distant molecular cloud in the extreme outer Galaxy with the Nobeyama 45 m telescope
Authors: Matsuo Mitsuhiro , Nakanishi Hiroyuki , Minamidani Tetsuhiro , Torii Kazufumi , Saito Masao , Kuno Nario , Sawada Tsuyoshi , Tosaki Tomoka , Kobayashi Naoto , Yasui Chikako , Mito Hiroyuki , Hasegawa Takashi , Hirota Akihiko 
Published: April 2017

Abstract
We report the discovery of a molecular cloud whose kinematic distance is the largest in the Galaxy at the present moment, named G213.042+0.003, at l = 213${^{\circ}_{.}}$042 and b = 0${^{\circ}_{.}}$003 in the 12CO(J = 1–0) line using the Nobeyama 45 m telescope and the BEARS multi-beam receiver. This molecular cloud is located at a heliocentric distance of $21_{-7}^{+12}\:$kpc and Galactocentric distance of 29$_{-7}^{+12}\:$kpc, which are estimated as the kinematic distances with the Galactic parameters obtained by Reid et al. (2014, ApJ, 783, 130). Its major and minor diameters and line width were measured to be $4.0_{-1.3}^{+2.3}\:$pc, 3.0$_{-1.0}^{+1.7}\:$pc, and 1.5 km s−1, respectively. The cloud mass was estimated to be 2.5$_{-1.4}^{+3.7}$ × 102 M⊙ using the CO-to-H2 conversion factor of 5.6 × 1020 cm−2 (K km s−1)−1 obtained in the far outer Galaxy.
Operating room team member role affects room traffic in orthopaedic surgery: a prospective observational study
Authors: DiBartola Alex C. , Patel Priya G. , Scharschmidt Thomas J. , Mayerson Joel L. , Phieffer Laura S. , Glassman Andrew H. , Moffatt-Bruce Susan D. , Quatman Carmen E. 
Published: April 2017

Background:
Operating room (OR) traffic is an increasing topic of concern for potential risks of surgical site infections (SSIs). We evaluated room traffic rates during orthopaedic surgery cases to better understand how OR team member roles contribute to room traffic. Our hypothesis was that OR traffic differs among team member groups.

Methods:
We evaluated 46 orthopaedic surgery cases involving implantation of a device at an academic medical center during the summer of 2015. Room traffic rates were recorded as the number of door openings per minute in each case. OR team member groups were defined as follows: Group (A) charge nurse, nurse, scrub technician, scrub technician student; (B) anesthesiology attending physician, anesthesiology resident, anesthesiology medical student, certified nurse anesthetist; (C) orthopaedic surgery attending, orthopaedic surgery resident, orthopaedic surgery medical student; (D) medical sales representative/vendor; (E) radiology technician.

Results:
The number of door openings ranged from 48 to 259 (mean 127±47). The overall mean room traffic rate per minute per case ranged from 0.2193-1.014 (mean 0.5856±0.1663). Operative length ranged from 90–521 min (mean 226±89.1). There was a statistically significance difference between the median room traffic rate per minute per case by different group (A, B, C, D, and E) types (χ

2

(4)
=127.085, P=0.0001).

Conclusions:
Room traffic rates and number of door openings per case are different among different OR team member groups. Better understanding of room traffic characteristics allows for strategic intervention to decrease room traffic among team members in each group.
Axial spondyloarthritis classification criteria: the debate continues
Authors: Dubreuil Maureen , Deodhar Atul A. 
Published: April 2017

Purpose of review
The Assessment of Spondyloarthritis International Society (ASAS) axial spondyloarthritis (axSpA) classification criteria marked a major step forward in SpA research, distinguishing axial from peripheral disease, and allowing earlier identification through MRI. This facilitated all aspects of research including epidemiology, therapeutics and patient outcomes.

Recent findings
The ASAS axSpA classification criteria have been applied broadly in research, and were validated in a recent meta-analysis of international studies. Concerns arose because of clinical differences between the clinical and imaging arms, which imply different risk for radiographic progression, and perform differently in validation studies. Low specificity of the MRI finding of sacroiliac joint bone marrow edema may lead to misclassification in populations with low axSpA prevalence. We suggest methodology to improve upon the criteria, including rigorous assessment of potential candidate criteria sets, discrete choice experiments to allow consideration of feature weights, and validation. Separately, assessment of structural and inflammatory MRI abnormalities should be performed to refine the MRI definition of sacroiliitis.

Summary
The debate regarding the validation and modification of the ASAS axSpA classification criteria should lead to international efforts to build upon the gains made by these criteria, to further refine the axSpA population definitions for research and ultimately improve patient outcomes.
The Children's Health Exposure Analysis Resource: enabling research into the environmental influences on children's health outcomes
Authors: Balshaw David M. , Collman Gwen W. , Gray Kimberly A. , Thompson Claudia L. 
Published: April 2017

Purpose of review
The Children's Health Exposure Analysis Resource (CHEAR) is a new infrastructure supported by the National Institute of Environmental Health Sciences to expand the ability of children's health researchers to include analysis of environmental exposures in their research and to incorporate the emerging concept of the exposome.

Recent findings
There is extensive discussion of the potential of the exposome to advance understanding of the totality of environmental influences on human health. Children's health is a logical choice to demonstrate the exposome concept due to the extensive existing knowledge of individual environmental exposures affecting normal health and development and the short latency between exposures and observable phenotypes. Achieving this demonstration will require access to extensive analytical capabilities to measure a suite of exposures through traditional biomonitoring approaches and to cross-validate these with emerging exposomic approaches.

Summary
CHEAR is a full-service exposure assessment resource, linking up-front consultation with both laboratory and data analysis. Analyses of biological samples are intended to enhance studies by including targeted analysis of specific exposures and untargeted analysis of small molecules associated with phenotypic endpoints. Services provided by CHEAR are made available without cost but require a brief application and adherence to policies detailed on the CHEAR web page at https://chearprogram.org/.
Digestion of Human Milk Oligosaccharides by Bifidobacterium breve in the Premature Infant
Authors: Underwood Mark A. , Davis Jasmine C.C. , Kalanetra Karen M. , Gehlot Sanjay , Patole Sanjay , Tancredi Daniel J. , Mills David A. , Lebrilla Carlito B. , Simmer Karen 
Published: April 2017

ABSTRACTObjective:The aim of this study was to measure consumption and absorption of human milk oligosaccharides (HMOs) in a cohort of premature infants treated with probiotic Bifidobacterium breve.Methods:Twenty‐nine premature infants (median gestational age 28 weeks, range 23–32 weeks) cared for in the neonatal intensive care unit of the King Edward and Princess Margaret Hospital in Perth, Australia, were treated with B breve at a dose of 1.66 billion organisms per day. Samples of feces, urine, and milk were obtained at initiation of the probiotic and again 3 weeks later. 16S ribosomal RNA from the feces was analyzed by next‐generation sequencing. Quantitation of HMO content of the milk, urine, and feces was performed using nano‐high‐performance liquid chromatography‐chip/time‐of‐flight mass spectrometry.Results:There was heterogeneity in colonization with bifidobacteria. “Responders” received milk with higher percentages of fucosylated HMOs and had higher percentages of bifidobacteria and lower percentages of Enterobacteriaceae in their feces than “nonresponders.” Several individual HMOs in the milk were associated with changes in fecal bifidobacteria over time. Changes over time in milk, fecal, and urine HMOs suggested heterogeneity among HMO structures in consumption by microbes in the gut lumen and absorption from the intestine.Conclusions:Colonization of the premature infant intestinal tract with probiotic B breve is influenced by prebiotic HMOs. B breve is a selective consumer of HMOs in the premature infant.
Dehydration bouts prompt increased activity and blood feeding by mosquitoes
Authors: Hagan Richard W. , Szuter Elise M. , Rosselot Andrew E. , Holmes Christopher J. , Siler Samantha C. , Rosendale Andrew J. , Hendershot Jacob M. , Elliott Kiaira S. B. , Jennings Emily C. , Rizlallah Alexandre E. , Xiao Yanyu , Watanabe Miki , Romick-Rosendale Lindsey E. , Rasgon Jason L. , Benoit Joshua B. 
Published: April 2017

AbstractMosquitoes are prone to dehydration and respond to this stress through multiple mechanisms, but previous studies have examined very specific responses and fail to provide an encompassing view of the role that dehydration has on mosquito biology. This study examined underlying changes in biology of the northern house mosquito,Culex pipiens, associated with short bouts of dehydration. We show that dehydration increased blood feeding propensity of mosquitoes, which was the result of both enhanced activity and a higher tendency to land on a host. Mosquitoes exposed to dehydrating conditions with access to water or rehydrated individuals experience no water loss and failed to display behavioral changes. RNA-seq and metabolome analyses following dehydration indicated that factors associated with energy metabolism are altered, specifically the breakdown of trehalose to yield glucose, which likely underlies changes in mosquito activity. Suppression of trehalose breakdown by RNA interference reduced phenotypes associated with dehydration. Comparable results were noted for two other mosquito species, suggesting this is a general response among mosquitoes. Lastly, field-based mesocosm studies usingC.pipiensrevealed that dehydrated mosquitoes were more likely to host feed, and disease modeling indicates dehydration bouts may increase transmission of West Nile virus. These results suggest that periods of dehydration prompt mosquitoes to utilize blood feeding as a mechanism to obtain water. This dehydration-induced increase in blood feeding is likely to intensify disease transmission during periods of low water availability.SignificanceDehydration stress has substantial impacts on the biology of terrestrial invertebrates. To date, no studies have elucidated the difference between dehydration exposure and realized water loss in relation to mosquito behavior and physiology. Our experiments show that direct dehydration stress increases mosquito activity and subsequent blood feeding, likely as a mechanism to locate and utilize a bloodmeal for rehydration. These dehydration-induced phenotypes were linked to altered carbohydrate metabolism that acts as a source of energy. This study provides important insight into the impact of mosquito-dehydration dynamics on disease transmission that is likely general among mosquitoes.
Differential Effects of LIS1 On Processive Dynein-Dynactin Motility
Authors: Gutierrez Pedro A. , McKenney Richard J. 
Published: April 2017

AbstractCytoplasmic dynein is the primary minus-end directed microtubule motor protein in cells. LIS1 is a highly conserved dynein regulatory factor that binds directly to the dynein motor domain, uncoupling the enzymatic and mechanical cycles of the motor, and stalling dynein on the microtubule track. Dynactin, another ubiquitous dynein regulatory factor, acts to release dynein from an autoinhibited state, leading to a dramatic increase in fast, processive dynein motility. How these opposing activities are integrated to control dynein motility is unknown. Here we used fluorescence single-molecule microscopy to study the interaction of LIS1 with the processive dynein-dynactin-BicD2N (DDB) complex. Surprisingly, in contrast to the prevailing model for LIS1 function established in the context of dynein alone, we find that binding of LIS1 to DDB does not strongly disrupt processive motility. Motile DDB complexes bind up to two LIS1 dimers, and mutational analysis suggests LIS1 binds directly to the dynein motor domains during DDB movement. Interestingly, LIS1 enhances DDB velocity in a concentration dependent manner, in contrast to observations of LIS1’s effects on the motility of isolated dynein. Thus, LIS1 exerts concentration dependent effects on dynein motility, and can synergize with dynactin to enhance processive movement in the absence of load.
Does foreign direct investment promote exports in China?
Authors: Li Xin , Chang Hsu Ling , Su Chi Wei , Dai Yin 
Published: April 2017

Purpose
The purpose of this paper is to investigate the causal link between foreign direct investment (FDI) and exports in China based on the knowledge capital model (KK model, Markusen, 2002).

Design/methodology/approach
The bootstrap Granger full-sample and sub-sample rolling window causality test is used to determine whether FDI can promote exports.

Findings
The full-sample causality test indicates no causal relationship from FDI to exports. However, considering structural changes of exports and FDI, the authors’ find that the full-sample test is not reliable. Instead, the authors use the rolling window causality test to revisit the dynamic causal relationship, and the results present significant effects from FDI on exports, mostly around periods in which the proportion of FDI from Hong Kong, Macao and Taiwan is increasing. Specifically, positive impacts of FDI on exports are stronger than the negative impacts in China.

Research limitations/implications
The findings in this study suggest a significant time-varying nature of the correlation between FDI and exports. The promotion effect of FDI to exports is proved by the rolling window approach; it thus supports the KK model that divides FDI into lateral FDI and vertical FDI and proves that the constitution of FDI is critical to the relationship between FDI and exports.

Practical implications
China has been facing adjustment of its economic structure in recent years, and in this situation, increasing the proportion of FDI that can bring advanced production function is critical for the industrial structural adjustment.

Originality/value
This paper uses the bootstrap rolling window causality test to investigate the time-varying nature of the causality between FDI and exports, considering structural changes for the first time. The authors further deepen the previous research and draw a more realistic conclusion.
The spillover effect between CSI 500 index futures market and the spot market
Authors: Fan Xuejun , Du De 
Published: April 2017

PurposeFocusing on the spillover effects between the CSI 500 stock index futures market and its underlying spot market during April to September 2015, the purpose of this paper is to explore whether Chinese stock index futures should be responsible for the 2015 stock market crash.Design/methodology/approachUsing both linear and non-linear econometric models, this paper empirically examines the mean spillover and the volatility spillover between the CSI 500 stock index futures market and the underlying spot market.FindingsThe results showed the following: the CSI 500 stock index futures market has significant one-way mean spillover effect on its spot market. The volatility in CSI 500 stock index futures market also has a significant positive spillover effect on its spot stock market, and the mean value of dynamic correlation coefficient between the two market volatility is 0.4848. The spillover effect of the CSI 500 stock index futures market on the underlying spot market is significantly asymmetric, characterized by relatively moderate and slow during the period of the markets rising, yet violent and rapid during the period of the markets falling. The findings suggest that although the stock index futures itself was not the “culprit” of Chinese stock market crash in 2015, its existence indeed accelerated and exacerbated the stock market’s decline under the imperfect trading system.Originality/valueDifferent from the existing literature mainly focusing on CSI 300 stock index futures, this paper empirically examines the impact of the introduction of CSI 500 stock index futures on 2015 Chinese stock market crash for the first time.