gebhart/patrepeval huggingface dataset:
Identifying the differences in mechanisms of mycophenolic acid controlling fucose content of glycoproteins expressed in different CHO cell lines (2016)

In the biopharmaceutical industry, glycosylation is a critical quality attribute that can modulate the efficacy of a therapeutic glycoprotein. Obtaining a consistent glycoform profile is desired because molecular function can be defined by its carbohydrate structures. Specifically, the fucose content of oligosaccharides in glycoproteins is one of the most important attributes that can significantly affect antibody-dependent cellular cytotoxicity (ADCC) activity. It is therefore important to understand the fucosylation pathway and be able to control fucosylation at the desired level to match predecessor materials in late stage and biosimilar programs. Several strategies were explored in this study and mycophenolic acid (MPA) was able to finely modulate the fucose content with the least undesired side effects. However, the response was significantly different between CHO cell lines of different lineages. Further experiments were then performed for a deeper understanding of the mechanism of fucosylation in different CHO cell lines. Results indicated that changes in the intracellular nucleotide involved in fucosylation pathway after MPA treatment are the main cause of the differences in fucosylation level response in different CHO cell lines. Differences in MPA metabolism in the various CHO cell lines directly resulted in different levels of afucosylation measured in antibodies produced by the CHO cell lines. Biotechnol. Bioeng. 2016;113: 2367-2376. © 2016 Wiley Periodicals, Inc.
Pulse shortening by RF breakdown in relativistic backward wave oscillator (2008)

Relativistic backward wave oscillator (RBWO) is the suitable source for generating high power electromagnetic wave (HPEM). The RBWO has a high efficiency by means of the interaction region between a backward wave and an electron beam. However, the pulse shortening problem occurs frequently in experiments of RBWO because of the RF breakdown on rippled slow wave structure. Experimental study is done 500 MW RBWO in progress.
N.m.r. Spectra of porphyrins. Part 35. An examination of the proposed models of the chlorophyll a dimer (1988)

The n.m.r. complexation shifts at 500 MHz of the protons of chlorophyll a have been obtained from titration experiments with [2H4]methanol and chlorophyll a dissolved in CDCl3 at such concentrations (3mM) that only the chlorophyll dimer is present. This more accurate and more complete set of complexation shifts than obtained previously has been used to examine critically proposed models of the chlorophyll a dimer, using the double-dipole model of the chlorophyll ring current to calculate the dimer shifts. Proposals based on the crystal structure of ethyl chlorophyllide-a dihydrate (the Strouse model), on exciton-theoretical and infrared data (the Shipman model), and the various skew structures, do not lead to any agreement with the observed complexation shifts. The face-to-face proposal (the Fong model) gives the correct overall pattern for the complexation shifts, but not quantitative agreement. The unsymmetrical head-to-tail (‘piggy-back’) structure does give quantitative agreement with the observed shifts for all the protons measured. These last two models appear to involve co-ordination of the C-10 methoxycarbonyl CO with the adjoining magnesium atom, which is not consistent with observations on the pyrochlorophyllide series, in which similar complexation shifts are observed. A new structure which both quantitatively fits the observed complexation shifts and which appears to satisfy these other observations is proposed. This is a back-to-back structure in which both the C-10 methoxycarbonyl groups in the dimer are exo to the dimer structure. The arrangement is not symmetric and the two chlorophyll molecules are in very different environments. In one molecule the C-9 CO is near to the neighbouring magnesium atom and could be co-ordinated to the magnesium via a bridging water molecule. In the other molecule the C-7 propionic CO is situated near to the neighbouring magnesium atom and could also be co-ordinated to it. The C-10 methoxycarbonyl groups are not involved in the dimer binding interaction.
Role of AMP-activated protein kinase in the regulation by glucose of islet beta cell gene expression (2000)

Elevated glucose concentrations stimulate the transcription of the pre-proinsulin (PPI), L-type pyruvate kinase (L-PK), and other genes in islet beta cells. In liver cells, pharmacological activation by 5-amino-4-imidazolecarboxamide riboside (AICAR) of AMP-activated protein kinase (AMPK), the mammalian homologue of the yeast SNF1 kinase complex, inhibits the effects of glucose, suggesting a key signaling role for this kinase. Here, we demonstrate that AMPK activity is inhibited by elevated glucose concentrations in MIN6 beta cells and that activation of the enzyme with AICAR prevents the activation of the L-PK gene by elevated glucose. Furthermore, microinjection of antibodies to the alpha2- (catalytic) or beta2-subunits of AMPK complex, but not to the alpha1-subunit or extracellular stimulus-regulated kinase, mimics the effects of elevated glucose on the L-PK and PPI promoter activities as assessed by single-cell imaging of promoter luciferase constructs. In each case, injection of antibodies into the nucleus and cytosol, but not the nucleus alone, was necessary, indicating the importance of either a cytosolic phosphorylation event or the subcellular localization of the alpha2-subunits. Incubation with AICAR diminished, but did not abolish, the effect of glucose on PPI transcription. These data suggest that glucose-induced changes in AMPK activity are necessary and sufficient for the regulation of the L-PK gene by the sugar and also play an important role in the regulation of the PPI promoter.
Current status of the Hobby-Eberly Telescope wide field upgrade (2012)

The Hobby-Eberly Telescope (HET) is an innovative large telescope of 9.2 meter aperture, located in West Texas at the McDonald Observatory (MDO). The HET operates with a fixed segmented primary and has a tracker which moves the four-mirror corrector and prime focus instrument package to track the sidereal and non-sidereal motions of objects. A major upgrade of the HET is in progress that will increase the pupil size to 10 meters and the field of view to 22′ by replacing the corrector, tracker and prime focus instrument package. In addition to supporting the existing suite of instruments, this wide field upgrade will feed a revolutionary new integral field spectrograph called VIRUS, in support of the Hobby-Eberly Telescope Dark Energy Experiment (HETDEXχ). This paper discusses the current status of this upgrade.
Manipulation in real, virtual and remote environments (2002)

In this paper we describe a novel experimental procedure for the evaluation of a telemanipulator performance. A group of subjects performed the same set of tasks directly on a physical setup, on a virtual implementation capable of providing visual and force feedback through an haptic display, and remotely on the real setup using a telemanipulation system. Using this experimental procedure we were able to decouple the effects on the overall telemanipulator performance introduced by the single components of the system, master manipulator, display, slave manipulator rind bilateral controller.
Urinary phytate concentration and risk of fracture determined by the FRAX index in a group of postmenopausal women (2019)

Background/aim: This study was designed to evaluate the relationship between urinary phytate concentration and risk of fracture at 10 years, determined by using the FRAX model, in women who had undergone menopause within 5 years of the time of enrollment. Materials and methods: Of the 212 postmenopausal women evaluated, 69 were excluded because they had urinary phytate concentrations between 0.51 and 0.99 mg/L. Of the remaining 143 women, 91 had low (≤0.50 mg/L) and 52 had high (≥1.0 mg/L) urinary phytate concentrations. The 10-year risk of fracture was calculated by using the FRAX model.Results: The risks of major osteoporotic fracture and hip fracture were higher in women with low urinary phytate levels (P &amp;amp;lt; 0.001 in both cases). Evaluation of the risk of hip fracture in women with and without risk factors for osteoporosis (e.g., tobacco, alcohol, and drug consumption) and according to urinary phytate concentrations indicated that, among women with no risk factors, those with low and high urinary phytate levels had a range of risks of 0%-0.6% and 0%-0.3%, respectively (P = 0.098). Moreover, among women with at least one risk factor, those with low and high urinary phytate had a range of risks of 0.1%-0.8% and 0.1%-0.4%, respectively (P = 0.002). Similar results were observed when the risks of major osteoporotic fracture were analyzed.Conclusion: These results indicate the relationship of phytate with the risks of major osteoporotic fracture and hip fracture, with these differences being more marked in women with risk factors for osteoporosis. From this study follows the importance of the consumption of phytate-rich products (nuts, legumes, whole cereals) to protect against the risk of fracture in 10 years, mainly in women with risk factors for osteoporosis.
Bifurcation and chaos of DC-DC converter as applied to micro-inverter with multi control parameters (2015)

In general, DC-DC converter is a highly nonlinear system. More than one decade ago, many researchers have approved that DC-DC converters are experiencing bifurcation and chaotic oscillations. In this paper, both DC-DC Buck and Boost converters are been studied and analyzed. The study showed that such DC-DC converters are experiencing a nonlinear behavior (chaotic behavior) under certain operation conditions. In this paper, we studied the bifurcation and chaos in the DC-DC buck converter with changing different control parameters. In addition, the bifurcation theory will be applied to DC-DC Boost converter. Bifurcation diagrams and state-space diagrams have been shown for changing some control parameters.
Nanomaterial-based Sensors for Volatile Biomarkers (2022)

This chapter provides an overview of the present and ongoing developments in the field of volatile organic compound (VOC) nanomaterial-based sensors that have been finding use in healthcare. It starts by briefly explaining the advantage of nanomaterials for sensing applications and reviewing the available and quickly progressing VOC sensing devices. There is a discussion of the main trends in material design with special attention given to nanostructuring and nanohybridization, while highlighting emerging sensing materials and strategies. An insightful summary of the field and suggestions of multiple worthy directions in which to choose nanomaterial-based sensors are discussed, while considering the profile of the targeted VOCs and the possible limitations of applying sensing approaches. The perspectives when taking VOC sensors to a new level in the field of diagnostics are made evident.
THE APPLICATION OF INSTABILITIES IN MICROFLUIDIC JETS TO DIGITAL OFFSET CLASS PRINTING (2008)

The tendency of fluid jets to break up into droplets of multiple sizes has been well known since the times of Lord Rayleigh. 1 However the ability to make and control individual droplets from arrays of such jets has come only recently, due in part to the availability of microstructure manufacturing technologies and to the recognition of the potential importance of such arrays to variable data printing. We describe a new inkjet printing technology based on thermally stimulated drop breakup of jets of complex fluids that allows variable data printing to move into "high-speed," "offset class" markets, which include publication and short-run commercial printing markets, often served today by offset lithography, and transactional printing markets, often served by imposition print technologies. The physics of microjet instabilities and the ability to make low-cost microfluidic devices enable such high-speed digital applications.
Real-time close-range 3D motion measurements for dental medicine (1990)

Dental medicine needs to observe the motion of the jaw with respect to the skull in three dimensions. This represents, therefore, a problem domain in which one has to observe, in real-time, the motion of one three- dimensional body in 3-D space (the jaw) with respect to another three-dimensional body in 3-D space (the skull) which both may move independently. This paper discusses an innovative solution to this requirement. The solution is implemented on a personal computer and is based on light-emitting diodes that are attached to the two moving 3-D objects. The innovation has been granted patent protection2. An element of the solution is the hand-held 3-D cursor whose position is also trackable as a separate three-dimensional body in 3-D space and allows the user to identify the XYZ coordinates of any point by a free-hand pointing action. Applications of this real-time 3-D measurement system are not only in dental medicine but may extend to mechanical engineering, medical gait analysis and other applications where 3-D motions need to be tracked in real time.
Virtual screening to enrich a compound collection with CDK2 inhibitors using docking, scoring, and composite scoring models (2005)

Docking programs can generate subsets of a compound collection with an increased percentage of actives against a target (enrichment) by predicting their binding mode (pose) and affinity (score), and retrieving those with the highest scores. Using the QXP and GOLD programs, we compared the ability of six single scoring functions (PLP, Ligscore, Ludi, Jain, ChemScore, PMF) and four composite scoring models (Mean Rank: MR, Rank-by-Vote: Vt, Bayesian Statistics: BS and PLS Discriminant Analysis: DA) to separate compounds that are active against CDK2 from inactives. We determined the enrichment for the entire set of actives (IC50 < 10 microM) and for three activity subsets. In all cases, the enrichment for each subset was lower than for the entire set of actives. QXP outperformed GOLD at pose prediction, but yielded only moderately better enrichments. Five to six scoring functions yielded good enrichments with GOLD poses, while typically only two worked well with QXP poses. For each program, two scoring functions generally performed better than the others (Ligscore2 and Ludi for GOLD; QXP and Jain for QXP). Composite scoring functions yielded better results than single scoring functions. The consensus approaches MR and Vt worked best when separating micromolar inhibitors from inactives. The statistical approaches BS and DA, which require training data, performed best when distinguishing between low and high nanomolar inhibitors. The key observation that all hit rate profiles for all four activity intervals for all scoring schemes for both programs are significantly better than random, is evidence that docking can be successfully applied to enrich compound collections.
OrgaPVnet: Building a Realistic Roadmap for Organic Based Photovoltaics (2008)

Solar cells with active layers, partially or fully based on organic materials, are the subject of large interest, both from R&amp;D-actors as from large investors. This interest is fuelled by the rapid developments in the field of organic based devices with certified efficiencies between 5 and 6% for full-organic devices and 11% for dye sensitized solar cells, the potentially very low cost of these devices, mechanical flexibility and light weight. The low cost potential is based on the use of low-cost materials and substrates and the very high production speeds which could be reached by roll-to-roll processing. In addition, organic photovoltaic devices take profit of the developments in neighbouring fields like Organic LED’s and thin-film transistors, which could create synergetic effects similar to what was observed for crystalline Si solar cells which took benefit from the large knowledge and equipment base, built up in the micro-electronics sector. Notwithstanding all these promises, there is a strong need to define correctly the technical and scientific challenges, to outline the way these challenges have to be tackled and to define the markets in which these organic photovoltaic devices could create large impact. This is done in the frame of the European Project ORGAPVNET. The paper aims at bringing this information in a concise form to the broader PV-community to improve the understanding of this emerging field, to explain how this information is going to be used to build a dedicated roadmap and to explain the synergies which exist with other fields of organic devices.
Optical spectroscopy of a GaAs/AlGaAs quantum wire structure using near-field scanning optical microscopy (1994)

We report the first spectroscopic study using a low temperature near-field scanning optical microscope. We have studied an array of GaAs/AlGaAs cleaved edge overgrowth quantum wires. The three luminescence peaks originate from different structures in the sample: The (001)-oriented multiple quantum wells, the (110)-oriented single quantum well, and the quantum wires. The linewidth of the quantum wire emission is related to roughness in the (110)-oriented single quantum well. Quenching of the multiple quantum wells and single quantum well emission near the quantum wires is attributed to diffusion of photoexcited carriers into the wires.
Hybrid OFDM for future DSRC applications (2002)

Future DSRC applications need flexible and robust air interface technology to support high and low data rate services in harsh mobile environments. First we analyze various DSRC applications for their data requirement and present typical DSRC channel scenarios with their parameters. To address this variety of scenarios, we propose a hybrid OFDM architecture that is a combination of single carrier and multicarrier (OFDM) communication systems for DSRC services. Single carrier devices communicate in an OFDMA scheme in the uplink for more spectral efficiency reasons. Simulation results shows that it is feasible to operate hybrid OFDM for a variety of DSRC applications.
Direct Monitoring of Fucosylated Glycopeptides of Alpha‐Fetoprotein in Human Serum for Early Hepatocellular Carcinoma by Liquid Chromatography–Tandem Mass Spectrometry with Immunoprecipitation (2018)

These findings suggest that glycopeptide-based LC-MS/MS is a promising method and that AFP-fuc% is a clinically useful parameter for differentiating between early HCC and liver cirrhosis.
<title>Increasing link utilization in IP over WDM networks</title> (2002)

In this paper we study an approach to Quality of Service that offers end-users the choice between two classes of service defined according to their level of transmission protection. The first class of service, called Fully Protected (FP), offers end-users a guarantee of survivability in the case of a single failure; all FP traffic is protected using either a 1:1 or 1+1 protection scheme at the WDM layer. The second class of service, called Best-Effort Protected (BEP), is not protected; when a failure occurs, the network does the best it can by restoring at the IP layer only as much BEP traffic as possible. The FP service class mimics what Internet users receive today. The motivation of this approach is to increase the amount of bandwidth used on backbone networks by offering a lower quality of service that does not affect the current QoS provided by the network. We design an ILP model, for finding primary and backup paths at the optical layer, that incorporates a number of carriers' common practices. Namely we allow the FP demand to be specified via a traffic matrix at the IP layer, we include an overprovisioning factor that specifies the portion of each link that must be left unused, and we incorporate a minimal fairness requirement on how the BEP traffic is allocated. Our goal is thus to quantify how much BEP traffic can be carried in addition to the FP traffic, without impacting the protection quality of the FP traffic even in the case of failure, and without impacting the FP load. We show that by having two such classes of service, the load on a network can be increased by a factor of 4 to 7 (depending upon the network). Even if carriers want to overprovision their networks by 50%, we can still triple the total network load. We illustrate that the location of the bottleneck can affect whether or not we see a difference in performance between 1:1 or 1+1 protection schemes. Finally we evaluate the tradeoff between the two carrier requirements of overprovisioning and minimal f
<title>Fluorescence spectroscopy of normal and cancerous human stomach tissue</title> (1994)

The autofluorescence of cancerous and normal human stomach tissues was measured in vitro, by fluorescence spectroscopy, within three hours of surgery ablation. A new fluorescence emission band, centered at about 380 nm for the cancerous stomach tissue is reported, for 340 nm excitation. This band is practically absent for the normal tissue when this is excited at the same wavelength. For UVB excitation (between 283 and 305 nm) the emission bands are centered around 350 nm and 470 nm, for both tissues, in agreement with the literature. The ratios of the fluorescence intensities for cancerous and normal tissues are measured at the center of the three bands, the intensity for the diseased tissue being always higher than for the normal one. The presence of a new band centered at 380 nm, combined with the intensity ratios, may prove of great relevance towards early in vivo detection of stomach cancer.
Automatic Segmentation of Walking Strides in Wearable Accelerometry Data with Adaptive Empirical Pattern Transformation (2019)

Quantifying gait parameters and ambulatory monitoring of changes in these parameters has become increasingly important for epidemiological and clinical studies. Wearable accelerometers provide objective high-density measurements of human gait dynamics through recording of acceleration. Many studies use accelerometry to objectively measure physical activity using the activity counts, vector magnitude, or number of steps. These measures use just a fraction of the information in the raw accelerometry data as they are typically summarized at the minute level. To address this problem, we focus on raw, sub-second level accelerometry data and define a set of gait characteristics based on these data. Additionally, to overcome the analytical challenges of these complex and voluminous data we develop automatic and unsupervised methodology for precise segmentation of stride patterns. PURPOSE: We propose Adaptive Empirical Pattern Transformation (ADEPT) and maximization-tuning procedure for automatic identification of individual walking strides from raw accelerometry data that uses data-derived baseline patterns, representing a population-specific strides. METHODS: Data were collected as a part of the study on Identification of Walking, Stair Climbing, and Driving Using Wearable Accelerometers, funded by the Indiana University CTSI grant and conducted at the Department of Biostatistics, RM Fairbanks School of Public Health at Indiana University. The study enrolled 32 healthy participants between 23 and 52 years of age. Participants wore accelerometers on a wrist, hip and both ankles during a 450-meter outdoor walk. RESULTS: ADEPT yields results that are in most cases visually indistinguishable from manual segmentation and reduces strides segmentation time radically. The average absolute deviation of estimated stride duration across study participants was 4.74, 1.42, 1.28 and 1.31 percent, for wrist, hip and both ankles respectively. CONCLUSIONS: : Our results indicate that the errors are small relative to the signal for all body locations suggesting that ADEPT is a robust and universal tool for segmentation of strides in accelerometry data.