gebhart/patrepeval huggingface dataset:
Functional elements DE2A, DE2B, and DE1A and the TATA box are required for activity of the chicken alpha A-crystallin gene in transfected lens epithelial cells. (1993)

alpha A-crystallin is an abundant soluble protein of the vertebrate eye lens. In addition to the TATA box, four positive cis-regulatory elements of the chicken alpha A-crystallin gene have been identified by linker scanning mutagenesis, DNase I footprinting, and gel mobility shift experiments. The regulatory elements described here have been named DE2A (at positions -144 to -134), DE2B (at positions -128 to -118), and DE1A (at positions -114 to -103). DE2A and DE2B form a dyad of symmetry between positions -141 and -118 (5'-AGACTGTCAT....AGGTCAGTCT-3'), consistent with the close similarity in the mobility of complexes formed with lens nuclear proteins by these two elements. Mutations in DE2A, DE2B, and DE1A leading to loss of promoter activity using the bacterial chloramphenicol acetyltransferase reporter gene transfected into primary embryonic chicken lens epithelial cells resulted in a corresponding loss in the ability to compete for complex formation with lens nuclear proteins in gel mobility shift assays. Mutation of the alpha A-CRYBP1-like site (-67/-57), necessary for function of the mouse alpha A-crystallin promoter, did not affect the activity of the chicken promoter. The DNase I footprinting and gel mobility shift experiments confirmed the previously noted binding of nuclear proteins to a dyad of symmetry at positions -153 to -140. In contrast to DE2A, DE2B, and DE1A, mutagenesis and gel mobility shift experiments failed to correlate function and protein binding for the -153/-140 dyad. DE2A, DE2B, and DE1A agree well with the regulatory elements alpha CE1 (-162/-134), alpha CE3 (-135/-121), and alpha CE2 (-119/-99) (Matsuo, I., and Yasuda, K. (1992) Nucleic Acids Res. 20, 3701-3712) for this gene. The present results suggest, however, that the lens enhancer activity of alpha CE1 is due to the sequence -141/-134, which forms the upper half of the DE2A/DE2B dyad of symmetry, rather than the -153/-140 dyad as previously suspected.
Small-Polaron Hopping and Low-Temperature (45–225 K) Photo-Induced Transient Absorption in Magnesium-Doped Lithium Niobate (2020)

A strongly temperature-dependent photo-induced transient absorption is measured in 6.5 mol% magnesium-doped lithium niobate at temperatures ranging from 45 K to 225 K. This phenomenon is interpreted as resulting from the generation and subsequent recombination of oppositely charged small polarons. Initial two-photon absorptions generate separated oppositely charged small polarons. The existence of these small polarons is monitored by the presence of their characteristic absorption. The strongly temperature-dependent decay of this absorption occurs as series of thermally assisted hops of small polarons that facilitate their merger and ultimate recombination. Our measurements span the high-temperature regime, where small-polaron jump rates are Arrhenius and strongly dependent on temperature, and the intermediate-temperature regime, where small-polaron jump rates are non-Arrhenius and weakly dependent on temperature. Distinctively, this model provides a good representation of our data with reasonable values of its two parameters: Arrhenius small-polaron hopping’s activation energy and the material’s characteristic phonon frequency.
Caracterisation biochimique, clonage et sequence de la proteine kinase de 50 kda specifique d'une classe particuliere de vesicules cytoplasmiques : les "coated vesicles" (ou vesicules recouvertes) (1988)

Caracterisation d'un systeme enzymatique de regulation propre aux vesicules recouvertes: determination de la structure complete d'une proteine kinase de 50 dka ca#2#+ calmoduline et ampc independante, et substrat d'une proteine phosphatase specifique aux vesicules
Cover Feature: Atomic Layer Fluorination of 5 V Class Positive Electrode Material LiCoPO4 for Enhanced Electrochemical Performance (Batteries & Supercaps 10/2020) (2020)

The Cover Feature shows an artistic view of a Li-ion battery with an atomic-layer-fluorinated cathode for improved electrochemical cycling. More information can be found in the Article by N. Louvain and co-workers.
Point defect scattering in silicon nanowires (2010)

A semi-empirical tight-binding Hamiltonian based on density functional theory is used to study scattering of defects in H-passivated (110)SiNWs. The effect of surface dangling bonds and the presence of oxygen on the coherent transport is considered. The scattering at Si vacancies is also studied.
Securing IoT Devices Running PureOS from Ransomware Attacks: Leveraging Hybrid Machine Learning Techniques (2023)

Internet-enabled (IoT) devices are typically small, low-powered devices used for sensing and computing that enable remote monitoring and control of various environments through the Internet. Despite their usefulness in achieving a more connected cyber-physical world, these devices are vulnerable to ransomware attacks due to their limited resources and connectivity. To combat these threats, machine learning (ML) can be leveraged to identify and prevent ransomware attacks on IoT devices before they can cause significant damage. In this research paper, we explore the use of ML techniques to enhance ransomware defense in IoT devices running on the PureOS operating system. We have developed a ransomware detection framework using machine learning, which combines the XGBoost and ElasticNet algorithms in a hybrid approach. The design and implementation of our framework are based on the evaluation of various existing machine learning techniques. Our approach was tested using a dataset of real-world ransomware attacks on IoT devices and achieved high accuracy (90%) and low false-positive rates, demonstrating its effectiveness in detecting and preventing ransomware attacks on IoT devices running PureOS.
Self-Consistent Anharmonic Theory and Its Application to Ferroelectric Crystal (2009)

Abstract The dielectric properties of barium titanate near the Curie temperature are studied using the variational principle method on a self-consistent anharmonic model. A trial Hamiltonian was devised using the terms of the anharmonic oscillator and asymmetric potential energy, which was adopted as the inter-atomic potential of the ferroelectric crystal. The temperature dependence of the dielectric property of barium titanate that was derived from this theory is in good agreement with the experimental result of the inter-atomic potential determined from first-principles ultrasoft pseudo potential calculations. Keywords: Ferroelectric crystalbarium titanatedielectric propertyvariational principle methodtrial Hmiltoniananharmonic oscillatorinter-atomic potentialfirst-principles calculationfree energyequilibrium condition
Cover Image (2021)

The cover image is based on the Original Article Automatic Recognition Method of Primary Path for Anastomosing River based on Its Typical Features by Wei Wu et al., https://doi.org/10.1111/tgis.12742.
Fiber type specific glycogen utilization in rat diaphragm during treadmill exercise (1987)

To examine the significance of endogenous stores of glycogen in specific fiber types (I, IIa, IIb) of the costal region of the diaphragm, adult male Wistar rats performed continuous running (25 m/min, 8 degrees grade) exercise for either 30 min or until fatigue. At 30 min of exercise, glycogen loss, as measured microphotometrically using the periodic acid-Schiff technique averaged between 73 and 80% (P less than 0.05) in the different fiber types. When exercise was performed to exhaustion, representing an additional 94 min, no further reduction in glycogen was observed in any fiber type. Biochemical determinations of glycogen from the diaphragm confirmed the extensive reduction in glycogen concentration with exercise. Large reductions (P less than 0.05) in glycogen were also noted in the soleus, plantaris, and vastus lateralis red. Although significant depletion (P less than 0.05) occurred in the vastus lateralis white, it was not as pronounced as in these other muscles. Repletion to preexercise glycogen concentration was complete by 4 h of recovery in all muscles except the vastus lateralis white. It is concluded that endogenous glycogen is a significant substrate in all muscles sampled regardless of fiber composition. In the case of the costal region of the diaphragm, the increased work of breathing resulting from heavy exercise leads to the recruitment of all fiber types, and each fiber type depends on glycogen as a substrate at least early in the exercise.
A Detailed Reaction Kinetics-Based Calculation Tool for Internal Combustion Engine-Related Ignition Processes (2022)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;Ignition delay times are major information needed to allow the simulation of auto-ignition and knocking combustion in internal combustion engines (ICEs). Due to their variance over changing boundary conditions (BC) and limitations of measurement processes, a common way to obtain them is via reaction kinetic simulations. To facilitate and accelerate the simulation process with varying operating conditions and gas composition definitions, an efficient tool that uses Cantera’s Python interface has been created. It allows the end-user to easily calculate the ignition delay data needed for engine simulation without the necessity for in-depth knowledge of the underlying processes. All calculations are based on the creation of a homogeneously mixed gaseous mixture corresponding to engine-based environmental conditions. Depending on the desired fuel, oxidizer, temperature, pressure, water, and exhaust gas recirculation (EGR) rate, the resulting reactant composition is computed. From there, the mixture is ignited in a constant-pressure (optional: constant-volume) reactor, and the result is evaluated with all popular ignition delay definitions. The whole concept is modular and can be easily expanded with alternative EGR and/or ignition delay definitions. Two more sophisticated additions are shortly mentioned and explained. First, the view on incomplete combustion caused by finite residency times (reflecting real engine operation). This approach results in additional nitrogen oxides (NO&lt;sub&gt;X&lt;/sub&gt;) in the recirculating exhaust gas and thus lowers the ignition delay times. Second, the admixture of lubricant oil contained in charge air. With this, the effects of externally added long-chained hydrocarbon molecules on, for example, methane (CH&lt;sub&gt;4&lt;/sub&gt;) combustion, can be addressed.&lt;/div&gt;&lt;/div&gt;
Foreign accent conversion through voice morphing (2013)

We present a voice morphing strategy that can be used to generate a continuum of accent transformations between a foreign speaker and a native speaker. The approach performs a cepstral decomposition of speech into spectral slope and spectral detail. Accent conversions are then generated by combining the spectral slope of the foreign speaker with a morph of the spectral detail of the native speaker. Spectral morphing is achieved by representing the spectral detail through pulse density modulation and averaging pulses in a pair-wise fashion. The technique is evaluated on parallel recordings from two ARCTIC speakers using objective measures of acoustic quality, speaker identity and foreign accent that have been recently shown to correlate with perceptual results from listening tests. Index Terms: voice morphing, accent conversion.
Synthesis of type‐C virus particles from murine cultured cells induced by iododeoxyuridine. VI. Biosynthesis of reverse transcriptase (1977)

Abstract Treatment with 5‐iodo‐2'‐deoxyuridine (IdUrd) of BALB/3T3 cells non‐productively transformed with Kirsten murine sarcoma virus (K‐BALB) results in the induction of extracellular type‐C virus production with a concomitant appearance of intracellular reverse transcriptase. Production of BALB virus‐2 (v‐2) and its Kirsten sarcoma virus pseudo‐type, occurring 2‐3 days after IdUrd treatment, is inhibited and stimulated by interferon and dexamethasone, respectively, By contrast, and as previously reported, neither compound affects synthesis of N‐tropic virus (BALB virus‐1) which is produced later (5‐7 days) after IdUrd treatment. The stimulatory and inhibitory activities of these compounds are partially antagonistic since: (1) the simultaneous presence of both dexamethasone and interferon results in a virus production level between those observed with either compound alone; and (2) increasing the dexamethasone concentration at a fixed interferon concentration increases virus production. However, the effects of these two compounds on the appearance of an intracellular viral protein (reverse transcriptase) after IdUrd treatment were unexpected. The post‐induction appearance of intracellular reverse transcriptase is inhibited by interferon but is not affected by dexamethasone. This suggests that dexamethasone stimulates a step after protein synthesis, and that interferon inhibits an earlier step (translational or pre‐translational) or that it enhances degradation of viral proteins. When interferon and dexamethasone are both present, no inhibition of the appearance of reverse transcriptase is observed. Thus, dexamethasone has a second effect on virus production, namely to prevent the inhibition by interferon of the appearance of intracellular reverse transcriptase. Since dexamethasone completely overcomes the inhibitory effect of interferon on intracellular reverse transcriptase levels, but only partially reverses the inhibition by interferon of virus production, interferon (in the presence of dexamethasone) must also inhibit a post‐translational step in virus production. This step may or may not be the same as the late dexamethasone‐sensitive step. Thus, both dexamethasone and interferon appear to have both translational (or pre‐translational) and post‐translational effects on the production of xenotropic (v‐2) mouse type‐C virus. This suggests that BALB/c mouse cells restrict the production of xenotropic endogenous virus at two distinct sites.
Intelligent coordination of multiple systems with neural networks (1991)

A multiple-system coordinator that combines the techniques of intelligent control and neural networks, and forms the high-level coordinator in a hierarchical structure, is proposed. The basic idea is to estimate the effects of the control commands to subsystems using a predictor and modify these commands using a knowledge-based coordinator so as to achieve the desired performance. The predictor was designed for multiple-input, multiple-output systems using neural networks. The knowledge-based coordinator is responsible for a goal-oriented search in its knowledge base and the overall system stability. As an example, the coordination of two two-link robots holding a single object is discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Identifying Factors Predicting Margin Positivity After Mastectomy (2022)

INTRODUCTION: Positive surgical margin after mastectomy occurs in approximately 10% of women and increases risk of recurrence and morbidity. The aim of this study was to identify factors which may confer a higher risk of margin positivity after mastectomy. METHODS: Women with Tis–T3 breast cancer who underwent mastectomy as definitive operation were retrospectively analyzed from 2014 to 2018. Comparison of clinicopathologic data was made between patients with negative margins (greater than or equal to 1 mm) and close (less than 1 mm) or positive margins by univariate and multivariate statistical analyses. RESULTS: During the study period, 942 women underwent mastectomy. Negative margins were reported for 798 (85%) women, whereas 144 (15%) women experienced close (97/144) or positive (33/144) margin. Re-excision of margin was performed for 37 patients (4%), and 9 of 37 (24%) had residual cancer after re-excision. On multivariate analysis, treatment with neoadjuvant chemotherapy (0.39 odds ratio [OR], 95% CI 0.22–0.70, p = 0.002) and increased age (0.97 OR, 95% CI 0.96–0.99, p = 0.003) decreased the risk of close or positive margin, whereas Asian race (5.72 OR, 95% CI 1.56–21.02, p < 0.009), increased tumor to breast size ratio (2.07 OR, 95% CI 1.57–2.73, p < 0.001), lower inner quadrant (LIQ) tumor location (3.24 OR, 95% CI 1.64–6.41, p < 0.001), and immediate reconstruction (1.66 OR, 95% CI 1.00–2.74, p = 0.048) increased the risk of close or positive margin status (Table). CONCLUSION: Increasing age, neoadjuvant chemotherapy, Asian race, increased tumor size to breast weight ratio, LIQ tumor location, and immediate reconstruction independently predict close or positive margin status after mastectomy. Table. - Multivariate Logistic Regression for Margin Positivity Characteristic Adjusted OR 95% CI p Value Neoadjuvant chemotherapy 0.39 0.22–0.70 0.002 Age (year) 0.97 0.96–0.99 0.003 Asian/Pacific Islander 5.72 1.56 –1.02 0.009 Tumor size/Breast weight (log[cm/kg+1]) 2.07 1.57–2.73 < 0.001 Tumor location (LIQ) 3.24 1.64–6.41 <0.001 Immediate recontruction 1.66 1.00–2.74 0.048
High Energy Density Lithium Batteries (2010)

Materials Engineering for High Density Energy Storage provides first-hand knowledge about the design of safe and powerful batteries and the methods and approaches for enhancing the performance of next-generation batteries. The book explores how the innovative approaches currently employed, including thin films, nanoparticles and nanocomposites, are paving new ways to performance improvement. The topic's tremendous application potential will appeal to a broad audience, including materials scientists, physicists, electrochemists, libraries, and graduate students.
Enzymatic process development for the extraction of ferulic acid from wheat bran (2010)

The agro-industries generate each year thousands of tons of by-products, such as cereal bran or sugar beet pulps. For instance, Walloon wheat transformation industry provides annually about 200.000 tons of bran. Most of those by-products are under-valorized as cattle feed. By the use of biorefinery, this biomass may constitute a renewable source for various value-added molecules like dietary fibres, proteins, antioxidants, and more.
ANALYSIS OF PROCESSING CONDITIONS FOR A NOVEL 3D-COMPOSITE PRODUCTION TECHNIQUE (2015)

A novel manufacturing process for a continuous fiber lattice fabrication (CFLF), inspired by 3D-printing, provides continuously extruded free form structures of reinforced thermoplastic material.
Treatment of experimental asthma by long-term gene therapy directed against IL-4 and IL-13 (2003)

The clinical manifestations of allergic asthma are believed to result from a dysregulated, T helper 2 lymphocyte (Th2)-biased response to antigen. Although asthma symptoms can be controlled acutely, there is a need for a therapy that will address the underlying immune dysfunction and provide continuous control of chronic airway inflammation. The Th2-type cytokines, IL-13 and IL-4, have been demonstrated to play a crucial role in asthma pathogenesis and their selective neutralization results in the alleviation of asthmatic symptoms in mouse models. The activity of both of these cytokines can be inhibited by a mutant IL-4 protein, IL-4 receptor antagonist (IL-4RA), and thus, continual IL-4RA therapy might be beneficial in treatment of chronic asthma. To explore the potential utility of long-term gene therapy for the treatment of asthma we used a recombinant adeno-associated virus (AAV) vector to deliver and provide sustained expression of IL-4RA in vivo. We show that AAV-mediated delivery of IL-4RA to the airways of mice reduces airway hyperresponsiveness (AHR) and airway eosinophilia triggered by either IL-13 or IL-4. Furthermore, AAV-delivered IL-4RA, expressed either systemically or in the airways of mice following allergen sensitization, significantly inhibited development of airway eosinophilia and mucus production and reduced the levels of asthma-associated Th2 cytokines and AHR in the experimental mouse model of allergic asthma. Thus, gene therapy can be a potential therapeutic option to treat and control chronic airway inflammation and asthmatic symptoms.
K[ZnBP2O8] and A[ZnBP2O8] (A=NH4+, Rb+, Cs+): Zincoborophosphates as a New Class of Compounds with Tetrahedral Framework Structures (1999)

Tetrahedral framework structures with topologies that show close relationships to the feldspar group or to gismondine are formed by the zincoborophosphates A[ZnBP2O8] (see picture). The compounds are readily accessible under mild hydrothermal conditions (Tmax=170°C) and are thermally remarkably stable (for example, 940°C for A=Cs). Metalloborophosphates are a new class of compounds, which are expected to provide access to zeolite-like microporous systems.
Recovery of ova and their re‐insertion into the hen's oviduct through a fistula (1989)

1. The first loop of the domestic hen's magnum was fistulated. A cannula mounted with a collecting tube served to trap the passing ova about 2.5 h following ovulation. 2. Nine out of 10 fistulated hens resumed ovulation about 2 to 5 weeks following surgery. A total of 63 magnal ova were collected. 3. Five of the magnal ova were successfully returned to the oviduct through the fistula and resulted in 5 normal soft-shelled eggs. The success of ova reimplantation was affected by prolapse of the posterior part of the oviduct and the timing of ova return.
Systems Science of Secure and Resilient Cyberphysical Systems (2020)

We are in the midst of a pervasive, profound shift in the way humans engineer physical systems and manage their physical environment using networking and IT. Because of these disruptive changes, physical systems can now be attacked through cyberspace, and cyberspace can be attacked through physical means.
Multi-articular passive exoskeleton for reducing the metabolic cost during human walking (2019)

Ankle passive exoskeleton has been demonstrated to enhance walking economy and reduce the metabolic cost during walking. How to develop multi-articular passive exoskeleton to further reduce the metabolic cost during human walking still remains a challenge. In this paper, we develop a hip-knee passive exoskeleton that uses springs to assist both hip extension and knee flexion. Springs in the exoskeleton are firstly stretched to store some of the negative mechanical power of knee joint during the late swing phase, then the stored energy in the springs is released to assist hip extension during the early stance phase. The whole process is controlled by a mechanical clutch. The experiment results show that the metabolic cost was reduced by 7.6 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">%</sup> compared to walking without the exoskeleton. To our knowledge, this is the first multi-articular passive exoskeleton that can reduce the metabolic cost of walking. This paper also discusses the possibility for the passive exoskeleton to exploit heel-strike energy for further reducing the metabolic cost of walking.