gebhart/patrepeval huggingface dataset:
Treatment of Pulp and Paper Mill Wastes (2005)

Pulp and paper mills are a major source of industrial pollution worldwide. The pulping and bleaching steps generate most of the liquid, solid, and gaseous wastes (Table 1) [1]. Pulping is a process in which the raw material is treated mechanically or chemically to remove lignin in order to facilitate cellulose and hemicellulose fiber separation and to improve the papermaking properties of fibers. Bleaching is a multistage process to whiten and brighten the pulp through removal of residual lignin. Pulping and bleaching operations are energy intensive and typically consume huge volumes of fresh water and large quantities of chemicals such as sodium hydroxide, sodium carbonate, sodium sulfide, bisulfites, elemental chlorine or chlorine dioxide, calcium oxide, hydrochloric acid, and so on. A partial list of the various types of compounds found in spent liquors generated from pulping and bleaching steps is shown in Table 2 [2–4]. The effluents generated by the mills are associated with the following major problems:
Circuit-quantum electrodynamics with direct magnetic coupling to single-atom spin qubits in isotopically enriched 28Si (2014)

Recent advances in silicon nanofabrication have allowed the manipulation of spin qubits that are extremely isolated from noise sources, being therefore the semiconductor equivalent of single atoms in vacuum. We investigate the possibility of directly coupling an electron spin qubit to a superconducting resonator magnetic vacuum field. By using resonators modified to increase the vacuum magnetic field at the qubit location, and isotopically purified 28Si substrates, it is possible to achieve coupling rates faster than the single spin dephasing. This opens up new avenues for circuit-quantum electrodynamics with spins, and provides a pathway for dispersive read-out of spin qubits via superconducting resonators.
Regulatory macrophages induced by infliximab are involved in healing in vivo and in vitro (2011)

These data show that regulatory macrophages may be involved in mucosal healing and provide a rationale for the superiority of infliximab/azathioprine combination treatment observed in the clinic.
Construction and Analysis of Two Genome-Scale Deletion Libraries for Bacillus subtilis (2017)

A systems-level understanding of Gram-positive bacteria is important from both an environmental and health perspective and is most easily obtained when high-quality, validated genomic resources are available. To this end, we constructed two ordered, barcoded, erythromycin-resistance- and kanamycin-resistance-marked single-gene deletion libraries of the Gram-positive model organism, Bacillus subtilis. The libraries comprise 3,968 and 3,970 genes, respectively, and overlap in all but four genes. Using these libraries, we update the set of essential genes known for this organism, provide a comprehensive compendium of B. subtilis auxotrophic genes, and identify genes required for utilizing specific carbon and nitrogen sources, as well as those required for growth at low temperature. We report the identification of enzymes catalyzing several missing steps in amino acid biosynthesis. Finally, we describe a suite of high-throughput phenotyping methodologies and apply them to provide a genome-wide analysis of competence and sporulation. Altogether, we provide versatile resources for studying gene function and pathway and network architecture in Gram-positive bacteria.
Effectively indexing uncertain moving objects for predictive queries (2009)

Moving object indexing and query processing is a well studied research topic, with applications in areas such as intelligent transport systems and location-based services. While much existing work explicitly or implicitly assumes a deterministic object movement model, real-world objects often move in more complex and stochastic ways. This paper investigates the possibility of a marriage between moving-object indexing and probabilistic object modeling. Given the distributions of the current locations and velocities of moving objects, we devise an efficient inference method for the prediction of future locations. We demonstrate that such prediction can be seamlessly integrated into existing index structures designed for moving objects, thus improving the meaningfulness of range and nearest neighbor query results in highly dynamic and uncertain environments. The paper reports on extensive experiments on the B x -tree that offer insights into the properties of the paper's proposal.
Localization of JPEG Double Compression Through Multi-domain Convolutional Neural Networks (2017)

When an attacker wants to falsify an image, in most of cases she/he will perform a JPEG recompression. Different techniques have been developed based on diverse theoretical assumptions but very effective solutions have not been developed yet. Recently, machine learning based approaches have been started to appear in the field of image forensics to solve diverse tasks such as acquisition source identification and forgery detection. In this last case, the aim ahead would be to get a trained neural network able, given a to-be-checked image, to reliably localize the forged areas. With this in mind, our paper proposes a step forward in this direction by analyzing how a single or double JPEG compression can be revealed and localized using convolutional neural networks (CNNs). Different kinds of input to the CNN have been taken into consideration, and various experiments have been carried out trying also to evidence potential issues to be further investigated.
The Abl and Arg non‐receptor tyrosine kinases regulate different zones of stress fiber, focal adhesion, and contractile network localization in spreading fibroblasts (2010)

Directed cell migration requires precise spatial control of F-actin-based leading edge protrusion, focal adhesion (FA) dynamics, and actomyosin contractility. In spreading fibroblasts, the Abl family kinases, Abl and Arg, primarily localize to the nucleus and cell periphery, respectively. Here we provide evidence that Abl and Arg exert different spatial regulation on cellular contractile and adhesive structures. Loss of Abl function reduces FA, F-actin, and phosphorylated myosin light chain (pMLC) staining at the cell periphery, shifting the distribution of these elements more to the center of the cell than in wild-type (WT) and arg(-/-) cells. Conversely, loss of Arg function shifts the distribution of these contractile and adhesion elements more to the cell periphery relative to WT and abl(-/-) cells. Abl/Arg-dependent phosphorylation of p190RhoGAP (p190) promotes its binding to p120RasGAP (p120) to form a functional RhoA GTPase inhibitory complex, which attenuates RhoA activity and downstream pMLC and FA formation. p120 and p190 colocalize both in the central region and at the cell periphery in WT cells. This p120:p190 colocalization redistributes to a more peripheral distribution in abl(-/-) cells and to a more centralized distribution in arg(-/-) cells, and these altered distributions can be restored to WT patterns via re-expression of Abl or Arg, respectively. Thus, the altered p120:p190 distribution in the mutant cells correlates inversely with the redistribution in adhesions, actin, and pMLC staining in these cells. Our studies suggest that Abl and Arg exert different spatial regulation on actomyosin contractility and focal adhesions within cells.
Activation of JNK1/2 and p38 MAPK signaling pathways promotes enterovirus 71 infection in immature dendritic cells (2014)

c-Jun NH2-terminal kinase/stress-activated kinase (JNK/SAPK) and the p38 mitogen-activated protein kinase (p38 MAPK) are important components of cellular signal transduction pathways, which have been reported to be involved in viral replication. However, little is known about JNK1/2 and p38 MAPK signaling pathways in enterovirus 71 (EV71)-infected immature dendritic cells (iDCs). Thus, iDCs were induced from peripheral blood mononuclear cells (PBMC) and performed to explore the expressions and phosphorylation of molecules in the two signaling pathways as well as secretions of inflammatory cytokines and interferons during EV71 replication. We showed that EV71 infection could activate both JNK1/2 and p38 MAPK in iDCs and phosphorylate their downstream transcription factors c-Fos and c-Jun, which further promoted the production of IL-2, IL-6, IL-10, and TNF-α. Moreover, EV71 infection also increased the release of IFN-β and IL-12 p40. Pretreatment of iDCs with SP600125 and SB203580 (20 μM) could severely impair viral replication and its induced phosphorylation of JNK1/2,p38 MAPK, c-Fos and c-Jun. In addition, treatment of EV71-infected iDCs with SP600125 and SB203580 could inhibit secretions of IL-6, IL-10 and TNF-α. JNK1/2 and p38 MAPK signaling pathways are beneficial to EV71 infection and positively regulate secretions of inflammatory cytokines in iDCs.
<i>In vivo</i> evidence for K<sub>Ca</sub> channel opening properties of acetazolamide in the human vasculature (2001)

1. The selective carbonic anhydrase inhibitor acetazolamide is known to increase blood flow in several organs. Acetazolamide directly dilates isolated resistance arteries associated with activation of calcium-activated potassium (K(Ca)) channels. We examined both the presence and mechanism of the direct vascular action of acetazolamide in vivo in humans. 2. Forearm vasodilator responses of 30 healthy volunteers to infusion of placebo and increasing doses of acetazolamide (1-3-10 mg min(-1) dl(-1)) into the brachial artery were recorded by venous occlusion plethysmography, before and after local administration of L-NMMA (0.2 mg min(-1) dl(-1), an inhibitor of NO-synthase, n=6), indomethacin (5.0 microg min(-1) dl(-1), an inhibitor of prostaglandin synthesis, n=6), glibenclamide (10 microg min(-1) dl(-1), an inhibitor of K(ATP) channels, n=6), tetraethylammonium (0.1 mg min(-1) dl(-1), an inhibitor of K(Ca) channels, n=6) or placebo (NaCl 0.9%, n=6). Lower dosages of acetazolamide did not affect vascular tone (n=6). 3. Acetazolamide infusions increased forearm blood flow from 2.41+/-0.17 to 2.99+/-0.18, 4.09+/-0.26 and 6.77+/-0.49 ml min(-1) dl(-1) in the infused forearm (P:<0.001), with no significant changes in the non-infused forearm, blood pressure or heart rate. Acetazolamide-induced vasodilation was not inhibited by L-NMMA, indomethacin, or glibenclamide but was significantly attenuated by TEA (vasodilation: 23+/-6, 82+/-19, 241+/-38% versus 27+/-8, 44+/-22, 42+/-35%). 4. We conclude that acetazolamide exerts a direct vasodilator effect in vivo in humans mediated by vascular K(Ca) channel activation. This makes acetazolamide the first drug known that specifically modulates this channel.
Utilizing RFID Signaling Scheme for Localization of Stationary Objects and Speed Estimation of Mobile Objects (2007)

Mapping the physical location of nodes within a wireless sensor network (WSN) is critical in many applications such as tracking and environmental sampling. Passive RFID tags pose an interesting solution to localizing nodes because an outside reader, rather than the tag, supplies the power to the tag. Thus, utilizing passive RFID technology allows a localization scheme to not be limited to objects that have wireless communication capability because the technique only requires that the object carries a RFID tag. This paper illustrates a method in which objects can be localized without the need to communicate received signal strength information between the reader and the tagged item. The method matches tag count percentage patterns under different signal attenuation levels to a database of tag count percentages, attenuations and distances from the base station reader.
A two-stage aerosol impactor with embedded MEMS resonant mass balances for particulate size segregation and mass concentration monitoring (2013)

This work reports on integration of MEMS resonant mass balances within a two-stage aerosol impactor capable of sampling and size separation of micro to nanoscale airborne particles. Two identical thin-film piezoelectric on substrate (TPoS) resonators acting as high resolution mass balances provide real-time information on mass concentration of size-segregated airborne particles adsorbed in each aerosol impactor stage. Tests performed on air samples from different environments with different particle mass concentrations ranging from 0.014-0.2μg/m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> (particles larger than 60nm) show a clear correlation between the resonator response and the expected particle concentrations. SEM images of the deposited particles clearly show a size difference between particles collected in the two stages with the cutoff sizes close to the values the impactor was originally designed for (230nm and 60nm for the first and second stages, respectively).
Adding Hyperlinks to Digital Television (1998)

Hyperlinked video is video in which specific objects are made selectable by some form of user interface, and the user's interactions with these objects modify the presentation of the video. Identifying and tracking the objects remains one of the chief difficulties in authoring hyperlinked video; we solve this problem through the use of a video tracking and segmentation algorithm that uses color, texture, motion, and position parameters. An author uses a computer mouse to scribble roughly on each desired object in a frame of video, and the system generates a segmentation mask for that frame and following frames. We have applied this technique in the production of a soap opera program, with the result that the user can inquire about purchasing clothing and furnishings used in the show. We will discuss this and other uses of the technology, describe our experiences in using the segmentation algorithm for hyperlinked video purposes in both broadcast and on-demand modes, and present several different user-interface methods appropriate for hyperlinked video.
Optical polarization characteristics of light emission from sidewalls of primary-color light-emitting diodes (2008)

The present communication reports a study on polarized light emission from sidewalls of light-emitting-diode (LED) dies with future interest in color display applications, e.g., liquid-crystal display (LCD) backlighting. Commercial LED dies with three primary colors were subjected to polarization characterization via a confocal microscope. AlInGaP red LED dies (cube shape) were shown to emit polarized light with a polarization ratio of 0.47. InGaN-based blue (sapphire substrate) and green (SiC substrate) LED dies were revealed to possess polarization ratios as high as 0.9 on side emission from epitaxial layers. These results ensure the potential of commercially available LED dies for LCD backlighting experiments. Discussions were made on improvement in polarization characteristics.
Therapeutic and prophylactic DNA vaccines for HIV-1 (2013)

Continued improvements in delivery technology, in particular electroporation, and the use of prime-boost vaccine strategies will aid in boosting the immunogenicity of DNA vaccines. Basic immunology research will also help discover new potential adjuvant targets that can be combined with DNA vaccination, such as inhibitors of inhibitory receptors.
Four-channel integrated-optic wavelength demultiplexer with weak polarization dependence (1991)

A planar four-channel wavelength demultiplexer with weak polarization dependence is proposed and demonstrated. This demultiplexer is based on an optical-phased array. An experimental device with dimensions 4.5*3.2 mm/sup 2/ was designed and fabricated, using conventional (high-quality) optical lithography. The demultiplexer operates in the wavelength range 776.5-781.2 nm, with a channel spacing of 1.55 nm. Insertion loss was 0.6 dB for the central channels and 1.2 dB for the outer channels for transverse-electric (TE) polarization, excluding 1.3-dB waveguide propagation loss. Crosstalk values measured 15.4-29.7 dB for the TE and 13.4-22.2 dB for the transverse-magnetic (TM) polarization.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Financial Anatomy of Biomedical Research (2005)

Enhancing research productivity and evaluation of benefit are pressing challenges, requiring (1) more effective translation of basic scientific knowledge to clinical application; (2) critical appraisal of rapidly moving scientific areas to guide investment where clinical need is greatest, not only where commercial opportunity is currently perceived; and (3) more specific information about sources and uses of research funds than is generally available to allow informed investment decisions. Responsibility falls on industry, government, and foundations to bring these changes about with a longer-term view of research value.
Young neurons from the adult subependymal zone proliferate and migrate along an astrocyte, extracellular matrix‐rich pathway (1996)

The subependymal zone (SEZ) of the lateral ventricle of adult rodents has long been known to be mitotically active. There has been increased interest in the SEZ, since it has been demonstrated that neuroepithelial stem cells residing there generate neurons in addition to glia in vitro. In the present study, we have examined parasagittal sections of the adult mouse brain using immunocytochemistry for extracellular matrix (ECM) molecules (tenascin and chondroitin sulfate-containing proteoglycans), glial fibrillary acidic protein (GFAP, a cytoskeletal protein prominently expressed by immature and reactive astrocytes), RC-2 (a radial glial and immature astrocyte cytoskeletal marker), TuJ1 (a class III β-tubulin isoform expressed solely by postmitotic and adult neurons), nestin (a cytoskeletal protein associated with stem cells), neuron-specific enolase, and bromodeoxyuridine (BrdU, which is taken up by dividing cells). Our results demonstrate that a population of young neurons reside within an ECM-rich, GFAP-positive astrocyte pathway from the rostral SEZ all the way into the olfactory bulb. Furthermore, BrdU labeling studies indicate that there is a high level of cell division along the entire length of this path, and double-labeling studies indicate that neurons committed to a neuronal lineage (i.e., TuJ1+) take up BrdU (suggesting they are in the DNA synthesis phase of the cell cycle), again along the entire length of the SEZ “migratory pathway.” Thus, the SEZ appears to retain the ability to produce neurons and glia throughout the life of the animal, functioning as a type of “brain marrow.” The implications of these findings are discussed in relation to the role that such a glial/ECM-rich boundary (as seen in the embryonic cortical subplate and other developing areas) may play in: confining the migratory populations and maintaining them in a persistent state of immaturity; facilitating their migration to the olfactory bulb, where they are incorporated into established adult circuitries; and potentially altering SEZ cell cycle dynamics that eventually lead to cell death. © 1996 Wiley-Liss, Inc.
Radically Different Antioxidants:  Thermally Generated Carbon-Centered Radicals as Chain-Breaking Antioxidants (2006)

A new class of thermally activated chain-breaking antioxidants is presented. Dimers of persistent carbon-centered radicals are able to inhibit the autoxidation of cumene and styrene with better rate constants than the commercial antioxidant Irganox HP-136 and 3,5-di-tert-butyl-4-hydroxyanisole. A dramatic increase in antioxidant activity is observed with increasing temperature as more dimers dissociate to their corresponding persistent radicals.
Cytosine Deaminase from<i>Escherichia coli</i>—Production, Purification, and Some Characteristics (1986)

We wanted to obtain a large amount of cytosine deaminase from Escherichia coli. This enzyme deaminates 5-fluorocytosine and is thermostable. It is needed for trial use in a novel chemotherapy for cancer in combination with 5-fluorocytosine. We improved the conditions of its production by examining the culture conditions. A pH-stat culture with the culture pH controlled at around 8.5 using citric acid gave efficient production of cell mass and enzyme activity. The enzyme was purified 1200-fold from the cell-free extract, to homogeneity, using two kinds of affinity adsorbents prepared for this purpose. The enzyme had a molecular weight of 200,000 (gel permeation), and seemed to be an SH-enzyme. The purified enzyme was thermostable.
Control of prostate cell growth, DNA damage and repair and gene expression by resveratrol analogues, in vitro (2010)

The chemopreventive potential of resveratrol is marred by its low bioavailability. Studies of modified resveratrol may reveal features that affect its bioefficacy and bioavailability. We compared the anti-proliferative and gene regulatory activities of resveratrol with trimethoxy-resveratrol and triacetyl-resveratrol using cultured human prostate cancer (CaP) cells. LNCaP cells were incubated with resveratrol and its analogues. Changes in proliferation, colony formation, cell cycle, apoptosis and prostate specific antigen (PSA) PSA were determined. DNA damage was assayed by phosphorylated-histone H2AX changes. Expression of total and serine-15-phosphorylated p53 and p53-inducible cell cycle regulatory protein p21 and ribonucleotide reductase subunit p53R2 involved in DNA repair were measured by immunobloting and reverse transcription-polymerase chain reaction. Exposure to resveratrol or triacetyl-resveratrol activated p53, increased p21 and p53R2 and decreased PSA expression in LNCaP cells. These changes were attenuated by the p53 inhibitor pifithrin-α. However, LNCaP cells exposed to trimethoxy-resveratrol showed induction of apoptosis, reduction in G₁ and prolongation of the SG₂M phases. Resveratrol and analogues were also studied in CWR22Rv1 (containing mutated p53) and p53-null PC-3 cells. CWR22Rv1 cells exposed to resveratrol and triacetyl-resveratrol showed a G₁S block, concomitant with increased p53 and p21 expression; however, identically treated PC-3 cells showed attenuated progression through the SG₂M phases. Trimethoxy-resveratrol did not affect CWR22Rv1 cell cycle but reduced and expanded PC-3 cells in the G₁ and SG₂M phases, respectively. These results suggest that triacetyl-resveratrol and trimethoxy-resveratrol are active against different stage CaP cells, using overlapping and distinct mechanisms.
miR-1, miR-10b, miR-155, and miR-191 are novel regulators of BDNF (2014)

Brain-derived neurotrophic factor (BDNF) is a secreted protein of the neurotrophin family that regulates brain development, synaptogenesis, memory and learning, as well as development of peripheral organs, such as angiogenesis in the heart and postnatal growth and repair of skeletal muscle. However, while precise regulation of BDNF levels is an important determinant in defining the biological outcome, the role of microRNAs (miRs) in modulating BDNF expression has not been extensively analyzed. Using in silico approaches, reporter systems, and analysis of endogenous BDNF, we show that miR-1, miR-10b, miR-155, and miR-191 directly repress BDNF through binding to their predicted sites in BDNF 3'UTR. We find that the overexpression of miR-1 and miR-10b suppresses endogenous BDNF protein levels and that silencing endogenous miR-10b increases BDNF mRNA and protein levels. Furthermore, we show that miR-1/206 binding sites within BDNF 3'UTR are used in differentiated myotubes but not in undifferentiated myoblasts. Finally, our data from two cell lines suggest that endogenous miR-1/206 and miR-10 family miRs act cooperatively in suppressing BDNF through their predicted sites in BDNF 3'UTR. In conclusion, our results highlight miR-1, miR-10b, miR-155, and miR-191 as novel regulators of BDNF long and short 3'UTR isoforms, supporting future research in different physiological and pathological contexts.