gebhart/patrepeval huggingface dataset:
Technologies for ballast water treatment: a review (2009)

Abstract Invasive aquatic species discharged through ballast water is one of the most serious problems posed nowadays in the marine environment. This review paper summarizes the available technologies applied for ballast water treatment. These technologies can be either port‐based or ship‐based, with the latter being easier to implement. Special emphasis was given to onboard treatment methods, which can be categorized as physical separation, mechanical or chemical methods. The efficiency of the methods, as well as the capacity of application and the target microorganisms were compiled and are presented in this review. Copyright © 2009 Society of Chemical Industry
Observing Single Molecules Complexing with Cucurbit[7]uril through Nanogap Surface-Enhanced Raman Spectroscopy (2016)

In recent years, single-molecule sensitivity achievable by surface-enhanced Raman spectroscopy (SERS) has been widely reported. We use this to investigate supramolecular host-guest chemistry with the macrocyclic host cucurbit[7]uril, on a few-to-single-molecule level. A nanogap geometry, comprising individual gold nanoparticles on a planar gold surface spaced by a single layer of molecules, gives intense SERS signals. Plasmonic coupling between the particle and the surface leads to strongly enhanced optical fields in the gap between them, with single-molecule sensitivity established using a modification of the well-known bianalyte method. Changes in the Raman modes of the host molecule are observed when single guests included inside its cavity internally stretch it. Anisotropic intermolecular interactions with the guest are found which show additional distinct features in the Raman modes of the host molecule.
Characterization of Amylolytic Enzymes, Having Both α-1,4 and α-1,6 Hydrolytic Activity, from the Thermophilic Archaea <i>Pyrococcus furiosus</i> and <i>Thermococcus litoralis</i> (1993)

Extracellular pullulanases were purified from cell-free culture supernatants of the marine thermophilic archaea Thermococcus litoralis (optimal growth temperature, 90 degrees C) and Pyrococcus furiosus (optimal growth temperature, 98 degrees C). The molecular mass of the T. litoralis enzyme was estimated at 119,000 Da by electrophoresis, while the P. furiosus enzyme exhibited a molecular mass of 110,000 Da under the same conditions. Both enzymes tested positive for bound sugar by the periodic acid-Schiff technique and are therefore glycoproteins. The thermoactivity and thermostability of both enzymes were enhanced in the presence of 5 mM Ca, and under these conditions, enzyme activity could be measured at temperatures of up to 130 to 140 degrees C. The addition of Ca also affected substrate binding, as evidenced by a decrease in K(m) for both enzymes when assayed in the presence of this metal. Each of these enzymes was able to hydrolyze, in addition to the alpha-1,6 linkages in pullulan, alpha-1,4 linkages in amylose and soluble starch. Neither enzyme possessed activity against maltohexaose or other smaller alpha-1,4-linked oligosaccharides. The enzymes from T. litoralis and P. furiosus appear to represent highly thermostable amylopullulanases, versions of which have been isolated from less-thermophilic organisms. The identification of these enzymes further defines the saccharide-metabolizing systems possessed by these two organisms.
Strategies to deal with the concern about marker genes in transgenic plants: Some environment-friendly approaches (2002)

Selectable marker genes, that confer resistance to antibiotics or herbicides, are generally incorporated along with the gene of interest in a transformation process so as to allow the recognition of the transformed cells from a background of untransformed ones. Subsequent to the generation of transgenic plants, the presence of these marker genes becomes no more of practical utility and thus arguably a matter of public euphoria, speculating the risk they can pose to the environment and health. Since the recurrent transformations to pyramid desirable genes are practically difficult with the same selectable markers used, novel strategies evolved to essentially eliminate these marker genes or to modulate their spatial/temporal expression, and by use of environmentally safe selectable markers and transplastomic plants. The article discusses the state-of-the-art applications and limitations associated with such systems.
Synergistic Antimicrobial Effects of Silver/Transition-metal Combinatorial Treatments (2017)

Due to the emergence of multi-drug resistant strains, development of novel antibiotics has become a critical issue. One promising approach is the use of transition metals, since they exhibit rapid and significant toxicity, at low concentrations, in prokaryotic cells. Nevertheless, one main drawback of transition metals is their toxicity in eukaryotic cells. Here, we show that the barriers to use them as therapeutic agents could be mitigated by combining them with silver. We demonstrate that synergism of combinatorial treatments (Silver/transition metals, including Zn, Co, Cd, Ni, and Cu) increases up to 8-fold their antimicrobial effect, when compared to their individual effects, against E. coli and B. subtilis. We find that most combinatorial treatments exhibit synergistic antimicrobial effects at low/non-toxic concentrations to human keratinocyte cells, blast and melanoma rat cell lines. Moreover, we show that silver/(Cu, Ni, and Zn) increase prokaryotic cell permeability at sub-inhibitory concentrations, demonstrating this to be a possible mechanism of the synergistic behavior. Together, these results suggest that these combinatorial treatments will play an important role in the future development of antimicrobial agents and treatments against infections. In specific, the cytotoxicity experiments show that the combinations have great potential in the treatment of topical infections.
Effect of Polymorphic Forms of Bulk Powders on Pharmaceutical Properties of Carbamazepine Granules. (1999)

The effects of polymorphic forms of bulk powder on the pharmaceutical properties of carbamazepine (CBZ)granules were investigated by using X-ray diffraction analysis, thermal analysis and Brunauer-Emmett-Teller surface area measurement. A mixture consisting of 50% CBZ forms I, II, III or IV (dehydrate) as a bulk powder, 35% crystalline α-lactose monohydrate and 15% corn starch was used as a pharmaceutical powder, with binder aqueous solutions containing 5% hydroxypropylcellulose (HPC). After kneading with the binder solution, granules were obtained using an extruding granulator. After granulation forms I, II and III were 2.5, 80.3 and 35.2%transformed into dihydrate, respectively. Next, the wet granules were dried at 60°C for 24 h, and the transformed dihydrates were dehydrated into fine particles containing form III. The yield of granules obtained from forms I, II, III and IV was 73.8, 0.0, 0.0 and 76.3%, respectively. The lower granule yields of forms II and III appeared to be due to a lack of kneading water due to absorption of CBZ as crystalline water. Therefore, to the granules of forms II and III was added extra water (60 and 30 ml/kg) to the mixture, respectively, which improved yield markedly, (to 65.1 and 69.2%), indicating the decrease in granule yield was caused by the absorption of water on transformation of dihydrate. The specific surface area (Sw) results suggested that the granules obtained from form II bulk powder had the largest Sw, and those from form I the lowest. In the order of Sw and tablet hardness of the granules, the powders ranked form II>III>IV>I. This indicated that the mechanical strength of the tablet was proportional to the Sw of the particles. The dissolution profiles of the CBZ tablets were investigated in JP XIII, 1st fluid (ph 1.2, 37±0.5°C), and the time required for 50% dissolution (T50) was measured. In the order of T50 ranking was IV≤I<III<II. These results suggested that the polymorphic transformation during the granulation and drying processes induced a change in pharmaceutical properties.
Regulation of nitric-oxide synthase mRNA expression by interferon-gamma and picolinic acid. (1994)

Picolinic acid, a catabolite of L-tryptophan, is a potent co-stimulatory agent for the induction of tumoricidal activity and the production of L-arginine-dependent reactive nitrogen intermediates (RNI) in murine macrophages. We studied whether picolinic acid could affect nitric-oxide synthase (NOS) expression at the gene level in the macrophage cell line ANA-1. NOS mRNA was neither constitutively expressed nor induced by treatment with picolinic acid alone. However, low levels of NOS mRNA were induced by interferon (IFN)-gamma alone. In contrast, a major increase of NOS mRNA expression was observed after treatment with IFN-gamma plus picolinic acid. The synergism was already detectable after 5-6 h and increased up to 20 h of treatment. The ability of picolinic acid to augment IFN-gamma-dependent NOS mRNA expression was associated with a parallel increase in transcription, as demonstrated by nuclear run-on experiments. Protein synthesis was required for the induction of NOS mRNA because addition of cycloheximide dramatically reduced IFN-gamma plus picolonic acid-induced NOS mRNA expression. Finally, interleukin-4 significantly decreased IFN-gamma plus picolinic acid-induced NOS mRNA expression and NOS transcription. These data provide evidence of a molecular event connecting arginine and tryptophan metabolic pathways in the generation of RNI, and they indicate that picolinic acid can induce transcriptional activation of gene expression.
Behavior of mitochondria, chloroplasts and their nuclei during the mitotic cycle in the ultramicroalga Cyanidioschyzon merolae. (1994)

The behavior of cell nuclei, mitochondria and chloroplasts was followed during the mitotic cycle in the primitive unicellular red alga Cyanidioschyzon merolae by epifluorescence microscopy after staining with 4',6-diamidino-2-phenylindole (DAPI) or 3,3'-dihexyloxacarbocyanine iodide (DIOC6), by fluorimetry using a video-intensified microscope photon-counting system (VIMPCS), and by electron microscopy. The cells were classified into five types based on differences in the shape, size, and distribution of organelles in each cell: type I, II, III, IV, and V. Types II, III, IV, and V appear in that order concomitant with a decrease in type I after the cells are subjected to darkness during synchronous culture, suggesting that the organelles divide in the following sequence: chloroplast, mitochondrion, and cell nucleus. The mitochondrial DNA (mt-DNA) and the chloroplast DNA (cp-DNA) are synthesized during stage I, while the cell-nuclear DNA (cn-DNA) is duplicated in stage II. The mitochondria- and chloroplast-nuclear divisions are completed in stage IV. The mitochondrial and chloroplast divisions begin simultaneously in stage II, and chloroplast division finishes just prior to mitochondrial division. The end result is that C. merolae multiplies by binary fission. Electron microscopic examination of serial thin sections of the chloroplast clearly show that the chloroplasts in types II and III are divided by a chloroplast dividing ring (CD-ring), which is located on the cytoplasmic side of the outer envelope at the equatorial region between the daughter chloroplasts. The CD-ring may be involved in chloroplast division throughout the plant kingdom in primitive unicellular algae and higher plants.
Orientation control of YBa2Cu3O7 thin films on MgO for epitaxial junctions (1992)

A low-temperature argon ion milling process has been used to induce growth of c-oriented YBa2Cu3O7 on (001) MgO substrates with the in-plane film axes rotated 45° with respect to those of the substrate, and with respect to those of films grown on untreated regions of the substrate. This process is compatible with standard photolithographic processing, and has been used to produce defined areas of the two orientations on the same substrate. Josephson junctions and dc SQUIDs have been fabricated using the resulting grain boundaries.
Telomeres and disease (2009)

The telomeres of most eukaryotes are characterized by guanine-rich repeats synthesized by the reverse transcriptase telomerase. Complete loss of telomerase is tolerated for several generations in most species, but modestly reduced telomerase levels in human beings are implicated in bone marrow failure, pulmonary fibrosis and a spectrum of other diseases including cancer. Differences in telomerase deficiency phenotypes between species most likely reflect a tumour suppressor function of telomeres in long-lived mammals that does not exist as such in short-lived organisms. Another puzzle provided by current observations is that family members with the same genetic defect, haplo-insufficiency for one of the telomerase genes, can present with widely different diseases. Here, the crucial role of telomeres and telomerase in human (stem cell) biology is discussed from a Darwinian perspective. It is proposed that the variable phenotype and penetrance of heritable human telomerase deficiencies result from additional environmental, genetic and stochastic factors or combinations thereof.
Lithium Based Metal−Organic Framework with Exceptional Stability (2009)

A three-dimensional lithium based metal−organic framework Li2(2,6-NDC) (1); UL-MOF-1, UL = ultralight; NDC = napthalenedicarboxylate; space group P21/c, a = 10.302(5), b = 5.345(2), c = 8.663(4) Å, β = 98.659(9)°, V = 471.6(4) Å3 was synthesized. The framework is stable to 610 °C. The synthesis of 1 was achieved using solvothermal methods in N,N-dimethylformamide at 180 °C and was characterized by single crystal X-ray diffraction. The structure consists of layers of two-dimensional antifluorite related LiO connected by the NDC linker.
Nebulization as a delivery method for mAbs in respiratory diseases (2015)

Overall, the inhalation of mAbs for therapeutic purposes is both appropriate and feasible. The size and structure of the biotherapeutic molecule are important properties to be taken into account when trying to achieve long-term retention. Mesh nebulizers currently appear to be the most appropriate devices for the safe delivery of large amounts of active mAb into the lungs. mAbs should be formulated so as to prevent their degradation and possible immunogenicity. General guidelines can be given for mAb aerosolization, but the formulation and device combination should be adapted for each therapeutic and clinical application.
Policy-based security channels for protecting network communication in mobile cloud computing (2011)

In this paper we present a set of policy-driven security protocols for ensuring the confidentiality and integrity of enterprise data in mobile cloud computing environments. The proposed protocols leverage trusted authority entities and the “elastic” virtualized nature of the cloud computing model to provide energy-efficient key management mechanisms and policy-driven data protection techniques that support the secure interaction of the mobile client with an assortment of cloud software and storage services. The main contribution lies in: (1) Offloading the intensive asymmetric key agreement mechanisms from the mobile client and delegating them to resource-lucrative trusted authority sites. This is achieved by aggregating the security associations, required to agree on symmetric keys between the client and the cloud services, in a single security association between the client and the trusted authority. The aggregation concept results in major energy savings especially when the client consumes a relatively large set of services as is the case in cloud computing today. (2) Designing a customizable policy-based security architecture that considers the sensitivity of cloud data to provide multi-level and fine-grained data protection methodologies that suit the energy-limited mobile devices and the low-bandwidth wireless networks characterizing current mobile cloud computing models. The system is implemented in a real cloud computing environment and the savings in terms of energy consumption and execution time are analyzed.
FREQ-Seq: A Rapid, Cost-Effective, Sequencing-Based Method to Determine Allele Frequencies Directly from Mixed Populations (2012)

Understanding evolutionary dynamics within microbial populations requires the ability to accurately follow allele frequencies through time. Here we present a rapid, cost-effective method (FREQ-Seq) that leverages Illumina next-generation sequencing for localized, quantitative allele frequency detection. Analogous to RNA-Seq, FREQ-Seq relies upon counts from the >10(5) reads generated per locus per time-point to determine allele frequencies. Loci of interest are directly amplified from a mixed population via two rounds of PCR using inexpensive, user-designed oligonucleotides and a bar-coded bridging primer system that can be regenerated in-house. The resulting bar-coded PCR products contain the adapters needed for Illumina sequencing, eliminating further library preparation. We demonstrate the utility of FREQ-Seq by determining the order and dynamics of beneficial alleles that arose as a microbial population, founded with an engineered strain of Methylobacterium, evolved to grow on methanol. Quantifying allele frequencies with minimal bias down to 1% abundance allowed effective analysis of SNPs, small in-dels and insertions of transposable elements. Our data reveal large-scale clonal interference during the early stages of adaptation and illustrate the utility of FREQ-Seq as a cost-effective tool for tracking allele frequencies in populations.
Environmentally robust differential resonant accelerometer in a wafer-scale encapsulation process (2017)

This work demonstrates a unique temperature-compensated differential resonant accelerometer fabricated in a wafer-scale encapsulation process. By utilizing a pair of ultra-stable, high quality factor (>50,000) resonant beams as a strain gauge, we show differential operation with a scale factor of 427Hz/g and a bias instability of 0.16μg at 21s integration time. Furthermore, matched temperature coefficients of frequency (TCf) of the two beams provide a first order cancellation of temperature drift, resulting in a scale factor stability of 0.38% over the temperature range from −20°C to 80°C.
Interactive 3D Modeling with a Generative Adversarial Network (2017)

This paper proposes the idea of using a generative adversarial network (GAN) to assist a novice user in designing real-world shapes with a simple interface. The user edits a voxel grid with a painting interface (like Minecraft). Yet, at any time, he/she can execute a SNAP command, which projects the current voxel grid onto a latent shape manifold with a learned projection operator and then generates a similar, but more realistic, shape using a learned generator network. Then the user can edit the resulting shape and snap again until he/she is satisfied with the result. The main advantage of this approach is that the projection and generation operators assist novice users to create 3D models characteristic of a background distribution of object shapes, but without having to specify all the details. The core new research idea is to use a GAN to support this application. 3D GANs have previously been used for shape generation, interpolation, and completion, but never for interactive modeling. The new challenge for this application is to learn a projection operator that takes an arbitrary 3D voxel model and produces a latent vector on the shape manifold from which a similar and realistic shape can be generated. We develop algorithms for this and other steps of the SNAP processing pipeline and integrate them into a simple modeling tool. Experiments with these algorithms and tool suggest that GANs provide a promising approach to computer-assisted interactive modeling.
Anisotropic Shape Memory Behaviors of Polylactic Acid/Citric Acid–Bentonite Composite with a Gradient Filler Concentration in Thickness Direction (2018)

To date, polylactic acid (PLA) composites with a uniform dispersion of fillers have been extensively studied. However, there is little research about the shape memory (SM) behavior of a PLA composite in which the nanoclays have a nonuniform dispersion. In this paper, the alkaline calcium bentonite (ACBT) was first modified by citric acid (CA) to improve the compatibility between bentonite (BT) and PLA. The structure of CA-modified bentonite (CABT) was characterized by Fourier transform infrared spectroscopy (FT-IR), thermogravimetric analysis (TGA), X-ray diffraction (XRD), and scanning electron microscopy (SEM). Then the CABT/PLA composite with gradient concentration of CABT in thickness direction was fabricated. Because of the good affinity between the grafted CA and the ester groups, the CABT imposed powerful restrictions on the PLA chains, which contributed to the anisotropic driving force for shape recovery. The relationship between the structure and the properties and the mechanism of anisotropic SM behavior of composite were studied.
Transcranial Magnetic Stimulation in Epilepsy (2003)

Transcranial magnetic stimulation (TMS) seems an attractive tool for the study of seizure disorders. It is simple to perform, relatively inexpensive, and generally safe, with the potential to provide noninvasive clinical measurements of neuronal excitability. Applications in patients with epilepsy include investigation of underlying cortical excitability and determination of the effects of antiepileptic drugs (AEDs); preoperative localization of epileptic foci; and functional mapping. Several review articles have been published on the use of TMS for epilepsy (1, 2, 3, 4, 5). Most intriguingly, TMS could become a new seizure treatment modality.

The parameters measured by TMS include motor threshold, which is the minimal threshold for motor response in target muscle and motor evoked potential (MEP) amplitude, both measured using single pulses (see Table 1). The cortical silent period (CSP) is a lapse in electromyogram (EMG), when a TMS pulse is given during tonic voluntary muscle contraction; its duration is related to stimulus intensity. Additional parameters are measured with paired-pulse stimulation techniques. For example, intracortical inhibition (ICI), a decrease in MEP amplitude from the first to the second stimulus, is seen when a subthreshold conditioning pulse is followed by a suprathreshold pulse after a 2- to 5-millisecond delay, whereas intracortical facilitation (ICF) occurs when the pulses are 7 to 20 milliseconds apart.

TABLE 1

TMS Parameters