Miracle-dz/UniFAR-FTUs huggingface dataset:
Hydrogen sulfide intervention in focal cerebral ischemia/reperfusion injury in rats

The present study aimed to explore the mechanism underlying the protective effects of hydrogen sulfide against neuronal damage caused by cerebral ischemia/reperfusion. We established the middle cerebral artery occlusion model in rats via the suture method. Ten minutes after middle cerebral artery occlusion, the animals were intraperitoneally injected with hydrogen sulfide donor compound sodium hydrosulfide. Immunofluorescence revealed that the immunoreactivity of P2X 7 in the cerebral cortex and hippocampal CA1 region in rats with cerebral ischemia/reperfusion injury decreased with hydrogen sulfide treatment. Furthermore, treatment of these rats with hydrogen sulfide significantly lowered mortality, the Longa neurological deficit scores, and infarct volume. These results indicate that hydrogen sulfide may be protective in rats with local cerebral ischemia/reperfusion injury by down-regulating the expression of P2X 7 receptors.
Increasing the sensitivity and information content of multi-dimensional and hyphenated LC-MS systems

The aims of this thesis were to investigate the potential of multi-dimensional separation platforms and their applicability in the analysis of complex mixtures, and to explore routes toward tackling their major drawbacks. Chapter 1 describes the effectiveness of one-dimensional liquid chromatography and limitations in applications addressed by this technique. In Chapter 2 the possibilities and limitations of stationary-phase-assisted modulation as a post-column focusing approach (“1,5D-LC system”) are described. “1,5D-LC” has great potential for improving the detectability of pure-compound standards. Chapter 3 describes the development of the online comprehensive two-dimensional LC×LC-MS separation of anabolic steroids in bovine-urine samples. The proposed strategy allowed to improve the detectability of trace-level anabolic residues and resulted in clear gains in signal intensities, increased signal-to-noise ratios for steroid compounds and in a greater number of detected compounds. In Chapter 4 a novel trapped-ion-mobility spectrometer (TIMS) is discussed. This multi-dimensional separation platform (LC-TIMS-MS) was applied for untargeted separation of lipids in human-plasma samples and was shown to provide more-detailed information in comparison with traditional LC-MS technology. Chapter 5 describes the results of the lipidomic mapping of the human-plasma samples performed by online comprehensive two-dimensional liquid chromatography (LC×LC-MS). A comparison of LC-TIMS-MS and LC×LC-MS techniques was made in terms of the main descriptors of separation power. Chapter 6 discusses the main achievements and also features some reflections on the future directions for development and improvement of extremely effective and accessible multi-dimensional separations.
A growth factor-repressible gene associated with protein kinase C- mediated inhibition of adipocyte differentiation

The conversion of determined adipoblasts to fully differentiated adipocytes requires appropriate environmental conditions. A strict dependence on cell confluence and a facilitation by glucocorticoid hormones have previously been described. We have found that agents that are capable of activating protein kinase C, such as basic fibroblast growth factor and phorbol esters, inhibit the differentiation of the adipogenic cell line TA1 without stimulating cell growth. Here we describe the sequence and characterization of a cDNA (clone 5) that detects an RNA, the expression of which is enhanced by glucocorticoids and increasing cell density. In contrast, activators of protein kinase C including basic fibroblast growth factor, phorbol esters, and synthetic diacylglycerols inhibit clone 5 gene expression. It appears that clone 5 expression is closely linked to environmental and hormonal factors that promote the differentiation of adipogenic cells.
Towards atomic and close-to-atomic scale manufacturing

Human beings have witnessed unprecedented developments since the 1760s using precision tools and manufacturing methods that have led to ever-increasing precision, from millimeter to micrometer, to single nanometer, and to atomic levels. The modes of manufacturing have also advanced from craft-based manufacturing in the Stone, Bronze, and Iron Ages to precision-controllable manufacturing using automatic machinery. In the past 30 years, since the invention of the scanning tunneling microscope, humans have become capable of manipulating single atoms, laying the groundwork for the coming era of atomic and close-to-atomic scale manufacturing (ACSM). Close-to-atomic scale manufacturing includes all necessary steps to convert raw materials, components, or parts into products designed to meet the user’s specifications. The processes involved in ACSM are not only atomically precise but also remove, add, or transform work material at the atomic and close-to-atomic scales. This review discusses the history of the development of ACSM and the current state-of-the-art processes to achieve atomically precise and/or atomic-scale manufacturing. Existing and future applications of ACSM in quantum computing, molecular circuitry, and the life and material sciences are also described. To further develop ACSM, it is critical to understand the underlying mechanisms of atomic-scale and atomically precise manufacturing; develop functional devices, materials, and processes for ACSM; and promote high throughput manufacturing.
Monitoring human papillomavirus prevalence in urine samples: a review

Human papillomavirus (HPV) is the main cause of cervical cancer, and many countries now offer vaccination against HPV to girls by way of government-funded national immunization programs. Monitoring HPV prevalence in adolescents could offer a near-term biological measure of vaccine impact, and urine sampling may be an attractive large-scale method that could be used for this purpose. Our objective was to provide an overview of the literature on HPV DNA detection in urine samples, with an emphasis on adolescents. We searched the PubMed database using the terms “HPV” and “urine” and identified 21 female and 14 male study populations in which HPV prevalence in urine samples was reported, four of which included only asymptomatic female adolescents. We provide herein an overview of the recruitment setting, age, urine sampling procedure, lesion type, HPV assay, and HPV prevalence in urine samples and other urogenital samples for the studies included in this review. In female study populations, concordance for any HPV type and type-specific concordance in paired urine and cervical samples are provided in addition to sensitivity and specificity. We concluded that few studies on HPV prevalence in urine samples have been performed in asymptomatic female adolescent populations but that urine samples may be a useful alternative to cervical samples to monitor changes in HPV prevalence in females in the post-HPV vaccination era. However, care should be taken when extrapolating HPV findings from urine samples to the cervix. In males, urine samples do not seem to be optimal for monitoring HPV prevalence due to a low human genomic DNA content and HPV DNA detection rate compared to other urogenital sites. In each situation the costs and benefits of HPV DNA detection in urine compared to alternative monitoring options should be carefully considered.
Role of insulin in work-induced growth of skeletal muscle.

Although insulin treatment was necessary for total body growth in alloxandiabetic rats, work-induced hypertrophy of the soleus and plantaris muscles could be induced in such animals without insulin. Compensatory growth proceeded to a similar extent in diabetic and normal rats. (Endocrinology 83: 1071, 1968)
Prediction of Power Grid Failure Using Neural Network Learning

Power Grid failures have the potential to drastically affect the population be it a localized outage or a large-scale blackout. Pre-event planning currently consists of preparation for all scenarios and some enthusiastic prognoses, leading to most resources spreading thin. Focus on a specific area of concern typically follows large scale power grid failures as post event analysis and does not include an overall analysis. In this study, a neural network is used to conduct “pre-event” analysis of a power grid to determine if it is susceptible to failure. This research study demonstrates that overall “pre-event” analysis can be beneficial with the use of a machine learning agent. The agent can also be used to determine areas that need the most attention. Future work with larger number of constraints and additional machine learning algorithms will be explored to further improve power grid analysis and performance.
Improving Privacy on Android Smartphones Through In-Vivo Bytecode Instrumentation

In this paper we claim that a widely applicable and efficient means to fight against malicious mobile Android applications is: 1) to per- form runtime monitoring 2) by instrumenting the application byte- code and 3) in-vivo, i.e. directly on the smartphone. We present a tool chain to do this and present experimental results showing that this tool chain can run on smartphones in a reasonable amount of time and with a realistic effort. Our findings also identify chal- lenges to be addressed before running powerful runtime monitoring and instrumentations directly on smartphones. We implemented two use-cases leveraging the tool chain: FineGPolicy, a fine-grained user centric permission policy system and AdRemover an adver- tisement remover. Both prototypes improve the privacy of Android systems thanks to in-vivo bytecode instrumentation.
Adaptive Route Selection Policy Based on Back Propagation Neural Networks

One of the key issues in the study of multiple route protocols in mobile ad hoc networks (MANETs) is how to select routes to the packet transmission destination. There are currently two route selection methods: primary routing policy and load-balancing policy. Many ad hoc routing protocols are based on primary (fastest or shortest but busiest) routing policy from the self-standpoint of traffic transmission optimization of each node. Load-balancing protocols equalize transmission load among multiple routes in the network. However, the lack of global perspective can cause congestion in primary policy and prolong delay time in load-balancing policy. So, although they are sometimes efficient, these two types of policies cannot adapt to intricately changing network conditions. We propose a new multiple route protocol with an Adaptive route selection Policy based on a Back propagation Neural network (APBN) to optimize selection policy. In our study, we used a gradient ascent algorithm to determine the relationship between different optimum route selection polices and varying conditions in the communication network and to make a neural network that learns this relationship using the Back Propagation (BP) algorithm to predict the next optimum route selection policy. We evaluated our protocol using Omnet simulator. The results show that the proposed scheme performs better than current protocols.
Improved internal quantum efficiency in high-quality BaSi2 films grown by molecular beam epitaxy

A new method has been developed for the formation of undoped BaSi<sub>2</sub> absorption layers on an Sb-doped n<sup>+</sup>-BaSi<sub>2</sub>/p<sup>+</sup>-Si tunnel junction (TJ) formed on Si(111). The diffusion of Sb atoms from the n<sup>+</sup>-BaSi<sub>2</sub> layer was effectively suppressed by inserting a thin Si layer between the n<sup>+</sup>-BaSi<sub>2</sub> and 400-nm-thick undoped BaSi<sub>2</sub> layers. The inserted Si layer was firstly deposited at room temperature, followed by annealing at 650°C by solid phase epitaxy (SPE). Both X-ray diffraction (XRD) and reflection high-energy electron diffraction (RHEED) patterns indicated the good crystalline quality of undoped BaSi<sub>2</sub> overlayers; the I-V characteristics revealed the excellent tunneling effect of the TJ. The photoresponsivity has been greatly improved by the new growth method and reached a maximum of 0.37 A/W at 1.55 eV under a bias voltage of 2 V; the corresponding external quantum efficiency (EQE) and internal quantum efficiency (IQE) increased up to 60% and 70%, respectively, which is the highest value ever reported for semiconducting silicides.
The Infection of Cucumber (Cucumis sativus L.) Roots by Meloidogyne incognita Alters the Expression of Actin-Depolymerizing Factor (ADF) Genes, Particularly in Association with Giant Cell Formation

Cucumber (Cucumis sativus L.) is threatened by substantial yield losses due to the south root-knot nematode (Meloidogyne incognita). However, understanding of the molecular mechanisms underlying the process of nematode infection is still limited. In this study, we found that M. incognita infection affected the structure of cells in cucumber roots and treatment of the cytoskeleton inhibitor (cytochalasin D) reduced root-knot nematode (RKN) parasitism. It is known that Actin-Depolymerizing Factor (ADF) affects cell structure, as well as the organization of the cytoskeleton. To address the hypothesis that nematode-induced abnormal cell structures and cytoskeletal rearrangements might be mediated by the ADF genes, we identified and characterized eight cucumber ADF (CsADF) genes. Phylogenetic analysis showed that the cucumber ADF gene family is grouped into four ancient subclasses. Expression analysis revealed that CsADF1, CsADF2-1, CsADF2-2, CsADF2-3 (Subclass I), and CsADF6 (Subclass III) have higher transcript levels than CsADF7-1, CsADF7-2 (Subclass II genes), and CsADF5 (Subclass IV) in roots. Members of subclass I genes (CsADF1, CsADF2-1, CsADF2-2, and CsADF2-3), with the exception of CsADF2-1, exhibited a induction of expression in roots 14 days after their inoculation (DAI) with nematodes. However, the expression of subclass II genes (CsADF7-1 and CsADF7-2) showed no significant change after inoculation. The transcript levels of CsADF6 (Subclass III) showed a specific induction at 21 DAI, while CsADF5 (Subclass IV) was weakly expressed in roots, but was strongly up-regulated as early as 7 DAI. In addition, treatment of roots with cytochalasin D caused an approximately 2-fold down-regulation of the CsADF genes in the treated plants. These results suggest that CsADF gene mediated actin dynamics are associated with structural changes in roots as a consequence of M. incognita infection.
KEPLER-445, KEPLER-446 AND THE OCCURRENCE OF COMPACT MULTIPLES ORBITING MID-M DWARF STARS

We confirm and characterize the exoplanetary systems Kepler-445 and Kepler-446: two mid-M dwarf stars, each with multiple, small, short-period transiting planets. Kepler-445 is a metal-rich ([Fe/H] = +0.25 ± 0.10) M4 dwarf with three transiting planets, and Kepler-446 is a metal-poor ([Fe/H] = −0.30 ± 0.10) M4 dwarf also with three transiting planets. Kepler-445c is similar to GJ 1214b: both in planetary radius and the properties of the host star. The Kepler-446 system is similar to the Kepler-42 system: both are metal-poor with large galactic space velocities and three short-period, likely rocky transiting planets that were initially assigned erroneously large planet-to-star radius ratios. We independently determined stellar parameters from spectroscopy and searched for and fitted the transit light curves for the planets, imposing a strict prior on stellar density in order to remove correlations between the fitted impact parameter and planet-to-star radius ratio for short-duration transits. Combining Kepler-445, Kepler-446, and Kepler-42, and isolating all mid-M dwarf stars observed by Kepler with the precision necessary to detect similar systems, we calculate that 21% of mid-M dwarf stars host compact multiples (multiple planets with periods of less than 10 days) for a wide range of metallicities. We suggest that the inferred planet masses for these systems support highly efficient accretion of protoplanetary disk metals by mid-M dwarf protoplanets.
Vascular progenitors derived from murine bone marrow stromal cells are regulated by fibroblast growth factor and are avidly recruited by vascularizing tumors

Bone marrow‐derived stromal cells (BMSC) possess a population of vascular progenitor cells that enable them to acquire a histology and immunophenotype coherent with endothelial cells (EC). Recent evidence indicates that a hypoxic environment such as that encountered in tumor masses regulates BMSC angiogenic properties by pathways that remain to be defined. It is also unclear as to what extent these marrow‐derived precursor cells could contribute to the growth of endothelium‐lined vessels at the vicinity of tumor masses. In this study, we found that BMSC exhibited the ability to generate three‐dimensional capillary‐like networks on Matrigel, and that this property was up‐regulated by growth factors‐enriched conditioned media isolated from several tumor‐derived cell lines. In particular, basic fibroblast growth factor, a key mediator of angiogenesis, was found to be the most potent growth factor for inducing BMSC proliferation, migration, and tubulogenesis. The setup of a new two‐dimensional in vitro co‐culture assay further showed that BMSC were massively recruited when cultured in the presence of either cancerous or differentiated EC lines. In vivo, subcutaneous co‐injection of BMSC with U‐87 glioma cells in nude mice resulted in the formation of highly vascularized tumors, where BMSC differentiated into CD31‐positive cells and localized at the lumen of vascular structures. Our data suggest that BMSC could be recruited at the sites of active tumor neovascularization through paracrine regulation of their angiogenic properties. These observations may have crucial implications in the development of novel therapies using BMSC engineered to secrete anti‐cancerous agents and to antagonize tumor progression. © 2004 Wiley‐Liss, Inc.
Distinct cytoskeletal domains revealed in sperm cells

Antibodies against different cytoskeletal proteins were used to study the cytoskeletal organization of human spermatozoa. A positive staining with actin antibodies was seen in both the acrosomal cap region and the principal piece region of the tail. However, no staining was obtained with nitrobenzoxadiazol-phallacidin, suggesting that most of the actin was in the nonpolymerized form. Most of the myosin immunoreactivity was confirmed to a narrow band in the neck region of spermatozoa. Tubulin was located to the entire tail, whereas vimentin was only seen in a discrete band-like structure encircling the sperm head, apparently coinciding with the equatorial segment region. Surface staining of the spermatozoa with fluorochrome-coupled Helix pomatia agglutinin revealed a similar band-like structure that co-distributed with the vimentin- specific staining. Instead, other lectin conjugates used labeled either the acrosomal cap region (peanut and soybean agglutinins), both the acrosomal cap and the postacrosomal region of the head (concanavalin A), or the whole sperm cell surface membrane (wheat germ and lens culinaris agglutinins and ricinus communis agglutinin l). In lectin blotting experiments, the Helix pomatia agglutinin-binding was assigned to a 80,000-mol-wt polypeptide which, together with vimentin, also resisted treatment with Triton X-100. Only the acrosomal cap and the principal piece of the tail were decorated with rabbit and hydridoma antibodies against an immunoanalogue of erythrocyte alpha-spectrin (p230). p230 appeared to be the major calmodulin-binding polypeptide in spermatozoa, as shown by a direct overlay assay of electrophoretic blots of spermatozoa with 125I-calmodulin. The results indicate that spermatozoa have a highly specialized cytoskeletal organization and that the distribution of actin, spectrin, and vimentin can be correlated with distinct surface specializations of the sperm cells. This suggest that cytoskeleton may regulate the maintenance of these surface assemblies and, hence, affect the spermatozoan function.
Max-Sum Diversity Via Convex Programming

Diversity maximization is an important concept in information retrieval, computational geometry and operations research. Usually, it is a variant of the following problem: Given a ground set, constraints, and a function $f(\cdot)$ that measures diversity of a subset, the task is to select a feasible subset $S$ such that $f(S)$ is maximized. The \emph{sum-dispersion} function $f(S) = \sum_{x,y \in S} d(x,y)$, which is the sum of the pairwise distances in $S$, is in this context a prominent diversification measure. The corresponding diversity maximization is the \emph{max-sum} or \emph{sum-sum diversification}. Many recent results deal with the design of constant-factor approximation algorithms of diversification problems involving sum-dispersion function under a matroid constraint. In this paper, we present a PTAS for the max-sum diversification problem under a matroid constraint for distances $d(\cdot,\cdot)$ of \emph{negative type}. Distances of negative type are, for example, metric distances stemming from the $\ell_2$ and $\ell_1$ norm, as well as the cosine or spherical, or Jaccard distance which are popular similarity metrics in web and image search.
Zone Identification in Biology Articles as a Basis for Information Extraction

Information extraction (IE) in the biomedical domain is now regarded as an essential technique for the dynamic management of factual information contained in archived journal articles and abstract collections. We aim to provide a technique serving as a basis for pinpointing and organizing factual information related to experimental results. In this paper, we enhance the idea proposed in (Mizuta and Collier, 2004); annotating articles in terms of rhetorical zones with shallow nesting. We give a qualitative analysis of the zone identification (ZI) process in biology articles. Specifically, we illustrate the linguistic and other features of each zone based on our investigation of articles selected from four major online journals. We also discuss controversial cases and nested zones, and ZI using multiple features. In doing so, we provide a stronger theoretical and practical support for our framework toward automatic ZI.
Contractile activation in scorpion striated muscle fibers. Dependence on voltage and external calcium

Excitation-contraction coupling was characterized in scorpion striated muscle fibers using standard microelectrode techniques as employed in studies on vertebrate skeletal muscle. The action potential of scorpion muscle consists of two phases of regenerative activity. A relatively fast, overshooting initial spike is followed by a prolonged after- discharge of smaller, repetitive spikes. This after-discharge is accompanied by a twitch that relaxes promptly upon repolarization. Twitches fail in Na-free, tetrodotoxin (TTX)-containing, or Ca-free media. However, caffeine causes contractures in muscles paralyzed by Na- and Ca-free solutions. Experiments on muscle fibers voltage-clamped at a point with two microelectrodes in Na-free or TTX-containing media indicate that: (a) the strength-duration relation for threshold contractions has a shape similar to that in frog muscle, but mean values are displaced approximately 20 mV in the positive direction; (b) tetracaine exerts a parallel effect on strength-duration curves from scorpion and frog; (c) contractile activation in scorpion is abolished in Ca-free media; and (d) the contractile threshold is highly correlated with the occurrence of inward Ca current for pulses of all durations. Thus, the voltage dependence of contractile activation in scorpion and frog muscle is similar. However, the preparations differ in their dependence on extracellular Ca for contraction. These results are discussed in relation to possible mechanisms coupling tubular depolarization to Ca release from the sarcoplasmic reticulum in vertebrate and invertebrate skeletal muscle.