Miracle-dz/UniFAR-FTUs huggingface dataset:
Imaging Pyrite Oxidation and Barite Precipitation in Gas and Oil Shales

The complex suite of chemicals that comprises fracture fluid may result in chemical alterations of shale matrices, which can in turn affect gas and oil transport through the matrices and across fracture-matrix interfaces. In this study, we examined chemical reactions in carbonate-poor Marcellus and carbonate-rich Eagle Ford matrices upon reaction with synthetic fracture fluid (initial pH = 2) at 77 bar and 80 oC for three weeks. A subset of the experiments was conducted with additional Ba2+ and SO4 ions in the fracture fluid to promote barite precipitation. Micro-CT and synchrotron x-ray fluorescence microscopy were used to identify the reaction zones in shale. In contrast with previous studies that focus on chemical reactions at the shale-fluid interface, we observe that the chemical reactions can penetrate a considerable distance into the shale matrix unless the matrix is devoid of any microcracks. The results show that, for shale cores with microcracks, both pyrite oxidation/dissolution and barite precipitation can extend millimeters into the matrix, depending on mineral compositions of the shale. Following 3 weeks of reaction, the carbonate-poor Marcellus system had final pH of 4. The altered zone of the shale core showed a pyrite oxidation zone > 5 mm into the matrix, while barite precipitation was limited to the surface (≤ 45 μm into the matrix). Conversely, the solution of the carbonate-rich Eagle Ford cores was completely neutralized during reaction. When compared to Marcellus, the Eagle Ford shale had a reversed trend with limited pyrite oxidation, and extensive barite precipitation (several millimeters into the matrix) in microcracks and in matrix pores. This comparison is consistent with earlier findings that compared to low pH, near-neutral pH promotes barite precipitation and Fe(II) oxidation. Our results also suggest that scale precipitation, even if formed only at the fracture-matrix interface, can limit transport of dissolved oxygen across the interface, and may also affect transport of gas and oil from shale matrices to fractures for recovery.
Correspondence between self-ratings and key-workers' ratings of depression in adults with mild learning disabilities.

OBJECTIVE This study assessed the association between self-ratings and key-worker ratings of depression in people with mild learning disabilities. METHOD The Zung Depression Scale was completed by 74 adults with mild learning disabilities and a modified version of the questionnaire was completed by two key-workers at two periods in time. RESULTS The correlations between ratings of depression by key-workers were high and key-worker ratings correlated significantly with self-rating. The depression scores were found to be temporally stable. CONCLUSIONS The findings suggest that proxy raters appear to be able to make reliable and valid judgements about other people's self-reported levels of depression.
Characterization of the Inflammatory Response to a Highly Selective PDE4 Inhibitor in the Rat and the Identification of Biomarkers that Correlate with Toxicity

The primary toxicity associated with repeated oral administration of the PDE4 inhibitor IC542 to the rat is an inflammatory response leading to tissue damage primarily in the gastrointestinal tract and mesentery. Although necrotizing vasculitis is frequently seen with other PDE4 inhibitors, blood vessel injury was rare following IC542 administration and was always associated with inflammation in the surrounding tissue. The incidence and severity of the histologic changes in these studies correlated with elevated peripheral blood leukocytes, serum IL-6, haptoglobin, and fibrinogen, and with decreased serum albumin. By monitoring haptoglobin, fibrinogen and serum albumin changes in IC542-treated rats, it was possible to identify rats with early histologic changes that were reversible. Since PDE4 inhibition is generally associated with anti-inflammatory activity, extensive inflammation in multiple tissues was unexpected with IC542. Co-administration of dexamethasone completely blocked IC542-induced clinical and histologic changes in the rat, confirming the toxicity resulted from inflammatory response. In addition, IC542 augmented release of the proinflammatory cytokine IL-6 in LPS-activated whole blood from rats but not monkeys or humans. The effect of IC542 on IL-6 release from rat leukocytes in vitro is consistent with the proinflammatory response observed in vivo and demonstrates species differences to PDE4 inhibition.
Memory B cells in the lung participate in protective humoral immune responses to pulmonary influenza virus reinfection

After pulmonary virus infection, virus-binding B cells ectopically accumulate in the lung. However, their contribution to protective immunity against reinfecting viruses remains unknown. Here, we show the phenotypes and protective functions of virus-binding memory B cells that persist in the lung following pulmonary infection with influenza virus. A fraction of virus-binding B-cell population in the lung expressed surface markers for splenic mature memory B cells (CD73, CD80, and CD273) along with CD69 and CXCR3 that are up-regulated on lung effector/memory T cells. The lung B-cell population with memory phenotype persisted for more than 5 mo after infection, and on reinfection promptly differentiated into plasma cells that produced virus-neutralizing antibodies locally. This production of local IgG and IgA neutralizing antibody was correlated with reduced virus spread in adapted hosts. Our data demonstrates that infected lungs harbor a memory B-cell subset with distinctive phenotype and ability to provide protection against pulmonary virus reinfection.
Evidence that Gonadotropin-Releasing Hormone (GnRH) II Stimulates Luteinizing Hormone and Follicle-Stimulating Hormone Secretion from Monkey Pituitary Cultures by Activating the GnRH I Receptor1

Abstract Mammalian gonadotropin-releasing hormone (GnRH) I is the neuropeptide that regulates reproduction. In recent years, a second isoform of GnRH, GnRH II, and its highly selective type II GnRH receptor were cloned and identified in monkey brain, but its physiological function remains unknown. We sought to determine whether GnRH II stimulates LH and FSH secretion by activating specific receptors in primary pituitary cultures from male monkeys. Dispersed pituitary cells were maintained in steroid-depleted media and stimulated with GnRH I and/or GnRH II for 6 h. Cells were also treated with Antide (Bachem, King of Prussia, PA), a GnRH I antagonist, to block gonadotropin secretion. In monkey as well as rat pituitary cultures, GnRH II was a less effective stimulator of LH and FSH secretion than was GnRH I. In both cell preparations, Antide completely blocked LH and FSH release provoked by GnRH II as well as GnRH I. Furthermore, the combination of GnRH I and GnRH II was no more effective than either agonist alone. These results indicate that GnRH II stimulates FSH and LH secretion, but they also imply that this action occurs through the GnRH I receptor. The GnRH II receptors may have a unique function in the monkey brain and pituitary other than regulation of gonadotropin secretion.
Effects of Exonuclease Activity and Nucleotide Selectivity of the Herpes Simplex Virus DNA Polymerase on the Fidelity of DNA Replication In Vivo

ABSTRACT A mutagenesis system was developed for the in vivo study of the fidelity of DNA replication mediated by wild-type herpes simplex virus type 1 (HSV-1) strain KOS and its polymerase (Pol) mutant derivatives PAAr5, Y7, and YD12. The pHOS1 shuttle plasmid, which contained the SupF mutagenesis marker gene and the HSVoris sequence, was used for analysis of the mutation frequency and the mutation spectrum. All three Pol mutants induced significant increases in the mutation frequencies of the target gene, despite the fact that PAAr5 was previously shown to have an antimutator phenotype by the thymidine kinase mutagenesis assay (J. D. Hall, D. M. Coen, B. L. Fisher, M. Weisslitz, S. Randall, R. E. Almy, P. Gelep, and P. A. Schaffer, Virology 132:26–37, 1984; C. B. C. Hwang and J.-H. Chen, Gene 152:191–193, 1995). Altered spectra of mutated target genes induced by these three mutants were also observed. The relative frequencies of both deletion and complex mutations found in mutants induced by exonuclease-proficient Pols were significantly higher than those induced by exonuclease-deficient Pols. On the other hand, the exonuclease-deficient Pols induced significant increases in the frequency of base substitutions, which comprised predominantly G · C-to-T · A transversions, as well as mutations at additional hot spots. These results suggest that the HSV-1 DNA Pol can incorporate purine-purine or pyrimidine-pyrimidine mispaired bases which may be preferentially proofread by its intrinsic exonuclease activity. Furthermore, the effects of the sequence context of the target gene and the assay method should also be considered carefully in any analysis of replication fidelity.
When Minority Labor Migrants Meet the Welfare State

Life cycle employment of minority labor migrants who entered Norway in the early 1970s diverges from that of natives. Immigrant employment was nearly complete during early years but declined to 50% by the year 2000 (compared to 87% for a native comparison group). We find that immigrant employment is particularly sensitive to the business cycle and that economic downturns of the 1980s and 1990s accelerated their labor market exit. We trace part of the decline to migrants being overrepresented in shrinking industries. But we also identify welfare disincentives that contribute to poor life cycle employment performance of immigrants with many dependent family members.
Unattended and attended visual change detection of motion as indexed by event-related potentials and its behavioral correlates

Visual mismatch negativity (vMMN) is a negative-going component amongst cognitive event-related potentials. It reflects an automatic change-detection process that occurs when an infrequent stimulus is presented that is incongruent with the representation of a frequent (standard) event. In our research we use visual motion (more specifically motion direction changes) to study vMMN. Since movement in the visual field is quite irresistible to our brain, the question in hand is, if the detection of motion direction changes is dependent on attention directed to the stimulus. We present a new continuous whole-display stimulus configuration, where the attention capturing primary task of motion onset detection is in the central part of the visual display and visual oddball sequence on the background. The visual oddball paradigm consisted of 85% standard and 15% deviant events, motion direction change being the deviant. We show that even though the unattended visual oddball sequence does not affect the performance in the demanding behavioral primary task, the differences appearing in that sequence are noticed by our brain and reflected in two distinguishable vMMN components in occipital and parietal scalp locations. When attention is directed toward the visual oddball sequence, we only see different processing of standards and deviants in later time-windows and task-related activity in frontal scalp location. Our results are obtained under strict attention manipulation conditions.
Modeling the Dynamics of Plasmodium vivax Infection and Hypnozoite Reactivation In Vivo

The dynamics of Plasmodium vivax infection is characterized by reactivation of hypnozoites at varying time intervals. The relative contribution of new P. vivax infection and reactivation of dormant liver stage hypnozoites to initiation of blood stage infection is unclear. In this study, we investigate the contribution of new inoculations of P. vivax sporozoites to primary infection versus reactivation of hypnozoites by modeling the dynamics of P. vivax infection in Thailand in patients receiving treatment for either blood stage infection alone (chloroquine), or the blood and liver stages of infection (chloroquine + primaquine). In addition, we also analysed rates of infection in a study in Papua New Guinea (PNG) where patients were treated with either artesunate, or artesunate + primaquine. Our results show that up to 96% of the P. vivax infection is due to hypnozoite reactivation in individuals living in endemic areas in Thailand. Similar analysis revealed the around 70% of infections in the PNG cohort were due to hypnozoite reactivation. We show how the age of the cohort, primaquine drug failure, and seasonality may affect estimates of the ratio of primary P. vivax infection to hypnozoite reactivation. Modeling of P. vivax primary infection and hypnozoite reactivation provides important insights into infection dynamics, and suggests that 90–96% of blood stage infections arise from hypnozoite reactivation. Major differences in infection kinetics between Thailand and PNG suggest the likelihood of drug failure in PNG.
Spatial schemas in depictions

Depictions, such as maps, that portray visible things are ancient whereas graphics, such as charts and diagrams, that portray things that are inherently not visible, are relatively modern inventions. An analysis of historical and developmental graphic inventions suggests that they convey meaning by using elements and space naturally. Elements are based on likenesses, "figures of depiction" and analogs to physical devices. Spatial relations are used metaphorically to convey other relations, based on proximity, at nominal, ordinal, and interval levels. Graphics serve a variety of functions, among them, attracting attention, supporting memory, providing models, and facilitating inference and discovery. Spatial Schemas in Depictions Barbara Tversky Stanford University
Scheduling Tree-Dags Using FIFO Queues: A Control-Memory Trade-Off

We study a combinatorial problem that is motivated by “client? server” schedulers for parallel computations. Such schedulers are often used, for instance, when computations are being done by a cooperating network of workstations. Our results expose and quantify a control? memory trade-off for such schedulers, when the computation being scheduled has the structure of a binary tree, with all arcs oriented either root-toward-leaves or leaves-toward-root. The combinatorial problem for the root-toward-leaves case takes the following form. (The leaves-toward-root case gives rise to a dual formulation, which yields the same trade-offs.) Consider, for integersk,N> 0, an algorithm that employskFIFO queues in order to schedule anN-leaf binary tree in such a way that each nonleaf node of the tree is executed before its children. We establish a trade-off between the number of queues used by the algorithm? which we view as measuring thecontrol complexityof the algorithm? and thememory requirementsof the algorithm, as embodied in the required capacity of the largest-capacity queue. Specifically, for each integerk? {1, 2, . , log2N}, letQk(N) denote the minimax per-queue capacity for ak-queue algorithm that schedules allN-leaf binary trees; letQ*k(N) denote the analogous quantity forcompletebinary trees. We establish the following bounds: For generalN-leaf binary trees, for allk,formula]? Qk(N) ? 2N1/k+ 1.For complete binary trees, we derive tighter bounds. We prove that for all constantk,Q*k(N) = ? formula]. For generalk, we obtain the following bounds:formula]? Q*k(N) ? (4k)1? 1/kformula]. Similar trade-offs are readily established for trees of any fixed branching factor.
Enhanced cell killing induced by the combination of radiation and the heat shock protein 90 inhibitor 17-allylamino-17- demethoxygeldanamycin: a multitarget approach to radiosensitization.

PURPOSE Current strategies for tumor cell radiosensitization focus on a target-based approach. However, the radioresponse of a tumor cell is influenced by a wide variety of signaling molecules existing in a number of different survival pathways. Therefore, in an attempt to increase the probability and/or degree of radiosensitization, we have begun to investigate a multitarget approach using the heat shock protein 90 inhibitor 17-allylamino-17-demethoxygeldanamycin (17AAG). EXPERIMENTAL DESIGN The effect of 17AAG on the levels of three proteins (Raf-1, ErbB2, and Akt) previously implicated in the regulation of radiosensitivity was determined in four human tumor cell lines. Tumor cell survival after exposure to corresponding concentrations of 17AAG combined with clinically relevant doses of X-rays was then evaluated using a clonogenic assay. The radiosensitivity of a nonimmortalized, normal fibroblast cell line was also determined after exposure to 17AAG. RESULTS Exposure to nanomolar concentrations of 17AAG reduced the levels of the three radiosensitivity-associated proteins in a cell type manner. Using corresponding concentrations, 17AAG enhanced the radiosensitivity of each of the tumor cell lines with enhancement factors ranging from 1.3 to 1.7. The enhancement appeared to be related to the number of radioresponse-regulatory proteins affected. In contrast to the tumor cell lines, 17AAG had no effect on the radiosensitivity of a normal, nonimmortalized human fibroblast cell line. CONCLUSIONS These data suggest that heat shock protein 90 may be an appropriate target for selectively enhancing the radiosensitivity of tumor cells over normal cells. Furthermore, they illustrate the potential of a multitarget approach to radiosensitization.
OpenCL-based hardware-software co-design methodology for image processing implementation on heterogeneous FPGA platform

Recently, the OpenCL hardware-software co-design methodology has gained traction in realizing effective parallel architecture designs in heterogeneous FPGA platforms. In fact, the portability of OpenCL on hardware ready platforms such as GPU or multicore CPU enables ease of design verification. This is true especially for parallel algorithms before implementing them using cumbersome HDL-based RTL design. In this paper we employed OpenCL programming platform based on Altera SDK for OpenCL (AOCL) to implement a Sobel filter algorithm as an image processing test case on a Cyclone V FPGA board. Using the portability of this platform, the performance of the kernel code is benchmarked against that of the GPU and multicore CPU implementations for different image and kernel sizes. Different optimization strategies are also applied for each platform. We found that increasing the Sobel filter kernel size from 3×3 to 5×5 results in only 11.3% increase in computation time for FPGA, while the effect was much more significant where the execution time was as high as 23.6% and 85.7% for CPU and GPU, respectively.
Evaluating Gene Expression Dynamics Using Pairwise RNA FISH Data

Recently, a novel approach has been developed to study gene expression in single cells with high time resolution using RNA Fluorescent In Situ Hybridization (FISH). The technique allows individual mRNAs to be counted with high accuracy in wild-type cells, but requires cells to be fixed; thus, each cell provides only a "snapshot" of gene expression. Here we show how and when RNA FISH data on pairs of genes can be used to reconstruct real-time dynamics from a collection of such snapshots. Using maximum-likelihood parameter estimation on synthetically generated, noisy FISH data, we show that dynamical programs of gene expression, such as cycles (e.g., the cell cycle) or switches between discrete states, can be accurately reconstructed. In the limit that mRNAs are produced in short-lived bursts, binary thresholding of the FISH data provides a robust way of reconstructing dynamics. In this regime, prior knowledge of the type of dynamics--cycle versus switch--is generally required and additional constraints, e.g., from triplet FISH measurements, may also be needed to fully constrain all parameters. As a demonstration, we apply the thresholding method to RNA FISH data obtained from single, unsynchronized cells of Saccharomyces cerevisiae. Our results support the existence of metabolic cycles and provide an estimate of global gene-expression noise. The approach to FISH data presented here can be applied in general to reconstruct dynamics from snapshots of pairs of correlated quantities including, for example, protein concentrations obtained from immunofluorescence assays.
Mayors and “their” land: Revealing approaches to flood risk management in small municipalities

The multilevel adaptive governance of flood risk reduction has been emphasised in the last decades and supported by the requirements of European Flood Directive (EC, 2007), while assigning an increasingly important role to municipalities. By contrast, only fragmented efforts have addressed the personal (expert knowledge), financial, and institutional limits of municipalities to achieve the flood risk management (FRM) goals. Starting with thorough literature review, we emphasise the key gaps in current understanding of municipal FRM and note that scarce attention has been paid to small‐sized municipalities (both in area and population). Next, we present an empirical case study based on semi‐structured interviews with 17 mayors of small municipalities in a flood‐prone area of northern Czechia. The aggregation of the mayors' opinions about flood threat and current and planned FRM measures as well as the perceived barriers in their implementation enabled the classification of different FRM strategies at a municipal level (herein referred to as “self‐confidence,” “fatalism,” and “active scepticism”). These strategies are then discussed in terms of the mayors' leadership styles and the significant consequences on the effectiveness and efficiency of FRM at a municipal level.
Both Cell Fusion and Transdifferentiation Account for the Transformation of Human Peripheral Blood CD34-Positive Cells Into Cardiomyocytes In Vivo

Background—Adult human peripheral blood CD34-positive (CD34+) cells appear to transform into cardiomyocytes in the injured hearts of severe combined immunodeficient mice. It remains unclear, however, whether the apparent transformation is the result of transdifferentiation of the donor stem cells or of fusion of the donor cell with the cardiomyocyte of the recipients. Methods and Results—We performed flow cytometry analyses of cells isolated from the hearts of mice that received human CD34+ cells. Human HLA-ABC antigen and cardiac troponin T or Nkx2.5 were used as markers for cardiomyocytes derived from human CD34+ cells, and HLA-ABC and VE-cadherin were used to identify the transformed endothelial cells. The double-positive cells were collected and interphase fluorescence in situ hybridization was used to detect the expression of human and mouse X chromosomes in these cells. We found that 73.3% of nuclei derived from HLA+ and troponin T+ or Nkx2.5+ cardiomyocytes contain both human and mouse X chromosomes and 23.7% contain only human X chromosome. In contrast, the nuclei of HLA−, troponin T+ cells contain only mouse X chromosomes. Furthermore, 97.3% of endothelial cells derived from CD34+ cells contained human X chromosome only. Conclusions—Thus, both cell fusion and transdifferentiation may account for the transformation of peripheral blood CD34+ cells into cardiomyocytes in vivo.