bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tight clustering for large datasets with an application to gene expression data
Authors: Karmakar Bikram , Das Sarmistha , Bhattacharya Sohom , Sarkar Rohan , Mukhopadhyay Indranil 
Published: February 2019

AbstractThis article proposes a practical and scalable version of the tight clustering algorithm. The tight clustering algorithm provides tight and stable relevant clusters as output while leaving a set of points as noise or scattered points, that would not go into any cluster. However, the computational limitation to achieve this precise target of tight clusters prohibits it from being used for large microarray gene expression data or any other large data set, which are common nowadays. We propose a pragmatic and scalable version of the tight clustering method that is applicable to data sets of very large size and deduce the properties of the proposed algorithm. We validate our algorithm with extensive simulation study and multiple real data analyses including analysis of real data on gene expression.
Ovarian Hormone-dependent and Spinal ERK Activation-regulated Nociceptive Hypersensitivity in Female Rats with Acid Injection-induced Chronic Widespread Muscle Pain
Authors: Chang Ju-Hsin , Tsai Shih-Ying , Zeng Yen-Jing , Liu Yu-Cheng , Li Chi-Yuan , Chen Kuen-Bao , Wen Yeong-Ray 
Published: February 2019

AbstractSymptoms of chronic widespread muscle pain (CWP) meet most of the diagnostic criteria for fibromyalgia syndrome, which is prevalent in females. We used an acid injection-induced muscle pain (AIMP) model to mimic CWP. After female rats received an ovariectomy (OVX), acid saline solution was injected into the left gastrocnemius muscle. Time courses of changes in pain behaviours and p-ERK in the spinal cord were compared between groups. Intrathecal injections of oestradiol (E2) to the OVX group before two acid injections and E2 or progesterone (P4) injections in male rats were compared to evaluate hormone effects. We found that repeated acid injections produced mechanical hypersensitivity and enhanced p-ERK expression in the spinal dorsal horn. OVX rats exhibited significantly less tactile allodynia than did the rats in the other groups. The ERK inhibitor U0126 alleviated mechanical allodynia with lower p-ERK expression in the sham females but did not affect the OVX rats. Intrathecal E2 reversed the attenuated mechanical hypersensitivity in the OVX group, and E2 or P4 induced transient hyperalgesia in male rats. Accordingly, our results suggested that ovarian hormones contribute to AIMP through a spinal p-ERK-mediated pathway. These findings may partially explain the higher prevalence of fibromyalgia in females than males.
Mixed stock analysis of juvenile green turtles aggregating at two foraging grounds in Fiji reveals major contribution from the American Samoa Management Unit
Authors: Piovano Susanna , Batibasaga Aisake , Ciriyawa Ana , LaCasella Erin L. , Dutton Peter H. 
Published: February 2019

AbstractIn this study we assessed the breeding population, or Management Unit (MU), origin of green turtles (Chelonia mydas) present at Yadua Island and Makogai Island foraging grounds in Fiji, central South Pacific. Based on analysis of mitochondrial (mt) DNA sequences from 150 immature green turtles caught during surveys carried out in 2015–2016, we identified a total of 18 haplotypes, the most common being CmP22.1 (44%) which is a primary haplotype characterizing the American Samoa breeding population. Results of a Bayesian mixed-stock analysis reveals that the two foraging grounds are used by green turtles from the American Samoa MU (72%, Credible Interval (CI): 56–87%), New Caledonia MU (17%, CI: 6–26%) and French Polynesia MU (7%, CI: 0–23%). The prominence of the contribution we found from the American Samoa MU compared to that of French Polynesia, both which have historic telemetry and tagging data showing connectivity with Fijian foraging areas, may reflect the current relative abundance of these two nesting populations and draws attention to a need to update population surveys and identify any significant nesting in Fiji that may have been overlooked.
Proteasome β5 subunit overexpression improves proteostasis during aging and extends lifespan in Drosophila melanogaster
Authors: Nguyen Nga N. , Rana Anil , Goldman Camille , Moore Rhiannon , Tai Justin , Hong Yongchan , Shen Jingyi , Walker David W. , Hur Jae H. 
Published: February 2019

AbstractThe β5 subunit of the proteasome has been shown in worms and in human cell lines to be regulatory. In these models, β5 overexpression results in upregulation of the entire proteasome complex which is sufficient to increase proteotoxic stress resistance, improve metabolic parameters, and increase longevity. However, fundamental questions remain unanswered, including the temporal requirements for β5 overexpression and whether β5 overexpression can extend lifespan in other species. To determine if adult-only overexpression of the β5 subunit can increase proteasome activity in a different model, we characterized phenotypes associated with β5 overexpression in Drosophila melanogaster adults. We find that adult-only overexpression of the β5 subunit does not result in transcriptional upregulation of the other subunits of the proteasome as they do in nematodes and human cell culture. Despite this lack of a regulatory role, boosting β5 expression increases the chymotrypsin-like activity associated with the proteasome, reduces both the size and number of ubiquitinated protein aggregates in aged flies, and increases longevity. Surprisingly, these phenotypes were not associated with increased resistance to acute proteotoxic insults or improved metabolic parameters.
deMix: Decoding Deuterated Distributions from Heterogeneous Protein States via HDX-MS
Authors: Na Seungjin , Lee Jae-Jin , Joo Jong Wha J. , Lee Kong-Joo , Paek Eunok 
Published: February 2019

AbstractCharacterization of protein structural changes in response to protein modifications, ligand or chemical binding, or protein-protein interactions is essential for understanding protein function and its regulation. Amide hydrogen/deuterium exchange (HDX) coupled with mass spectrometry (MS) is one of the most favorable tools for characterizing the protein dynamics and changes of protein conformation. However, currently the analysis of HDX-MS data is not up to its full power as it still requires manual validation by mass spectrometry experts. Especially, with the advent of high throughput technologies, the data size grows everyday and an automated tool is essential for the analysis. Here, we introduce a fully automated software, referred to as ‘deMix’, for the HDX-MS data analysis. deMix deals directly with the deuterated isotopic distributions, but not considering their centroid masses and is designed to be robust over random noises. In addition, unlike the existing approaches that can only determine a single state from an isotopic distribution, deMix can also detect a bimodal deuterated distribution, arising from EX1 behavior or heterogeneous peptides in conformational isomer proteins. Furthermore, deMix comes with visualization software to facilitate validation and representation of the analysis results.
Peri-hand space expands beyond reach in the context of walk-and-reach movements
Authors: Berger Michael , Neumann Peter , Gail Alexander 
Published: February 2019

AbstractThe brain incorporates sensory information across modalities to be able to interact with our environment. The peripersonal space (PPS), defined by a high level of crossmodal interaction, is centered on the relevant body part, e.g. the hand, but can spatially expand to encompass tools or reach targets during goal-directed behavior. Previous studies considered expansion of the PPS towards goals within immediate or tool-mediated reach, but not the translocation of the body as during walking. Here, we used the crossmodal congruency effect (CCE) to quantify the extension of the PPS and test if PPS can also expand further to include far located walk-and-reach targets accessible only by translocation of the body. We tested for orientation specificity of the hand-centered reference frame, asking if the CCE inverts with inversion of the hand orientation during reach. We show a high CCE with onset of the movement not only towards reach targets but also walk-and-reach targets. When participants must change hand orientation, the CCE decreases, if not vanishes, and does not simply invert. We conclude that the PPS can expand to the action space beyond immediate or tool-mediated reaching distance but is not purely hand-centered with respect to orientation.
Cancer associated fibroblasts sculpt tumour microenvironment by recruiting monocytes and inducing immunosuppressive PD-1+ TAMs
Authors: Gok Yavuz Betul , Gunaydin Gurcan , Gedik M. Emre , Kosemehmetoglu Kemal , Karakoc Derya , Ozgur Figen , Guc Dicle 
Published: February 2019

AbstractFibroblasts turn into cancer associated fibroblasts (CAFs) in the tumour microenvironment. CAFs have recently attracted attention for their function as a regulator of immune cell recruitment and function in addition to their tumour-promoting roles. In this study, we aimed to determine the role of CAFs on monocyte recruitment and macrophage polarization in breast cancer. CAFs, which were α-SMA expressing fibroblasts in contrast to normal fibroblasts (NFs), effectively recruited monocytes. Recruitment of monocytes by CAFs might be mediated by monocyte chemotactic protein-1 (MCP-1) as well as stromal cell-derived factor-1 (SDF-1) cytokines. CAFs differentiated the recruited monocytes into M2-like macrophages which are capable of exerting their immunosuppressive roles via the PD-1 axis. CAF-educated monocytes exhibited strong immune suppression unlike NF-educated monocytes and enhanced the motility/invasion of breast cancer cells in addition to increasing the expressions of epithelial–mesenchymal transition (EMT)-related genes and vimentin protein in cancer cells. CAF-educated M1 macrophages displayed increased expression of M2 markers and production of anti-inflammatory cytokine IL-10 in contrast to decreased production of pro-inflammatory cytokine IL-12 compared with control M1 macrophages; suggesting that CAFs were also able to induce the trans-differentiation of M1 macrophages to M2 macrophages. We then investigated the relationship between the infiltration of CAFs and tumour associated macrophages (TAMs) using tissue samples obtained from breast cancer patients. High grade of CAFs significantly correlated with the number of TAMs in human breast cancer tissue samples. It was also associated with higher Ki-67 proliferation index, and higher tumour volume. This result is in line with our finding of increased breast cancer cell proliferation due to the effects of CAF-educated monocytes in vitro. Our results concluded that CAFs play pivotal roles in sculpturing the tumour microenvironment in breast cancer, and therapeutic strategies to reverse the CAF-mediated immunosuppressive microenvironment should be taken into consideration.
Low density lipoprotein mimics insulin action on autophagy and glucose uptake in endothelial cells
Authors: Zhu Lin , Wu Guangjie , Yang Xiaoyan , Jia Xiong , Li Juyi , Bai Xiangli , Li Wenjing , Zhao Ying , Li Ye , Cheng Wenzhuo , Liu Shuli , Jin Si 
Published: February 2019

AbstractElevated plasma low density lipoprotein (LDL) is an established risk factor for cardiovascular disease. In addition to being able to cross the endothelial barrier to become accumulated in subendothelial space and thereby initiate atherosclerosis, LDL may exert a direct effect on vascular endothelial cells through activation of LDL receptor and its downstream signaling. Whether LDL can modulate the signaling for autophagy in endothelial cells is not clear. The present study firstly demonstrated that LDL can suppress endothelial autophagy through activation of the PI3K/Akt/mTOR signaling pathway and can promote glucose uptake by translocating glucose transporter 1 (GLUT1) from cytoplasm to cell membrane, actions similar to those of insulin. A co-immunoprecipitation assay found that LDL receptor (LDLR) and insulin receptor (IR) formed a complex in HUVECs. Knock down of the insulin receptor by small interfering RNA blocked the suppression of autophagy by LDL, as well as the signaling pathway involved. We conclude that LDL may mimic the action of insulin in endothelial cells, which might partly explain the increased incidence of diabetes in patients receiving some LDL-lowering therapy.
Streptomyces monashensis sp. nov., a novel mangrove soil actinobacterium from East Malaysia with antioxidative potential
Authors: Law Jodi Woan-Fei , Ser Hooi-Leng , Ab Mutalib Nurul-Syakima , Saokaew Surasak , Duangjai Acharaporn , Khan Tahir Mehmood , Chan Kok-Gan , Goh Bey-Hing , Lee Learn-Han 
Published: February 2019

AbstractA new Streptomyces species discovered from Sarawak mangrove soil is described, with the proposed name – Streptomyces monashensis sp. nov. (strain MUSC 1JT). Taxonomy status of MUSC 1JT was determined via polyphasic approach. Phylogenetic and chemotaxonomic properties of strain MUSC 1JT were in accordance with those known for genus Streptomyces. Based on phylogenetic analyses, the strains closely related to MUSC 1JT were Streptomyces corchorusii DSM 40340T (98.7%), Streptomyces olivaceoviridis NBRC 13066T (98.7%), Streptomyces canarius NBRC 13431T (98.6%) and Streptomyces coacervatus AS-0823T (98.4%). Outcomes of DNA–DNA relatedness between strain MUSC 1JT and its closely related type strains covered from 19.7 ± 2.8% to 49.1 ± 4.3%. Strain MUSC 1JT has genome size of 10,254,857 bp with DNA G + C content of 71 mol%. MUSC 1JT extract exhibited strong antioxidative activity up to 83.80 ± 4.80% in the SOD assay, with significant cytotoxic effect against colon cancer cell lines HCT-116 and SW480. Streptomyces monashensis MUSC 1JT (=DSM 103626T = MCCC 1K03219T) could potentially be a producer of novel bioactive metabolites; hence discovery of this new species may be highly significant to the biopharmaceutical industry as it could lead to development of new and useful chemo-preventive drugs.
Peer effects on control-averse behavior
Authors: Rudorf Sarah , Baumgartner Thomas , Knoch Daria 
Published: February 2019

AbstractThe urge to rebel against external control affects social interactions in many domains of our society with potentially far-reaching consequences. Nevertheless, it has remained unclear to what degree this control-averse behavior might be influenced by the people in our surroundings, our peers. In an experimental paradigm with real restrictions of the subjects’ freedom of choice and no systematic incentives to follow the peer, we are able to demonstrate both negative and positive peer effects on control-averse behavior. First, we find that information about a peer’s strongly control-averse behavior, although irrelevant for the subjects’ outcome, increases the subjects’ individual control-averse behavior. Second, we find that information about a peer’s more generous and only weakly control-averse behavior increases subjects’ generous behavior, even though it is associated with greater costs for the subjects. Critically, each subject’s behavior determined the monetary payoff of both the subject and a third person, thereby constituting a social behavior with actual consequences. Interestingly, these peer effects are not moderated by self-assessments of the general resistance to peer influence or the general tendency to rebel against restrictions of one’s freedom of choice. Contributing new insights into a complex and highly relevant social phenomenon, our results indicate that information about a single peer’s behavior can influence individual control-averse behavior.
The impact of cation concentration on Microcystis (cyanobacteria) scum formation
Authors: Drugă Bogdan , Buda Doriana-Mădălina , Szekeres Edina , Chiş Ciprian , Chiş Iuliana , Sicora Cosmin 
Published: February 2019

AbstractCyanobacterial scums at the surface of the lakes are potentially harmful phenomena with increasing occurrence in the last decades, and the causes that lead to their formation are still an unresolved issue. In order to better understand what triggers the scums, we investigated the effect of several Mg2+ and Ca2+ ion concentrations in promoting them in eight Microcystis aeruginosa strains. The possibility to prevent scum formation by using the ion chelator EDTA was also explored. We found that in some strains the cell aggregation takes place under lower ion source concentrations (20 mM MgSO4 or CaCl2), while in others this phenomenon does not occur even at 60 mM concentration. The scum formation correlated to the amount of extracellular polymeric substances (between 234 and 351 µg/cell). EDTA failed to prevent the scum formation in most strains, and in turn it caused cell lysis followed by the release of cellular content into the culture medium. We emphasize the relevance of these results for cyanobacterial scum formation in the environment and we also suggest that controlling the salinity of the medium (by manipulating the ion concentration) is a potentially efficient method for biomass harvesting in large ponds/tanks.
Diverse nature of femtosecond laser ablation of poly(L-lactide) and the influence of filamentation on the polymer crystallization behaviour
Authors: Stępak Bogusz , Gazińska Małgorzata , Nejbauer Michał , Stepanenko Yuriy , Antończak Arkadiusz 
Published: February 2019

AbstractOver the past few years we have witnessed growing interest in ultrafast laser micromachining of bioresorbable polymers for fabrication of medical implants and surface modification. In this paper we show that surface structuring of poly(L-lactide) with 300 fs laser pulses at 515 and 1030 nm wavelength leads to formation of defects inside the polymer as a result of laser beam filamentation. Filament-induced channels have diameter around 1 μm and length of hundreds of micrometers. SEM images of microchannels cross-sections are presented. The influence of wavelength and pulse spacing on bulk modification extent was investigated and parameters limiting filamentation were determined. We show that filamentation can be used for controlling properties of PLLA. The presence of filament-induced modifications such as empty microchannels and pressure wave-induced stress lead to increased ability of polymer to crystallize at lower temperature. Crystallization behaviour and crystal morphology after laser treatment was investigated in details using different analytical techniques such as WAXD, DSC and FTIR/ATR. Hydrolytic degradation experiment was performed. Presented method can be applied for controllable, spatially distributed modification of polymer crystallinity, crystalline phase structure and hydrolytic degradation profile.
Air pollutants associated with smoking in indoor/outdoor of waterpipe cafés in Tehran, Iran: Concentrations, affecting factors and health risk assessment
Authors: Masjedi Mohammad Reza , Taghizadeh Farhad , Hamzehali Sanaz , Ghaffari Sonia , Fazlzadeh Mehdi , Jafari Ahmad Jonidi , Niazi Sadegh , Mehrizi Ehsan Abouee , Moradi Masoud , Pasalari Hasan , Arfaeinia Hossein 
Published: February 2019

AbstractDespite increasingly growth in waterpipe smoking in Tehran, so far no study has been conducted on the air quality of the waterpipe and cigarette cafés. Thirty-six cafés were selected and the concentration of three pollutants including formaldehyde, carbon monoxide and nicotine were measured in both indoor and outdoor air of cafés two times (week-day and weekend’s session). Air sampling was performed for 180 min for each pollutant. It was observed that the concentration of pollutants inside the cafés was higher during weekend session (with a higher number of “active waterpipe heads”) compared with findings during the week-day sessions. Furthermore, the concentration of pollutants in the indoor air of the cafés was significantly higher than that of the outdoors (p < 0.05). According to path analysis, the number of “active waterpipe heads” had the maximum impact on generation of pollutants inside the cafés, followed by the type of tobacco as the second influential factor. The average of lifetime cancer risk (LTCR) resulted by formaldehyde exposure through inhalation in waterpipe (WS), cigarette (CS), waterpipe and cigarette (WCS) and none-smoking (NS) cafés in week-day and weekend sessions were estimated to be 111 × 10−5 and 61.2 × 10−5, 33.7 × 10−5 and 39.4 × 10−5, 271 × 10−5 and 322 × 10−5, and 4.80 × 10−5 and 5.90 × 10−5, respectively, which exceed the limit value by the U.S.EPA and WHO. The concentration of pollutants in the indoor air of smoking cafés in Tehran is significantly high, such that it can pose serious risks for the health of both personnel and customers. Therefore, decision makers are expected to enact applicable and strict policies so as to abate this public health risk.
Remote temporal wavepacket narrowing
Authors: Sedziak-Kacprowicz Karolina , Lasota Mikołaj , Kolenderski Piotr 
Published: February 2019

AbstractQuantum communication protocols can be significantly enhanced by careful preparation of the wavepackets of the utilized photons. Following the theoretical proposal published recently by our group, we experimentally demonstrate the effect of remote temporal wavepacket narrowing of a heralded single photon produced via spontaneous parametric down-conversion. This is done by utilizing a time-resolved measurement on the heralding photon which is frequency-entangled with the heralded photon. We then investigate optimal photon pair source characteristics to minimize heralded wavepacket width.
Cav3.2 T-type calcium channels shape electrical firing in mouse Lamina II neurons
Authors: Candelas Miriam , Reynders Ana , Arango-Lievano Margarita , Neumayer Christoph , Fruquière Antoine , Demes Elsa , Hamid Jawed , Lemmers Céline , Bernat Claire , Monteil Arnaud , Compan Vincent , Laffray Sophie , Inquimbert Perrine , Le Feuvre Yves , Zamponi Gerald W. , Moqrich Aziz , Bourinet Emmanuel , Méry Pierre-François 
Published: February 2019

AbstractThe T-type calcium channel, Cav3.2, is necessary for acute pain perception, as well as mechanical and cold allodynia in mice. Being found throughout sensory pathways, from excitatory primary afferent neurons up to pain matrix structures, it is a promising target for analgesics. In our study, Cav3.2 was detected in ~60% of the lamina II (LII) neurons of the spinal cord, a site for integration of sensory processing. It was co-expressed with Tlx3 and Pax2, markers of excitatory and inhibitory interneurons, as well as nNOS, calretinin, calbindin, PKCγ and not parvalbumin. Non-selective T-type channel blockers slowed the inhibitory but not the excitatory transmission in LII neurons. Furthermore, T-type channel blockers modified the intrinsic properties of LII neurons, abolishing low-threshold activated currents, rebound depolarizations, and blunting excitability. The recording of Cav3.2-positive LII neurons, after intraspinal injection of AAV-DJ-Cav3.2-mcherry, showed that their intrinsic properties resembled those of the global population. However, Cav3.2 ablation in the dorsal horn of Cav3.2GFP-Flox KI mice after intraspinal injection of AAV-DJ-Cav3.2-Cre-IRES-mcherry, had drastic effects. Indeed, it (1) blunted the likelihood of transient firing patterns; (2) blunted the likelihood and the amplitude of rebound depolarizations, (3) eliminated action potential pairing, and (4) remodeled the kinetics of the action potentials. In contrast, the properties of Cav3.2-positive neurons were only marginally modified in Cav3.1 knockout mice. Overall, in addition to their previously established roles in the superficial spinal cord and in primary afferent neurons, Cav3.2 channel appear to be necessary for specific, significant and multiple controls of LII neuron excitability.