Miracle-dz/UniFAR-FTUs huggingface dataset:
Yield stress and strength of saline cemented tailings materials in sub-zero environments: slag-paste backfill

This paper presents the results of an investigation that aimed to evaluate the influence of sodium chloride (NaCl or salt) on the yield stress and evolution of the strength of a cemented tailings material (called cemented paste backfill, CPB) that contains ground granulated blast furnace slag (Slag-CPB) in sub-zero environments. About 200 CPB specimens with different NaCl concentrations (0, 5, 35, and 100 g/L) and cured at −6 °C are tested at different curing times (0, 0.25, 1, 2, and 4 h for yield stress measurement; 7, 28, and 90 days for uniaxial compressive testing). Moreover, microstructural analyses are conducted on cement-slag paste and Slag-CPB samples with various concentrations of NaCl. The results show that the addition of NaCl provides better flowability of the fresh Slag-CPB and significantly affects the strength development of Slag-CPB. The results presented in this study have significant implications for backfill practices in permafrost and cold regions.
The Nature of Premaximum Halts of Classical Nova Outbursts: V723 Cassiopeiae and V463 Scuti

We present a new interpretation of long premaximum halts of nova outbursts. For V723 Cas (Nova Cas 1995) and V463 Sct (Nova Sct 2000), we have reproduced light curves, excluding the brightness maxima, starting from the long premaximum halt through the late decay phase of the outbursts using a steady state optically thick wind model. When the hydrogen-rich envelope of the white dwarf (WD) is massive enough, the star expands to ~100 R☉ or over, and its surface temperature decreases to below 7000 K. At this supergiant mimicry stage, the changes in both the photospheric radius and the temperature are small against the large increase in the envelope mass. These changes cause a saturation in visual magnitude that lasts a long time before it begins to decline. This saturation is known as the premaximum halt of a classical nova outburst. The visual magnitude during the saturation is close to the bolometric magnitude, which is an upper limit for a given WD mass. Since the WD masses are estimated to be 0.59 M☉ for V723 Cas and 1.1 M☉ for V463 Sct by fitting the decline rate of nova light curves, we can determine the absolute magnitude of premaximum halts. It is a refined Eddington luminosity. Thus, the premaximum halt of a nova works as a standard candle.
Adaptive differentiation of murine lymphocytes. IV. (Responder × Nonresponder) F(1) T cells can be taught to preferentially help nonresponder,rather than responder, B cells

Responses to the synthetic terpolymer L-glutamic acid, L-lysine, L-tyrosine (GLT) in the mouse are controlled by H-2-1inked Ir-GLTgenes. (Responder × nonresponder) F(1) hybrid mice, themselves phenotypic responders, can be primed with GLT to develop specific helper cells capable of interacting with 2,4-dinitrophenyl hapten (DNP)-primed F(1) B cells in response to DNP-GLT. Unlike the indiscriminant ability of F(1) helper T cells for conventional antigens (i.e. not Ir gene-controlled), which can help B cells of either parental type (as well as F(1)) equally well, GLT-primed F(1) T cells can only provide help under normal circumstances for B lymphocytes of responder parent origin; they are unable to communicate effectively with nonresponder parental B cells (1, and the present studies). The present studies reveal, however, that the induction of a parental cell-induced allogeneic effect during priming of F(1) mice to GLT actually dictates the direction of cooperating preference that will be displayed by such F(1) helper cells for B cells of one parental type or the other. Thus, F(1) T cells, primed to GLT under the influence of an allogeneic effect induced by parental BALB/c cells, develop into effective helpers for nonresponder A/J B cells, but fail to develop effective helpers for responder BALB/c B cells, and vice-versa. In contrast, F(1) T cells, primed to GLT under the influence of an allogeneic effect induced by either parental type, display significantly enhanced levels of helper activity for B cells derived from F(1) donors. These results are interpreted to reflect the existence of two interdependent events provoked by the allogeneic effect: one event augments the differentiation of GLT-specific helper T cells belonging to the subset corresponding to the opposite parental type; this would explain the development of increased helper activity provided to partner B cells of opposite parental type (as well as of F(1) origin). The second event, we postulate, involves the production of responses against the receptors which normally self-recognize native cell interaction determinants; this form of anti-idiotype response is restricted against self- recognizing receptors of the same parental type used for induction of the allogeneic effect, hence explaining diminished helper activity of such F(1) cells for partner B lymphocytes of corresponding parental type.
Activin/Smad2-induced Histone H3 Lys-27 Trimethylation (H3K27me3) Reduction Is Crucial to Initiate Mesendoderm Differentiation of Human Embryonic Stem Cells*

Differentiation of human embryonic stem cells into mesendoderm (ME) is directed by extrinsic signals and intrinsic epigenetic modifications. However, the dynamics of these epigenetic modifications and the mechanisms by which extrinsic signals regulate the epigenetic modifications during the initiation of ME differentiation remain elusive. In this study, we report that levels of histone H3 Lys-27 trimethylation (H3K27me3) decrease during ME initiation, which is essential for subsequent differentiation induced by the combined effects of activin and Wnt signaling. Furthermore, we demonstrate that activin mediates the H3K27me3 decrease via the Smad2-mediated reduction of EZH2 protein level. Our results suggest a two-step process of ME initiation: first, epigenetic priming via removal of H3K27me3 marks and, second, transcription activation. Our findings demonstrate a critical role of H3K27me3 priming and a direct interaction between extrinsic signals and epigenetic modifications during ME initiation.
Added Prognostic Value of Cerebrospinal Fluid Biomarkers in Predicting Decline in Memory Clinic Patients in a Prospective Cohort.

BACKGROUND Limited information is available on short-term prognosis of Alzheimer's disease (AD) biomarkers in cerebrospinal fluid (CSF) in addition to routine diagnostic workup. OBJECTIVE This study aims to investigate the added prognostic value of AD CSF biomarkers. METHODS In a prospective cohort study, clinical experts predicted cognitive and functional symptoms in 114 memory clinic patients by assessing comprehensive routine diagnostic test information (patient history, and physical, neurological, psychiatric, neuropsychological, and MRI examinations), without and with CSF biomarkers. The reference standard was the 'observed clinically relevant decline' using baseline and 1- and 2-year follow-up information. RESULTS Decline over a 2-year period was observed in 51% of all participants (3% in SMC, 48% in MCI, 90% in mild dementia). In the total sample, the accuracy of predicted decline did not differ significantly between routine assessment without (79% correctly predicted) and with (74% correctly predicted) CSF biomarkers. Subgroup analyses revealed 25 (83%) correct predictions in SMC, 30 (68%) in MCI, and 35 (88%) in dementia without the use of CSF; and 21 (70%), 27 (61%), and 36 (90%), respectively, with the use of CSF in addition to the routine assessment. CONCLUSION AD CSF biomarkers did not increase accuracy of 2-year prognosis of cognitive and functional decline when added to routine diagnostic workup. This suggests that the standard diagnostic workup without CSF biomarkers allows fairly accurate predictions for the short-term course of symptoms. Routine AD biomarkers in CSF have limited prognostic value over 2 years in persons with a suspected cognitive disorder.
Homologous Recombination and Translesion DNA Synthesis Play Critical Roles on Tolerating DNA Damage Caused by Trace Levels of Hexavalent Chromium

Contamination of potentially carcinogenic hexavalent chromium (Cr(VI)) in the drinking water is a major public health concern worldwide. However, little information is available regarding the biological effects of a nanomoler amount of Cr(VI). Here, we investigated the genotoxic effects of Cr(VI) at nanomoler levels and their repair pathways. We found that DNA damage response analyzed based on differential toxicity of isogenic cells deficient in various DNA repair proteins is observed after a three-day incubation with K2CrO4 in REV1-deficient DT40 cells at 19.2 μg/L or higher as well as in TK6 cells deficient in polymerase delta subunit 3 (POLD3) at 9.8 μg/L or higher. The genotoxicity of Cr(VI) decreased ~3000 times when the incubation time was reduced from three days to ten minutes. TK mutation rate also significantly decreased from 6 day to 1 day exposure to Cr(VI). The DNA damage response analysis suggest that DNA repair pathways, including the homologous recombination and REV1- and POLD3-mediated error-prone translesion synthesis pathways, are critical for the cells to tolerate to DNA damage caused by trace amount of Cr(VI).
Using a Nonparametric Multilevel Latent Markov Model to Evaluate Diagnostics for Trachoma

In disease control or elimination programs, diagnostics are essential for assessing the impact of interventions, refining treatment strategies, and minimizing the waste of scarce resources. Although high-performance tests are desirable, increased accuracy is frequently accompanied by a requirement for more elaborate infrastructure, which is often not feasible in the developing world. These challenges are pertinent to mapping, impact monitoring, and surveillance in trachoma elimination programs. To help inform rational design of diagnostics for trachoma elimination, we outline a nonparametric multilevel latent Markov modeling approach and apply it to 2 longitudinal cohort studies of trachoma-endemic communities in Tanzania (2000–2002) and The Gambia (2001–2002) to provide simultaneous inferences about the true population prevalence of Chlamydia trachomatis infection and disease and the sensitivity, specificity, and predictive values of 3 diagnostic tests for C. trachomatis infection. Estimates were obtained by using data collected before and after mass azithromycin administration. Such estimates are particularly important for trachoma because of the absence of a true “gold standard” diagnostic test for C. trachomatis. Estimated transition probabilities provide useful insights into key epidemiologic questions about the persistence of disease and the clearance of infection as well as the required frequency of surveillance in the postelimination setting.
Multiset Ordering Constraints

We identify a new and important global (or nonbinary) constraint which ensures that the values taken by two vectors of variables, when viewed as multisets, are ordered. This constraint is useful for a number of different applications including breaking symmetry and fuzzy constraint satisfaction. We propose and implement a linear time algorithm for enforcing generalised arc-consistency on such a multiset ordering constraint. Experimental results show considerable promise.
Fine Mapping of a Gene (ER4.1) that Causes Epidermal Reticulation of Tomato Fruit and Characterization of the Associated Transcriptome

The hydrophobic cuticle that covers the surface of tomato (Solanum lycopersicum) fruit plays key roles in development and protection against biotic and abiotic stresses, including water loss, mechanical damage, UV radiation, pathogens, and pests. However, many details of the genes and regulatory mechanisms involved in cuticle biosynthesis in fleshy fruits are not well understood. In this study, we describe a novel tomato fruit phenotype, characterized by epidermal reticulation (ER) of green fruit and a higher water loss rate than wild type (WT) fruit. The ER phenotype is controlled by a single gene, ER4.1, derived from an introgressed chromosomal segment from the wild tomato species S. pennellii (LA0716). We performed fine mapping of the single dominant gene to an ~300 kb region and identified Solyc04g082540, Solyc04g082950, Solyc04g082630, and Solyc04g082910as potential candidate genes for the ER4.1 locus, based on comparative RNA-seq analysis of ER and WT fruit peels. In addition, the transcriptome analysis revealed that the expression levels of genes involved in cutin, wax and flavonoid biosynthesis were altered in the ER fruit compared with WT. This study provides new insights into the regulatory mechanisms and metabolism of the fruit cuticle.
Wind Field Estimation for Small Unmanned Aerial Vehicles

This paper describes a method for estimating wind field (wind velocity, rate of change of wind velocity, and wind gradient) for small and mini unmanned aerial vehicles. The approach uses sensors that are already part of a standard autopilot sensor suite (Global Positioning System, inertial measurement unit, airspeed, and magnetometer). The primary motivation is enabling energy harvesting; a secondary motivation is development of a low-cost atmospheric measurement and sampling system. The paper presents an error analysis and discusses the primary contributions to error in the estimated wind field. Results of Monte Carlo simulations compare predicted errors in wind estimates with actual errors and show the effect of using estimated winds for energy harvesting from gusts.
An efficient algorithm for detecting frequent subgraphs in biological networks

MOTIVATION With rapidly increasing amount of network and interaction data in molecular biology, the problem of effectively analyzing this data is an important one. Graph theoretic formalisms, commonly used for these analysis tasks, often lead to computationally hard problems due to their relation with subgraph isomorphism. RESULTS This paper presents an innovative new algorithm for detecting frequently occurring patterns and modules in biological networks. Using an innovative graph simplification technique, which is ideally suited to biological networks, our algorithm renders these problems computationally tractable. Indeed, we show experimentally that our algorithm can extract frequently occurring patterns in metabolic pathways extracted from the KEGG database within seconds. The proposed model and algorithm are applicable to a variety of biological networks either directly or with minor modifications. AVAILABILITY Implementation of the proposed algorithms in the C programming language is available as open source at http://www.cs. purdue.edu/homes/koyuturk/pathway/
(Almost) optimal parallel block access to range queries

This guarantee is true for any number of dimensions. Subsequent to this work, Bhatia et al. [4] have proved that such a performance bound is essentially optimal for this kind of scheme, and have also extended our results to the case where the number of disks is a product of the form &kgr;1 * &kgr;2 * … * &kgr;t where the &kgr;ts need not all be 2.
A DIRECT MEASUREMENT OF THE BARYONIC MASS FUNCTION OF GALAXIES AND IMPLICATIONS FOR THE GALACTIC BARYON FRACTION

We use both an H i-selected and an optically selected galaxy sample to directly measure the abundance of galaxies as a function of their “baryonic” mass (stars + atomic gas). Stellar masses are calculated based on optical data from the Sloan Digital Sky Survey and atomic gas masses are calculated using atomic hydrogen (H i) emission line data from the Arecibo Legacy Fast ALFA survey. By using the technique of abundance matching, we combine the measured baryonic function of galaxies with the dark matter halo mass function in a ΛCDM universe, in order to determine the galactic baryon fraction as a function of host halo mass. We find that the baryon fraction of low-mass halos is much smaller than the cosmic value, even when atomic gas is taken into account. We find that the galactic baryon deficit increases monotonically with decreasing halo mass, in contrast with previous studies which suggested an approximately constant baryon fraction at the low-mass end. We argue that the observed baryon fractions of low-mass halos cannot be explained by reionization heating alone, and that additional feedback mechanisms (e.g., supernova blowout) must be invoked. However, the outflow rates needed to reproduce our result are not easily accommodated in the standard picture of galaxy formation in a ΛCDM universe.
Flocculation in Azospirillum brasilense and Azospirillum lipoferum: exopolysaccharides and cyst formation

The phenomena of flocculation and floc formation by Azospirillum brasilense Sp7 (ATCC 29145) and Azospirillum lipoferum Sp59b (ATCC 29707) were studied in aerobic liquid cultures. Carbon sources representative of various entry pathways in combination with various nitrogen sources induced flocculation in both species of azospirilla. Noticeably, the combination of fructose and nitrate was the most effective in terms of floc yields. Phase-contrast microscopic observations revealed a transition in cell morphology from freely motile, vibrioid cells to nonmotile, highly refractile encysting forms during the formation of flocs. The nonmotile forms in flocs appeared to be entangled within a fibrillar matrix, and the cells were highly resistant to desiccation. Dried flocs kept for almost 6 months still maintained the highly refractile encysting forms, and their viability was confirmed by pellicle formation and acetylene reduction in semisolid malate medium. Electron microscopic observations of the desiccated flocs revealed the presence of cell forms containing abundant poly beta-hydroxybutyrate granules within a central body and surrounded by a thick layer of exopolysaccharides. The latter were characterized by alkali and acid digestion, crude cellulase hydrolysis, and calcofluor staining. It was concluded that the overproduction of exocellular polymers induces the flocculent growth and is associated with the concomitant transformation of vegetative cells to the desiccation-resistant encysting forms under limiting cultural conditions.
The Cornish-Fisher-Expansion in the Context of Delta - Gamma - Normal Approximations

Qualitative and quantitative properties of the Cornish-Fisher-Expansion in the context of Delta-Gamma-Normal approaches to the computation of Value at Risk are presented. Some qualitative deficiencies of the Cornish-Fisher-Expansion – the monotonicity of the distribution function as well as convergence are not guaranteed – make it seem unattractive. In many practical situations, however, its actual accuracy is more than sufficient and the Cornish-Fisher-approximation can be computed faster (and simpler) than other methods like numerical Fourier inversion. This paper tries to provide a balanced view on when and when not to use Cornish-Fisher in this context.
Cascaded Photonic Crystal Fiber Interferometers for Refractive Index Sensing

We present a cascaded fiber device based on photonic crystal fiber (PCF) interferometers for refractive index (RI) sensing. The PCF modal interferometers have microbubbles at both sides of the splice regions. The microbubbles act as thick diverging lens that scatter light for efficient excitation of higher order cladding modes and attenuation of the core modes in the transmitted spectrum. Three resonance wavelengths are monitored, and their corresponding RI sensitivities are found to be 252, 187, and 207 nm/refractive index unit (RIU). The results, to our best knowledge, demonstrate that PCF interferometers with microbubbles are repeatable for high RI sensitivity, and the best crosstalk achievable is 0.295 nm/RIU.
Fyn Regulates Adipogenesis by Promoting PIKE-A/STAT5a Interaction

ABSTRACT Fyn is a tyrosine kinase with multiple roles in a variety of cellular processes. Here we report that Fyn is a new kinase involved in adipocyte differentiation. Elevated Fyn protein is detected specifically in the adipocytes of obese mice. Moreover, Fyn expression increases progressively in 3T3-L1 cells during in vitro adipogenesis, which correlates with its kinase activity. Inhibition of Fyn by either genetic or pharmacological manipulation restrains the 3T3-L1 preadipocytes from fully differentiating into mature adipocytes. Mechanistically, Fyn regulates the activity of the adipogenic transcription factor signal transducer and activator of transcription 5a (STAT5a) through enhancing its interaction with the GTPase phosphoinositide 3-kinase enhancer A (PIKE-A). The STAT5a activity is therefore reduced in Fyn- or PIKE-ablated adipose tissues, leading to diminished expression of adipogenic markers and adipocyte differentiation. Our data thus demonstrate a novel functional interaction between Fyn, PIKE-A, and STAT5a in mediating adipogenesis.
Differences in Gamma Interferon Production In Vitro Predict the Pace of the In Vivo Response to Leishmania amazonensis in Healthy Volunteers

ABSTRACT The initial encounter of Leishmania cells and cells from the immune system is fundamentally important in the outcome of infection and determines disease development or resistance. We evaluated the anti-Leishmania amazonensis response of naive volunteers by using an in vitro priming (IVP) system and comparing the responses following in vivo vaccination against the same parasite. In vitro stimulation allowed us to distinguish two groups of individuals, those who produced small amounts of gamma interferon (IFN-γ) (n = 16) (low producers) and those who produced large amounts of this cytokine (n = 16) (high producers). IFN-γ production was proportional to tumor necrosis factor alpha and interleukin 10 (IL-10) levels but did not correlate with IL-5 production. Volunteers who produced small amounts of IFN-γ in vitro remained low producers 40 days after vaccination, whereas high producers exhibited increased IFN-γ production. However, 6 months after vaccination, all individuals tested produced similarly high levels of IFN-γ upon stimulation of their peripheral blood mononuclear cells with Leishmania promastigotes, indicating that low in vitro producers respond slowly in vivo to vaccination. In high IFN-γ producers there was an increased frequency of activated CD8+ T cells both in vitro and in vivo compared to the frequency in low producers, and such cells were positive for IFN-γ as determined by intracellular staining. Such findings suggest that IVP responses can be used to predict the pace of postvaccination responses of test volunteers. Although all vaccinated individuals eventually have a potent anti-Leishmania cell-mediated immunity (CMI) response, a delay in mounting the CMI response may influence resistance against leishmaniasis.
A Model of Relevance for Reuse-Driven Media Retrieval

An often criticized fact in multimedia retrieval is, that user needs are not appropriately taken into account. Both knowledge about how end users search and how they assess the relevance of retrieved multimedia objects can provide invaluable hints for the design of multimedia retrieval systems. This paper reports on an end user study on multimedia retrieval behavior of media professionals who intend to reuse media objects in media productions. We present a conceptual model which contains empirically validated information on how users in the media production domain search for content to be reused and how relevance is assessed by them. Finally we sketch how this information can be used to improve ranking of media objects in multi-faceted retrieval scenarios.