gebhart/patrepeval huggingface dataset:
A modular data analysis pipeline for the discovery of novel RNA motifs (2006)

This dissertation presents a modular software pipeline that searches collections of RNA sequences for novel RNA motifs. In this case the motifs incorporate elements of primary and secondary structure. The motif search pipeline breaks up sets of RNA sequences into shortened segments of RNA primary sequence. The shortened segments are then folded to obtain low energy secondary structures. The distance estimation module of the pipeline then calculates distances between the folded bricks, and then analyzes the resulting distance matrices for patterns. 
An initial implementation of the pipeline is applied to synthetic and biological data sets. This implementation introduces a new distance measure for comparing RNA sequences based on structural annotation of the folded sequence as well as a new data analysis technique called non-linear projection. The modular nature of the pipeline is then used to explore the relationships between several different distance measures on random data, synthetic data, and a biological data set consisting of iron response elements. It is shown that the different distance measures capture different relationships between the RNA sequences. The non-linear projection algorithm is used to produce 2-dimensional projections of the distance matrices which are examined via inspection and k-means multiclustering. The pipeline is able to successfully cluster synthetic RNA sequences based only on primary sequence data as well as the iron response elements data set. The dissertation also presents a preliminary analysis of a large biological data set of HIV sequences.
A 16-channel low-noise programmable system for the recording of neural signals (2011)

The current migration from passive to active neuroprobes, the increasing density in multielectrode arrays, as well as the introduction of new materials and processes for electrode fabrication, are imposing important challenges on the implementation of optimal integrated neural recording systems. In this paper, we present the design and implementation of an integrated neural acquisition system with 16 fully-differential input channels with individual channel programmability for the recording of neural activity in in vitro and in vivo experiments. Each channel consists of ac-coupled low-power, low-noise programmable amplification (from 100 to 6000 V/V) and programmable band-pass filtering, achieving 37nV/√Hz input-referred noise density while consuming a maximum of 70 µA per channel from a single 3.3V. The ASIC was implemented in a 0.35 µm CMOS technology and has a total area of 5.6 × 4.5 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . The system has been successfully tested in in vitro experiments, achieving simultaneous extracellular recordings of action potentials and showing satisfactory signal-to-noise ratios.
Time-frequency hop codes based upon extended quadratic congruences (1988)

Time-frequency hop codes are developed that can be used for coherent multiuser echolocation and asynchronous spread spectrum communication systems. They represent a compromise between Costas codes, which have nearly ideal autoambiguity but not so good cross-ambiguity properties, and linear congruential codes, which have nearly ideal cross-ambiguity but unattractive autoambiguity properties. Extended quadratic congruential code words are shown to have reasonably good autoambiguity and cross-ambiguity properties across the whole class of code sets considered. A uniform upper bound is placed on the entire cross-ambiguity function surface, and bounds are placed on the position and amplitude of spurious peaks in the autoambiguity function. These bounds depend on the time/bandwidth product and code length exclusively and lead naturally to a discussion of the design tradeoffs for these two parameters. Examples of typical autoambiguity and cross-ambiguity functions are given to illustrate the performance of the new codes.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Concomitant ventilatory and circulatory functions of the diaphragm and abdominal muscles (2010)

Expulsive maneuvers (EMs) caused by simultaneous contraction of diaphragm and abdominal muscles shift substantial quantities of blood from the splanchnic circulation to the extremities. This suggests that the diaphragm assisted by abdominal muscles might accomplish ventilation and circulation simultaneously by repeated EMs. We tested this hypothesis in normal subjects by measuring changes (Δ) in body volume (Vb) by whole body plethysmography simultaneously with changes in trunk volume (Vtr) by optoelectronic plethysmography, which measures the same parameters as whole body plethysmography plus the volume of blood shifts (Vbs) between trunk and extremities: Vbs = ΔVtr-ΔVb. We also measured abdominal pressure, pleural pressure, the arterial pressure wave, and cardiac output (Qc). EMs with abdominal pressure ~100 cmH(2)O for 1 s, followed by 2-s relaxations, repeated over 90 s, produced a "stroke volume" from the splanchnic bed of 0.35 ± 0.07 (SD) liter, an output of 6.84 ± 0.75 l/min compared with a resting Qc of 5.59 ± 1.14 l/min. Refilling during relaxation was complete, and the splanchnic bed did not progressively empty. Diastolic pressure increased by 25 mmHg during each EM. Between EMs, Qc increased to 7.09 ± 1.14 l/min due to increased stroke volume and heart rate. The circulatory function of the diaphragm assisted by simultaneous contractions of abdominal muscles with appropriate pressure and duration at 20 min(-1) can produce a circulatory output as great as resting Qc, as well as ventilation. These combined functions of the diaphragm have potential for cardiopulmonary resuscitation. The abdominal circulatory pump can act as an auxiliary heart.
A linear space of admittance control laws that guarantees force-assembly with friction (1997)

Force-assembly has been defined as an assembly process for which the use of a single, properly designed, admittance control law will guarantee the proper assembly of a given pair of mating parts. In previous work in workpart-into-fixture insertion, the conditions on a manipulators accommodation control law that ensure proper insertion despite infinitesimal positional error and finite (but bounded) friction have been identified. Through the use of an optimization routine, a control law that satisfies these force-assembly conditions at or below a friction maximum value can be obtained. This single control law, however, is not unique-there exists many other control laws that will satisfy the conditions of force-assembly at the same value of friction. This paper addresses the identification and construction of a linear space of accommodation control law parameters that ensure force-assembly with friction. First, linear sufficient conditions that ensure force-assembly with friction are identified. These linear sufficient conditions are then modified to separate the N/sup 2/+N dimensional space of accommodation control law parameters into N+1 different N-dimensional subspaces. A means of efficiently generating basis nominal velocity vectors and basis accommodation matrices is presented. A nominal velocity selected using any positive linear combination of the nominal velocity basis vectors and an accommodation matrix selected using any positive linear combination of the accommodation basis matrices will guarantee force-assembly (for any value of friction less than that used in generating the basis matrices). A planar example of the construction of each accommodation control law subspace is presented and illustrated in the geometry of the fixturing task.
Identification of an oncogenic RAB protein (2015)

In a short hairpin RNA screen for genes that affect AKT phosphorylation, we identified the RAB35 small guanosine triphosphatase (GTPase)-a protein previously implicated in endomembrane trafficking-as a regulator of the phosphatidylinositol 3'-OH kinase (PI3K) pathway. Depletion of RAB35 suppresses AKT phosphorylation in response to growth factors, whereas expression of a dominant active GTPase-deficient mutant of RAB35 constitutively activates the PI3K/AKT pathway. RAB35 functions downstream of growth factor receptors and upstream of PDK1 and mTORC2 and copurifies with PI3K in immunoprecipitation assays. Two somatic RAB35 mutations found in human tumors generate alleles that constitutively activate PI3K/AKT signaling, suppress apoptosis, and transform cells in a PI3K-dependent manner. Furthermore, oncogenic RAB35 is sufficient to drive platelet-derived growth factor receptor α to LAMP2-positive endomembranes in the absence of ligand, suggesting that there may be latent oncogenic potential in dysregulated endomembrane trafficking.
Measurement of Spurious Voltages in ZnO Piezoelectric Nanogenerators (2016)

The recent development and commercialization of microelectromechanical systems (MEMS)/nanoelectromechanical systems (NEMS) has brought the related challenge of independently powering such systems. The concept of the nanogenerator (NG) has shown potential for harvesting energy from the ambient environment to power MEMS/NEMS. Kinetic energy harvesting NGs based on the piezoelectric properties of ZnO nanowires have attracted much interest. In this paper, we have fabricated hydrothermally synthesized ZnO-based NGs following the procedures standardized in the published literature. Likewise, reference NGs without ZnO piezoelectric material were fabricated in parallel with the ZnO NGs. The voltage output of both the ZnO NG and the reference NG was measured given a 10-Hz cyclic vertical load. Unexpectedly, both the ZnO and the reference NG were found to produce 3 mV with 0.451 N of load. A finite-element model was created to determine that the voltage potential of the NG should be about 1 mV with the given load. A possible explanation for this unexpected behavior is that the measured signals are not entirely piezoelectric in nature. Rather, the signals recorded from the NGs may be some alternate phenomenon, such as the triboelectric, flexoelectric, or electret effect.
Characterization of Interaction between Fe‐Infiltrates and LSM Backbone in Solid Oxide Fuel Cells (2018)

In this paper, detailed materials characterization analyses on the interaction between FeO x nanoparticles infiltrated onto a La 0.8 Sr 0.2 MnO 3 (LSM) backbone cathode in a solid oxide fuel cell (SOFC) are reported. The infiltration process leads to an increase of 3.4% in cell performance. X‐ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM), transmission electron microscopy (TEM) as well as energy dispersive X‐ray spectroscopy (EDS) and electron energy loss spectroscopy (EELS) are utilized to perform a comprehensive examination of the microstructure and chemical properties at the interface of the infiltrate and backbone materials. Mn from the LSM backbone diffuses into the FeO x infiltrate and forms a Fe‐Mn‐O spinel. A small amount of Fe also diffuses into the LSM backbone, which could partially be responsible for the enhanced performance of the cell. The valence state of Mn increases from the surface of the Fe‐Mn‐O particle into bulk LSM, with the highest value being at the interface of the Fe‐Mn‐O/LSM backbone. Possible mechanisms are discussed for the change in Mn valence state within the LSM phase. Trace amounts of Mn and La are found in the YSZ phase, as a result of interdiffusion between LSM and YSZ.
ChemInform Abstract: Reductions with Lithium in Low Molecular Weight Amines and Ethylenediamine. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Pragmatic Pertinence: A Learnable Confidence Metric to Assess the Subjective Quality of LM-Generated Text (2023)

To be perceived as trustworthy, artificially generated text must be sufficiently congruent with the available discourse history.Pre-trained language models (LMs) operating in generative mode are capable of predicting locally coherent phrases, but those do not always reflect salient syntactic, semantic, or pragmatic facets of prior content.This paper introduces a learnable evaluation metric to assess the pragmatic pertinence of LM-generated text for a given history.Pertinence is closely aligned with qualitative human judgments of acceptability, thereby emerging as a blend of sensibleness and specificity.Experiments conducted across different domains using different learning architectures show that this approach circumvents the issue of multiple valid ground-truths, while providing a reliable quantitative ranking of generated text completion candidates in context.Pertinence scoring could thus prove useful for the detection of hallucinations.
56Gb/s ring modulator on a 300mm silicon photonics platform (2015)

We present a compact low-voltage high-speed silicon ring modulator fabricated in a 300mm CMOS platform. 56Gb/s modulation is demonstrated with 4dB dynamic extinction ratio using 2.5Vpp drive swing.
Using a Random Forest to Inspire a Neural Network and Improving on It (2017)

Neural networks have become very popular in recent years because of the astonishing success of deep learning in various domains such as image and speech recognition. In many of these domains, specific architectures of neural networks, such as convolutional networks, seem to fit the particular structure of the problem domain very well, and can therefore perform in an astonishingly effective way. However, the success of neural networks is not universal across all domains. Indeed, for learning problems without any special structure, or in cases where the data is somewhat limited, neural networks are known not to perform well with respect to traditional machine learning methods such as random forests. In this paper, we show that a carefully designed neural network with random forest structure can have better generalization ability. In fact, this architecture is more powerful than random forests, because the back-propagation algorithm reduces to a more powerful and generalized way of constructing a decision tree. Furthermore, the approach is efficient to train and requires a small constant factor of the number of training examples. This efficiency allows the training of multiple neural networks in order to improve the generalization accuracy. Experimental results on 10 real-world benchmark datasets demonstrate the effectiveness of the proposed enhancements.
Millimeter-Wave GaN HEMTs With Cavity-Gate Structure Using MSQ-Based Inter-Layer Dielectric (2016)

We have fabricated millimeter-wave gallium nitride high electron mobility transistors (GaN HEMTs) using methyl silsesquioxane (MSQ)-based inter-layer dielectric to suppress current collapse by enhancing the moisture resistance, and removed MSQ around the gate electrode for reducing parasitic capacitance. We clarified that the moisture resistance of conventional benzocyclobutene (BCB) is insufficient to suppress current collapse because water molecules easily permeate BCB, especially when using a cavity-gate structure. On the other hand, the moisture resistance of MSQ is very high because of the excellent hydrophobic property, and the current collapse due to moisture was effectively suppressed. So, improving the moisture resistance with hydrophobic low-k films plays a key role in reducing the current collapse of GaN HEMTs, especially when using a cavity-gate structure. Moreover, the parasitic capacitance of GaN HEMTs was successfully reduced by using the MSQ-cavity, and RF performance was improved by around 20%.
Orientation of Membrane Vesicles from Escherichia coli as Detected by Freeze-Cleave Electron Microscopy (1974)

The application of freeze-cleave electron microscopy to whole cells of Escherichia coli revealed that the particles exposed on the resulting two inner membrane faces are asymmetrically distributed. This method can therefore be used to determine the orientation of membrane vesicles from E. coli. Membrane vesicles freshly prepared in potassium phosphate buffer (K(+)-vesicles) by osmotic lysis of spheroplasts consisted almost entirely of right-side-out vesicles. Their size suggested that each cell gives rise to one vesicle. When the membrane vesicles were subjected to one cycle of freezing and thawing, the number of inside-out vesicles rose to about 25%. However, due to the small size of most of the inside-out vesicles, these contribute only 2 to 3% of the total membrane surface area of the preparation. The inside-out vesicles appear to arise from infoldings of the membrane of right-side-out vesicles. They also accumulate within the latter, thus producing multivesicular membrane sacs. Na(+)-vesicles (vesicles prepared in sodium phosphate buffer) subjected to freezing and thawing appeared to lose structural rigidity more than did K(+)-vesicles. In contrast to the membrane vesicles prepared by the osmotic lysis of spheroplasts, those obtained by breaking intact cells by a single passage through a French pressure cell were uniformly very small (only 40 to 110 nm in diameter); approximately 60 to 80% were inside-out. To reconcile the polarity of the membrane vesicles with the enzymic activities of such preparations, we propose that "dislocation" of membrane proteins occurs during osmotic lysis of spheroplasts.
Anterolaterale Rotationsinstabilität (2023)

Zusammenfassung Hintergrund Verletzungen des vorderen Kreuzbands (VKB), der Kaplan-Fasern (KF), der anterolateralen Kapsel/des anterolateralen Ligaments (C/ALL) und der posterioren Wurzel des lateralen Meniskus (LMPR) wurden getrennt voneinander mit anterolateraler Instabilität assoziiert. Ziel war es, die Bedeutung dieser Strukturen für die Kniestabilität zu untersuchen. Methoden Zehn fresh-frozen humane Kniekadaver wurden robotergestützt von 0° bis 90° Flexion getestet. Eine anterior-posteriore Kraft von 88 N, ein Innen-Außen-Rotationsdrehmoment von 5 N/m und ein Valgus-Varus-Drehmoment von 8 N/m wurden aufgebracht und die Kinematik des intakten Knies aufgezeichnet. Weitere 10 Kniegelenke wurden in einem Kinematikprüfstand mit optischem Tracking getestet, um die Knielaxität nach sequenziellem Durchtrennen der o. g. Strukturen über 0° bis 110° Flexion zu messen. Ergebnisse Das VKB war der primäre Hemmer für die anteriore tibiale Translation (ATT); andere Strukturen waren unbedeutend (&lt; 10 %). Die KF und C/ALL hemmten die Innenrotation (IR) und erreichten 44 % ± 23 % ( p &lt; 0,01) und 14 % ± 13 % ( p &lt; 0,05) bei 90°. Die LMPR hemmte die Valgus-, aber nicht die Innenrotation. Die ATT erhöhte sich bei VKB-Insuffizienz ( p &lt; 0,001) und nach der Durchtrennung der lateralen Strukturen von 70° auf 100° ( p &lt; 0,05). Die anterolaterale Rotationsinstabilität beim Pivot-Shift-Manöver wurde nach VKB-Durchtrennung von 0° auf 40° ( p &lt; 0,05) und weiter nach Durchtrennung der lateralen Strukturen von 0° auf 100° ( p &lt; 0,01) erhöht. Schlussfolgerung Der anterolaterale Komplex fungiert als funktionelle Einheit und sorgt für Rotationsstabilität. Das VKB ist der primäre Stabilisator für die ATT. Die KF sind der wichtigste Hemmer der IR ab 30° Flexion. Eine kombinierte Verletzung der KF mitsamt der C/ALL erhöhte die anterolaterale Rotationsinstabilität beträchtlich, während eine isolierte Verletzung der KF oder C/ALL dies nicht tat. Eine LMPR-Insuffizienz verursachte keine signifikante Instabilität bei intaktem VKB.
Analysis of a break in chromosome 14 mapping to the region of the immunoglobulin heavy chain locus. (1983)

We have detected restriction fragment length polymorphisms associated with the immunoglobulin heavy chain C gamma genes. DNA from both parents of an individual having an unbalanced rearrangement of the long arm of chromosome 14, region q32 [Cox, D. W., Markovic, V. D. & Teshima, I. E. (1982) Nature (London) 297, 428-430], revealed distinctive patterns of BamHI fragments which hybridized with cloned probes from the C gamma 2-C gamma 4 gene cluster. The number of hybridizing fragments in both cases (five) equaled the number of known C gamma genes. Pedigree and densitometric analyses indicated that the proband did not have any maternal complement of C gamma gene-hybridizing fragments. Included on the deleted chromosomal segment was a C gamma gene having properties of the previously reported C gamma pseudogene. We also examined DNA from this family with a probe for the highly polymorphic locus D14S1, which recently was demonstrated to be tightly linked to the C gamma 1 gene locus [Balazs, I., Purrello, M., Rubinstein, P., Alhadeff, B. & Siniscalco, M. (1982) Proc. Natl. Acad. Sci. USA 79, 7395-7399]. EcoRI and EcoRI-BamHI fragments from both parents hybridized with a probe for this locus in DNA from the proband, indicating that, unlike the C gamma gene family, D14S1 was not deleted from the abnormal chromosome. Thus, the chromosomal breakpoint in the proband lies within region 14q32 between the two tightly linked markers, D14S1 and the C gamma 1 heavy chain gene locus. The D14S1 locus must lie proximal to the centromere relative to the C gamma gene family. The genetic variability detected with C gamma gene probes may prove useful for genetic analysis of structural rearrangements involving this region of chromosome 14.
Effect of ambient temperature on cyclic creep. (1989)

The behavior of a pure copper subject to pure creep and cyclic creep under an imposed load is examined at room temperature, and at 250, 300, 350, 400 and 450°C to show the relation between these two kinds of phenomena. Formulating the cyclic creep behavior using not the cycle number but the real time during deformation, cyclic creep strain as well as creep strain are represented well by the function of stress, stress ratio and the ambient temperature both in the primary and the secondary stages. The examination of temperature dependency on cyclic creep shows the existence of the critical temperature, at which cyclic creep and pure creep with same amount of the maximum stress produce same amount of strain. Then over the critical temperature pure creep governs the material behavior, and under the temperature cyclic creep become prominent.
Effects of granulocyte/macrophage colony-stimulating factor on the development and differentiation of CD5-positive macrophages and their potential derivation from a CD5-positive B-cell lineage in mice. (1998)

In co-cultures of either the murine pre-B cell line J13, fetal liver cells, or adult peritoneal or bone marrow cells with ST2 mouse bone marrow stromal cells in the presence of granulocyte/macrophage colony-stimulating factor (GM-CSF), the development of CD5+ macrophages was demonstrated by immunohistochemical staining and flow cytometry. Although CD5+ macrophages were not present in the peritoneal cavities of normal mice, approximately 30% of the peritoneal macrophages in viable motheaten (mev/mev) mice, deficient in SHP-1 protein tyrosine phosphatase, expressed cell surface CD5 and B220, markers for B cells. In the mev/mev mice, GM-CSF level in peritoneal fluid was increased significantly. At 5 days after daily intravenous injection with GM-CSF, many CD5+ macrophages appeared in the peritoneal cavity and in omental milky spots of normal mice but fewer in osteopetrosis (op) mutant mice, deficient in macrophage (M)-CSF. These results indicate that GM-CSF, in combination with M-CSF, induces the development and differentiation of CD5+ macrophages in the peritoneal cavity, particularly in the omental milky spots of mice. In the peritoneal cavity of GM-CSF-treated mice, the percentages of hematopoietic progenitor cells doubly positive for CD5 and CD34 or c-kit and of macrophage precursor cells doubly positive for CD5 and ER-MP58 or ER-MP20 were increased significantly during the development of CD5+ macrophages and CD5 B cells, suggesting that CD5+ macrophages and B cells may share a bipotential progenitor in vivo.