bluuebunny/crossref_metadata_2025_split huggingface dataset:
An additive Gaussian process regression model for interpretable non-parametric analysis of longitudinal data
Authors: Cheng Lu , Ramchandran Siddharth , Vatanen Tommi , Lietzén Niina , Lahesmaa Riitta , Vehtari Aki , Lähdesmäki Harri 
Published: April 2019

AbstractBiomedical research typically involves longitudinal study designs where samples from individuals are measured repeatedly over time and the goal is to identify risk factors (covariates) that are associated with an outcome value. General linear mixed effect models are the standard workhorse for statistical analysis of longitudinal data. However, analysis of longitudinal data can be complicated for reasons such as difficulties in modelling correlated outcome values, functional (time-varying) covariates, nonlinear and non-stationary effects, and model inference. We present LonGP, an additive Gaussian process regression model that is specifically designed for statistical analysis of longitudinal data, which solves these commonly faced challenges. LonGP can model time-varying random effects and non-stationary signals, incorporate multiple kernel learning, and provide interpretable results for the effects of individual covariates and their interactions. We demonstrate LonGP’s performance and accuracy by analysing various simulated and real longitudinal -omics datasets.
Self-organization of swimmers drives long-range fluid transport in bacterial colonies
Authors: Xu Haoran , Dauparas Justas , Das Debasish , Lauga Eric , Wu Yilin 
Published: April 2019

AbstractMotile subpopulations in microbial communities are believed to be important for dispersal, quest for food, and material transport. Here, we show that motile cells in sessile colonies of peritrichously flagellated bacteria can self-organize into two adjacent, centimeter-scale motile rings surrounding the entire colony. The motile rings arise from spontaneous segregation of a homogeneous swimmer suspension that mimics a phase separation; the process is mediated by intercellular interactions and shear-induced depletion. As a result of this self-organization, cells drive fluid flows that circulate around the colony at a constant peak speed of ~30 µm s−1, providing a stable and high-speed avenue for directed material transport at the macroscopic scale. Our findings present a unique form of bacterial self-organization that influences population structure and material distribution in colonies.
Data from the Human Penguin Project, a cross-national dataset testing social thermoregulation principles
Authors: Hu Chuan-Peng , Yin Ji-Xing , Lindenberg Siegwart , Dalğar İlker , Weissgerber Sophia C. , Vergara Rodrigo C. , Cairo Athena H. , Čolić Marija V. , Dursun Pinar , Frankowska Natalia , Hadi Rhonda , Hall Calvin J. , Hong Youngki , Joy-Gaba Jennifer , Lazarević Dušanka , Lazarević Ljiljana B. , Parzuchowski Michal , Ratner Kyle G. , Rothman David , Sim Samantha , Simão Cláudia , Song Mengdi , Stojilović Darko , Blomster Johanna K. , Brito Rodrigo , Hennecke Marie , Jaume-Guazzini Francisco , Schubert Thomas W. , Schütz Astrid , Seibt Beate , Zickfeld Janis H. , IJzerman Hans 
Published: April 2019

AbstractIn the Human Penguin Project (N = 1755), 15 research groups from 12 countries collected body temperature, demographic variables, social network indices, seven widely-used psychological scales and two newly developed questionnaires (the Social Thermoregulation and Risk Avoidance Questionnaire (STRAQ-1) and the Kama Muta Frequency Scale (KAMF)). They were collected to investigate the relationship between environmental factors (e.g., geographical, climate etc.) and human behaviors, which is a long-standing inquiry in the scientific community. More specifically, the present project was designed to test principles surrounding the idea of social thermoregulation, which posits that social networks help people to regulate their core body temperature. The results showed that all scales in the current project have sufficient to good psychometrical properties. Unlike previous crowdsourced projects, this dataset includes not only the cleaned raw data but also all the validation of questionnaires in 9 different languages, thus providing a valuable resource for psychological scientists who are interested in cross-national, environment-human interaction studies.
Territoriality and variation in home range size through the entire annual range of migratory great spotted cuckoos (Clamator glandarius)
Authors: Rühmann Josse , Soler Manuel , Pérez-Contreras Tomás , Ibáñez-Álamo Juan Diego 
Published: April 2019

AbstractVariation in home range size throughout the year and its causes are not well understood yet. Migratory brood parasites offer a unique opportunity to incorporate this spatio-temporal dimension into the study of the factors regulating home range dynamics. Using satellite transmitters, we tracked sixteen migratory great spotted cuckoos (Clamator glandarius) of both sexes for up to three years. We constructed home ranges in all major staging areas, from the Spanish breeding areas to the African wintering grounds, analyzed their temporal and geographical variation and investigated their main potential determinants (e.g. food and host availability). We found that home ranges were significantly larger in the breeding area compared to non-breeding areas. Using NDVI as a proxy for food availability, we showed that breeding area home ranges have significantly lower food availability per km2 than home ranges elsewhere which could explain why cuckoos use alternative areas with higher food availability before initiating migration. We also found some evidence for sex differences. Additionally, we found no indications of territoriality in this species, providing novel information into the current debate on brood parasite territoriality. Overall, food availability seems to be an important factor regulating home range dynamics and influencing migratory patterns throughout the year in great spotted cuckoos.
Slowing less than 1 Hz is decreased near the seizure onset zone
Authors: Lundstrom Brian Nils , Boly Melanie , Duckrow Robert , Zaveri Hitten P. , Blumenfeld Hal 
Published: April 2019

AbstractFocal slowing (<4 Hz) of brain waves is often associated with focal cerebral dysfunction and is assumed to be increased closest to the location of dysfunction. Prior work suggests that slowing may be comprised of at least two distinct neural mechanisms: slow oscillation activity (<1 Hz) may reflect primarily inhibitory cortical mechanisms while power in the delta frequency (1–4 Hz) may correlate with local synaptic strength. In focal epilepsy patients, we examined slow wave activity near and far from the seizure onset zone (SOZ) during wake, sleep, and postictal states using intracranial electroencephalography. We found that slow oscillation (0.3–1 Hz) activity was decreased near the SOZ, while delta activity (2–4 Hz) activity was increased. This finding was most prominent during sleep, and accompanied by a loss of long-range intra-hemispheric synchrony. In contrast to sleep, postictal slowing was characterized by a broadband increase of spectral power, and showed a reduced modulatory effect of slow oscillations on higher frequencies. These results suggest slow oscillation focal slowing is reduced near the seizure onset zone, perhaps reflecting reduced inhibitory activity. Dissociation between slow oscillation and delta slowing could help localize the seizure onset zone from interictal intracranial recordings.
Novel screening system revealed that intracellular cholesterol trafficking can be a good target for colon cancer prevention
Authors: Miyamoto Shingo , Narita Takumi , Komiya Masami , Fujii Gen , Hamoya Takahiro , Nakanishi Ruri , Tamura Shuya , Kurokawa Yurie , Takahashi Maiko , Mutoh Michihiro 
Published: April 2019

AbstractIn conventional research methods for cancer prevention, cell proliferation and apoptosis have been intensively targeted rather than the protection of normal or benign tumor cells from malignant transformation. In this study, we aimed to identify candidate colon cancer chemopreventive drugs based on the transcriptional activities of TCF/LEF, NF-κB and NRF2, that play important roles in the process of malignant transformation. We screened a “validated library” consisting of 1280 approved drugs to identify hit compounds that decreased TCF/LEF and NF-κB transcriptional activity and increased NRF2 transcriptional activity. Based on the evaluation of these 3 transcriptional activities, 8 compounds were identified as candidate chemopreventive drugs for colorectal cancer. One of those, itraconazole, is a clinically used anti-fungal drug and was examined in the Min mouse model of familial adenomatous polyposis. Treatment with itraconazole significantly suppressed intestinal polyp formation and the effects of itraconazole on transcriptional activities may be exerted partly through inhibition of intracellular cholesterol trafficking. This screen represents one of the first attempts to identify chemopreventive agents using integrated criteria consisting of the inhibition of TCF/LEF, NF-κB and induction of NRF2 transcriptional activity.
Intracellular Fe2+ accumulation in endothelial cells and pericytes induces blood-brain barrier dysfunction in secondary brain injury after brain hemorrhage
Authors: Imai Takahiko , Iwata Sena , Hirayama Tasuku , Nagasawa Hideko , Nakamura Shinsuke , Shimazawa Masamitsu , Hara Hideaki 
Published: April 2019

AbstractAfter intracranial hemorrhage (ICH), iron is released from the hematoma and induces secondary brain injury. However, the detail effect of iron on blood-brain barrier (BBB) function is still unknown. We investigated whether hemoglobin (Hb), ferrous ammonium sulfate (FAS) or hemin which contains iron have the detrimental effect on both human brain microvascular endothelial cells and pericytes by cellular function analysis in vitro. We developed an iron (Fe2+)-detectable probe, Si-RhoNox-1, to investigate intracellular Fe2+ accumulation (Fe2+intra). After FAS treatment, there was the correlation between Fe2+intra and cell death. Moreover, Hb or hemin treatment induced cell death, increased reactive oxygen species and promoted Fe2+intra in both cells. These changes were inhibited by the Fe2+ chelator, 2,2′-bipyridil (BP). Furthermore, hemin induced endothelial barrier dysfunction via disruption of junction integrity. Based on in vitro studies, we used a hemin-injection ICH mice model in vivo. Hemin injection (10 mM/10 µL, i.c.) induced deleterious effects including BBB hyper-permeability, neuronal deficits, neuronal damage, altered proteins expression, and Fe2+intra in BBB composed cells. Lastly, BP (40 mg/kg, i.p.) administration attenuated neuronal deficits at 3 days after surgery. Collectively, Hb or hemin damaged BBB composed cells via Fe2+intra. Therefore, the regulation of the Fe2+ movement in BBB might be effective for treatment of ICH.
Near full-length HIV-1 subtype B sequences from the early South African epidemic, detecting a BD unique recombinant form (URF) from a sample in 1985
Authors: Obasa Adetayo Emmanuel , Engelbrecht Susan , Jacobs Graeme Brendon 
Published: April 2019

AbstractHIV-1 subtype C is the most prevalent subtype in South Africa. Although subtype B was previously detected in South Africa, there is limited sequence information available. We characterized near full-length HIV-1 subtype B sequences from samples collected at the start of the South African HIV-1 epidemic, in the 1980s. Five samples were analysed by PCR amplification, Sanger DNA sequencing and phylogenetic analyses. The viral genomes were amplified in two overlapping fragments of 5.5 kb and 3.7 kb. The sequences were subtyped using REGA version 3.0, RIP version 3.0 and jpHMM. Maximum Likelihood phylogenetic trees were inferred with MEGA version 6. Four HIV-1 patient sequences were subtyped as pure HIV-1 subtype B. One sequence was characterized as a novel HIV-1 subtype B and D recombinant. The sequences clustered phylogenetically with other HIV-1 subtype B sequences from South Africa, Europe and the USA. We report the presence of an HIV-1 subtype B and D recombinant strain detected in the beginning of the epidemic. This indicates that viral recombination events were already happening in 1985, but could have been missed as sequence analyses were often limited to small genomic regions of HIV-1.
Enabling cell recovery from 3D cell culture microfluidic devices for tumour microenvironment biomarker profiling
Authors: Virumbrales-Muñoz María , Ayuso Jose M. , Lacueva Alodia , Randelovic Teodora , Livingston Megan K. , Beebe David J. , Oliván Sara , Pereboom Desirée , Doblare Manuel , Fernández Luis , Ochoa Ignacio 
Published: April 2019

AbstractThe tumour microenvironment (TME) has recently drawn much attention due to its profound impact on tumour development, drug resistance and patient outcome. There is an increasing interest in new therapies that target the TME. Nonetheless, most established in vitro models fail to include essential cues of the TME. Microfluidics can be used to reproduce the TME in vitro and hence provide valuable insight on tumour evolution and drug sensitivity. However, microfluidics remains far from well-established mainstream molecular and cell biology methods. Therefore, we have developed a quick and straightforward collagenase-based enzymatic method to recover cells embedded in a 3D hydrogel in a microfluidic device with no impact on cell viability. We demonstrate the validity of this method on two different cell lines in a TME microfluidic model. Cells were successfully retrieved with high viability, and we characterised the different cell death mechanisms via AMNIS image cytometry in our model.
Estimation of swine movement network at farm level in the US from the Census of Agriculture data
Authors: Moon Sifat A. , Ferdousi Tanvir , Self Adrian , Scoglio Caterina M. 
Published: April 2019

AbstractSwine movement networks among farms/operations are an important source of information to understand and prevent the spread of diseases, nearly nonexistent in the United States. An understanding of the movement networks can help the policymakers in planning effective disease control measures. The objectives of this work are: (1) estimate swine movement probabilities at the county level from comprehensive anonymous inventory and sales data published by the United States Department of Agriculture - National Agriculture Statistics Service database, (2) develop a network based on those estimated probabilities, and (3) analyze that network using network science metrics. First, we use a probabilistic approach based on the maximum information entropy method to estimate the movement probabilities among different swine populations. Then, we create a swine movement network using the estimated probabilities for the counties of the central agricultural district of Iowa. The analysis of this network has found evidence of the small-world phenomenon. Our study suggests that the US swine industry may be vulnerable to infectious disease outbreaks because of the small-world structure of its movement network. Our system is easily adaptable to estimate movement networks for other sets of data, farm animal production systems, and geographic regions.
Functional Analysis of Conserved Transmembrane Charged Residues and a Yeast Specific Extracellular Loop of the Plasma Membrane Na+/H+ Antiporter of Schizosaccharomyces pombe
Authors: Dutta Debajyoti , Ullah Asad , Bibi Sana , Fliegel Larry 
Published: April 2019

AbstractThe Na+/H+ exchanger of the plasma membrane of S. pombe (SpNHE1) removes excess intracellular sodium in exchange for an extracellular proton. We examined the functional role of acidic amino acids of a yeast specific periplasmic extracellular loop 6 (EL6) and of Glu74 and Arg77 of transmembrane segment 3. Glu74 and Arg77 are conserved in yeast species while Glu74 is conserved throughout various phyla. The mutation E74A caused a minor effect, while mutation R77A had a larger effect on the ability of SpNHE1 to confer salt tolerance. Mutation of both residues to Ala or Glu also eliminated the ability to confer salt tolerance. Arg341 and Arg342 were also necessary for SpNHE1 transport in S. pombe. Deletion of 3 out of 4 acidic residues (Asp389, Glu390, Glu392, Glu397) of EL6 did not greatly affect SpNHE1 function while deletion of all did. Replacement of EL6 with a segment from the plant Na+/H+ exchanger SOS1 also did not affect function. We suggest that EL6 forms part of a cation coordination sphere, attracting cations for transport but that the region is not highly specific for the location of acidic charges. Overall, we identified a number of polar amino acids important in SpNHE1 function.
Magnetic moment inversion at giant flux jump: dynamical property of critical state in type-II superconductors
Authors: Chabanenko Viktor , Nabiałek Adam , Puźniak Roman , Kuchuk Olena , Chumak Oleksandr , Pérez-Rodríguez Felipe , Pal Umapada , Garcia-Vazquez Valentin , Cortés-Maldonado Raul , Qian Jun , Yao Xin , Szymczak Henryk 
Published: April 2019

AbstractExperimental evidence of tremendous magnetic moment dynamical inversion, from metastable trapping state to the state with essentially the same moment oriented in the opposite direction, appearing during giant flux jump connected to thermomagnetic avalanche process in superconducting YBa2Cu3O7−δ single crystal, is presented. Magnetization inversion takes place in the system, without thermal contact between sample and sample holder, with a tremendous stored energy once the avalanche process is completed in quasi-adiabatic conditions. A model of magnetic moment inversion, caused by the jump between two metastable states of superconductor with the same energy storage, is presented and discussed in terms of the critical state with peculiar evolution of the critical-current spatial distribution. Importantly, knowledge of conditions of the appearance of such a phenomenon is crucial for applications of bulk superconductors as “permanent” magnets, for example, in superconducting levitation devices, etc.
Quantitative dynamics of reversible platelet aggregation: mathematical modelling and experiments
Authors: Filkova Aleksandra A. , Martyanov Alexey A. , Garzon Dasgupta Andrei K. , Panteleev Mikhail A. , Sveshnikova Anastasia N. 
Published: April 2019

AbstractAlthough reversible platelet aggregation observed in response to ADP stimulation in the presence of calcium is a well-known phenomenon, its mechanisms are not entirely clear. To study them, we developed a simple kinetic mass-action-law-based mathematical model to use it in combination with experiments. Light transmission platelet aggregometry (LTA) induced by ADP was performed for platelet-rich plasma or washed platelets using both conventional light transmission and aggregate size monitoring method based on optical density fluctuations. Parameter values of the model were determined by means of parameter estimation techniques implemented in COPASI software. The mathematical model was able to describe reversible platelet aggregation LTA curves without assuming changes in platelet aggregation parameters over time, but with the assumption that platelet can enter the aggregate only once. In the model, the mean size of platelet aggregates correlated with the solution transparency. This corresponded with flow cytometry analysis and with optical density fluctuations data on aggregate size. The predicted values of model parameters correlated with ADP concentration used in experiments. These data suggest that, at the start of the aggregation, when platelet integrins switch “on”, large unstable platelet aggregates are rapidly formed, which leads to an increase in light transmission. However, upon fragmentation of these aggregates, the probability of the post-aggregate platelets’ attachment to each other decreases preventing new aggregation and resulting in the reversible aggregation phenomenon.
Loss of PKM2 in Lgr5+ intestinal stem cells promotes colitis-associated colorectal cancer
Authors: Kim Yeji , Lee Yong-Soo , Kang Sung Wan , Kim Seungil , Kim Tae-Young , Lee Su-Hyun , Hwang Sung Wook , Kim Jihun , Kim Eun Na , Ju Jin-Sung , Park Yun-Yong , Kweon Mi-Na 
Published: April 2019

AbstractThe regulatory properties of pyruvate kinase M2 isoform (PKM2), the key glycolytic enzyme, influence altered energy metabolism including glycolysis in cancer. In this study, we found that PKM2 was highly expressed in patients with ulcerative colitis or colorectal cancer (CRC). We then investigated the effectiveness of conditionally ablating PKM2 in Lgr5+ intestinal stem cells (ISC) using a mouse model of colitis-associated CRC (AOM plus DSS). Tamoxifen-inducible Lgr5-driven deletion of PKM2 in ISC (PKM2ΔLgr5-Tx) significantly promoted tumor incidence and size in the colon and lower body weight compared with findings in vehicle-treated mice (PKM2ΔLgr5-Veh). Histopathologic analysis revealed considerable high-grade dysplasia and adenocarcinoma in the colon of PKM2ΔLgr5-Tx mice while PKM2ΔLgr5-Veh mice had low- and high-grade dysplasia. Loss of PKM2 was associated with dominant expression of PKM1 in Lgr5+ ISC and their progeny cells. Further, the organoid-forming efficiency of whole cancer cells or Lgr5+ cells obtained from colon polyps of PKM2ΔLgr5-Tx mice was significantly increased when compared with PKM2ΔLgr5-Veh mice. Cancer organoids from PKM2ΔLgr5-Tx mice exhibited increased mitochondrial oxygen consumption and a shift of metabolites involved in energy metabolism. These findings suggest that loss of PKM2 function in ISC promotes colitis-associated CRC.
Phenazine-1-carboxamide functionalized mesoporous silica nanoparticles as antimicrobial coatings on silicone urethral catheters
Authors: Kanugala Sirisha , Jinka Sudhakar , Puvvada Nagaprasad , Banerjee Rajkumar , Kumar C. Ganesh 
Published: April 2019

AbstractMicrobial infections due to biofilms on medical implants can be prevented by antimicrobial coatings on biomaterial surfaces. Mesoporous silica nanoparticles (MSNPs) were synthesized via base-catalyzed sol-gel process at room temperature, functionalized with phenazine-1-carboxamide (PCN) and characterized by UV-visible, FT-IR, DLS, XRD spectroscopic techniques, SEM, TEM, TGA and BET analysis. Native MSNPs, PCN and PCN-MSNPs were evaluated for anti-Candida minimum inhibitory concentration (MIC), minimum fungicidal concentration (MFC), Candida albicans (C. albicans) biofilms and C. albicans-Staphylococcus aureus (S. aureus) polymicrobial biofilm inhibition. PCN-MSNPs were four-fold effective (MIC 3.9 µg mL−1; 17.47 µM) and MFC (7.8 µg mL−1; 34.94 µM) as compared to pure PCN (MIC 15.6 µg mL−1; 69.88 µM) and MFC (31.2 µg mL−1; 139.76 µM). PCN-MSNPs inhibited in vitro C. albicans MTCC 227-S. aureus MTCC 96 biofilms at very low concentration (10 µg mL−1; 44.79 µM) as compared to pure PCN (40 µg mL−1; 179.18 µM). Mechanistic studies revealed that PCN induced intracellular ROS accumulation in C. albicans MTCC 227, S. aureus MTCC 96 and S. aureus MLS-16 MTCC 2940, reduction in total ergosterol content, membrane permeability, disruption of ionic homeostasis followed by Na+, K+ and Ca2+ leakage leading to cell death in C. albicans MTCC 227 as confirmed by confocal laser scanning micrographs. The silicone urethral catheters coated with PCN-MSNPs (500 µg mL−1; 2.23 mM) exhibited no formation of C. albicans MTCC 227 - S. aureus MTCC 96 and C. albicans MTCC 227 - S. aureus MLS -16 MTCC 2940 biofilms. This is the first report on PCN-MSNPs for use as antimicrobial coatings against microbial adhesion and biofilm formation on silicone urethral catheters.