gebhart/patrepeval huggingface dataset:
Changes in the force development characteristics of muscle following repeated maximum force and power exercise (2005)

There is some evidence to suggest that ability to develop force in skeletal muscle can be improved for a short period following repeated maximal strength exercise. Some studies have suggested the phenomenon known as post-activation potentiation (PAP) to explain this immediate response to such exercise. However, little is known about the physical and temporal characteristics of the changes in muscle function due to PAP when induced using whole-body maximal strength exercise. The purpose of this study was to establish the physical and temporal characteristics of PAP of muscle function in elite male athletes following maximum strength and power exercise. Fifteen participants performed one of repeated maximal strength exercise or maximal power exercise or a control protocol on separate occasions. Changes in maximum isometric voluntary force (iMF), maximum isometric rate of force development (iRFD) and maximum vertical counter-movement jump (CMJ) were assessed. Results suggest that post-activation potentiation of iRFD occurs but is preceded by an initial suppression of force development capability following repeated maximal strength exercise. Following repeated maximal power exercise, however, post-activation potentiation of iRFD occurs immediately but is not seen over as long a period as that observed following maximal strength exercise. These results suggest that post-activation potentiation does bring about increased force development capability following intense exercise and that the temporal profile of the post-activation potentiation changes with intensity of the exercise used to induce it.
Improving CRISPR–Cas specificity with chemical modifications in single-guide RNAs (2017)

CRISPR systems have emerged as transformative tools for altering genomes in living cells with unprecedented ease, inspiring keen interest in increasing their specificity for perfectly matched targets. We have developed a novel approach for improving specificity by incorporating chemical modifications in guide RNAs (gRNAs) at specific sites in their DNA recognition sequence ('guide sequence') and systematically evaluating their on-target and off-target activities in biochemical DNA cleavage assays and cell-based assays. Our results show that a chemical modification (2'-O-methyl-3'-phosphonoacetate, or 'MP') incorporated at select sites in the ribose-phosphate backbone of gRNAs can dramatically reduce off-target cleavage activities while maintaining high on-target performance, as demonstrated in clinically relevant genes. These findings reveal a unique method for enhancing specificity by chemically modifying the guide sequence in gRNAs. Our approach introduces a versatile tool for augmenting the performance of CRISPR systems for research, industrial and therapeutic applications.
Electrical Resistivity of a Composite of Conducting Particles in an Insulating Matrix (1972)

A model rationalizing the curve of resistivity vs volume percent of a metal-powder component in a metal/polymer composite is considered. It shows the conductivity to be directly dependent on the surface area of the conducting particles and also shows a 2/3 power dependence on their volume. Comparison with experimental results shows a good fit.
Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes (2002)

Sequence similarity and profile searching tools were used to analyze the genome sequences of Arabidopsis thaliana, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Caenorhabditis elegans and Drosophila melanogaster for genes encoding three families of histone deacetylase (HDAC) proteins and three families of histone acetyltransferase (HAT) proteins. Plants, animals and fungi were found to have a single member of each of three subfamilies of the GNAT family of HATs, suggesting conservation of these functions. However, major differences were found with respect to sizes of gene families and multi-domain protein structures within other families of HATs and HDACs, indicating substantial evolutionary diversification. Phylogenetic analysis identified a new class of HDACs within the RPD3/HDA1 family that is represented only in plants and animals. A similar analysis of the plant-specific HD2 family of HDACs suggests a duplication event early in dicot evolution, followed by further diversification in the lineage leading to Arabidopsis. Of three major classes of SIR2-type HDACs that are found in animals, fungi have representatives only in one class, whereas plants have representatives only in the other two. Plants possess five CREB-binding protein (CBP)-type HATs compared with one to two in animals and none in fungi. Domain and phylogenetic analyses of the CBP family proteins showed that this family has evolved three distinct types of CBPs in plants. The domain architecture of CBP and TAF(II)250 families of HATs show significant differences between plants and animals, most notably with respect to bromodomain occurrence and their number. Bromodomain-containing proteins in Arabidopsis differ strikingly from animal bromodomain proteins with respect to the numbers of bromodomains and the other types of domains that are present. The substantial diversification of HATs and HDACs that has occurred since the divergence of plants, animals and fungi suggests a surprising degree of evolutionary plasticity and functional diversification in these core chromatin components.
Infrared multiple photon dissociation in the quadrupole ion trap via a multipass optical arrangement (1994)

The design of a novel multipass optical arrangement for use with infrared multiple photon dissociation (IRMPD) in the quadrupole ion trap is presented. This design circumvents previous problems of limited IR laser power, small IR absorption cross sections for many molecules, and the limited ion statistics of trapping and detection of ions for IRMPD in the quadrupole ion trap. In contrast to previous designs that utilized the quadrupole ion store, the quadrupole ion trap was operated in the mass selective instability mode with concurrent resonance ejection. The instrumental design consisted of a modified ring electrode with three spherical concave mirrors mounted on the inner surface of the ring. This modified design allowed for eight laser passes across the radial plane of the ring electrode. IRMPD of protonated bis(2-methoxyethyl)ether (diglyme) was used to characterize the performance of the multipass ring electrode. Two consecutive reactions for the IRMPD of protonated diglyme were observed with a lower energy channel predominant at less than 0.6 J (irradiation times from 1 to 30 ms) and a second channel predominant at energies greater than 0.6 J (irradiation times > 30 ms). Other studies presented include a discussion of the dissociation kinetics of protonated diglyme, the use of a pulsed valve for increased trapping efficiency of parent ion populations, and the effects of laser wavelength and of ion residence time in the radial plane of the ring electrode on photodissociation efficiency.
Self-Refereed On-Chip Jitter Measurement Circuit Using Vernier Oscillators (2005)

Among many recently proposed on-chip jitter measurement designs, Vernier delay line (VDL) is one of the most widely adopted methods that can achieve fine resolution. However, there are two major design challenges: the first is the mismatching of delay buffers; the second is the unavailability of an on-chip jitter free reference signal. To overcome these two challenges, we propose a self-refereed on-chip jitter measurement circuit. This measurement circuit eliminates the requirement to a jitter free reference signal. In addition, it utilizes Vernier oscillators to alleviate the mismatching effect in Vernier lines. Using this design, the jitter distribution and jitter RMS value can be characterized. To validate the design, the circuit has been implemented using IBM 7 HP 0.18um CMOS technology.
Toward leukocyte recognition using morphometry, texture and color (2005)

Although blood cell morphological analysis has been progressively replaced by new technologies, it is often possible and necessary to diagnose some types of leukemia by visual inspection. In order to automate this process, pattern recognition methods are used in the present work for computer-aided diagnosis, considering a variety of morphometric features, expressing size and shape, color and texture, which are combined in order to achieve more accurate results. The large number of measurements implies selection methods to be applied to the identification of the most discriminative subset. This paper describes 62 cell morphological attributes extracted, selected and analyzed using a system under development. We validate our results by using the Weka (Waikato environment knowledge analysis) machine learning algorithms. The obtained results illustrate the importance of feature selection for improving the classification of leukocytes from blood smears.
Handwritten zip code recognition with multilayer networks (2002)

An application of back-propagation networks to handwritten zip code recognition is presented. Minimal preprocessing of the data is required, but the architecture of the network is highly constrained and specifically designed for the task. The input of the network consists of size-normalized images of isolated digits. The performance on zip code digits provided by the US Postal Service is 92% recognition, 1% substitution, and 7% rejects. Structured neural networks can be viewed as statistical methods with structure which bridge the gap between purely statistical and purely structural methods.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A Deacylation Enzyme for Aculeacin A, a Neutral Lipopeptide Antibiotic, from Actinoplanes utahensis: Purification and Characterization (1989)

An enzyme, tentatively termed aculeacin A acylase, useful in preparing deacylated peptides which are used as starting material for semisynthetic antifungal antibiotics, was purified from the culture filtrate of Actinoplanes utahensis NRRL12052. The purification involved ultrafiltration and column chromatographies on DEAE-cellulose, hydroxyapatite, and Butyl-Toyopearl 650M. The purified enzyme was composed of two dissimilar subunits with molecular weights of 55,000 and 19,000. The subunits were dissociated in the presence of 0.1% SDS or 6 M guanidine hydrochloride; the dissociation accompanied loss of acylase activity. The enzyme was fully active at pH 7.0 and at 60 degrees C. Its pI was estimated to be above 10.25. The Km and Vmax for aculeacin A were 1.53 mM and 39.7 mumol/min/mg-protein, respectively.
The protein product of the oncogene bcl-2 is a component of the nuclear envelope, the endoplasmic reticulum, and the outer mitochondrial membrane. (1994)

The protein product of the oncogene bcl-2 is a potent inhibitor of apoptotic cell death. The Bcl-2 protein has variously been reported to reside in the nuclear envelope and endoplasmic reticulum or exclusively in the inner membrane of mitochondria. We therefore undertook a detailed analysis of the intracellular distribution of Bcl-2 by immunofluorescence, immunogold electron microscopy, and subcellular fractionation in three mouse cell lines expressing a human bcl-2 transgene and measured its importation into isolated mitochondria. By these methods, the protein was localized to the nuclear envelope, the endoplasmic reticulum, and the outer mitochondrial membrane. Any proposal for the mechanism by which Bcl-2 inhibits apoptosis must therefore accommodate the fact that Bcl-2 localizes to cytoplasmic membranes facing the cytosol.
A frequency diversity spread spectrum system for communication in the presence of in-band interference (1995)

Protection against in-band interference is required in antijam systems and when low level spread spectrum signals are overlaid on top of existing narrow-band users. We propose a secure spread-spectrum system whose optimum receiver is easy to build. We use frequency diversity which allows the receiver to distinguish unjammed signal replicas from their jammed versions. The system can also resist bandlimited partial-time jamming. The only choice left to a wise jammer to maximize our error probability is to spread his signal like ours. We derive the optimum receiver which jointly performs symbol detection and interference rejection. Side information, needed by this receiver, can easily be estimated. However, if the interference bandwidth is narrow enough compared to the signal bandwidth, side information is not needed by a simpler and near-optimum receiver. The bit error probability is evaluated for QPSK modulation and compared with that of direct sequence spread-spectrum.
Bioinspired Materials for Controlling Stem Cell Fate (2009)

Although researchers currently have limited ability to mimic the natural stem cell microenvironment, recent work at the interface of stem biology and biomaterials science has demonstrated that control over stem cell behavior with artificial microenvironments is quite advanced. Embryonic and adult stem cells are potentially useful platforms for tissue regeneration, cell-based therapeutics, and disease-in-a-dish models for drug screening. The major challenge in this field is to reliably control stem cell behavior outside the body. Common biological control schemes often ignore physicochemical parameters that materials scientists and engineers commonly manipulate, such as substrate topography and mechanical and rheological properties. However, with appropriate attention to these parameters, researchers have designed novel synthetic microenvironments to control stem cell behavior in rather unnatural ways. In this Account, we review synthetic microenvironments that aim to overcome the limitations of natural niches rather than to mimic them. A biomimetic stem cell control strategy is often limited by an incomplete understanding of the complex signaling pathways that drive stem cell behavior from early embryogenesis to late adulthood. The stem cell extracellular environment presents a miscellany of competing biological signals that keep the cell in a state of unstable equilibrium. Using synthetic polymers, researchers have designed synthetic microenvironments with an uncluttered array of cell signals, both specific and nonspecific, that are motivated by rather than modeled after biology. These have proven useful in maintaining cell potency, studying asymmetric cell division, and controlling cellular differentiation. We discuss recent research that highlights important biomaterials properties for controlling stem cell behavior, as well as advanced processes for selecting those materials, such as combinatorial and high-throughput screening. Much of this work has utilized micro- and nanoscale fabrication tools for controlling material properties and generating diversity in both two and three dimensions. Because of their ease of synthesis and similarity to biological soft matter, hydrogels have become a biomaterial of choice for generating 3D microenvironments. In presenting these efforts within the framework of synthetic biology, we anticipate that future researchers may exploit synthetic polymers to create microenvironments that control stem cell behavior in clinically relevant ways.
α, β-DIAMINOBUTYRIC ACID OBTAINED FROM ASPARTOCIN (1969)

α, β-Diaminobutyric acid, isolated from the acid hydrolysate of aspartocin, was resolved into two of the four possible isomers with a Technicon amino acid autoanalyzer. ORD and NMR studies of the isolated isomers indicated that one had the D-erythro and the other the L-threo configuration. The difference in NMR spectra of the two isomers was quite likely a consequence of restricted rotation about the Cα-Cβ bonds due to electrostatic repulsion of charged amino groups. Whether the antibiotic contains both isomers or one was formed by racemization during hydrolysis was not determined.
Gene mutations in inherited amyloidopathies of the nervous system. (1991)

Three papers published in this issue of the Journal (Bakker et al. 1991; Hiltunen et al. 1991; Schellenberg et al. 1991a) involve gene mutations responsible for amyloidoses affecting the nervous system. All three of these amyloidopathies are inherited in an autosomally dominant manner and involve the extracellular accumulation of amyloid. Amyloid is a general term for deposits of insoluble proteinaceous debris possessing specific tinctorial properties. In two of these disorders-an inherited form of dementia of the Alzheimer type and Dutch hereditary cerebral hemorrhage with amyloidosis (HCHWA-D)-the amyloid beta protein precursor (APP) serves as the substrate for amyloid formation. In the third disorderfamilial amyloidosis of Finnish type (FAF) -the substrate for amyloid formation is the actin-binding protein, gelsolin. In each case, the production of large amounts of amyloid in different forms is associated with specific clinical symptoms, ultimately leading to death. The APP gene encodes a set of normal membraneassociated proteins which are ubiquitously distributed in most peripheral and central nervous system tissues (Goldgaber et al. 1987; Kang et al. 1987; Robakis et al. 1987; Tanzi et al. 1987a). The principle component of the amyloid cores found in senile plaques in patients with Alzheimer disease (AD) and Down syndrome (DS) and, to lesser extent, in normal elderly individuals, is the 39-43-amino-acid peptide termed OiA4 (Glenner and Wong 1984). 13A4 is also the chief constituent of cerebral vessel amyloid deposits found in patients with AD, DS, and HCHWA-D (Glenner and Wong 1984; Van Duinen et al. 1987). The com-
Design for broadband high-efficiency grating couplers (2012)

In this Letter, we propose general optimization methods to design broadband high-efficiency grating couplers for planar waveguides. We attribute the coupling bandwidth to the mismatch of effective indices between the diffracted beam and the actual grating structure around the operation wavelength for fiber to waveguide excitation. The coupling bandwidth formula is deduced. A simple parameter-separate optimization procedure is proposed for general layered grating couplers for high coupling efficiency. Using our principle, we optimized a grating coupler for a horizontal slot waveguide operating at wavelength 1.55 μm for TM polarization. The grating coupler has 1 dB bandwidth of 60 nm and coupling efficiency of 65% with incident light from single-mode optical fiber (SMF) at 8°.
Large-scale, real-time visual–inertial localization revisited (2020)

The overarching goals in image-based localization are scale, robustness, and speed. In recent years, approaches based on local features and sparse 3D point-cloud models have both dominated the benchmarks and seen successful real-world deployment. They enable applications ranging from robot navigation, autonomous driving, virtual and augmented reality to device geo-localization. Recently, end-to-end learned localization approaches have been proposed which show promising results on small-scale datasets. However, the positioning accuracy, scalability, latency, and compute and storage requirements of these approaches remain open challenges. We aim to deploy localization at a global scale where one thus relies on methods using local features and sparse 3D models. Our approach spans from offline model building to real-time client-side pose fusion. The system compresses the appearance and geometry of the scene for efficient model storage and lookup leading to scalability beyond what has been demonstrated previously. It allows for low-latency localization queries and efficient fusion to be run in real-time on mobile platforms by combining server-side localization with real-time visual–inertial-based camera pose tracking. In order to further improve efficiency, we leverage a combination of priors, nearest-neighbor search, geometric match culling, and a cascaded pose candidate refinement step. This combination outperforms previous approaches when working with large-scale models and allows deployment at unprecedented scale. We demonstrate the effectiveness of our approach on a proof-of-concept system localizing 2.5 million images against models from four cities in different regions of the world achieving query latencies in the 200 ms range.
Continuous Inertial Focusing and Separation of Particles by Shape (2012)

Inertial effect of a flowing fluid, often a complicating factor in hydrodynamics, offers a way to high-purity, high-throughput shape-based separation of manmade particles or biological cells in microfluidic channels.
A Novel Approach Using Pharmacophore Ensemble/Support Vector Machine (PhE/SVM) for Prediction of hERG Liability (2007)

A novel approach by using a panel of plausible pharmacophore hypothesis candidates to constitute the pharmacophore ensemble (PhE) and subject them to regression by support vector machine (SVM) has been developed for predicting the liability of human ether-a-go-go-related gene (hERG). This PhE/SVM scheme takes into account the protein conformational flexibility while interacting with structurally diverse ligands, which is crucial yet often neglected by most of the analogue-based modeling methods. Thirty-nine molecules were carefully selected and cross-examined from the literature data for this study, of which 26 and 13 molecules were deliberately treated as the training set and the test set to generate the model and to validate the generated model, respectively. The final PhE/SVM model gave rise to an r(2) value of 0.97 for observed vs predicted pIC(50) values for the training set, a q(2) value of 0.89 by the 10-fold cross-validation and an r(2) value of 0.94 for the test set. Thus, this PhE/SVM model provides a fast and accurate tool for predicting liability of hERG and can be utilized to guide medicinal chemistry to avoid molecules with an inhibition potential of this potassium channel.
ACE inhibitors and statins for bone marrow failure following myocardial infarction? (2006)

See article by Thum et al. [4] (pages 50–60) in this issue .

Since their initial description a decade ago, endothelial precursor cells (EPCs) have been intensively studied, especially in relation to vascular injury or pathology and their clinical consequences. However, there is no consensus on the precise phenotypic definition of EPCs. Nonetheless, it has been established that these EPCs contribute to neovascularization in a variety of tissues [1] and they may even play a role in tissue regeneration if they transdifferentiate and integrate into functional tissue, for instance myocardium. The latter, however, is highly controversial.

Recruitment of EPCs from the bone marrow appears to be a natural mechanism to restore vascular function or even tissue function. Many acute tissue injuries, including myocardial infarction (MI), lead to a transient rise in circulating EPCs [2]. The functional importance of this rise in EPCs after MI is suggested by a correlation with better prognosis through reduced incidence of cardiac failure or death from cardiac cause. Multiple mechanisms have been described for this presumed interaction between peripheral organs and the bone marrow, mostly involving circulating factors such as VEGF [2] and perhaps CSFs [3]. It is therefore surprising that … 

* Corresponding author. Tel.: +31 43 3881200; fax: +31 43 3884166. Email address: m.post{at}fys.unimaas.nl
Antimetastatic and Antitumor Activities of Interleukin 10 in a Murine Model of Breast Cancer (1996)

Based on the recent observation of others that IL-10 has little toxicity when administered systemically to human volunteers and also on the findings of this study that it has antitumor and antimetastitic properties in mice, possible use of IL-10 in the treatment of human metastatic cancers deserves consideration.