bluuebunny/crossref_metadata_2025 huggingface dataset:
Free and Unfree Labor in Atlantic and Indian Ocean Port Cities (Seventeenth–Nineteenth Centuries)
Authors: Brandon Pepijn , Frykman Niklas , Røge Pernille
Published: March 2019

Colonial and postcolonial port cities in the Atlantic and Indian Ocean regions functioned as crucial hubs in the commodity flows that accompanied the emergence and expansion of global capitalism. They did so by bringing together laboring populations of many different backgrounds and statuses – legally free or semi-free wage laborers, soldiers, sailors, and the self-employed, indentured servants, convicts, and slaves. Focusing on the period from the seventeenth to the mid-nineteenth centuries, a crucial moment in the establishment of the world market, the transformation of colonial states, and the reorganization of labor and labor migration on a transoceanic scale, the contributions in this special issue address the consequences of the presence of these “motley crews” on and around the docks and the neighborhoods that stretched behind them. The introduction places the articles within the context of the development of the field of Global Labor History more generally. It argues that the dense daily interaction that took place in port cities makes them an ideal vantage point from which to investigate the consequences of the “simultaneity” of different labor relations for questions such as the organization of the work process under developing capitalism, the emergence of new forms of social control, the impact of forced and free migration on class formation, and the role of social diversity in shaping different forms of group and class solidarity. The introduction also discusses the significance of the articles presented in this special issue for three prevailing but problematic dichotomies in labor historiography: the sharp borders drawn between so-called free and unfree labor, between the Atlantic and the Indian oceans, and the pre-modern and modern eras.
History Below the Waterline: Enslaved Salvage Divers Harvesting Seaports’ Hinter-Seas in the Early Modern Atlantic
Authors: Dawson Kevin
Published: March 2019

This article considers how enslaved salvage divers cooperated and conspired with slaveholders and white employers to salvage shipwrecks and often smuggle recovered goods into homeports, permitting them to exchange their expertise for semi-independent lives of privileged exploitation. Knowing harsh treatment could preclude diving, white salvagers cultivated reciprocal relationships with divers, promoting arduousness by avoiding coercive discipline while nurturing a sense of mutual obligation arising from collective responsibilities and material rewards. Enslaved salvagers were, in several important ways, treated like free, wage-earning men. They were well fed, receiving daily allowances of fresh meat. Most resided in seaports, were hired out, and received equal shares of recovered goods, allowing many to purchase their freedom and that of family members. Divers produced spectacular amounts of wealth for their mother countries, owners, and colonial governments, especially in the maritime colonies of Bermuda, the Bahamas, and Cayman Islands. Their expertise was not confined to maritime colonies. Even as plantation slavery was taking root during the mid-seventeenth century, salvage divers provided an important source of income for planter-merchants.
Afterword: Reflections on the Motley Crew as Port City Proletariat
Authors: Rediker Marcus
Published: March 2019

This essay reflects on the workers in Atlantic and Indian Ocean port cities who made possible the rapidly expanding system of global capitalism between 1650 and 1850. In all of the ports treated in this volume, a mixture of multi-ethnic, male and female, unskilled, often unwaged laborers collectively served as the linchpins that connected local hinterlands (and seas) to bustling waterfronts, tall ships, and finally the world market. Although the precise combination of workers varied from one port to the next, all had an occupational structure in which half or more of the population worked in trade or the defense of trade, for example in shipbuilding/repair, the hauling of commodities to and from ships, and the building of colonial infrastructure, the docks and roads instrumental to commerce. This “motley crew” – a working combination of enslaved Africans, European/Indian/Chinese indentured servants, sailors, soldiers, convicts, domestic workers, and artisans – were essential to the production and worldwide circulation of commodities and profits.
Acceptability and feasibility of a school-based contraceptive clinic in a low-income community in South Africa
Authors: Khoza Nondumiso , Zulu Phindile , Shung-King Maylene
Published: March 2019

Aim

To investigate how acceptable and feasible a school-based contraceptive clinic (SBCC) would be in a low-income South African community.

Background

Teenage pregnancy is an important issue in South Africa, with significant health and social consequences. Issues regarding lack of confidentiality in an intimate community, unwelcoming health workers, long distances to clinics and perceptions of contraceptive side effects may all inhibit contraceptive use by adolescents. Although SBCC has been initiated and investigated in other countries, this approach is inadequately researched in South Africa.

Methods

A mixed method study was conducted to assess the attitudes of one community towards establishment of an SBCC in their area. Methods of data collection included: focus group discussions (FGDs) with teenage girls from a local high school; a key informant interview with the school principal; a structured survey, including open-ended questionnaires with randomly selected parents of teenage girls from the same community; and a documentary analysis to explore relevant legal and policy considerations.

Findings

Teenage girls, the school principal and parents with teenage daughters largely supported the idea of an SBCC, but with concerns about confidentiality, the possibility of increased promiscuity and contraceptive side effects. While legal statutes and policies in South Africa do not pose any barriers to the establishment of an SBCC, some logistical barriers remain.
Workload Perception of Air Traffic Control Officers and Pilots During	Continuous Descent Operations Approach Procedures
Authors: Efthymiou Marina , Fichert Frank , Lantzsch Olaf
Published: March 2019

Abstract. The paper examines the workload perceived by air traffic control officers (ATCOs) and pilots during continuous descent operations (CDOs), applying closed- and open-path procedures. CDOs reduce fuel consumption and noise emissions. Therefore, they are supported by airports as well as airlines. However, their use often depends on pilots asking for CDOs and controllers giving approval and directions. An adapted NASA Total Load Index (TLX) was used to measure the workload perception of ATCOs and pilots when applying CDOs at selected European airports. The main finding is that ATCOs’ workload increased when giving both closed- and open-path CDOs, which may have a negative impact on their willingness to apply CDOs. The main problem reported by pilots was insufficient distance-to-go information provided by ATCOs. The workload change is important when considering the use of CDOs.
A Migration Model for the Polar Spiral Troughs of Mars
Authors: Bramson A. M. , Byrne S. , Bapst J. , Smith I. B. , McClintock T.
Published: March 2019

Mars' iconic polar spiral troughs are 400–1,000‐m‐deep depressions in the north polar layered deposits. As the north polar layered deposits accumulate, troughs migrate approximately poleward, anti‐parallel to the local wind patterns. Insolation is suspected to drive ice retreat through sublimation. Sublimation at the trough wall produces a growing sublimation lag that modulates further retreat; however, winds move material off the retreating slope faces, thinning the lag. Discontinuities in stratigraphy seen by radar highlight Trough Migration Paths (TMPs), which provide a record of the troughs' position, formation, and evolution to the present day. We investigate two adjacent troughs presently near 87°N to evaluate the mass balance conditions at those sites. We constrain the contribution of insolation‐induced sublimation to the migration in the observed TMPs. We present a phenomenological model that combines our simulations of the sublimation conditions at paleo‐trough surfaces with accumulation rates to create synthetic TMPs that are tunable to the observations. Models using nominal values of lag diffusivity, albedo, and atmospheric water vapor abundance and in which the trough walls have been covered in a lag on the order of millimeters thick and formed ~2.3 Myr ago match the observed trough migration and align with expectations of trough ages. Thicker lags, and/or older troughs, would generate TMPs of constant slope, which does not match the observed paths. We demonstrate the viability of our new theoretical model for predicting conditions that lead to trough migration, allowing us to connect observable TMPs to Martian climate processes.
Let’s Start Teaching Scientists How to Withstand Attacks on Fact
Authors: Paasche �yvind , �kesson Henning
Published: March 2019

We need to imbue students with a central value: Adherence to the scientific method is, in itself, good citizenship.
Widespread losses of pollinating insects in Britain
Authors: Powney Gary D. , Carvell Claire , Edwards Mike , Morris Roger K. A. , Roy Helen E. , Woodcock Ben A. , Isaac Nick J. B.
Published: March 2019

Pollination is a critical ecosystem service underpinning the productivity of agricultural systems across the world. Wild insect populations provide a substantial contribution to the productivity of many crops and seed set of wild flowers. However, large-scale evidence on species-specific trends among wild pollinators are lacking. Here we show substantial inter-specific variation in pollinator trends, based on occupancy models for 353 wild bee and hoverfly species in Great Britain between 1980 and 2013. Furthermore, we estimate a net loss of over 2.7 million occupied 1 km2 grid cells across all species. Declines in pollinator evenness suggest that losses were concentrated in rare species. In addition, losses linked to specific habitats were identified, with a 55% decline among species associated with uplands. This contrasts with dominant crop pollinators, which increased by 12%, potentially in response agri-environment measures. The general declines highlight a fundamental deterioration in both wider biodiversity and non-crop pollination services.
Rapid mantle flow with power-law creep explains deformation after the 2011 Tohoku mega-quake
Authors: Agata Ryoichiro , Barbot Sylvain D. , Fujita Kohei , Hyodo Mamoru , Iinuma Takeshi , Nakata Ryoko , Ichimura Tsuyoshi , Hori Takane
Published: March 2019

The deformation transient following large subduction zone earthquakes is thought to originate from the interaction of viscoelastic flow in the asthenospheric mantle and slip on the megathrust that are both accelerated by the sudden coseismic stress change. Here, we show that combining insight from laboratory solid-state creep and friction experiments can successfully explain the spatial distribution of surface deformation in the first few years after the 2011 Mw 9.0 Tohoku-Oki earthquake. The transient reduction of effective viscosity resulting from dislocation creep in the asthenosphere explains the peculiar retrograde displacement revealed by seafloor geodesy, while the slip acceleration on the megathrust accounts for surface displacements on land and offshore outside the rupture area. Our results suggest that a rapid mantle flow takes place in the asthenosphere with temporarily decreased viscosity in response to large coseismic stress, presumably due to the activation of power-law creep during the post-earthquake period.
IL-4 together with IL-1β induces antitumor Th9 cell differentiation in the absence of TGF-β signaling
Authors: Xue Gang , Jin Guangxu , Fang Jing , Lu Yong
Published: March 2019

IL-9-producing CD4+(Th9) cells are a subset of CD4+T-helper cells that are endowed with powerful antitumor capacity. Both IL-4 and TGF-β have been reported to be indispensable for Th9 cell-priming and differentiation. Here we show, by contrast, that Th9 cell development can occur in the absence of TGF-β signaling. When TGF-β was replaced by IL-1β, the combination of IL-1β and IL-4 efficiently promoted IL-9-producing T cells (Th9IL-4+IL-1β). Th9IL-4+ IL-1βcells are phenotypically distinct T cells compared to classic Th9 cells (Th9IL-4+TGF-β) and other Th cells, and are enriched for IL-1 and NF-κB gene signatures. Inhibition of NF-κB but not TGF-β-signaling negates IL-9 production by Th9IL-4+IL-1βcells. Furthermore, when compared with classic Th9IL-4+TGF-βcells, Th9IL-4+IL-1βcells are less exhausted, exhibit cytotoxic T effector gene signature and tumor killing function, and exert a superior antitumor response in a mouse melanoma model. Our study thus describes an alternative pathway for Th9 cell differentiation and provides a potential avenue for antitumor therapies.
Probing boundary conditions of Productive Failure and analyzing the role of young students’ collaboration
Authors: Mazziotti Claudia , Rummel Nikol , Deiglmayr Anne , Loibl Katharina
Published: March 2019

Productive Failure (PF) facilitates students’ conceptual knowledge by delaying instruction until after problem solving. While PF is well investigated in middle and high school students, little is known about its effectiveness in younger students. Studies in younger samples, which implemented delayed instruction designs similar to those used in PF studies, showed mixed results. However, these studies did not implement two core design components of PF: (1) contrasting and comparing student-generated solutions and the canonical solution during the instructional phase (contrasting activity), and (2) students’ collaboration in small groups during the initial problem-solving phase. Both components can be expected to contribute to the effectiveness of PF. In a quasi-experimental study with 228 fifth graders, we implemented the first component (contrasting activity) with all students to establish whether under this condition, problem solving prior to instruction would be more effective for younger students’ conceptual knowledge acquisition than direct instruction (i.e., problem solving after instruction). Further, we experimentally tested the effect of the second component (collaborative vs. individual problem solving) on students’ conceptual knowledge and the number of solution ideas generated during initial problem solving. We found no empirical support for either of our hypotheses. To explore the extent to which students’ collaboration actually achieved its potential and relates to students’ conceptual knowledge and solution ideas in PF, we conducted analyses of collaborative processes. Our study adds to the mixed results regarding the superiority of problem solving prior to instruction for young students, thus opening the discussion about age-related prerequisites as boundary conditions for PF.
Author Correction: Draft genomic and transcriptome resources for marine chelicerate Tachypleus tridentatus
Authors: Liao Yong Yan , Xu Peng Wei , Kwan Kit Yue , Ma Zhi Yun , Fang Huai Yi , Xu Jun Yang , Wang Peng Liang , Yang Shao Yu , Xie Shang Bo , Xu Shu Qing , Dan Qian  , Li Wei Feng , Bai Li Rong , Zhou Da Jie , Zhang Yan Qiu , Lei Juan , Liu Ke , Li Fan , Li Jian , Zhu Peng , Wang Yu Jun , Wu Hai Ping , Xu You Hou , Huang Hu , Zhang Chi , Liu Jin Xia , Han Jun Feng
Published: March 2019

In the original version of this Data Descriptor the word “Gulf” was incorrectly spelled in the affiliation “Ocean College, Beibu Gulf University, Qinzhou, 535011, Guangxi, China”. This has now been corrected in both the HTML and PDF versions.
Suboptimal human multisensory cue combination
Authors: Arnold Derek H. , Petrie Kirstie , Murray Cailem , Johnston Alan
Published: March 2019

Information from different sensory modalities can interact, shaping what we think we have seen, heard, or otherwise perceived. Such interactions can enhance the precision of perceptual decisions, relative to those based on information from a single sensory modality. Several computational processes could account for such improvements. Slight improvements could arise if decisions are based on multiple independent sensory estimates, as opposed to just one. Still greater improvements could arise if initially independent estimates are summed to form a single integrated code. This hypothetical process has often been described as optimal when it results in bimodal performance consistent with a summation of unimodal estimates weighted in proportion to the precision of each initially independent sensory code. Here we examine cross-modal cue combination for audio-visual temporal rate and spatial location cues. While suggestive of a cross-modal encoding advantage, the degree of facilitation falls short of that predicted by a precision weighted summation process. These data accord with other published observations, and suggest that precision weighted combination is not a general property of human cross-modal perception.
A compact tunable quadrupole lens for brighter and sharper ultra-fast electron diffraction imaging
Authors: Yang Xi , Yu Lihua , Smaluk Victor , Wang Guimei , Hidaka Yoshitreu , Shaftan Timur , Doom Lewis , Padrazo Danny , Li Junjie , Fedurin Mikhail , Wan Weishi , Zhu Yimei
Published: March 2019

In this article, we report our proof-of-principle design and experimental commissioning of a broadly tunable and low-cost transverse focusing lens system for MeV-energy electron beams. The lens system based on electromagnetic (EM) quadrupoles has been built as a part of the existing instrument for ultra-fast electron diffraction (UED) experiments at the Accelerator Test Facility II (ATF-II) at Brookhaven National Laboratory (BNL). We experimentally demonstrated the independent control of the size and divergence of the beam with the charge ranging from 1 to 13 pC. The charge density and divergence of the beam at the sample are the most important factors determining the quality of the Bragg-diffraction image (BDI). By applying the Robust Conjugate Directional Search (RCDS) algorithm for online optimization of the quadrupoles, the transverse beam size can be kept constant down to 75 µm from 1 to 13 pC. The charge density is nearly two orders of magnitude higher than the previously achieved value using a conventional solenoid. Using the BDI method we were able to extract the divergence of the beam in real-time and apply it to the emittance measurement for the first time. Our results agree well with simulations and with the traditional quadrupole scan method. The real-time divergence measurement opens the possibility of online optimization of the beam divergence (<0.2 mrad) at the sample with the increased beam charge. This optimization is crucial for the future development of single-shot ultra-fast electron microscope (UEM). Finally, we demonstrated BDI with significant improvement, up to 3 times higher peak intensity and 2 times sharper Bragg-diffraction peaks at 13 pC. The charge is now limited by the laser power and increasing charge may improve the quality of BDI further. The capability we demonstrated here provides us with opportunities for new sciences using near-parallel, bright and ultrafast electron beams for single-shot imaging, to directly visualize the dynamics of defects and nanostructured materials, or even record molecular movie, which are impossible using present electron-beam technologies.
Mitochondria transfer from mesenchymal stem cells structurally and functionally repairs renal proximal tubular epithelial cells in diabetic nephropathy in vivo
Authors: Konari Naoto , Nagaishi Kanna , Kikuchi Shin , Fujimiya Mineko
Published: March 2019

The underlying therapeutic mechanism of renal tubular epithelium repair of diabetic nephropathy (DN) by bone marrow-derived mesenchymal stem cells (BM-MSCs) has not been fully elucidated. Recently, mitochondria (Mt) transfer was reported as a novel action of BM-MSCs to rescue injured cells. We investigated Mt transfer from systemically administered BM-MSCs to renal proximal tubular epithelial cells (PTECs) in streptozotocin (STZ)-induced diabetic animals. BM-MSCs also transferred their Mt to impaired PTECs when co-cultured in vitro, which suppressed apoptosis of impaired PTECs. Additionally, BM-MSC-derived isolated Mt enhanced the expression of mitochondrial superoxide dismutase 2 and Bcl-2 expression and inhibited reactive oxygen species (ROS) production in vitro. Isolated Mt also inhibited nuclear translocation of PGC-1α and restored the expression of megalin and SGLT2 under high glucose condition (HG) in PTECs. Moreover, isolated Mt directly injected under the renal capsule of STZ rats improved the cellular morphology of STZ-PTECs, and the structure of the tubular basement membrane and brush border in vivo. This study is the first to show Mt transfer from systemically administered BM-MSCs to damaged PTECs in vivo, and the first to investigate mechanisms underlying the potential therapeutic effects of Mt transfer from BM-MSCs in DN.
Development of model web-server for crop variety identification using throughput SNP genotyping data
Authors: Singh Rajender , Iquebal M. A. , Mishra C. N. , Jaiswal Sarika , Kumar Deepender , Raghav Nishu , Paul Surinder , Sheoran Sonia , Sharma Pradeep , Gupta Arun , Tiwari Vinod , Angadi U. B. , Kumar Neeraj , Rai Anil , Singh G. P. , Kumar Dinesh , Tiwari Ratan
Published: March 2019

Crop varieties or genotypes of a given species are pivotal for agricultural production and ownership, management and improvement of their germplasm is a great challenge. Its morphological identification requires time, cost and descriptors are often compromised statistically due to phenotypic plasticity. Development of DNA based signature of varieties can overcome these limitations. There is a global need to implement world trade organization (WTO) and intellectual property rights (IPR) guidelines of Plant Breeders Rights (PBR) where DUS (distinctness, uniformity and stability) testing can be supplemented by DNA profile. Universalization and minimization of SNP number without compromising identification accuracy is the major challenge in development of varietal profile by rapid genotype assay. Besides this, there is no server-based approach reducing computational skill with global accessibility of referral phenotypic and genotypic data. We report world’s first model web server for crop variety identification using >350 Indian wheat varieties and Axiom 35 K SNP chip data. Standard filtering and linkage disequilibrium approach were used to develop varietal signature in Linux using HTML, Java, PHP and MySQL with provision of QR code generator to facilitate bar-coding. Phylogenetic tree constructed by selected SNPs confirms six major trait based clusters of varieties and their pedigree. Our user friendly server based tool, VISTa (Variety Identification System of Triticum aestivum) (http://webtom.cabgrid.res.in/vista) can be used in DUS testing having dispute resolution of sovereignty and access benefit sharing (ABS) issues. This model approach can be used in other crops with pan-global level management of crop germplasm in endeavour of crop productivity.
Practical realization of a sub-λ/2 acoustic jet
Authors: Veira Canle Daniel , Kekkonen Tuukka , Mäkinen Joni , Puranen Tuomas , Nieminen Heikki J. , Kuronen Antti , Franssila Sami , Kotiaho Tapio , Salmi Ari , Hæggström Edward
Published: March 2019

Studies in optics and acoustics have employed metamaterial lenses to achieve sub-wavelength localization, e.g. a recently introduced concept called ‘acoustojet’ which in simulations localizes acoustic energy to a spot smaller than λ/2. However previous experimental results on the acoustojet have barely reached λ/2-wide localization. Here we show, by simulations and experiments, that a sub-λ/2 wide localization can be achieved by translating the concept of a photonic jet into the acoustic realm. We performed nano- to macroscale molecular dynamics (MD) and finite element method (FEM) simulations as well as macroscale experiments. We demonstrated that by choosing a suitable size cylindrical lens, and by selecting the speed-of-sound ratio between the lens material(s) and the surrounding medium, an acoustic jet (‘acoustic sheet’) is formed with a full width at half maximum (FWHM) less than λ/2. The results show, that the acoustojet approach can be experimentally realized with easy-to-manufacture acoustic lenses at the macroscale. MD simulations demonstrate that the concept can be extended to coherent phonons at nanoscale. Finally, our FEM simulations identify some micrometer size structures that could be realized in practice. Our results may contribute to starting a new era of super resolution acoustic imaging: We foresee that jet generating constructs can be readily manufactured, since suitable material combinations can be found from nanoscale to macroscale. Tight focusing of mechanical energy is highly desirable in e.g. electronics, materials science, medicine, biosciences, and energy harvesting.
The putative tumour suppressor protein Latexin is secreted by prostate luminal cells and is downregulated in malignancy
Authors: Seed Robert I. , Taurozzi Alberto J. , Wilcock Daniel J. , Nappo Giovanna , Erb Holger H. H. , Read Martin L. , Gurney Mark , Archer Leanne K. , Ito Saburo , Rumsby Martin G. , Petrie John L. , Clayton Aled , Maitland Norman J. , Collins Anne T.
Published: March 2019

Loss of latexin (LXN) expression negatively correlates with the prognosis of several human cancers. Despite association with numerous processes including haematopoietic stem cell (HSC) fate, inflammation and tumour suppression, a clearly defined biological role for LXN is still lacking. Therefore, we sought to understand LXN expression and function in the normal and malignant prostate to assess its potential as a therapeutic target. Our data demonstrate that LXN is highly expressed in normal prostate luminal cells but downregulated in high Gleason grade cancers. LXN protein is both cytosolic and secreted by prostate cells and expression is directly and potently upregulated by all-trans retinoic acid (atRA). Whilst overexpression of LXN in prostate epithelial basal cells did not affect cell fate, LXN overexpression in the luminal cancer line LNCaP reduced plating efficiency. Transcriptome analysis revealed that LXN overexpression had no direct effects on gene expression but had significant indirect effects on important genes involved in both retinoid metabolism and IFN-associated inflammatory responses. These data highlight a potential role for LXN in retinoid signaling and inflammatory pathways. Investigating the effects of LXN on immune cell function in the tumour microenvironment (TME) may reveal how observed intratumoural loss of LXN affects the prognosis of many adenocarcinomas.
Progesterone elevation on the day of hCG trigger has detrimental effect on live birth rate in low and intermediate ovarian responders, but not in high responders
Authors: Wu Ze , Dong Yunhua , Ma Yanping , Li Yonggang , Li Lei , Lin Na , Li Yunxiu , Zhuan Li , Bai Yun , Luo Xi , Kang Xiaomin
Published: March 2019

Progesterone elevation (PE) on the day of hCG trigger is associated with decreased pregnancy outcome in fresh cycles. Evidence for this comes from overall patient estimates that mostly ignore different ovarian responses. To compare the impacts of PE on the day of hCG trigger on live birth rates (LBs) in low, intermediate and high ovarian responders and to explore the cut-off value for PE in different populations according to the ovarian response, we retrospectively analyzed a total of 2,351 patients receiving fresh assisted reproduction technology (ART) transfer cycles with GnRH agonist using a long or short protocol. Trend and multivariate logistic regression analyses were performed to identify the cutoff values of PE and to evaluate the effects of PE on LB rates (LBRs) in different ovarian responders. The study found that PE has a detrimental effect on LBRs in low to intermediate ovarian responders rather than in high responders. The cut-off values for PE were 1.0 ng/mL and 2.0 ng/mL for low and intermediate ovarian responders, respectively. The different associations between PE and LBRs according to ovarian response could more accurately predict the prognosis of the IVF cycle and could be used to optimize the treatment of patients undergoing In Vitro Fertilization (IVF)/ Intracytoplasmic Sperm Injection (ICSI).
Identification and characterization of the lncRNA signature associated with overall survival in patients with neuroblastoma
Authors: Yerukala Sathipati Srinivasulu , Sahu Divya , Huang Hsuan-Cheng , Lin Yenching , Ho Shinn-Ying
Published: March 2019

Neuroblastoma (NB) is a commonly occurring cancer among infants and young children. Recently, long non-coding RNAs (lncRNAs) have been using as prognostic biomarkers for therapeutics and interventions in various cancers. Considering the poor survival of NB, the lncRNA-based therapeutic strategies must be improved. This work proposes an overall survival time estimator called SVR-NB to identify the lncRNA signature that is associated with the overall survival of patients with NB. SVR-NB is an optimized support vector regression (SVR)-based method that uses an inheritable bi-objective combinatorial genetic algorithm for feature selection. The dataset of 231 NB patients that contains overall survival information and expression profiles of 783 lncRNAs was used to design and evaluate SVR-NB from the database of gene expression omnibus accession GSE62564. SVR-NB identified a signature of 35 lncRNAs and achieved a mean squared correlation coefficient of 0.85 and a mean absolute error of 0.56 year between the actual and estimated overall survival time using 10-fold cross-validation. Further, we ranked and characterized the 35 lncRNAs according to their contribution towards the estimation accuracy. Functional annotations and co-expression gene analysis of LOC440896, LINC00632, and IGF2-AS revealed the association of co-expressed genes in Kyoto Encyclopedia of Genes and Genomes pathways.
Synergy between the alteration in the N-terminal region of butyrylcholinesterase K variant and apolipoprotein E4 in late-onset Alzheimer’s disease
Authors: Jasiecki Jacek , Limon-Sztencel Anna , Żuk Monika , Chmara Magdalena , Cysewski Dominik , Limon Janusz , Wasąg Bartosz
Published: March 2019

While the life expectancy of the population has increased, Alzheimer’s disease (AD) has emerged as one of the greatest health problems of old age. AD is characterized by neuronal loss and cognitive decline. In the AD brain, there is a decrease in levels of acetylcholinesterase (AChE) and an increase in the levels of the related enzyme butyrylcholinesterase (BChE), that accumulate in plaques and tangles. Apolipoprotein E (ApoE) is a major cholesterol carrier and plays an important role in maintaining lipid homeostasis. APOE-ε4 constitutes the most important known genetic risk factor for late-onset AD. It has been proposed that the BCHE-K allele (Ala539Thr) acts in synergy with the APOE-ε4 allele to promote risk for AD. However, there is insufficient evidence to support a correlation. Most studies focused only on the coding regions of the genes. In this study, we analyzed sequence regions beyond the BCHE coding sequence. We found synergy between APOE-ε4 and SNPs localized in 5′UTR (rs1126680) and in intron 2 (rs55781031) of the BCHE-K allele (rs1803274) in 18% of patients with late-onset AD (n = 55). The results show that the coexistence of the APOE-ε4 allele and 3 SNPs in the BCHE gene is associated with a highly elevated risk of late-onset AD. SNP (rs1126680) in 5′UTR of the BCHE gene is located 32 nucleotides upstream of the 28 amino acid signal peptide. Mass spectrometry analysis of the BChE protein produced by SNP (rs1126680) showed that the mutation caused an in frame N-terminal extension of 41 amino acids of the BChE signal peptide. The resultant variant with a 69 amino acid signal peptide, designated N-BChE, may play a role in development of AD.
Genetic structure in the paternal lineages of South East Spain revealed by the analysis of 17 Y-STRs
Authors: Saiz María , Alvarez-Cubero Maria Jesus , Lorente José Antonio , Alvarez Juan Carlos , Martinez-Gonzalez Luis Javier
Published: March 2019

The genetic data of 17 Y chromosome short tandem repeats in 146 unrelated donor residents in the provinces of Granada, Málaga, and Almería (GMA) were analyzed to determine the genetic legacy of the male inhabitants of the former Kingdom of Granada. A total of 139 unique haplotypes were identified. Observed allele frequencies and haplogroup frequencies were also analyzed. By AMOVA and STRUCTURE analysis, the populations of the 3 provinces could be treated genetically as a single population. The most frequent haplogroup was R1b1b2 (58.22%). By network analysis of all individuals, we observed a distribution according to haplogroup assignment. To improve the characterization of GMA population, it was compared with those of North Africa, the Iberian Peninsula, and southern Europe. In our analysis of allele frequencies and genetic distances, the GMA population lay within the Spanish population group. Further, in the STRUCTURE analysis, there was no African component in the GMA population, confirming that, based on our genetic markers, the GMA population does not reflect any male genetic influence of the North African people. The presence of African haplogroups in the GMA population is irrelevant when their frequency is compared with those in other European populations.
The physiology of forager hydration and variation among harvester ant (Pogonomyrmex barbatus) colonies in collective foraging behavior
Authors: Friedman Daniel A. , Greene Michael J. , Gordon Deborah M.
Published: March 2019

Ants are abundant in desiccating environments despite their high surface area to volume ratios and exposure to harsh conditions outside the nest. Red harvester ant (Pogonomyrmex barbatus) colonies must spend water to obtain water: colonies lose water as workers forage outside the nest, and gain water metabolically through seeds collected in foraging trips. Here we present field experiments showing that hydratedP. barbatusforagers made more foraging trips than unhydrated nestmates. The positive effect of hydration on foraging activity is stronger as the risk of desiccation increases. Desiccation tests showed that foragers of colonies that reduce foraging in dry conditions are more sensitive to water loss, losing water and motor coordination more rapidly in desiccating conditions, than foragers of colonies that do not reduce foraging in dry conditions. Desiccation tolerance is also associated with colony reproductive success. Surprisingly, foragers that are more sensitive to water loss are from colonies more likely to produce offspring colonies. This could be because the foragers of these colonies conserve water with a more cautious response to desiccation risk. An ant’s hydration status may influence its response to the olfactory interactions that regulate its decision to leave the nest to forage. Thus variation among ant colonies in worker physiology and response to ambient conditions may contribute to ecologically significant differences among colonies in collective behavior.
Quantifying circulating cell-free DNA in humans
Authors: Meddeb Romain , Dache Zahra Al Amir , Thezenas Simon , Otandault Amaëlle , Tanos Rita , Pastor Brice , Sanchez Cynthia , Azzi Joelle , Tousch Geoffroy , Azan Simon , Mollevi Caroline , Adenis Antoine , El Messaoudi Safia , Blache Philippe , Thierry Alain R.
Published: March 2019

To our knowledge, this is the first comprehensive study on the influence of several pre-analytical and demographic parameters that could be a source of variability in the quantification of nuclear and mitochondrial circulating DNA (NcirDNA and McirDNA). We report data from a total of 222 subjects, 104 healthy individuals and 118 metastatic colorectal cancer (mCRC) patients. Approximately 50,000 and 3,000-fold more mitochondrial than nuclear genome copies were found in the plasma of healthy individuals and mCRC patients, respectively. In healthy individuals, NcirDNA concentration was statistically influenced by age (p = 0.009) and gender (p = 0.048). Multivariate analysis with logistic regression specified that age over 47 years-old was predictive to have higher NcirDNA concentration (OR = 2.41; p = 0.033). McirDNA concentration was independent of age and gender in healthy individuals. In mCRC patients, NcirDNA and McirDNA levels were independent of age, gender, delay between food intake and blood collection, and plasma aspect, either with univariate or multivariate analysis. Nonetheless, ad hoc study suggested that menopause and blood collection time might have tendency to influence cirDNA quantification. In addition, high significant statistical differences were found between mCRC patients and healthy individuals for NcirDNA (p < 0.0001), McirDNA (p < 0.0001) and McirDNA/NcirDNA ratio (p < 0.0001). NcirDNA and McirDNA levels do not vary in the same way with regards to cancer vs healthy status, pre-analytical and demographic factors.
Should the outcome of focal photocoagulation for center-sparing diabetic macular edema require expanding the definition of center involvement?
Authors: Somilleda-Ventura Selma Alin , Razo Blanco-Hernández Dulce M. , Serafín-Solís Surisadai , Lima-Gómez Virgilio
Published: March 2019

Photocoagulation may still be a therapeutic choice for center-sparing diabetic macular edema. We compared the visual evolution after photocoagulation, in eyes with focal diabetic macular edema, stratified per the location of thickening with optical coherence tomography. We evaluated people with type 2 diabetes and focal diabetic macular edema, before and three weeks after focal photocoagulation. We divided the sample by edema location: central (group1); paracentral (group 2) and pericentral (group 3) and compared the proportions of eyes with baseline visual impairment, visual improvement, and visual deterioration between groups; central edema was evaluated with logistic regression, as an explaining variable of baseline visual impairment and visual improvement. The study included 160 eyes: 77 in group 1, 20 in group 2, 63 in group 3; baseline visual impairment was more frequent in groups 1 and 2 (52.6%) than in group 3 (28.6%, p = 0.002, OR 2.77) and as common in groups 1 (51.9%) and 2 (55.0%, p = 0.8). The proportions of visual improvement and visual deterioration did not differ between groups (p > 0.05). The outcome after focal photocoagulation was similar in paracentral (considered center-sparing) and central macular edema; the definition of center involvement, which needs intravitreal antiangiogenics, should expand to include paracentral thickening.
Octacosanol and policosanol prevent high-fat diet-induced obesity and metabolic disorders by activating brown adipose tissue and improving liver metabolism
Authors: Sharma Rahul , Matsuzaka Takashi , Kaushik Mahesh K. , Sugasawa Takehito , Ohno Hiroshi , Wang Yunong , Motomura Kaori , Shimura Takuya , Okajima Yuka , Mizunoe Yuhei , Ma Yang , Saber Zahara M. , Iwasaki Hitoshi , Yatoh Shigeru , Suzuki Hiroaki , Aita Yuichi , Han Song-iee , Takeuchi Yoshinori , Yahagi Naoya , Miyamoto Takafumi , Sekiya Motohiro , Nakagawa Yoshimi , Shimano Hitoshi
Published: March 2019

Brown adipose tissue (BAT) is an attractive therapeutic target for treating obesity and metabolic diseases. Octacosanol is the main component of policosanol, a mixture of very long chain aliphatic alcohols obtained from plants. The current study aimed to investigate the effect of octacosanol and policosanol on high-fat diet (HFD)-induced obesity. Mice were fed on chow, or HFD, with or without octacosanol or policosanol treatment for four weeks. HFD-fed mice showed significantly higher body weight and body fat compared with chow-fed mice. However, mice fed on HFD treated with octacosanol or policosanol (HFDo/p) showed lower body weight gain, body fat gain, insulin resistance and hepatic lipid content. Lower body fat gain after octacosanol or policosanol was associated with increased BAT activity, reduced expression of genes involved in lipogenesis and cholesterol uptake in the liver, and amelioration of white adipose tissue (WAT) inflammation. Moreover, octacosanol and policosanol significantly increased the expression of Ffar4, a gene encoding polyunsaturated fatty acid receptor, which activates BAT thermogenesis. Together, these results suggest that octacosanol and policosanol ameliorate diet-induced obesity and metabolic disorders by increasing BAT activity and improving hepatic lipid metabolism. Thus, these lipids represent promising therapeutic targets for the prevention and treatment of obesity and obesity-related metabolic disorders.
From Louvain to Leiden: guaranteeing well-connected communities
Authors: Traag V. A. , Waltman L. , van Eck N. J.
Published: March 2019

Community detection is often used to understand the structure of large and complex networks. One of the most popular algorithms for uncovering community structure is the so-called Louvain algorithm. We show that this algorithm has a major defect that largely went unnoticed until now: the Louvain algorithm may yield arbitrarily badly connected communities. In the worst case, communities may even be disconnected, especially when running the algorithm iteratively. In our experimental analysis, we observe that up to 25% of the communities are badly connected and up to 16% are disconnected. To address this problem, we introduce the Leiden algorithm. We prove that the Leiden algorithm yields communities that are guaranteed to be connected. In addition, we prove that, when the Leiden algorithm is applied iteratively, it converges to a partition in which all subsets of all communities are locally optimally assigned. Furthermore, by relying on a fast local move approach, the Leiden algorithm runs faster than the Louvain algorithm. We demonstrate the performance of the Leiden algorithm for several benchmark and real-world networks. We find that the Leiden algorithm is faster than the Louvain algorithm and uncovers better partitions, in addition to providing explicit guarantees.
Low Lattice Thermal Conductivity of a Two-Dimensional Phosphorene Oxide
Authors: Lee Seungjun , Kang Seoung-Hun , Kwon Young-Kyun
Published: March 2019

A fundamental understanding of the phonon transport mechanism is important for optimizing the efficiency of thermoelectric devices. In this study, we investigate the thermal transport properties of the oxidized form of phosphorene called phosphorene oxide (PO) by solving phonon Boltzmann transport equation based on first-principles density functional theory. We reveal that PO exhibits a much lower thermal conductivity (2.42–7.08 W/mK at 300 K) than its pristine counterpart as well as other two-dimensional materials. To comprehend the physical origin of such low thermal conductivity, we scrutinize the contribution of each phonon branch to the thermal conductivity by evaluating various mode-dependent quantities including Grüneisen parameters, anharmonic three-phonon scattering rate, and phase space of three-phonon scattering processes. Our results show that its flexible puckered structure of PO leads to smaller sound velocities; its broken-mirror symmetry allows more ZA phonon scattering; and the relatively-free vibration of dangling oxygen atoms in PO gives rise to additional scattering resulting in further reduction in the phonon lifetime. These results can be verified by the fact that PO has larger phase space for three-phonon processes than phosphorene. Furthermore we show that the thermal conductivity of PO can be optimized by controlling its size or its phonon mean free path, indicating that PO can be a promising candidate for low-dimensional thermoelectric devices.
Green synthesis of nitrogen-doped self-assembled porous carbon-metal oxide composite towards energy and environmental applications
Authors: Ghosh Arpita , Ghosh Sreetama , Seshadhri Garapati Meenakshi , Ramaprabhu Sundara
Published: March 2019

Increasing environmental pollution, shortage of efficient energy conversion and storage devices and the depletion of fossil fuels have triggered the research community to look for advanced multifunctional materials suitable for different energy-related applications. Herein, we have discussed a novel and facile synthesis mechanism of such a carbon-based nanocomposite along with its energy and environmental applications. In this present work, nitrogen-doped carbon self-assembled into ordered mesoporous structure has been synthesized via an economical and environment-friendly route and its pore generating mechanism depending on the hydrogen bonding interaction has been highlighted. Incorporation of metal oxide nanoparticles in the porous carbon network has significantly improved CO2 adsorption and lithium storage capacity along with an improvement in the catalytic activity towards Oxygen Reduction Reaction (ORR). Thus our present study unveils a multifunctional material that can be used in three different fields without further modifications.
Familiarization with treadmill walking: How much is enough?
Authors: Meyer Christian , Killeen Tim , Easthope Christopher S. , Curt Armin , Bolliger Marc , Linnebank Michael , Zörner Björn , Filli Linard
Published: March 2019

Treadmill-based gait analysis is widely used to investigate walking pathologies and quantify treatment effects on locomotion. Differential sensorimotor conditions during overground vs. treadmill walking necessitate initial familiarization to treadmill walking. Currently, there is no standardized treadmill acclimatization protocol and insufficient familiarization potentially confounds analyses. We monitored initial adaptations to treadmill walking in 40 healthy adults. Twenty-six walking parameters were assessed over 10 minutes with marker-based kinematic analysis and acclimatization profiles were generated. While 16 walking parameters demonstrated initial acclimatization followed by plateau performance, ten parameters remained stable. Distal lower limb control including ankle range of motion, toe trajectory and foot clearance underwent substantial adaptations. Moreover, intralimb coordination and gait variability also demonstrated acclimatization, while measures of symmetry and interlimb coordination did not. All parameters exhibiting a plateau after acclimatization did so within 6–7 minutes (425 strides). Older participants and those naïve to treadmill walking showed adaptations with higher amplitudes but over similar timescales. Our results suggest a minimum of 6 minutes treadmill acclimatization is required to reach a stable performance, and that this should suffice for both older and naïve healthy adults. The presented data aids in optimizing treadmill-based gait analysis and contributes to improving locomotor assessments in research and clinical settings.