Miracle-dz/UniFAR-FTUs huggingface dataset:
Creation of Engineered Cardiac Tissue In Vitro From Mouse Embryonic Stem Cells

Background— Embryonic stem (ES) cells can terminally differentiate into all types of somatic cells and are considered a promising source of seed cells for tissue engineering. However, despite recent progress in in vitro differentiation and in vivo transplantation methodologies of ES cells, to date, no one has succeeded in using ES cells in tissue engineering for generation of somatic tissues in vitro for potential transplantation therapy. Methods and Results— ES-D3 cells were cultured in a slow-turning lateral vessel for mass production of embryoid bodies. The embryoid bodies were then induced to differentiate into cardiomyocytes in a medium supplemented with 1% ascorbic acid. The ES cell–derived cardiomyocytes were then enriched by Percoll gradient centrifugation. The enriched cardiomyocytes were mixed with liquid type I collagen supplemented with Matrigel to construct engineered cardiac tissue (ECT). After in vitro stretching for 7 days, the ECT can beat synchronously and respond to physical and pharmaceutical stimulation. Histological, immunohistochemical, and transmission electron microscopic studies further indicate that the ECTs both structurally and functionally resemble neonatal native cardiac muscle. Markers related to undifferentiated ES cell contamination were not found in reverse transcriptase–polymerase chain reaction analysis of the Percoll-enriched cardiomyocytes. No teratoma formation was observed in the ECTs implanted subcutaneously in nude mice for 4 weeks. Conclusions— ES cells can be used as a source of seed cells for cardiac tissue engineering. Additional work remains to demonstrate engraftment of the engineered heart tissue in the case of cardiac defects and its functional integrity within the host’s remaining healthy cardiac tissue.
Daily Sampling of an HIV-1 Patient with Slowly Progressing Disease Displays Persistence of Multiple env Subpopulations Consistent with Neutrality

The molecular evolution of HIV-1 is characterized by frequent substitutions, indels and recombination events. In addition, a HIV-1 population may adapt through frequency changes of its variants. To reveal such population dynamics we analyzed HIV-1 subpopulation frequencies in an untreated patient with stable, low plasma HIV-1 RNA levels and close to normal CD4+ T-cell levels. The patient was intensively sampled during a 32-day period as well as approximately 1.5 years before and after this period (days −664, 1, 2, 3, 11, 18, 25, 32 and 522). 77 sequences of HIV-1 env (approximately 3100 nucleotides) were obtained from plasma by limiting dilution with 7–11 sequences per time point, except day −664. Phylogenetic analysis using maximum likelihood methods showed that the sequences clustered in six distinct subpopulations. We devised a method that took into account the relatively coarse sampling of the population. Data from days 1 through 32 were consistent with constant within-patient subpopulation frequencies. However, over longer time periods, i.e. between days 1…32 and 522, there were significant changes in subpopulation frequencies, which were consistent with evolutionarily neutral fluctuations. We found no clear signal of natural selection within the subpopulations over the study period, but positive selection was evident on the long branches that connected the subpopulations, which corresponds to >3 years as the subpopulations already were established when we started the study. Thus, selective forces may have been involved when the subpopulations were established. Genetic drift within subpopulations caused by de novo substitutions could be resolved after approximately one month. Overall, we conclude that subpopulation frequencies within this patient changed significantly over a time period of 1.5 years, but that this does not imply directional or balancing selection. We show that the short-term evolution we study here is likely representative for many patients of slow and normal disease progression.
On the throughput of Wireless Underground Sensor Networks using magneto-inductive waveguides

Wireless Underground Sensor Networks (WUSNs) present a variety of new research challenges. Recently, a magneto-inductive (MI) waveguide technique has been proposed to cope with the very harsh propagation conditions in WUSNs. This approach allows for an extension of the transmission range, which can be quite limited if relays are not deployed. In this paper, tree-based WUSNs are considered with sensors connected via MI-waveguides. The objective of our work is to determine the optimal system parameters and topology in order to avoid bottlenecks in the system and achieve optimal network throughput.
Provided for Non-commercial Research and Education Use Only. Not for Reproduction, Distribution or Commercial Use. Scaling Relationships among Drivers of Aquatic Respiration in Temperate Lakes: from the Smallest to the Largest Freshwater Ecosystems

Freshwater Biological Association. The attached offprint is provided to the author for research and education use (including use by others within their institution for such purposes) and for sharing with interested colleagues, provided the use of the article is for non-commercial purposes, and copies offered are not for sale and are not distributed in a systematic way. Please note that posting of the published version of the article to personal/academic websites or institutional repositories is not permitted, except for authors who have paid an 'open early' fee. All authors are permitted to post the submitted version of their manuscript (as prior to peer-review), provided it is clearly stated that the manuscript is unpublished, and full bibliographic reference to the published article is given. Authors who have paid an 'open early' fee are permitted to post the final published version of the article to their personal/ academic website or institutional repository, provided that it is non-commercial and there is a link to the published article on the journal website, Abstract To address how various environmental parameters control or constrain planktonic respiration (PR), we used geometric scaling relationships and established biological scaling laws to derive quantitative predictions for the relationships among key drivers of PR. We then used empirical measurements of PR and environmental (soluble reactive phosphate [SRP], carbon [DOC], chlorophyll a [Chl-a)], and temperature) and landscape parameters (lake area [LA] and watershed area [WA]) from a set of 44 lakes that varied in size and trophic status to test our hypotheses. We found that landscape-level processes affected PR through direct effects on DOC and temperature and indirectly via SRP. In accordance with predictions made from known relationships and scaling laws, scale coefficients (the parameter that describes the shape of a relationship between 2 variables) were found to be negative and have an absolute value <1. Biological parameters scaled positively with physical and chemical processes in accordance with those predicted from theory or previous studies (i.e., temperature >1, others <1). We also found evidence of a significant relationship between temperature and SRP. Because our dataset included measurements of respiration from small pond catchments to the largest body of freshwater on the planet, Lake Superior, these findings should be applicable to controls of PR for the great majority of temperate aquatic ecosystems.
Automated Electrophysiological and Pharmacological Evaluation of Human Pluripotent Stem Cell-Derived Cardiomyocytes

Automated planar patch clamp systems are widely used in drug evaluation studies because of their ability to provide accurate, reliable, and reproducible data in a high-throughput manner. Typically, CHO and HEK tumorigenic cell lines overexpressing single ion channels are used since they can be harvested as high-density, homogenous, single-cell suspensions. While human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) are physiologically more relevant, these cells are fragile, have complex culture requirements, are inherently heterogeneous, and are expensive to produce, which has restricted their use on automated patch clamp (APC) devices. Here, we used high efficiency differentiation protocols to produce cardiomyocytes from six different hPSC lines for analysis on the Patchliner (Nanion Technologies GmbH) APC platform. We developed a two-step cell preparation protocol that yielded cell catch rates and whole-cell breakthroughs of ∼80%, with ∼40% of these cells allowing electrical activity to be recorded. The protocol permitted formation of long-lasting (>15 min), high quality seals (>2 GΩ) in both voltage- and current-clamp modes. This enabled density of sodium, calcium, and potassium currents to be evaluated, along with dose–response curves to their respective channel inhibitors, tetrodotoxin, nifedipine, and E-4031. Thus, we show the feasibility of using the Patchliner platform for automated evaluation of the electrophysiology and pharmacology of hPSC-CMs, which will enable considerable increase in throughput for reliable and efficient drug evaluation.
Evidence for Remobilization of Barite Affecting Radiometric Dating Using 228Ra, 228Th, and 226Ra/Ba Values: Implications for the Evolution of Sea-Floor Volcanogenic Massive Sulfides

Samples of chimneys (black smokers) and other volcanogenic massive sulfide (VMS) mineralization were collected from hydrothermal vent fields associated with submarine arc and back-arc volcanoes in the western Pacific. Each specimen was dated using radiometric techniques to establish the frequency and duration of hydrothermal activity at that site, information that is vital when establishing the time elapsed to amass an ore deposit. In each case, the radiometric dating relied on the radium isotopes 228 Ra and 226 Ra with half-lives of 5.75 and 1,600 years, respectively, which coprecipitate with barite and then decay. We began dating VMS mineralization 15 years ago, knowing that the 226 Ra/Ba decreases with time, with the Ba and Ra assumed to be from a common source such that the initial 226 Ra/Ba value, i.e., the value at the onset of mineralization, was constant. Thus, the age of an “old” chimney (up to 15,000 yr) was calculated by comparing its 226 Ra/Ba value with the initial value established from nearby “young” chimneys ( 228 Ra. Since then, we have discovered that chimneys and other forms of sea-floor VMS mineralization can contain barite from two or more hydrothermal events. That is, older barite can be dissolved and reprecipitated (remobilized) from earlier mineralization deposited subseafloor, or earlier sea-floor mineralization overprinted (crosscut) by new. In many cases, the 226 Ra/Ba dating did not provide an absolute age for the older material but, rather, a difference in age between two samples that had incorporated varying proportions of older barite that was low or “dead” (i.e., >15,000 yr) with respect to 226 Ra, due to radioactive decay. Remobilizing of older barite is consistent with zone refining of metals in large VMS deposits, but we have only considered this recently. However, our investigations show that this can affect the initial 226 Ra/Ba values for VMS mineralization from arc and back-arc volcanoes, and also from mid-ocean ridges. Where sufficient samples contained 228 Ra, we estimated an age for the remobilized barite by plotting a 226 Ra/Ba versus 228 Ra/Ba mixing line for the VMS at the time of mineralization and found that hydrothermal activity has occurred at some arc volcanoes for >15,000 years. Such long histories of hydrothermal activity indicate the propensity for producing large metal-rich deposits on the seafloor.
Effects of information quality on inventory management

This paper investigated how different IQ categories affect the quality of inventory control decisions. The result has shown that intrinsic IQ and contextual IQ are positively related to inventory decision quality, indicating that intrinsic IQ and contextual IQ are the underlying concerns in improving inventory decision quality. It is also found that the effect of representational IQ on inventory decision quality is non-significant. However, under just-in-time inventory policy, representational IQ and contextual IQ jointly affect inventory decision quality. This result indicates that improving representational IQ may intensify the positive effects of contextual IQ.
First Evidence of Intraclonal Genetic Exchange in Trypanosomatids Using Two Leishmania infantum Fluorescent Transgenic Clones

Background The mode of reproduction in Leishmania spp has been argued to be essentially clonal. However, recent data (genetic analysis of populations and co-infections in sand flies) have proposed the existence of a non-obligate sexual cycle in the extracellular stage of the parasite within the sand fly vector. In this article we propose the existence of intraclonal genetic exchange in the natural vector of Leishmania infantum. Methodology/Principal findings We have developed transgenic L. infantum lines expressing drug resistance markers linked to green and red fluorescent reporters. We hypothesized whether those cells with identical genotype can recognize each other and mate. Both types of markers were successfully exchanged within the sand fly midgut of the natural vector Phlebotomus perniciosus when individuals from these species were fed with a mixture of parental clones. Using the yellow phenotype and drug resistance markers, we provide evidence for genetic exchange in L. infantum. The hybrid progeny appeared to be triploid based on DNA content analysis. The hybrid clone analyzed was stable throughout the complete parasite life cycle. The progress of infections by the hybrid clone in BALB/c mice caused a reduction in parasite loads in both spleen and liver, and provided weight values similar to those obtained with uninfected mice. Spleen arginase activity was also significantly reduced relative to parental strains. Conclusions/Significance A L. infantum hybrid lineage was obtained from intraclonal genetic exchange within the midgut of the natural vector, suggesting the ability of this parasite to recognize the same genotype and mate. The yellow hybrid progeny is stable throughout the whole parasite life cycle but with a slower virulence, which correlates well with the lower arginase activity detected both in vitro and in vivo infections.
Toward Improving Short‐Term Predictions of Fine Particulate Matter Over the United States Via Assimilation of Satellite Aerosol Optical Depth Retrievals

This study develops a new approach to improve simulations of the particulate matter of aerodynamic diameter smaller than 2.5 μm (PM2.5) in the Community Multiscale Air Quality (CMAQ) model via assimilation of Moderate Resolution Imaging Spectroradiometer (MODIS) aerosol optical depth (AOD) retrievals using the Gridpoint Statistical Interpolation (GSI) system. In contrast to previous studies that only consider errors due to transport, our computation of the background error covariance matrix incorporates uncertainties in anthropogenic emissions. To understand the impact of this approach, three experiments (one background and two assimilations) are performed over the contiguous United States (CONUS) from 15 July to 14 August 2014. The background CMAQ experiment significantly underestimates both the MODIS AOD and surface PM2.5 levels. MODIS AOD assimilation pushes both the CMAQ AOD and surface PM2.5 distributions toward the observed distributions, but CMAQ still underestimates the observations. Averaged over CONUS, the two assimilation experiments with and without including the anthropogenic emission uncertainties improve the correlation coefficient between the model and independent observations of PM2.5 by ~67% and ~48%, respectively, and reduces the mean bias by ~38% and ~10%, respectively. The assimilation improves the model performance everywhere over CONUS, except the New York and Wisconsin, where CMAQ overestimates the observed PM2.5 during nighttime after assimilation likely because of overcorrection of aerosol mass concentrations by the AOD assimilation. Future work should incorporate uncertainties in other processes (biomass burning and biogenic emissions, deposition, chemistry, transport, and boundary conditions) to further enhance the value of assimilating spaceborne AOD retrievals.
CODS

Database evolution is the process of updating the schema of a database or data warehouse (schema evolution) and evolving the data to the updated schema (data evolution). Database evolution is often necessitated in relational databases due to the changes of data or workload, the suboptimal initial schema design, or the availability of new knowledge of the database. It involves two steps: updating the database schema, and evolving the data to the new schema. Despite the capability of commercial RDBMSs to well optimize query processing, evolving the data during a database evolution through SQL queries is shown to be prohibitively costly. We designed and developed CODS, a platform for efficient data level data evolution in column oriented databases, which evolves the data to the new schema without materializing query results or unnecessary compression/decompression as occurred in traditional query level approaches. CODS ameliorates the efficiency of data evolution by orders of magnitude compared with commercial or open source RDBMSs.
Electronic structure of aqueous solutions: Bridging the gap between theory and experiments

A predictive and efficient computational framework for describing the electronic properties of aqueous solutions is presented. Predicting the electronic properties of aqueous liquids has been a long-standing challenge for quantum mechanical methods. However, it is a crucial step in understanding and predicting the key role played by aqueous solutions and electrolytes in a wide variety of emerging energy and environmental technologies, including battery and photoelectrochemical cell design. We propose an efficient and accurate approach to predict the electronic properties of aqueous solutions, on the basis of the combination of first-principles methods and experimental validation using state-of-the-art spectroscopic measurements. We present results of the photoelectron spectra of a broad range of solvated ions, showing that first-principles molecular dynamics simulations and electronic structure calculations using dielectric hybrid functionals provide a quantitative description of the electronic properties of the solvent and solutes, including excitation energies. The proposed computational framework is general and applicable to other liquids, thereby offering great promise in understanding and engineering solutions and liquid electrolytes for a variety of important energy technologies.
Knee moments of anterior cruciate ligament reconstructed and control participants during normal and inclined walking

Objectives Prior injury to the knee, particularly anterior cruciate ligament (ACL) injury, is known to predispose one to premature osteoarthritis (OA). The study sought to explore if there was a biomechanical rationale for this process by investigating changes in external knee moments between people with a history of ACL injury and uninjured participants during walking: (1) on different surface inclines and (2) at different speeds. In addition we assessed functional differences between the groups. Participants 12 participants who had undergone ACL reconstruction (ACLR) and 12 volunteers with no history of knee trauma or injury were recruited into this study. Peak knee flexion and adduction moments were assessed during flat (normal and slow speed), uphill and downhill walking using an inclined walkway with an embedded Kistler Force plate, and a ten-camera Vicon motion capture system. Knee injury and Osteoarthritis Outcome Score (KOOS) was used to assess function. Multivariate analysis of variance (MANOVA) was used to examine statistical differences in gait and KOOS outcomes. Results No significant difference was observed in the peak knee adduction moment between ACLR and control participants, however, in further analysis, MANOVA revealed that ACLR participants with an additional meniscal tear or collateral ligament damage (7 participants) had a significantly higher adduction moment (0.33±0.12 Nm/kg m) when compared with those with isolated ACLR (5 participants, 0.1±0.057 Nm/kg m) during gait at their normal speed (p<0.05). A similar (non-significant) trend was seen during slow, uphill and downhill gait. Conclusions Participants with an isolated ACLR had a reduced adductor moment rather an increased moment, thus questioning prior theories on OA development. In contrast, those participants who had sustained associated trauma to other key knee structures were observed to have an increased adduction moment. Additional injury concurrent with an ACL rupture may lead to a higher predisposition to osteoarthritis than isolated ACL deficiency alone.
Exploiting local similarity for indexing paths in graph-structured data

XML and other semi-structured data may have partially specified or missing schema information, motivating the use of a structural summary which can be automatically computed from the data. These summaries also serve as indices for evaluating the complex path expressions common to XML and semi-structured query languages. However, to answer all path queries accurately, summaries must encode information about long, seldom-queried paths, leading to increased size and complexity with little added value. We introduce the A(k)-indices, a family of approximate structural summaries. They are based on the concept of k-bisimilarity, in which nodes are grouped based on local structure, i.e., the incoming paths of length up to k. The parameter k thus smoothly varies the level of detail (and accuracy) of the A(k)-index. For small values of k, the size of the index is substantially reduced. While smaller, the A(k) index is approximate, and we describe techniques for efficiently extracting exact answers to regular path queries. Our experiments show that, for moderate values of k, path evaluation using the A(k)-index ranges from being very efficient for simple queries to competitive for most complex queries, while using significantly less space than comparable structures.
Medroxyprogesterone Acetate Alters Mycobacterium Bovis BCG-Induced Cytokine Production in Peripheral Blood Mononuclear Cells of Contraceptive Users

Most individuals latently infected with Mycobacterium tuberculosis (M.tb) contain the infection by a balance of effector and regulatory immune responses. This balance can be influenced by steroid hormones such as glucocorticoids. The widely used contraceptive medroxyprogesterone acetate (MPA) possesses glucocorticoid activity. We investigated the effect of this hormone on immune responses to BCG in household contacts of active TB patients. Multiplex bead array analysis revealed that MPA demonstrated both glucocorticoid and progestogenic properties at saturating and pharmacological concentrations in peripheral blood mononuclear cells (PBMCs) and suppressed antigen specific cytokine production. Furthermore we showed that PBMCs from women using MPA produced significantly lower levels of IL-1α, IL-12p40, IL-10, IL-13 and G-CSF in response to BCG which corresponded with lower numbers of circulating monocytes observed in these women. Our research study is the first to show that MPA impacts on infections outside the genital tract due to a systemic effect on immune function. Therefore MPA use could alter susceptibility to TB, TB disease severity as well as change the efficacy of new BCG-based vaccines, especially prime-boost vaccine strategies which may be administered to adult or adolescent women in the future.