gebhart/patrepeval huggingface dataset:
Analysis of Membrane-Binding Properties of Dermaseptin Analogues:  Relationships between Binding and Cytotoxicity (2003)

To understand relationships between membrane-binding properties of cytolytic peptides and resulting cytotoxicity, we investigated interactions of dermaseptin analogues with model bilayers by means of surface plasmon resonance. First, we tested the system by comparing two native dermaseptins, S1 and S4, whose binding properties were previously characterized in different experimental systems. Validation experiments revealed deviations from the one-to-one interaction model and indicated the binding to proceed by a two-stage mechanism. By calculation of apparent affinity constants and individual affinities for both steps of the interaction, the biosensor technology was able to distinguish between surface-bound peptides that subsequently penetrated into the bilayer and peptides that remained essentially superficially bound. This data interpretation was sustained after analysis of a series of dermaseptin S4 derivatives whose binding data were compared with cytotoxicity, revealing cytolytic activity to correlate mainly with insertion affinity. The data indicate that the potency of highly cytolytic peptides such as K(4)K(20)-S4 is not due to the highest membrane adhesion affinity but to the highest propensity for the inserted state. Similarly, truncated derivatives of 16, 13, and 10 residues showed a progressive reduction in cytotoxicity that best correlated with progressive reduction in insertion affinity. Support for the adhesion versus inserted states was provided by proteolytic experiments with RBC-bound peptides that demonstrated K(4)K(20)-S4 to be protected from enzymatic cleavage, unlike its 13-mer derivative. Overall, using the two-stage model proved instrumental in investigating membrane-binding properties of antimicrobial peptides and capable of explaining the cytolytic properties of closely related analogues.
Early aging and age-related pathologies in mice deficient in BMAL1, the core componentof the circadian clock (2006)

Mice deficient in the circadian transcription factor BMAL1 (brain and muscle ARNT-like protein) have impaired circadian behavior and demonstrate loss of rhythmicity in the expression of target genes. Here we report that Bmal1(-/-) mice have reduced lifespans and display various symptoms of premature aging including sarcopenia, cataracts, less subcutaneous fat, organ shrinkage, and others. The early aging phenotype correlates with increased levels of reactive oxygen species in some tissues of the Bmal1(-/- )animals. These findings, together with data on CLOCK/BMAL1-dependent control of stress responses, may provide a mechanistic explanation for the early onset of age-related pathologies in the absence of BMAL1.
A new methodology for the synthesis of β-amino acids (2000)

A differentially functionalized succinic acid unit 6 undergoes alkylation with excellent regio- and high stereocontrol at the carbon α to the imide to furnish the alkylated product 7 in 60–83% yield. Selective removal of the imide provides 8 in 80–90% yields. Curtius rearrangement of 8 with retention of stereochemistry provides N-protected β-amino acids (9) in 70–83% yields. Alternatively, selective deprotection of the ester group followed by Curtius rearrangement provides isomeric β-amino acids 14a, 14b, and 14e in good yields. The methodology has been successfully applied to the synthesis of N-Boc-iturinic acid and 2-methyl-3-aminopropanoic acid, components of the antifungal peptide iturin and the cytotoxic depsipeptide cryptophycin respectively.
A new toroidal TFT structure for future generation SRAMs (2002)

A new toroidal TFT structure has been developed for future generation SRAM products. This new TFT provides excellent device performance at scaled power supply voltages and offers significant savings in bitcell area.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A NOVEL METHOD FOR THE SYNTHESIS OF β-LACTAMS BY MEANS OF PHASE TRANSFER SYSTEM (1981)

Abstract The reaction of β-amino acids with methanesulfonyl chloride in a chloroform-water bilayer system in the presence of 15 mol% of tetrabutylammonium hydrogen sulfate gives the corresponding β-lactams in good yields.
Aggregation Induced by Calcium Chloride and Subsequent Thermal Gelation of Whey Protein Isolate (1998)

The aggregation of whey proteins that was induced by CaCl 2 was investigated by measuring turbidity and aggregate size. The effect of the aggregation on thermal gelation was determined by measuring gel hardness. Standard conditions were set at 10% whey protein solution, 20 mM CaCl 2 , and 45C in order to observe the influence of different variable levels on the aggregation. The addition of 20 mM CaCl 2 to a 10% whey protein isolate solution resulted in a continuous increase in turbidity during 5 h of incubation at room temperature (21C). As expected, an increase in temperature (21 to 45C ) or CaCl 2 concentration ( 5 to 50 mM) increased the rate and extent of the aggregation. Stable colloidal aggregates were formed with 10 to 30 mM CaCl 2 . An increase in protein concentration from 5 to 20% remarkably reduced the rate and extent of the aggregation during the 5-h incubation. The aggregation was dependent on the weight ratio of CaCl 2 to whey proteins. Aggregation induced by CaCl 2 before heat-induced gelation greatly affected the hardness of the gels that were formed by heat treatment (80C for 30 min). The formation of the hardest gels required the optimal extent of aggregation or aggregate size.
Determination of the phase change on reflection from two-beam interference (1994)

Light reflected by a nondielectric material experiences a phase change on reflection that differs from light reflected by a dielectric material and other nondielectric materials. The complex degree of coherence for small optical path differences is derived for two-beam interference when the illumination source is extended, incoherent, and quasi-monochromatic. An analysis of the two-beam interference pattern reveals a simple relationship between the phase of the interference pattern at the point of maximum fringe visibility and the material-dependent phase change on reflection.
Uncalibrated Dynamic Visual Servoing (2004)

A dynamic quasi-Newton method for uncalibrated, vision-guided robotic tracking control with fixed imaging is developed and demonstrated. This method does not require calibrated kinematic and camera models. Robotic control is achieved at each step through minimizing a nonlinear objective function, by taking quasi-Newton steps and estimating the composite Jacobian at each step. The Jacobian is estimated using a dynamic recursive least-squares algorithm. Experimental results demonstrate the validity of this approach.
Preliminary experience with process modeling in the MARVEL software development environment kernel (2002)

The authors define a software development environment kernel called MARVEL. Implementing several prototypes and small environments has uncovered some significant flaws and revealed open design problems. Problems connected with the construction and debugging of a process model, with envelope construction, and with support of multiple users are considered. The authors note that they have investigated only a small fraction of the potential for rule-based process modeling and controlled automation. They observe that they do not yet fully understand how rule-based process modeling or controlled automation works and whether the combination is indeed a solid foundation for a software-development environment architecture.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Analyzing highway flow patterns using cluster analysis (2005)

Historical traffic patterns can be used for the prediction of traffic flows, as input for macroscopic traffic models, for the imputation of missing or erroneous data and as a basis for traffic management scenarios. This paper investigates the determination of historical traffic patterns by means of Ward's hierarchical clustering procedure. Days were clustered before and after a pre-classification into working days and non-working days, using two different definitions of a daily traffic profile. The results of the clustering after preclassification are clearly better than before classification. Moreover, working days are easier to classify into distinctive, recurrent traffic patterns than non-working days. Finally, clustering on the basis of 15 minutes traffic flows resulted in a better classification of working days than the two-step clustering that used the total daily traffic flow, peak flows, peak times and ratios. The clustering on the basis of 15 minutes traffic flows resulted in a classification into five clusters that show distinct daily flow profiles and are representative for the days within the clusters. The day of the week and vacation periods are determinative for the cluster a working day is classified to.
Robust indoor positioning fusing PDR and RF technologies: The RFID and UWB case (2013)

Indoor positioning is usually based on individual technologies that provide estimates of the trajectory of the person, or measures the ranges or angles between the user and known positions. Each technique has its advantages and problems, and a common way to overcome the drawbacks of single-technology solutions is to fuse the information from several system, but due to their non linear measurements, there is no optimal linear solution. We propose the use of a particle filter to fuse foot mounted inertial measurements with any additional Radio Frequency (RF) measurement. The information fusion is achieved propagating the position of the particles using the relative step displacements obtained from foot mounted Pedestrian Dead Reckoning (PDR), and updating the weights of the particles according to the RF measurements. In our experiments the inertial unit was located in the foot of the user, and the RF system consisted in a Radio Frequency Identification (RFID) receiver in the waist, and an Ultra Wide band (UWB) tag in the chest, but the scheme can be used in any sensor configuration. As the UWB measurements have a significant amount of outliers due to non line of sight conditions generated by the position of the tag in the body, received reflections, etc., we propose a new outlier rejection algorithm based on the compatibility of groups of measurements. The fusion was tested evaluating the inclusion of each of the RF systems and varying the number RFID tags used. The proposed method is able to locate a person with less than 2 m of error (for 90 % of the obtained estimations) in the studied trajectory. This particle filter scheme offers robust indoor positioning with 100 % availability and smooth trajectory estimation thanks to the PDR and limited error due to the RF measurements.
The Development of Ni/Dolomite Catalyst in Simultaneous Biomass Gasification and Reforming in Fluidized Bed (2009)

Simultaneous gasification and steam reforming of t he biomass on Ni/dolomite catalyst in fluidized bed reactor were studied in the gaseous p roduction in the one stage reactor. Problem statement: The parameters such as temperature, steam flow rat e, biomass feed rate, gas flow rate for fluidization, oxygen flow rate and catalyst types w ere studied to produce the high gaseous products including tar elimination. Approach: The temperature at 780°C, steam flow rate of 222 mmoL h -1 , gas flow rate for fluidization 450 mL min -1 and oxygen input 50 mL min -1 were found to be the suitable conditions. The Ni/Dolomite and the developed Ni/Dolomite were studied about their performance. Results: It was confirmed that Ni/Dolomite and newly developed Ni-WO 3/Dolomite show high performance in biomass gasification. Conclusion/Recommendations: It was claimed that Ni/Dolomite catalyst was the effective and give bes t performance for tar cracking. Newly developed Ni-WO 3/Dolomite catalyst was investigated to resist sulfu r nd coking. Three types of catalyst were used in the biomass gasification, which are Ni/Dolo mite, Ni/Dolomite+Silica binder and Ni- WO 3/Dolomite. From the XRD analysis, structures of typ e 1 (Ni/dolomite) and type 2 (Ni/Dolomite+Silica binder) were similar which were in CaCO 3, MgNiO 2, NiO and MgO forms. Type 3 (Ni-WO 3/Dolomite) was CaWO 4, MgNiO 2, NiO and MgO forms. When the catalytic gasification was operated, newly Ni- WO 3/Dolomite catalyst was the best catalyst for bamboo and palm shell biomasses, which could produce the high carbon monoxide and hydrogen but low methane and carbon dioxide were found. Carbon deposition on catalyst was around 0.37 mg according to the TG analysis.
Bacterial genes modifying hormonal balances in plants (1994)

A number of microorganisms that interact with plants use the same hormonal signals as plants. Four phytopathogenic bacteria causing either «olive knot» disease, «leafy galls», «crown gall» or «hairy root» disease in plants are among those most studied. The last two species induce proliferation resembling normal tissue and organ formation. Crown gall and hairy root are due to the expression of oncogenes carried on a bacterial DNA figment, which is transferred and integrated into the plant genome during infection. These oncogenes modify the plant hormonal balances or the hormone signal perception of the cells. In this review, we describe the different types of oncogenes present in several microorganisms, their functions when they are known, and the morphological, physiological, and developmental modifications that are induced when these oncogenes are introduced into plants
Electronic-band parameters in strained<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">Si</mml:mi></mml:mrow><mml:mrow><mml:mn>1</mml:mn><mml:mi mathvariant="normal">−</mml:mi><mml:mi mathvariant="italic">x</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math><mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">Ge</mml:mi></mml:mrow><mml:mrow><mml:mi mathvariant="italic">x</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math>alloys on<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">Si</mml:mi></mml:mrow><mml:mrow><mml:mn>1</mml:mn><mml:mi mathvariant="normal">−</mml:mi><mml:mi mathvariant="italic">y</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math><mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">Ge</mml:mi></mml:mrow><mml:mrow><mml:mi mathvariant="italic">y</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math>substrates (1993)

A systematic theoretical study of the electronic properties of pseudomorphic (100)-strained ${\mathrm{Si}}_{1\mathrm{\ensuremath{-}}\mathit{x}}$${\mathrm{Ge}}_{\mathit{x}}$ alloys grown on unstrained ${\mathrm{Si}}_{1\mathrm{\ensuremath{-}}\mathit{y}}$${\mathrm{Ge}}_{\mathit{y}}$ substrates is presented. Based on nonlocal empirical pseudopotential calculations with spin-orbit interactions, realistic estimates of the conduction- and valence-band-edge energies, higher-energy-band minima, effective masses, deformation potentials, and heterostructure band offsets for the whole range of alloy compositions x and y and strain are presented. The theory predicts that the band edges of weakly stressed Ge fall within the wider gap of the ${\mathrm{Si}}_{1\mathrm{\ensuremath{-}}\mathit{y}}$${\mathrm{Ge}}_{\mathit{y}}$ substrate for 0.7y1 (type-I alignment), in contrast to any Si-rich combination of active layer and substrate.
Rapidly Reversible Dissociation of Polysomes in <italic>Escherichia coli</italic> by <italic>n</italic>-Butanol (1969)

When 0.1M n-butanol was added to a culture of exponentially growing E. coli, the polysomal structure of the bacteria was lost within 2 min. This was prevented by addition of chloramphenicol. With 0.1M butanol, both RNA and protein syntheses in the bacteria were severely inhibited. On diluting the affected culture with 3 volumes of butanol-free medium, the bacteria quickly recovered their polysomal structure and resumed normal growth without any appreciable latent period. The mode of action of butanol with respect to membrane function is discussed.
Spectrally coded O-CDMA system with four users at 2.5 Gbit/s using low power nonlinear processing (2004)

A four-user 2.5 Gbit/s optical code-division multiple-access (O-CDMA) system is demonstrated at ≤10−11 BER utilising programmable spectral phase encoding, an ultrasensitive (<0.4 pJ/bit) PPLN-waveguide nonlinear waveform discriminator, and a 10G Ethernet receiver.
p53: A new player in reproduction (2008)

The roles of the p53 protein in tumor suppression have been firmly established. However, the functions of this protein under normal conditions or in the absence of stress, if any, have remained a mystery. In humans, some alleles containing a functional single nucleotide polymorphism in the p53 gene and its negative regulator, the Mdm2 gene, are under positive selection over evolutionary time frames, suggesting that the p53 pathway might have important functions that are optimized and selected for by evolutionary or reproductive pressures. Indeed, a recent study demonstrated a new function for the p53 protein in the regulation of maternal reproduction in mice, through transcriptional regulation of leukemia inhibitory factor (LIF), a novel p53 target gene. Sufficient uterine LIF levels are essential for the implantation of blastocysts or early embryos into the uterus. p53 deficient (p53(-/-)) female mice have a reduced pregnancy rate and litter size, due to impaired implantation resulting from decreased uterine LIF levels. Administration of LIF to pregnant p53(-/-) mice restored maternal reproduction by improving implantation. An association has been reported between women carrying the p53 codon 72 polymorphism (a proline to arginine change) with recurrent implantation failure, suggesting a similar function for p53 in humans. These findings of a new function for the p53 protein in reproduction may help to explain the observed evolutionary selection of some alleles of the p53 and Mdm2 genes. This may also be an excellent example of antagonistic pleiotrophy.
Novel compact model for multi-level spin torque magnetic tunnel junctions (2016)

Spin-transfer torque (STT) and spin-orbit torque (SOT) based magnetic tunnel junction (MTJ) devices are emerging as strong contenders for the next generation memories. Conventional STT magneto-resistive random access memory (MRAM) offers lower power, non-volatility and CMOS process compatibility. However, higher current requirement during the write operation leads to tunnel barrier reliability issues and larger access devices. SOT-MRAM eliminates the reliability issues with strong spin polarized current (100%) and separate read/write current paths; however, the additional two access transistors in SOT-MRAM results into increased cell area. Multilevel cell (MLC) structure paves a way to circumvent the problems related to the conventional STT/SOT based MTJ devices and provides enhanced integration density at reduced cost per bit. Conventional STT/SOT-MRAM requires a unit cell area of ~10-60 F<sup>2</sup> and reported simulations have been based on available single-level MTJ compact models. However, till date no compact model exists that can capture the device physics of MLC-MTJ accurately. Hence, a novel compact model is proposed in this paper to capture the accurate device physics and behaviour of the MLC-MTJs. It is designed for MLCs with different MTJ configurations demonstrated so far, such as series and parallel free layer based MLC-MTJs. The proposed model is coded in Verilog-A, which is compatible with SPICE for circuit level simulations. The model is in close agreement with the experimental results exhibiting an average error of less than 15%.
Magnetic imaging in the presence of an external field: erasure process of thin film recording medium (1995)

The evolution of microscopic magnetic structures on a thin film recording medium has been imaged by applying a progressively increasing external magnetic field. Images from magnetic force microscopy with an in situ magnetic field revealed features attributable to probe-induced and sample-induced effects. The probe effects result in the preferential sensitivity of the MFM imaging to the component of the local sample field in the direction of the probe's magnetization. The reorientation of the probe's magnetization with respect to the sample plane direction causes the change in instrument response from detecting surface magnetic charges (magnetization divergence sensing) to detecting the surface magnetization distribution. Sample effects are more prominent at higher fields and the micromagnetic features of the recorded patterns follow characteristic sequence as the unfavorably magnetized features of the recorded patterns follow a characteristic sequence as the unfavorably magnetized areas switch in the direction of the external field.
Keratinocyte growth factor-induced proliferation of rat airway epithelium is restricted to Clara cells<i>in vivo</i> (2002)

Keratinocyte growth factor (KGF) is a potent mitogen of pulmonary bronchial and alveolar epithelial cells. However, it is unclear which type(s) of airway epithelial cells (AEC) proliferate(s) in response to KGF. AEC proliferation was induced in rats by either endobronchial instillation of 5 mg recombinant human (rHu) KGF per kg body weight or by adenoviral transfer of the human KGF gene (Ad5-HuKGF). Alterations in terminal airway AEC were followed for up to 7 days after rHuKGF, and for up to 28 days after Ad5-HuKGF. Cell proliferation, as assessed by immunohistochemistry (IHC) for incorporated 5-bromo-2'-deoxyuridine (BrdU) and quantified by stereology, peaked at days 1-2 and was resolved by day 7 after rHuKGF and by day 21 after Ad5-HuKGF. Double immunofluorescence labelling for BrdU or Ki-67 on the one hand, and for Clara cell specific protein 10 (CC10) and calcitonin-gene related peptide on the other hand, demonstrated that Clara cells, not pulmonary neuroendocrine cells, proliferated in response to human KGF. TUNEL (terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate nick end-labelling) method in conjunction with IHC for MNF116 failed to detect significant numbers of apoptotic AEC. IHC in conjunction with stereology revealed transient phenotypic alterations with a decrease in CC10, an increase in surfactant protein D and an increase in CD44v6 in AEC. The authors conclude that Clara cells responded to human keratinocyte growth factor in vivo by proliferation as well as by changes in protein expression, whereas no significant response was observed in pulmonary neuroendocrine cells. As Clara cells are intimately involved in airway epithelial repair, ion and fluid transport, and modulate lung inflammation, the potential of human keratinocyte growth factor to protect the lung may in part rely on the response of Clara cells.
Comparing 2.5%, 5%, and 10% Benzoyl Peroxide on Inflammatory Acne Vulgaris (1986)

A 2.5% formulation of benzoyl peroxide was compared with its vehicle, and with a 5% and a 10% proprietary benzoyl peroxide gel preparation in three double-blind studies involving 153 patients with mild to moderately severe acne vulgaris. The 2.5% benzoyl peroxide formulation was more effective than its vehicle and equivalent to the 5% and 10% concentrations in reducing the number of inflammatory lesions (papules and pustules). Desquamation, erythema, and symptoms of burning with the 2.5% gel were less frequent than with the 10% preparation but equivalent to the 5% gel. The 2.5% formulation also significantly reduced Propionibacterium acnes and the percentage of free fatty acids in the surface lipids after 2 weeks of topical application.