gebhart/patrepeval huggingface dataset:
Antibody-directed targeting of lysostaphin adsorbed onto polylactide nanoparticles increases its antimicrobial activity against<i>S. aureus</i><i>in vitro</i> (2011)

The objective of this paper was to study the effect of antibody-directed targeting of S. aureus by comparing the activities of lysostaphin conjugated to biodegradable polylactide nanoparticles (NPs) in the presence and in the absence of co-immobilized anti-S. aureus antibody. Lysostaphin-antibody-NP conjugates were synthesized through physical adsorption at different enzyme:antibody:NP ratios. The synthesized enzyme-NP conjugates were characterized by means of dynamic light scattering and zeta potential analysis, and the total protein binding yield on the NPs was characterized using Alexa Fluor 350 and 594 dyes for the S. aureus antibody and lysostaphin respectively. We observed enhanced antimicrobial activity for both enzyme-coated and enzyme-antibody-coated NPs for lysostaphin coatings corresponding to ∼ 40% of the initial monolayer and higher compared to the free enzyme case (p < 0.05). At the highest antibody coating concentration, bacterial lysis rates for antibody-coated samples were significantly higher than for lysostaphin-coated samples lacking the antibody (p < 0.05). Such enzyme-NP conjugates thus have the potential for becoming novel therapeutic agents for treating antibiotic-resistant S. aureus infections.
A 56M&#x03A9; CMOS TIA for MEMS applications (2009)

We present the analysis, design, and measurement results of a high-gain, low-noise differential transimpedance amplifier (TIA) designed to interface with electrostatic microelectromechanical systems (MEMS) resonators. A capacitive-feedback current amplifier drives current into an active load to obtain a 56 MOmega transimpedance gain, 1.8 MHz bandwidth, phase response near 0deg, and 65 fA/radicHz input-referred noise. The TIA was fabricated in 0.18 mum CMOS technology and dissipates 436 muW from a 1.8 V supply.
High‐precision measurements of ionospheric TEC gradients with the Very Large Array VHF system (2012)

We have used a relatively long, contiguous VHF observation of a bright cosmic radio source (Cygnus A) with the Very Large Array (VLA) to demonstrate the capability of this instrument to study the ionosphere. This interferometer, and others like it, can observe ionospheric total electron content (TEC) fluctuations on a much wider range of scales than is possible with many other instruments. We have shown that with a bright source, the VLA can measure differential TEC values between pairs of antennas ( δ TEC) with a precision of 3 × 10 −4 TECU. Here, we detail the data reduction and processing techniques used to achieve this level of precision. In addition, we demonstrate techniques for exploiting these high‐precision δ TEC measurements to compute the TEC gradient observed by the array as well as small‐scale fluctuations within the TEC gradient surface. A companion paper details specialized spectral analysis techniques used to characterize the properties of wave‐like fluctuations within this data.
Improving cancer subtype diagnosis and grading using clinical decision support system based on computer-aided tissue image analysis (2013)

This research focuses towards the development of a clinical decision support system (CDSS) based on cellular and tissue image analysis and classification system that improves consistency and facilitates the clinical decision making process. In a typical cancer examination, pathologists make diagnosis by manually reading morphological features in patient biopsy images, in which cancer biomarkers are highlighted by using different staining techniques. This process is subjected to pathologist's training and experience, especially when the same cancer has several subtypes (i.e. benign tumor subtype vs. malignant subtype) and the same cancer tissue biopsy contains heterogeneous morphologies in different locations. The variability in pathologist's manual reading may result in varying cancer diagnosis and treatment.\nThis Ph.D. research aims to reduce the subjectivity and variation existing in traditional histo-pathological reading of patient tissue biopsy slides through Computer-Aided Diagnosis (CAD). Using the CAD, quantitative molecular profiling of cancer biomarkers of stained biopsy images are obtained by extracting and analyzing texture and cellular structure features. In addition, cancer sub-type classification and a semi-automatic grade scoring (i.e. clinical decision making) for improved consistency over a large number of cancer subtype images can be performed. The CAD tools do have their own limitations and in certain cases the clinicians, however, prefer systems which are flexible and take into account their individuality when necessary by providing some control rather than fully automated system. Therefore, to be able to introduce CDSS in health care, we need to understand users' perspectives and preferences on the new information technology. This forms as the basis for this research where we target to present the quantitative information acquired through the image analysis, annotate the images and provide suitable visualization which can facilitate the process of decision making in a clinical setting.
The research of adaptive weighted congestion control in MPTCP (2011)

As the traditional TCP which has greatly restricted is no longer able to meet the requirements of the existing data transmittal.so Multipath Transport Protocol is proposed.Focus on the issue of fairness on the bottleneck link in multipath transmission,and analyzes the limitations of the algorithms of EWTCP with equal round-trip time,We investigate a congestion control scheme that addresses this problem with the adaptive weighted congestion control approach(AWTCP). In our scheme, an According to the simulation experiments by NS2 show that when RTT changes, AWTCP algorithm also able to adaptive changes the weight to each sub-flow, end-to-end connection that uses flows along multiple paths can fairly compete with TCP flows at the shared bottleneck.
Testing and Developing a Remote Controlled and Supervised Container Handling Equipment (2017)

The introduction of Automation is gaining speed in many application fields due the latest technological, social and economic developments. The field of harbour terminals is not an exception, with up to 500 large scale terminals searching for new automation systems.\nThis MSc thesis was carried out at Kalmar and it is taking into consideration company policies and procedures in order to provide a realistic scenario. However, the literature review was not limited to Kalmar solutions and is taking into consideration other practices, especially those related to networks and video and audio protocols.\nThe main objective of this MSc thesis is the development of an automatic rubber tyred gantry crane. Special consideration is provided on how the crane can remotely be controlled and supervised within a specific area. The supervision is desired because by safety reasons the operator supervises the automatic movements of the gantry direction in X coordinate and the Y trolley coordinate for a potential “dead man´s” switch. The hoist direction along Z and the truck lane operation are remotely controlled by the operator.\nAs an engineering requirement, Kalmar´s Software Architecture, and its reconfiguration features, play an important role at the time of configuring and installing the system. The Thesis pays special attention on how to solve network issues due the increase of crane´s load. The final approach is complemented by the development of a User Interface in order to host the increased amount of information due the new automation system. The Thesis also presents the results for testing the new solution on Cargotec final product, and outline the main issues reported during the testing period. The resulting solution is a market ready product.
Temperature-Dependent $I$– $V$ Characteristics of a Vertical $\hbox{In}_{0.53}\hbox{Ga}_{0.47}\hbox{As}$ Tunnel FET (2010)

We report on the experimental temperature-dependent characteristics of vertical In <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.53</sub> Ga <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.47</sub> As tunnel field-effect transistors (TFETs) at low drain bias to provide key insight into its device operation and design. Leakage floor (I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">OFF</sub> ) is determined by the ungated p <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> -i-n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> reverse bias leakage and is dominated by Shockley-Read-Hall generation-recombination current. The temperature dependence of subthreshold slope arises from tunneling into mid-gap states at the oxide-semiconductor interface, followed by thermal emission into the conduction band. At intermediate gate voltages, pure band-to-band tunneling dominates, while at higher gate voltages, current transport is diffusion limited. The temperature-dependent study of In <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.53</sub> Ga <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.47</sub> As TFET highlights the importance of passivating the III-V and dielectric interface.
Upgrading Wastewater Treatment by Water Hyacinth in Developing Countries (1990)

With increasing stress on existing wastewater treatment systems, it is necessary either to upgrade the treatment unit(s) or install an entirely new treatment plant. Obviously, the upgrading is preferred over the alternative of having a new system. Keeping this in view, in the present project, an attempt has been made to explore the possibility of upgrading existing facultative ponds using water hyacinth. Bench-scale batch studies were designed to compare the performance of hyacinth treatment system with facultative ponds. Investigations were carried out with synthetic wastewater having COD in the range of 32.5-1090 mg/l. The efficiency of COD removal in water hyacinth ponds was 15-20 percent more than the facultative ponds. Based on the results, an empirical model has been proposed for COD removal kinetics. In the second phase of the project a hyacinth pond was continuously operated. BOD, COD, TS, TN, TP, pH, and DO were regularly monitored. However, the DO of the effluent from hyacinth treatment system was considerably reduced. Effluent should be aerated before it is discharged. The results indicate that the existing facultative ponds can be stalked with water hyacinth to improve their performance as well as hyacinth treatment systems can be installed to support the conventional treatment.
[Viscoelastic property of human brain -for the analysis of impact injury (author's transl)]. (1981)

1. Viscoelasticity of the human brain was investigated in order to understand the physical properties of the brain and to apply it to the analysis of the head injury mechanisms. 2. Static shear modulus (G) of the human white matter was 2.4 X 10(3) dyne/cm2. 3. Complex Young's modulus (E*(omega) = E' + iE") of the white matter, the gray matter, and the brain stem was measured in the range of 3-36 degrees C and 3-35 Hz using the dynamic viscoelastometer. Storage Young's modulus (E') of both white and gray matters of human brain was in the figures of 10(5) dyne/cm2 and loss Young's modulus (E") of those showed 10(4)-15(5) dyne/cm2. 4. The viscoelasticity of human brain is illustrated in Fig. 4 on the assumption of the equivalence of time and temperature. In case of head injury with impact duration of 5 msec it is proper to use the following value : E' = 4 X 10(5) dyne/cm2, E" = 2 X 10(5) dyne/cm2 in the white matter and E' = 3 X 10(5) dyne/cm 2, in the gray matter. 5. The visoelasticity of gelatin and bean curds were also examined to know whether or not simulation of the brain was possible. The viscoelasticity of 5-15% gelatin with an addition of 5% formalin was decreased 1-2 figures compared with that of the brain. The viscoelasticity of bean curds was about the same as that of the brain.
A Finite Element Investigation into the Changing Channel Angular Extrusion of Brass Alloy (2008)

This study investigates a novel changing channel angular (CCA) extrusion process, in which high strains are induced within the billet by passing it through a series of channels of unequal cross-sections arranged such that they form specified internal angles. Using commercial DEFORMTM 2D rigid-plastic finite element code, the plastic deformation behavior of CuZn37 brass alloy is examined during one-turn and two-turn CCA extrusion processing in dies with internal angles of φ =90o, 120o, 135o or 150o, respectively. The simulations focus specifically on the effects of the processing conditions on the effective strain, the rotation angle and the effective stress induced within the extruded billet. The numerical results provide valuable insights into the shear plastic deformation behavior of CuZn37 brass alloy during the CCA extrusion process.
Logic gates and memory cells based on single C<sub>60</sub>electromechanical transistors (2001)

The equivalent electrical circuit of a single C60 electromechanical transistor in a planar lay-out is presented using its experimental STM characteristics. This circuit is used to demonstrate that such a hybrid molecular electronic device can be used as a class A amplifier, a NOT or NOR gate and to implement an SRAM memory point. All the devices are simulated using the SPICE routine to find their optimum load resistance and cantilever grid size. The class A amplifier can operate with a cut-off frequency of a few gigahertz while the logic gate and memory are limited to a few tens of megahertz, but for a very small power design in the picowatt range.
Combining high‐throughput screening of caspase activity with anti‐apoptosis genes for development of robust CHO production cell lines (2010)

A set of anti-apoptotic genes were over-expressed, either singly or in combination, in an effort to develop robust Chinese Hamster Ovary host cell lines suitable for manufacturing biotherapeutics. High-throughput screening of caspase 3/7 activity enabled a rapid selection of transfectants with reduced caspase activity relative to the host cell line. Transfectants with reduced caspase 3/7 activity were then tested for improved integrated viable cell count (IVCC), a function of peak viable cell density and longevity. The maximal level of improvement in IVCC could be achieved by over-expression of either single anti-apoptotic genes, e.g., Bcl-2Δ (a mutated variant of Bcl-2) or Bcl-XL, or a combination of two or three anti-apoptotic genes, e.g., E1B-19K, Aven, and XIAPΔ. These cell lines yielded higher transient antibody production and a greater number of stable clones with high antibody yields. In a 5 L fed-batch bioreactor system, BΔ31-1, a stable clone expressing Bcl-2Δ, had a product titer that was 180% as compared to an optimal clone (Con-1) from the control cell line. Although lactate accumulated to more than 5 g/L in the control culture, its concentration was reduced in the anti-apoptotic BΔ31-1 cultures to below 1 g/L, confirming our earlier findings that cells over-expressing anti-apoptotic genes consume the lactate that would otherwise accumulate as a by-product in the culture medium. To the best of our knowledge, this is the first study to use the high throughput caspase screening method to identify CHO host cell lines with superior anti-apoptotic characteristics.
EM-seq: Detection of DNA Methylation at Single Base Resolution from Picograms of DNA (2019)

Abstract Bisulfite sequencing is widely used to detect 5mC and 5hmC at single base resolution. However, bisulfite treatment damages DNA resulting in fragmentation, loss of DNA and biased sequencing data. To overcome this, we developed Enzymatic Methyl-seq (EM-seq), an enzymatic based approach that uses as little as 100 pg of DNA. EM-seq outperformed bisulfite converted libraries in all metrics examined including coverage, duplication, sensitivity and nucleotide composition. EM-seq libraries displayed even GC distribution, improved correlation across input amounts as well as increased representation of genomic features. These data indicate that EM-seq is more accurate and reliable than whole genome bisulfite sequencing (WGBS).
Robust voice activity detector for real world applications using harmonicity and modulation frequency (2011)

The task of robustly detecting distant speech in low SNR environments for automatic speech recognition is examined using a two-stage approach based on two distinguishing features of speech, namely harmonicity and modulation frequency (MF). A modified metric for harmonicity is used as a gating function to a set of parallel classifiers that incorporate MFs computed on different frequency bands. Performance is evaluated on both the frame-level discriminative power and also the system level ASR results on a real-world robotic forklift task. Compared to other previously proposed features such as relative spectral entropy, and classification strategies involving MFs, the combined approach shows good generalization across different kinds of dynamic noise conditions, and obtains a significant improvement on the false alarm rate at low speech miss rate settings. The overall ASR results also improved significantly compared to the ESTI AMR-VAD2, while reducing the number of false alarms by a factor of two. Index Terms: voice activity detection, modulation frequency, harmonicity, human-robot interaction.
Structure-activity relationship analysis and therapeutic potential of peptide deformylase inhibitors. (2004)

Peptide deformylase inhibitors (PDFIs) appear to be one of the most exciting classes of antibacterial agents discovered to date. Rapid progress in the development of PDFIs has been possible because peptide deformylase is a metalloprotease, and this class of enzymes shows a high degree of structure-function conservation, and because the most potent PDFIs are hydroxamate derivatives, a well known category of pharmacophores. The current challenge in structure-activity relationship analysis is obtaining molecules with potent in vivo antibacterial activity against a range of drug-resistant pathogens. The PDFIs currently in clinical trials target community-based bacterial infections, with a potential major pharmaceutical market.
Compression of a Flapping Mechanophore Accompanied by Thermal Void Collapse in a Crystalline Phase (2018)

Mechanical control of the molecular energy landscape is an important issue in modern materials science. Mechanophores play a unique role in that the mechanical responses are induced against the activation barrier for intramolecular transformation with the aid of external forces. Here we report an unprecedented activation process of a flexible flapping mechanophore. Namely, thermal void collapse in a crystalline phase triggers mechanophore compression in a definite proportion. Unfavored conformational planarization of the flapping mechanophore is compulsorily induced by packing force, leading to a total energy gain in crystal packing. Fluorescence chromism indicates extended π conjugation resulting from the mechanophore compression, giving rise to an energy transfer from the unpressed to compressed conformers.
Managing and Mining Large Graphs: Systems and implementations (tutorial) (2012)

We are facing challenges at all levels ranging from infrastructures to programming models for managing and mining large graphs. A lot of algorithms on graphs are ad-hoc in the sense that each of them assumes that the underlying graph data can be organized in a certain way that maximizes the performance of the algorithm. In other words, there is no standard graph systems based on which graph algorithms are developed and optimized. In response to this situation, a lot of graph systems have been proposed recently. In this tutorial, we discuss several representative systems. Still, we focus on providing perspectives from a variety of standpoints on the goals and the means for developing a general purpose graph system. We highlight the challenges posed by the graph data, the constraints of architectural design, the different types of application needs, and the power of different programming models that support such needs.
Structures buckling under tensile dead load (2011)

Some 250 years after the systematic experiments by Musschenbroek and their rationalization by Euler, for the first time we show that it is possible to design structures (i.e. mechanical systems whose elements are governed by the equation of the elastica) exhibiting bifurcation and instability (‘buckling’) under tensile load of constant direction and point of application (‘dead’). We show both theoretically and experimentally that the behaviour is possible in elementary structures with a single degree of freedom and in more complex mechanical systems, as related to the presence of a structural junction, called ‘slider’, allowing only relative transversal displacement between the connected elements. In continuous systems where the slider connects two elastic thin rods, bifurcation occurs both in tension and in compression, and is governed by the equation of the elastica, employed here for tensile loading, so that the deformed rods take the form of the capillary curve in a liquid, which is in fact governed by the equation of the elastica under tension. Since axial load in structural elements deeply influences dynamics, our results may provide application to innovative actuators for mechanical wave control; moreover, they open a new perspective in the understanding of failure within structural elements.
Contribution of reactive oxygen species to ovarian cancer cell growth arrest and killing by the anti-malarial drug artesunate (2016)

Ovarian cancer is a leading cause of cancer-related death in women and the most lethal gynecological malignancy in the developed world. The morbidity and mortality of ovarian cancer underscore the need for novel treatment options. Artesunate (ART) is a well-tolerated anti-malarial drug that also has anti-cancer activity. In this study, we show that ART inhibited the in vitro growth of a panel of ovarian cancer cell lines, as well as the growth of ovarian cancer cells isolated from patients. Moreover, ART decreased tumor growth in vivo in a mouse model of ovarian cancer. ART-treated ovarian cancer cells showed a strong induction of reactive oxygen species (ROS) and reduced proliferation. ROS-dependent cell cycle arrest occurred in the G2/M phase whereas ROS-independent cell cycle arrest occurred in the G1 phase, depending on the concentration of ART to which ovarian cancer cells were exposed. The anti-proliferative effect of ART was associated with altered expression of several key cell cycle regulatory proteins, including cyclin D3, E2F-1, and p21, as well as inhibition of mechanistic target of rapamycin signaling. Exposure of ovarian cancer cells to higher concentrations of ART resulted in ROS-dependent DNA damage and cell death. Pretreatment of ovarian cancer cells with a pan-caspase inhibitor or ferroptosis inhibitor decreased but did not completely eliminate ART-mediated cytotoxicity, suggesting the involvement of both caspase-dependent and caspase-independent pathways of killing. These data show that ART has potent anti-proliferative and cytotoxic effects on ovarian cancer cells, and may therefore be useful in the treatment of ovarian cancer. © 2016 Wiley Periodicals, Inc.