gebhart/patrepeval huggingface dataset:
Analysis of Regulatory Regions of Emilin1 Gene and Their Combinatorial Contribution to Tissue-specific Transcription (2005)

The location of regions that regulate transcription of the murine Emilin1 gene was investigated in a DNA fragment of 16.8 kb, including the entire gene and about 8.7 and 0.6 kb of 5'- and 3'-flanking sequences, respectively. The 8.7-kb segment contains the 5'-end of the putative 2310015E02Rik gene and the sequence that separates it from Emilin1, whereas the 0.6-kb fragment covers the region between Emilin1 and Ketohexokinase genes. Sequence comparison between species identified several conserved regions in the 5'-flanking sequence. Most of them contained chromatin DNase I-hypersensitive sites, which were located at about -950 (HS1), -3100 (HS2), -4750 (HS3), and -5150 (HS4) in cells expressing Emilin1 mRNA. Emilin1 transcription initiates at multiple sites, the major of which correspond to two Initiator sequences. Promoter assays suggest that core promoter activity was mainly dependent on Initiator1 and on Sp1-binding sites close to the Initiators. Moreover, one important regulatory region was contained between -1 and -169 bp and a second one between -630 bp and -1.1 kb. The latter harbors a putative binding site for transcription factor AP1 matching the location of HS1. The function of different regions was studied by expressing lacZ constructs in transgenic mice. The results show that the 16.8-kb segment contains regulatory sequences driving high level transcription in all the tissues where Emilin1 is expressed. Moreover, the data suggest that transcription in different tissues is achieved through combinatorial cooperation between various regions, rather than being dependent on a single cis-activating region specific for each tissue.
Surface-acoustic-wave attenuation in a β-alumina thin film (1992)

The attenuation of surface acoustic waves (SAW) in a \ensuremath{\beta}-alumina thin film prepared by the rf-sputtering method has been measured in the frequency region from 130 to 600 MHz at temperatures from 80 to 300 K. Two types of methods are employed for the measurement of the SAW attenuation, which are termed ``air-gap method'' and ``nonpiezoelectric method,'' to elucidate the coupling mode between mobile ions and the SAW. In both methods, clear peaks in the temperature-dependence curve of the SAW attenuation are observed, which are responsible for the piezoelectric coupling and the local strain coupling, respectively. The attempt frequency of ion jumps is estimated to be 0.9\ifmmode\times\else\texttimes\fi{}${10}^{12}$ ${\mathrm{s}}^{\mathrm{\ensuremath{-}}1}$. And the activation energy is estimated to be 0.13 eV, which is consistent with the value (0.14 eV) calculated with a paired-interstitialcy mechanism of ${\mathrm{Na}}^{+}$ ions.
Copolymer effects on microglia and T cells in the central nervous system of humanized mice (2005)

The random amino acid copolymers FYAK and VWAK ameliorate EAE in a humanized mouse model expressing both a human transgenic myelin basic protein (MBP)85-99-specific T cell receptor and HLA-DR2. Here we show that microglia isolated from the central nervous system (CNS) of humanized mice with EAE induced by MBP85-99 and treated with these copolymers had reduced expression of HLA-DR, and thus reduced capacity to present MBP85-99 and activate transgenic T cells. In vitro microglia up-regulated empty HLA-DR2 upon activation with GM-CSF with or without LPS or IFN-gamma, but not with IL-4 or IL-10. Correspondingly, gene chip arrays showed that the CNS of untreated and YFAK-treated mice differentially expressed pro- and anti-inflammatory molecules during MBP85-99-induced EAE. Interestingly, microglia expressed the full-length gammabeta and alphabeta subunits of the tetrameric adaptor protein complexes AP-1 and AP-2 respectively, but after treatment with GM-CSF these complexes were cleaved, as had been found in immature dendritic cells derived from bone marrow. Strikingly, in vivo the perivascular lymphocyte infiltration seen in untreated mice immunized with MBP85-99 was composed of equal numbers of hVbeta2+ MPB85-99-specific transgenic and hVbeta2- endogenous T cells, while the much smaller infiltration seen after treatment with YFAK was composed predominantly of hVbeta2- endogenous T cells.
Prefetch Side-Channel Attacks (2016)

Modern operating systems use hardware support to protect against control-flow hijacking attacks such as code-injection attacks. Typically, write access to executable pages is prevented and kernel mode execution is restricted to kernel code pages only. However, current CPUs provide no protection against code-reuse attacks like ROP. ASLR is used to prevent these attacks by making all addresses unpredictable for an attacker. Hence, the kernel security relies fundamentally on preventing access to address information. We introduce Prefetch Side-Channel Attacks, a new class of generic attacks exploiting major weaknesses in prefetch instructions. This allows unprivileged attackers to obtain address information and thus compromise the entire system by defeating SMAP, SMEP, and kernel ASLR. Prefetch can fetch inaccessible privileged memory into various caches on Intel x86. It also leaks the translation-level for virtual addresses on both Intel x86 and ARMv8-A. We build three attacks exploiting these properties. Our first attack retrieves an exact image of the full paging hierarchy of a process, defeating both user space and kernel space ASLR. Our second attack resolves virtual to physical addresses to bypass SMAP on 64-bit Linux systems, enabling ret2dir attacks. We demonstrate this from unprivileged user programs on Linux and inside Amazon EC2 virtual machines. Finally, we demonstrate how to defeat kernel ASLR on Windows 10, enabling ROP attacks on kernel and driver binary code. We propose a new form of strong kernel isolation to protect commodity systems incuring an overhead of only 0.06-5.09%.
Co-expression network analysis identifies gonad- and embryo-associated protein modules in the sentinel species Gammarus fossarum (2019)

Next generation sequencing and mass spectrometry technologies have recently expanded the availability of whole transcriptomes and proteomes beyond classical model organisms in molecular biology, even in absence of an annotated genome. However, the fragmented nature of transcriptomic and proteomic data reduces the ability to interpret the data, notably in non-model organisms. Network-based approaches may help extracting important biological information from -omics datasets. The reproductive cycle of the freshwater crustacean Gammarus fossarum.provides an excellent case study to test the relevance of a network analysis in non-model organisms. Here, we illustrated how the use of a co-expression network analysis (based on Weighted Gene Co-expression Network Analysis algorithm, WGCNA) allowed identifying protein modules whose expression profiles described germ cell maturation and embryonic development in the freshwater crustacean Gammarus fossarum. Proteome datasets included testes, ovaries or embryos samples at different maturation or developmental stages, respectively. We identified an embryonic module correlated with mid-developmental stages corresponding to the organogenesis and it was characterized by enrichment in proteins involved in RNA editing and splicing. An ovarian module was enriched in vitellogenin-like proteins and clottable proteins, confirming the diversity of proteins belonging to the large lipid transfer family involved in oocytes maturations in this freshwater amphipod. Moreover, our results found evidence of a fine-tuned regulation between energy production by glycolysis and actin-myosin-dependent events in G. fossarum spermatogenesis. This study illustrates the importance of applying systems biology approaches to emergent animal models to improve the understanding of the molecular mechanisms regulating important physiological events with ecological relevance.
ChemInform Abstract: SYNTHESIS AND CARBON‐13 NMR SPECTROSCOPY OF MAN3LYS2‐RAFFINOSE CONJUGATE (1983)

Abstract Raffinose (II) wird mit Galactoseoxidase zur 6"‐Aldehydoraffinose oxidiert und mit dem Peptid (I) reduktiv aminiert zum Glycopeptid (III).
Optical imaging of pattern formation: reflection anisotropy microscopy applied to globally coupled oscillatory CO-oxidation (2007)

A reflection anisotropy microscope (RAM) creates the contrast in its images from a change in the polarization orientation of reflected light from a surface. This may stem from local variations of the reconstruction of a surface, being initiated by changes in an adsorption layer. The advantages and disadvantages of a recently improved RAM versus other optical imaging techniques are discussed. We demonstrate the unique features of RAM and present the first experimental findings of so called 2pi phase kinks in the globally coupled CO-oxidation on Pt(110).
A multi-hop wireless sensor network for in-situ agricultural applications (2019)

This paper presents the design and implementation of a wireless sensor network (WSN) for agricultural monitoring applications using a multi-hop tree based architecture. Each sensor node is equipped with different sensors such as soil moisture (custom built), atmospheric temperature and relative humidity sensors. The nodes use TelosB modules for wireless communication. The implemented testbed consists of 20 nodes covering an area of 120 m×150 m. Each node reported its sensor data at every 1 hour interval to the base station along the data collection tree following a time synchronized periodic sleep wake-up schedule. The maximum depth of the constructed data collection tree was observed as 5 hops in the implemented network. The performance of the in-house developed soil moisture sensors are evaluated through the implemented WSN and the difference between the measured soil moisture and the commercial time domain reflectrometry is observed as ±3%. © 2019 URSI. All rights reserved.
Perchlorate reduction from a highly contaminated groundwater in the presence of sulfate‐reducing bacteria in a hydrogen‐fed biofilm (2013)

We used a hydrogen (H2 )-based biofilm to treat a groundwater contaminated with perchlorate (ClO(4)(-) ) at ~10 mg/L, an unusually high concentration. To enhance ClO(4)(-) removal, we either increased the H2 pressure or decreased the electron-acceptor surface loading. The ClO(4)(-) removal increased from 94% to 98% when the H2 pressure was increased from 1.3 to 1.7 atm when the total acceptor surface loading was 0.49 g H2 /m(2) day. We then decreased the acceptor surface loading stepwise from 0.49 to 0.07 g H2 /m(2) day, and the ClO(4)(-) removal improved to 99.6%, giving an effluent ClO(4)(-) concentration of 41 µg/L. However, the tradeoff was that sulfate (SO(4)(2-) ) reduction occurred, reaching 85% conversion at the lowest acceptor surface loading (0.07 g H(2) /m(2) day). In two steady states with the highest ClO(4)(-) reduction, we assayed for the presence of perchlorate-reducing bacteria (PRB), denitrifying bacteria (DB), and sulfate-reducing bacteria (SRB) by quantitative polymerase chain reaction (qPCR) targeting characteristic reductases. The qPCR results documented competition between PRB and SRB for space within the biofilm. A simple model analysis for a steady-state biofilm suggests that competition from SRB pushed the PRB to locations having a higher detachment rate, which prevented them from driving the ClO(4)(-) concentration below 41 µg/L.
Rapid Application Evolution and Integration Through Document Metamorphosis (2001)

The Harland document management system implements a data model in which document (object) structure can be altered by mixin-style multiple inheritance at any time. This kind of structural fluidity has long been supported by knowledge-base management systems, but its use has primarily been in support of reasoning and inference. In this paper, we report our experiences building and supporting several non-trivial applications on top of this data model. Based on these experiences, we argue that structural fluidity is convenient for data-intensive applications other than knowledge-base management. Specifically, we suggest that this flexible data model is a natural fit for the decoupled programming methodology that arises naturally when using enterprise component frameworks.
Purification of Carbon Nanotube Sheets (2014)

Large volumes of carbon nanotube (CNT) sheets and yarns are required to enable practical applications such as structural reinforcements, electrical conductors, electromagnetic interference shielding, and energy storage. Although these macroscopic assemblages of CNTs are commercially available, reports on their handling and processing have been quite limited. In this article, we report a systematic study of the purification of commercially available CNT sheets produced directly from as‐grown nanotubes. These CNT sheets contain residual metal catalysts encapsulated in graphitic carbon nanoparticles known to contaminate common powdery pristine CNT materials. Although many purification methods effective for powdery CNTs are known, they cannot be directly applied to CNT sheets because these processes often involve sonication and/or reflux, which are too aggressive and deleterious to the integrity of the sheets. Therefore, alternative physically benign processes were chosen and evaluated in detail. Assessment of the purification method included characterization of parameters such as residual metal content, weight retention, and changes in the Raman D‐to‐G intensity ratio. Importantly, the purification methodology was also placed in the context of the targeted application as a structural reinforcement in advanced composites. In this application, the mechanical properties of the CNT sheets are crucial, thus specific strength and modulus were evaluated and compared for the purified CNT sheets and the nanocomposites produced therefrom. Several important processing parameters were identified that resulted in purified CNT sheets with not only low catalyst content but also reasonable retention of mechanical properties. In addition, the scalability of the purification method and a procedure to prevent CNT sheet wrinkling after purification were demonstrated. Assessment criteria of CNT sheet purification techniques toward other potential applications are also discussed.
Atrial “J” Pacing Lead Retention Wire Fracture: Radiographic Assessment, Incidence of Fracture, and Clinical Management (1995)

The incidence of retention wire fracture in the Accufix 330-801 lead is significantly higher than originally reported. Patients should be notified of the potential dangers associated with this lead. Cardiac digital fluoroscopy is an effective method of screening for wire fracture. Leads with fractured retention wires should be extracted and those with normal fluoroscopic appearance should undergo regular fluoroscopic screening.
Cyclooxygenase-2 (COX-2)-Inhibition induziert im hepatozellulären Karzinom Apoptose und Chemosensitivität (2006)

Die Cycloxygenase-2 (COX-2), ein Schlüsselenzym des Arachidonsäuremetabolismus, ist im hepatozellulären Karzinom häufig dysreguliert. Wir konnten zeigen, dass die selektive Inhibition von COX-2 durch NSAIDS (Celecoxib) über die Modulation von Apoptose das Wachstum von Hepatomzellen in vitro und in vivo hemmt.
Cryptographically Protected Prefixes for Location Privacy in IPv6. (2013)

Abstract. There is a growing concern with preventing unauthorized agents from discovering the geographical location of Internet users, a kind of security called location privacy. Typical deployments of IPv6 make it possible to deduce the approximate geographical location of a device from its IPv6 address. We present a scheme called Cryptographically Protected Prefixes (CPP) 1, to address this problem at the level of IPv6 addressing and forwarding. CPP randomizes the address space of a defined topological region (privacy domain), thereby making it infeasible to infer location information from an IP address. CPP can be deployed incrementally. We present an adversary model and show that CPP is secure within the model, assuming the existence of pseudorandom functions. We have implemented CPP as a pre-processing step within the forwarding algorithm in the FreeBSD 4.8 kernel. Our performance testing indicates that CPP pre-processing results in a 40–50 percent overhead for packet forwarding in privacy domain routers. The additional end to end per packet delay is roughly 20 to 60 microseconds. We also give an attack against the address encryption scheme in [Raghavan et al. 2009]. We show that the CPP forwarding algorithm is resilient in the event of network failures.
General description and operation of the agro-environmental system: Crop management modeling (1981)

Input for a data management system to provide farmers with information to improve crop management practices in Virginia requires monitoring of control crops at field stations, crop surveys derived from remotely sensed aircraft data, meteorological data from synchronous satellites, and details of local agricultural conditions. Presently models are under development for determining pest problems, water balance in the soil, stages of plant maturity, and optimum planting date. The status of the Cerospora leafspot model for peanut crop management is considered. Other models under development planned relate to Cylindtocladium Blackrot and Sclerotinia blight of peanuts, cyst nematode (Globerdena solanacearum) of tobacco, and red crown rot of soybeans. A software for program for estimating precipitation and solar radiation on a statewise basis is also being developed.
Learning Sparse Polynomial Functions (2013)

We study the question of learning a sparse multivariate polynomial over the real domain. In particular, for some unknown polynomial f(x) of degree-d and k monomials, we show how to reconstruct f, within error ∊, given only a set of examples xi drawn uniformly from the n-dimensional cube (or an n-dimensional Gaussian distribution), together with evaluations f(i) on them. The result holds even in the “noisy setting”, where we have only values f(i) + g where g is noise (say modeled as a Gaussian random variable). The runtime of our algorithm is polynomial in n, k, 1/∊ and Cd where Cd depends only on d. Note that, in contrast, in the “boolean version” of this problem, where is drawn from the hypercube, the problem is at least as hard as the “noisy parity problem,” where we do not know how to break the nΩ(d) time barrier, even for k = 1, and some believe it may be impossible to do so.
Selective substitution of an imido ligand in alkyl- and aryl-imido rhenium(VII) complexes; crystal structures of (2,6-dimethylphenyl)ammonium trichlorobis(2,6-dimethylphenyl-imido)methylrhenate(VII) and bis(2,6-dimethylphenylimido)methylbis(neopentyl)rhenium(VII) (1991)

Reaction of ReMeO3 and 2,6-dimethylphenyl isocyanate gives the imido complex [ReMe(NR)3](R = 2,6-Me2C6H3). Complexes of the type [ReMe(NR)3] or [ReMe(NBut)3] undergo selective substitution of only one imido ligand to form bis(imido) derivatives. Thus, [ReMe(NBut)3] reacts with the weak acid catechol via protonation of one imido ligand to form a stable five-co-ordinate complex [ReMe(NBut)2(O2C6H4)]. In contrast, [ReMe(NR)3] forms a complex which can only be isolated in a pure state by the addition of pyridine (py) to give the six-co-ordinate [ReMe(NR)2(O2C6H4)(py)]. The complex [ReMe(NR)3] also reacts with thiophenol to give five-co-ordinate [ReMe(NR)2(SPh)2]. Reaction of [ReMe(NR)3] with HCl gives the ionic complex [NH3R][ReMeCl3(NR)2]. The crystal structure of this complex was determined by X-ray crystallography. The neutral dihalide complexes [ReMe(NR)2X2(py)](X = Cl or Br) are prepared from [ReMe(NR)3] by the addition of 2 equivalents of pyridinium halide. Alkylation of the dichloro or dibromo derivative with neopentylmagnesium chloride gives the novel mixed-alkyl complex [ReMe(CH2But)2(NR)2] as a mixture of two isomers, the structure of one of which was determined by X-ray crystallography.
EthnoHERBS: Conservation of European Biodiversity through Exploitation of Traditional Herbal Knowledge for the Development of Innovative Products (2022)

EthnoHERBS is a H2020-MSCA-RISE project aiming to record and evaluate information on SE European traditional knowledge, explore in a high-throughput manner the biodiversity of Balkan Peninsula flora and elaborate cutting-edge technologies in Natural Products Chemistry to discover and develop innovative cosmeceutical products against skin disorders.Within the
Detecting Mild Lower-limb Skeletal Muscle Fatigue with Stimulated-echo q-space Imaging (2020)

The feasibility of detecting mild exercise-related muscle fatigue via stimulated echo (STE) and q-space imaging (qsi) was evaluated. The right calves of seven healthy volunteers were subjected to mild exercise loading, and qsi was generated using spin echo (Δ: 45.6 ms) and three different STE (Δ: 114, 214, and 414 ms) acquisitions. We concluded that qsi with an increased STE diffusion time can detect mild fatigue in the gastrocnemius muscle.
Analysis of elastic micro optical components under large deformation (2002)

We describe a technique for analyzing the mechanical and optical properties of deformable optical elements that combines the finite element method, ray-tracing and birefringence measurement. We fabricated a pneumatically actuated microlens array on an elastic polydimethylsiloxane (PDMS) film to assess the proposed analysis technique. The lenses are 120 μm in diameter and arranged on the top surface of a 200 μm thick base film. The lenses are displaced by pneumatic actuators at the bottom of the film. The measured mechanical–optical properties of the PDMS test materials showed a good match with the calculation. The paths and retardation of light beams transmitted in the microlens array under several actuating conditions were then analyzed. The lens displacement of 21.8 μm was measured at an applied pressure of −45 kPa. At the same pressure, a ray-trace analysis showed that the actuator changed the visual axis of each lens by 5°, while the retardation was estimated to be within the order of 5 × 10−3 nm.
Nitride Metal/Semiconductor Superlattices for High Temperature Direct Thermal-to-Electrical Energy Conversion (2007)

We have identified TiN/GaN and ZrN/ScN as two possible pure rocksalt structured metal/semiconductor combinations for fabrication of solid-state thermionic energy converters for high operational temperatures. The selection of the materials was constrained by issues that are critical to the integration of heterogeneous materials such as crystallographic compatibility and thermodynamic stability of the metal/semiconductor combinations at high operating temperatures. The first nitride superlattice system consists of TiN as the metal layer and GaN, in its metastable rocksalt phase, as the semiconductor layer, grown on rocksalt MgO substrates. The metastable rocksalt GaN (rs-GaN) phase is stabilized by pseudomorphic epitaxy on a metallic rocksalt TiN underlayer, and its existence has been verified using high-resolution x-ray diffraction and transmission electron microscopy. The critical thickness for the rocksalt-to-wurtzite phase transition has been empirically determined to be between 1 and 2 nm, although much thicker rocksalt GaN films, up to approximately 6 nm, can be maintained for several superlattice periods. The second pure rocksalt-structured superlattice system analyzed consists of alternating layers of metallic ZrN and semiconducting ScN. These epitaxial superlattices were grown on rocksalt MgO substrates using dc magnetron sputtering in a nitrogen-argon ambient.