gebhart/patrepeval huggingface dataset:
A Digital 1.6 pJ/bit Chip Identification Circuit Using Process Variations (2008)

A 128-bit, 1.6 pJ/bit, 96% stable chip ID generation circuit utilizing process variations is designed in a 0.13 mum CMOS process. The circuit consumes 162 nW from a 1 V supply at low readout frequencies and 1.6 muW at 1 Mb/s. Cross-coupled logic gates were employed to simultaneously generate, amplify, and digitize the random circuit offset to create a stable unique digital chip ID code. A thorough statistical analysis is presented in order to explore the ID circuit reliability and stability. Two ID generators with different layout techniques were designed and fabricated to provide a performance comparison of power consumption, ID stability, and ID statistical robustness.
Rapid and Sensitive Fingerprinting of Wine Proteins by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (MALDI-TOF) Mass Spectrometry (1998)

To obtain fast and accurate protein and peptide fingerprints, eight wines were analyzed by both matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) and surface enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF). Most of the major proteins detected were common to all wines analyzed. The major protein had a mass of 21.3 kDa. Other significant peaks were observed with masses of 7.2, 9.1, 13.1, and 22.2 kDa. A broad peak centered at 16.6 to 16.8 kDa was variable in intensity among vintages and cultivars. The greatest variation was seen in the peptide region: the two Chardonnay wines contained less peptide material than Sauvignon blanc or Muscat of Alexandria wines. In SELDI-TOF iminodiacetate chelated copper ions were used to selectively bind proteins and peptides from wine. This effectively concentrated minor components in wine, permitting detection. On the other hand, several other, more abundant proteins did not interact with the immobilized copper ion functional group, suggesting different surface chemistries. A heat-generated haze from a commercially produced Sauvignon blanc wine was also evaluated. MALDI-TOF analyses revealed an enrichment of the 16.6 kDa material, but with very little 21.3 kDa, present in the haze. Both MALDI-TOF and SELDI-TOF are excellent tools for analysis of wine proteins and haze.
Global analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants (2013)

Cys2-His2 zinc finger proteins (ZFPs) are the largest group of transcription factors in higher metazoans. A complete characterization of these ZFPs and their associated target sequences is pivotal to fully annotate transcriptional regulatory networks in metazoan genomes. As a first step in this process, we have characterized the DNA-binding specificities of 129 zinc finger sets from Drosophila using a bacterial one-hybrid system. This data set contains the DNA-binding specificities for at least one encoded ZFP from 70 unique genes and 23 alternate splice isoforms representing the largest set of characterized ZFPs from any organism described to date. These recognition motifs can be used to predict genomic binding sites for these factors within the fruit fly genome. Subsets of fingers from these ZFPs were characterized to define their orientation and register on their recognition sequences, thereby allowing us to define the recognition diversity within this finger set. We find that the characterized fingers can specify 47 of the 64 possible DNA triplets. To confirm the utility of our finger recognition models, we employed subsets of Drosophila fingers in combination with an existing archive of artificial zinc finger modules to create ZFPs with novel DNA-binding specificity. These hybrids of natural and artificial fingers can be used to create functional zinc finger nucleases for editing vertebrate genomes.
Multilayers on Solid Planar Substrates: From Structure to Function (2002)

This chapter contains sections titled: Introduction Formation and Structure of LbL Multilayers Adsorption Kinetics of Polyelectrolytes LbL Multilayer Formation ζ-potential Effect of Polymer Charge Influence of Ionic Strength Permeability of Polyelectrolyte Multilayer Internal Structure Implementing Metallosupramolecular Devices in Thin Layered Films Introduction Metallosupramolecular Coordination Polyelectrolytes Polyoxometalate Clusters
Enzymatic Degradation of Phenazines Can Generate Energy and Protect Sensitive Organisms from Toxicity (2015)

Phenazine production by Pseudomonas spp. can shape microbial communities in a variety of environments ranging from the cystic fibrosis lung to the rhizosphere of dryland crops. For example, in the rhizosphere, phenazines can protect plants from infection by pathogenic fungi. The redox activity of phenazines underpins their antibiotic activity, as well as providing pseudomonads with important physiological benefits. Our discovery that soil mycobacteria can catabolize phenazines and thereby protect other organisms against phenazine toxicity suggests that phenazine degradation may influence turnover in situ. The identification of genes involved in the degradation of phenazines opens the door to monitoring turnover in diverse environments, an essential process to consider when one is attempting to understand or control communities influenced by phenazines.
Pitfalls in establishing the diagnosis of deep venous thrombophlebitis by indium-111 platelet scintigraphy. (1988)

Forty-seven 111In-platelet scintigraphs (In-PS) were analyzed retrospectively to identify sources of diagnostic error and to optimize the diagnostic criteria for active deep venous thrombophlebitis (DVT). The results of In-PS were compared with contrast venography, additional diagnostic studies, and clinical outcome. Three patterns of platelet localization emerged as the best predictors of active DVT: (a) focal or (b) linear 4-hr localization, or (c) an asymmetric blood-pool pattern on 4-hr imaging that evolved into a focal or linear pattern by 16 to 24 hr. All false-positive studies had abnormal patterns confined to the inguinal region at 24 hr. All patients with false-negative studies had received heparin between 4 and 24 hr. The potential pitfalls encountered in the evaluation of the iliac, femoral, and popliteal veins are reviewed and the importance of delayed imaging in selected cases is emphasized.
A randomized double-blind controlled study on the efficacy of laser zona pellucida thinning on live birth rates in cases of advanced female age (2006)

The present study indicates that AH does not improve IVF-embryo transfer outcome in women aged > or =37 years.
Radiofrequency Catheter Modification of the Sinus Node for “Inappropriate” Sinus Tachycardia (1995)

Sinus node modification is feasible in humans and should be considered as an alternative to complete atrioventricular junctional ablation for patients with disabling inappropriate sinus tachycardia refractory to medical management. Sinus node modification may be aided by ICE.
Asymmetric Numb distribution is critical for asymmetric cell division of mouse cerebral cortical stem cells and neuroblasts (2002)

Stem cells and neuroblasts derived from mouse embryos undergo repeated asymmetric cell divisions, generating neural lineage trees similar to those of invertebrates. In Drosophila, unequal distribution of Numb protein during mitosis produces asymmetric cell divisions and consequently diverse neural cell fates. We investigated whether a mouse homologue m-numb had a similar role during mouse cortical development. Progenitor cells isolated from the embryonic mouse cortex were followed as they underwent their next cell division in vitro. Numb distribution was predominantly asymmetric during asymmetric cell divisions yielding a beta-tubulin III(-) progenitor and a beta-tubulin III(+) neuronal cell (P/N divisions) and predominantly symmetric during divisions producing two neurons (N/N divisions). Cells from the numb knockout mouse underwent significantly fewer asymmetric P/N divisions compared to wild type, indicating a causal role for Numb. When progenitor cells derived from early (E10) cortex undergo P/N divisions, both daughters express the progenitor marker Nestin, indicating their immature state, and Numb segregates into the P or N daughter with similar frequency. In contrast, when progenitor cells derived from later E13 cortex (during active neurogenesis in vivo) undergo P/N divisions they produce a Nestin(+) progenitor and a Nestin(-) neuronal daughter, and Numb segregates preferentially into the neuronal daughter. Thus during mouse cortical neurogenesis, as in Drosophila neurogenesis, asymmetric segregation of Numb could inhibit Notch activity in one daughter to induce neuronal differentiation. At terminal divisions generating two neurons, Numb was symmetrically distributed in approximately 80% of pairs and asymmetrically in 20%. We found a significant association between Numb distribution and morphology: most sisters of neuron pairs with symmetric Numb were similar and most with asymmetric Numb were different. Developing cortical neurons with Numb had longer processes than those without. Numb is expressed by neuroblasts and stem cells and can be asymmetrically segregated by both. These data indicate Numb has an important role in generating asymmetric cell divisions and diverse cell fates during mouse cortical development.
The Acyltransferase GPAT5 Is Required for the Synthesis of Suberin in Seed Coat and Root of Arabidopsis (2007)

Suberin and cutin are fatty acid- and glycerol-based plant polymers that act as pathogen barriers and function in the control of water and solute transport. However, despite important physiological roles, their biosynthetic pathways, including the acyl transfer reactions, remain hypothetical. We report the characterization of two suberin mutants (gpat5-1 and gpat5-2) of Arabidopsis thaliana GPAT5, encoding a protein with acyl-CoA:glycerol-3-phosphate acyltransferase activity. RT-PCR and beta-glucuronidase-promoter fusion analyses demonstrated GPAT5 expression in seed coat, root, hypocotyl, and anther. The gpat5 plants showed a 50% decrease in aliphatic suberin in young roots and produced seed coats with a severalfold reduction in very long chain dicarboxylic acid and omega-hydroxy fatty acids typical of suberin but no change in the composition or content of membrane or storage glycerolipids or surface waxes. Consistent with their altered suberin, seed coats of gpat5 mutants had a steep increase in permeability to tetrazolium salts compared with wild-type seed coats. Furthermore, the germination rate of gpat5 seeds under high salt was reduced, and gpat5 seedlings had lower tolerance to salt stress. These results provide evidence for a critical role of GPAT5 in polyester biogenesis in seed coats and roots and for the importance of lipid polymer structures in the normal function of these organs.
Nanosecond pulsed electric field effects on human cells (2003)

Electric fields have been used on intact cells for decades, most notably for effects on plasma membranes for cell fusion and transient electroporation to allow the entry of xenomolecules. Compared to electroporation pulses, new pulse power technology generates non-thermal pulses with shorter durations and higher electric fields (nsPEF) such that the charging time of the plasma membrane is not reached, but subcellular membranes and intracellular functions are affected independent of heating. Here we investigated nsPEF-induced programmed cell death (apoptosis) in intact human cells with pulse durations between 10-300 nanoseconds over a range of electric field intensities and energy densities. nsPEF effects are observed on the plasma membrane integrity and caspase activation using fluorescent markers, flow cytometry, biochemical assays. The results indicate that once a critical electric field intensity threshold is reached, nsPEF-induced apoptosis is dependent on the pulse duration and is independent of the electric field intensity. Relatively long pulses (300 ns), which have greater plasma membrane effects and lesser intracellular effects, recruit apoptosis mechanisms that rapidly advance through apoptosis to loss of membrane integrity in minutes. Shorter pulses (10 ns), which have greater intracellular effects and lesser plasma membrane effects, induce apoptosis, but require longer times (tens of minutes to hours). We conclude that nsPEF-induced apoptosis does not require plasma membrane effects related to electroporation. nsPEF affect a continuum of cellular mechanisms from the plasma membrane to intracellular targets. Longer pulses recruit multiple and perhaps synergistic pathways while shorter pulses recruit more time-dependent pathways. These studies promote a better understand of the effects of nsPEF on basic functions during cellular responses to intrinsic and extrinsic stresses and suggest the potential for nsPEF applications for therapeutic purposes.
Functional evidence for an extracellular calcium receptor mechanism triggering tyrosine kinase activation associated with mouse keratinocyte differentiation. (1994)

Calcium-induced keratinocyte differentiation is associated with tyrosine phosphorylation of a p62 protein which associates with the ras-GTPase activating protein (GAP). We have examined the nature of the calcium signal triggering p62 phosphorylation. EGTA, a specific chelator of calcium, was able to completely block calcium-induced p62 phosphorylation, even after using conditioned medium from calcium-treated keratinocytes. Preventing calcium-induced cell-cell contacts by anti-cadherin antibodies did not inhibit tyrosine phosphorylation. Slight increases in extracellular calcium concentrations (0.15 or 0.30 mM) were already sufficient to induce p62 phosphorylation. Other divalent cations, such as magnesium, zinc, nickel, and cobalt, but not the trivalent cation lanthanum, induced p62 phosphorylation to a similar extent as calcium. There was no close correlation between the ability of the various ions to induce p62 phosphorylation and increase free intracellular calcium. Similarly, treatment of primary keratinocytes with the calcium ionophores A23187 or X537A did not induce p62 phosphorylation, although it increased free intracellular calcium levels. Finally, blockers of potassium uptake, which is induced by calcium, did not inhibit p62 phosphorylation. Thus, in keratinocyte differentiation, calcium is likely to provide the primary signal for p62 tyrosine phosphorylation and may act directly at the cell membrane through a "cationic receptor mechanism" analogous to that described in other cell types.
Donor Islet Endothelial Cells Participate in Formation of Functional Vessels Within Pancreatic Islet Grafts (2005)

Pancreatic islet transplantation has emerged as a therapy for type 1 diabetes and is today performed using both freshly isolated and cultured islets. Islet blood vessels are disrupted during islet isolation; therefore, proper revascularization of the transplanted islets is of great importance for islet graft function and survival. We have studied intraislet endothelial cells after islet isolation, during islet culture, and following islet transplantation. By isolating islets from the transgenic Tie2-GFP (green fluorescent protein) mouse, characterized by an endothelial cell-specific expression of GFP, living endothelial cells could be studied in intact islets utilizing two-photon laser-scanning microscopy (TPLSM). Intraislet endothelial cells were found to survive islet transplantation but to rapidly disappear during islet culture. By transplanting freshly isolated Tie2-GFP islets and applying a novel ex vivo model for simultaneous perfusion and TPLSM imaging of the graft-bearing kidneys, GFP fluorescent endothelial cells were found to extensively contribute to vessels within the islet graft vasculature. Real-time imaging of the flow through the islet graft vasculature confirmed that the donor-derived vessels were functionally integrated. Hence, intraislet endothelial cells have the capability of participating in revascularization of pancreatic islets subsequent to transplantation. Therefore, preservation of intraislet endothelial cell mass may improve long-term graft function.
Diets high in resistant starch and arabinoxylan modulate digestion processes and SCFA pool size in the large intestine and faecal microbial composition in pigs (2014)

The effects of a high level of dietary fibre (DF) either as arabinoxylan (AX) or resistant starch (RS) on digestion processes, SCFA concentration and pool size in various intestinal segments and on the microbial composition in the faeces were studied in a model experiment with pigs. A total of thirty female pigs (body weight 63.1 (sem 4.4) kg) were fed a low-DF, high-fat Western-style control diet (WSD), an AX-rich diet (AXD) or a RS-rich diet (RSD) for 3 weeks. Diet significantly affected the digestibility of DM, protein, fat, NSP and NSP components, and the arabinose:xylose ratio, as well as the disappearance of NSP and AX in the large intestine. RS was mainly digested in the caecum. AX was digested at a slower rate than RS. The digesta from AXD-fed pigs passed from the ileum to the distal colon more than twice as fast as those from WSD-fed pigs, with those from RSD-fed pigs being intermediate (P< 0.001). AXD feeding resulted in a higher number of Faecalibacterium prausnitzii, Roseburia intestinalis, Blautia coccoides-Eubacterium rectale, Bifidobacterium spp. and Lactobacillus spp. in the faeces sampled at week 3 of the experimental period (P< 0.05). In the caecum, proximal and mid colon, AXD feeding resulted in a 3- to 5-fold higher pool size of butyrate compared with WSD feeding, with the RSD being intermediate (P <0.001). In conclusion, the RSD and AXD differently affected digestion processes compared with the WSD, and the AXD most efficiently shifted the microbial composition towards butyrogenic species in the faeces and increased the large-intestinal butyrate pool size.
Use of Epidemiologic Methods in Studying Diseases Caused by Toxic Chemicals (1993)

Epidemiologic methods are primarily used for the study of the determinants and occurrence of human illnesses. They have also been applied widely for the discovery of etiologic agents. Because we did not implemented a system of hazard communication e.q. material safety data sheet (MSDS) in Taiwan before 1991, it has been relatively difficult for clinicians to recognize diseases caused by toxic chemicals. By carefully falsifying alternative hypotheses, we have documented 10 kinds of diseases caused by industrial toxic chemicals during 1 983-1992 through the application of epidemiologic methods, which can be considered as a game of conjectures and refutations. We shall share this experience on the documentation of bipyridyl and its isomers as the cause of occupational skin cancer. Epidemiologic methods can also be used to set up early diagnostic criteria and to quantitatively assess the health risk of potential hazards. We have recently found 31 cases (48% of all examined workers) of lead poisoning in a lead recycling factory, and found both an increased lead absorption and a decreased intelligence quotient (IQ) of kindergarten children nearby the factory. Their blood leads decreased and IQ improved significantly after being moved 2 kilometers away from the factory for 2.5 years. These two examples illustrate how the epidemiologic methods can be used on the study and prevention of diseases caused by toxic chemicals.
Machine Learning of Three-dimensional Right Ventricular Motion Enables Outcome Prediction in Pulmonary Hypertension: A Cardiac MR Imaging Study (2017)

Purpose To determine if patient survival and mechanisms of right ventricular failure in pulmonary hypertension could be predicted by using supervised machine learning of three-dimensional patterns of systolic cardiac motion. Materials and Methods The study was approved by a research ethics committee, and participants gave written informed consent. Two hundred fifty-six patients (143 women; mean age ± standard deviation, 63 years ± 17) with newly diagnosed pulmonary hypertension underwent cardiac magnetic resonance (MR) imaging, right-sided heart catheterization, and 6-minute walk testing with a median follow-up of 4.0 years. Semiautomated segmentation of short-axis cine images was used to create a three-dimensional model of right ventricular motion. Supervised principal components analysis was used to identify patterns of systolic motion that were most strongly predictive of survival. Survival prediction was assessed by using difference in median survival time and area under the curve with time-dependent receiver operating characteristic analysis for 1-year survival. Results At the end of follow-up, 36% of patients (93 of 256) died, and one underwent lung transplantation. Poor outcome was predicted by a loss of effective contraction in the septum and free wall, coupled with reduced basal longitudinal motion. When added to conventional imaging and hemodynamic, functional, and clinical markers, three-dimensional cardiac motion improved survival prediction (area under the receiver operating characteristic curve, 0.73 vs 0.60, respectively; P < .001) and provided greater differentiation according to difference in median survival time between high- and low-risk groups (13.8 vs 10.7 years, respectively; P < .001). Conclusion A machine-learning survival model that uses three-dimensional cardiac motion predicts outcome independent of conventional risk factors in patients with newly diagnosed pulmonary hypertension. Online supplemental material is available for this article.
A Flexible Tool for Model Building: the Relevant Transformation of the Inputs Network Approach (RETINA)* (2003)

Abstract A new method, called Relevant Transformation of the Inputs Network Approach is proposed as a tool for model building. It is designed around flexibility (with nonlinear transformations of the predictors of interest), selective search within the range of possible models, out‐of‐sample forecasting ability and computational simplicity. In tests on simulated data, it shows both a high rate of successful retrieval of the data generating process, which increases with the sample size and a good performance relative to other alternative procedures. A telephone service demand model is built to show how the procedure applies on real data.
A study of field emission microtriodes (1991)

Structures simulating integrated field emission microtriodes have been successfully fabricated and tested. These microtriodes use Spindt-type molybdenum field emission cathodes with the anodes in three different configurations. The anodes are located at a distance d>5 mm, approximately 1.25 mm, and approximately 2-20 mu m from the gate electrode and the emitter tip. The effects of device operation on the performance of the Mo field emission tips operating in close proximity to anodes were presented. A transconductance of 0.5 mS (5 mu S/tip or 12 S/cm/sup 2/) and a cutoff frequency of 0.8 MHz have been measured. Extension of these results indicates that transconductances of 250 mS/mm and cutoff frequencies of 100 GHz may be possible.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>