gebhart/patrepeval huggingface dataset:
Glycosaminoglycan Composition of the Large Freshwater Mollusc Bivalve <i>Anodonta </i><i>a</i><i>nodonta</i> (2005)

In this paper, glycosaminoglycans from the body of the large freshwater mollusc bivalve Anodonta anodonta were recovered at about 0.6 mg/g of dry tissue, composed of chondroitin sulfate (approximately 38%), nonsulfated chondroitin (about 21%), and heparin (41%). This last polysaccharide was found to consist of a large percentage (approximately 88%) of a fast-moving species possessing a lower molecular mass and sulfate group amount and about 12% of a more sulfated, slow-moving component having a greater molecular mass. The chondroitin sulfate was composed of approximately 28% of the 6-sulfated disaccharide, 46% of the 4-sulfated disaccharide, and about 26% of the nonsulfated disaccharide, with a charge density value of 0.74. Heparin was subjected to the oligosaccharide mapping after treatment with heparinase and then separation of the resulting unsaturated oligosaccharides by SAX-HPLC. A heparin sample from Anodonta anodonta showed a degree of sulfation similar to that of bovine mucosal heparin because of the presence of approximately the same mol % of the trisulfated disaccharide (DeltaUA2S(1-->4)-alpha-D-GlcN2S6S), a slight modification of the other oligosaccharides, and a significant increase of the disaccharide bearing the sulfate group in position 3 of the N-sulfoglucosamine 6-sulfate (-->4)-beta-D-GlcA(1-->4)-alpha-D-GlcN2S3S6S(1-->) part of the ATIII-binding region. However, the anticoagulant activity of mollusc heparin was quite similar to that of pharmaceutical grade heparin. The data obtained again emphasize the heterogeneity of GAGs from molluscs.
Saccadic eye movements evoked by microstimulation of the fastigial nucleus of macaque monkeys (1988)

1. Systematic exploration throughout the deep cerebellar nuclei and white matter disclosed that the region from which saccadic eye movements (saccades) were evoked with weak currents (less than 10 microA) was confined to the fastigial nucleus and the adjacent white matter. 2. When an electrode for stimulation was advanced in the cerebellum, saccades were evoked in the direction of the stimulated side (ipsilateral saccades) as it entered the low-threshold region. In some tracks, particularly when the electrode was advanced in the medial portion of the fastigial nucleus, the direction of the evoked saccades changed from the ipsilateral to the contralateral. 3. The mappings with microstimulation disclosed that the ipsilateral saccades were elicited from a relatively wide region that included almost the full extent of the fastigial nucleus. The low-threshold region continued in the white matter caudally into vermal lobule VII and rostrally into the dorsal aspect of the brachium conjunctivum. On the other hand, the contralateral saccades were evoked from a relatively circumscribed region in the ventromedial portion of the fastigial nucleus. 4. The reversal in the direction of the horizontal component occurred always in a narrow zone in the core of the fastigial nucleus. The caudal part of this zone coincided with an ellipsoidal region where anterogradely labeled axons of the Purkinje cells terminated when HRP was injected into vermal lobule VII. 5. When bicuculline (0.2-1 microgram) was injected in the ellipsoidal region, the ipsilateral saccades evoked from the dorsocaudal aspect of the region were suppressed for several hours. On the other hand, the contralateral saccades evoked from the ventromedial portion of the fastigial nucleus were either unchanged or enhanced. 6. Because the ipsilateral saccades were suppressed by bicuculline, they were most probably evoked by stimulation of the presynaptic component of gamma-amino-butyric acid-(GABA) mediated synapses, namely the axons of Purkinje cells. 7. Because stimulation of the presynaptic component of the inhibitory synapses evoked ipsilateral saccades, activation of the postsynaptic component would evoke contralateral saccades. In fact, the distribution of the fastigial sites yielding contralateral saccades coincided with the course of axons of fastigial neurons arising in the ellipsoidal region. It is most likely, therefore, that the contralateral saccades were evoked by stimulation of fastigial neurons.(ABSTRACT TRUNCATED AT 400 WORDS)
ARC: a self-tuning, low overhead replacement cache (2003)

Abstract — We consider the problem of cache management in a demand paging scenario with uniform page sizes. We propose a new cache management policy, namely, Adaptive Replacement Cache (ARC), that has several advantages. In response to evolving and changing access patterns, ARC dynamically, adaptively, and continually balances between the recency and frequency components in an online and selftuning fashion. The policy ARC uses a learning rule to adaptively and continually revise its assumptions about the workload. The policy ARC is empirically universal, that is, it empirically performs as well as a certain fixed replacement policy– even when the latter uses the best workload-specific tuning parameter that was selected in an offline fashion. Consequently, ARC works uniformly well across varied workloads and cache sizes without any need for workload specific a priori knowledge or tuning. Various policies such as LRU-2, 2Q, LRFU, and LIRS require user-defined parameters, and, unfortunately, no single choice works uniformly well across different workloads and cache sizes. The policy ARC is simple-to-implement and, like LRU, has constant complexity per request. In comparison, policies LRU-2 and LRFU both require logarithmic time complexity in the cache size. The policy ARC is scan-resistant: it allows one-time sequential requests to pass through without polluting the cache. On ¢¡ real-life traces drawn from numerous domains, ARC leads to substantial performance gains over LRU for a wide range of cache sizes. For example, for a SPC1 like synthetic benchmark, at 4GB cache, LRU delivers a hit ratio £¥¤§¦¨£�© of while ARC achieves a hit ratio of ¢� I.
The Dark Side of Glia (2005)

Long ignored, the nervous system9s glial cells may turn out to be key players in disease and prime targets for therapy.
Decreasing Incidence of Acute Kidney Injury in Patients with COVID-19 Critical Illness in New York City (2021)

AKI impacts a high proportion of admitted patients with COVID-19 and is associated with high mortality, particularly when RRT is required. AKI incidence appears to be decreasing over time and kidney function frequently recovers in those who survive.
Cloning and functional expression of the mouse epithelial sodium channel (1999)

The epithelial sodium channel (ENaC) plays a major role in the transepithelial reabsorption of sodium in the renal cortical collecting duct, distal colon, and lung. ENaCs are formed by three structurally related subunits, termed alpha-, beta-, and gammaENaC. We previously isolated and sequenced cDNAs encoding a portion of mouse alpha-, beta-, and gammaENaC (alpha-, beta-, and gammamENaC). These cDNAs were used to screen an oligo-dT-primed mouse kidney cDNA library. Full-length betamENaC and partial-length alpha- and gammamENaC clones were isolated. Full-length alpha- and gammamENaC cDNAs were subsequently obtained by 5'-rapid amplification of cDNA ends (5'-RACE) PCR. Injection of mouse alpha-, beta-, and gammaENaC cRNAs into Xenopus oocytes led to expression of amiloride-sensitive (K(i) = 103 nM), Na(+)-selective currents with a single-channel conductance of 4.7 pS. Northern blots revealed that alpha-, beta-, and gammamENaC were expressed in lung and kidney. Interestingly, alphamENaC was detected in liver, although transcript sizes of 9.8 kb and 3.1 kb differed in size from the 3.2-kb message observed in other tissues. A partial cDNA clone was isolated from mouse liver by 5'-RACE PCR. Its sequence was found to be nearly identical to alphamENaC. To begin to identify regions within alphamENaC that might be important in assembly of the native heteroligomeric channel, a series of functional experiments were performed using a construct of alphamENaC encoding the predicted cytoplasmic NH(2) terminus. Coinjection of wild-type alpha-, beta-, and gammamENaC with the intracellular NH(2) terminus of alphamENaC abolished amiloride-sensitive currents in Xenopus oocytes, suggesting that the NH(2) terminus of alphamENaC is involved in subunit assembly, and when present in a 10-fold excess, plays a dominant negative role in functional ENaC expression.
Demonstration of BACE (β-secretase) phosphorylation and its interaction with GGA1 in cells by fluorescence-lifetime imaging microscopy (2004)

beta-Secretase (BACE) carries out the first of two proteolysis steps to generate the amyloid-beta peptides that accumulate in the senile plaques in Alzheimer's disease (AD). Because most BACE activity occurs in endosomes, signals regulating its trafficking to these compartments are important to an understanding of AD pathogenesis. A DISLL sequence near the BACE C-terminus mediates binding of BACE to the VHS domains of Golgi-localized gamma-ear-containing ARF-binding (GGA) proteins, which are involved in the sorting of proteins to endosomes. Phosphorylation of the motif's serine residue regulates BACE recycling back to the cell surface from early endosomes and enhances the interaction of BACE with GGA proteins in isolated protein assays. We found that BACE phosphorylation influences BACE-GGA interactions in cells using a new fluorescence-resonance-energy-transfer-based assay of protein proximity, fluorescence lifetime imaging. Although serine-phosphorylated BACE was distributed throughout the cell, interaction of GGA1 with the wild-type protein occurred in juxtanuclear compartments. Pseudo-phosphorylated and non-phosphorylated BACE mutants remained localized with GGA1 in the Golgi body, but the latter mutation diminished the two proteins' FRET signal. Because BACE phosphorylated at serine residues can be identified in human brain, these data suggest that serine phosphorylation of BACE is a physiologically relevant post-translational modification that regulates trafficking in the juxtanuclear compartment by interaction with GGA1.
The H-phosphonate approach to the solution phase synthesis of linear and cyclic oligoribonucleotides (1999)

The solution phase synthesis of the tetraribonucleoside triphosphate r(ApCpGpU) 18 and the corresponding cyclic tetraribonucleotide 19 is described. The synthetic methodology is based on 5'- O -(DMTr)-2'- O -(Fpmp)-ribonucleoside-3'- H -phosphonate building blocks 10. Coupling, which is rapid and quantitative, is effected with di-(2-chlorophenyl) phosphorochloridate 5 at -40 degreesC; it is followed by in situ treatment with 2-(4-methyl-phenyl)sulphanyl-1 H -isoindole-1,3(2 H )-dione 6b. The resulting sulphur transfer reaction also proceeds rapidly and quantitatively at -40 degreesC. The same coupling and sulphur transfer steps are used in the cyclization reaction, but a 5'- H -phosphonate intermediate 24 is involved. The final three-step unblocking process involves treatment with (i) E -2-nitrobenzaldoxime 7 and N 1, N 1, N 3, N 3-tetramethylguanidine (TMG) 8 in aceto-nitrile, (ii) concentrated aqueous ammonia at 50 degreesC and (iii) 0.5 mol/dm3sodium acetate buffer (pH 4.0) at 40 degreesC. The fully unblocked products 18 and 19 were characterized by NMR spectroscopy and by enzymatic digestion.
Functions of Prefabricated Chunks in the Development of Language Competence (2005)

Based on a review of the theories of prefabricated chunks of language,and an analysis of their important functions in language communication and the development of language competence,this paper proposes that chunks should be systematically incorporated in the curriculum of language teaching because chunks work in the four aspects:1.accelerating automatic processing of the low-end language data,thus raising reading speed;2.increasing listening efficiency with rational allocation of the cognitive resources in high-end data processing;3.facilitating the easy and fluent speaking with reinforced priority and continuity in communication;4.improving writing in a way of language variation as a result of short-term memory in language transformation.
On-Chip CNN Accelerator for Image Super-Resolution. (2018)

To implement convolutional neural networks (CNN) in hardware, the state-of-the-art CNN accelerators pipeline computation and data transfer stages using an off-chip memory and simultaneously execute them on the same timeline. However, since a large amount of feature maps generated during the operation should be transmitted to the off-chip memory, the pipeline stage length is determined by the off-chip data transfer stage. Fusion architectures that can fuse multiple layers have been proposed to solve this problem, but applications such as super-resolution (SR) require a large amount of an on-chip memory because of the high resolution of the feature maps. In this paper, we propose a novel on-chip CNN accelerator for SR to optimize the CNN dataflow in the on-chip memory. First, the convolution loop optimization technique is proposed to prevent using a frame buffer. Second, we develop a combined convolutional layer processor to reduce the buffer size used to store the feature maps. Third, we explore how to perform low-cost multiply-and-accumulate operations in the deconvolutional layer used in SR. Finally, we propose a two-stage quantization algorithm to select the optimized hardware size for the limited number of DSPs to implement the on-chip CNN accelerator. We evaluate our proposed accelerator with FSRCNN, which is most popular as the CNN-based SR algorithm. Experimental results show that the proposed accelerator requires 9.21ms to achieve an output image with the 2560x1440 pixel resolution, which is 36 times faster than the conventional method. In addition, we reduce the on-chip memory usage and DSP usage by 4 times and 1.44 times, respectively, compared to the conventional methods.
A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes (2013)

RNA molecules transmit the information encoded in the genome and generally reflect its content. Adenosine-to-inosine (A-to-I) RNA editing by ADAR proteins converts a genomically encoded adenosine into inosine. It is known that most RNA editing in human takes place in the primate-specific Alu sequences, but the extent of this phenomenon and its effect on transcriptome diversity are not yet clear. Here, we analyzed large-scale RNA-seq data and detected ∼1.6 million editing sites. As detection sensitivity increases with sequencing coverage, we performed ultradeep sequencing of selected Alu sequences and showed that the scope of editing is much larger than anticipated. We found that virtually all adenosines within Alu repeats that form double-stranded RNA undergo A-to-I editing, although most sites exhibit editing at only low levels (<1%). Moreover, using high coverage sequencing, we observed editing of transcripts resulting from residual antisense expression, doubling the number of edited sites in the human genome. Based on bioinformatic analyses and deep targeted sequencing, we estimate that there are over 100 million human Alu RNA editing sites, located in the majority of human genes. These findings set the stage for exploring how this primate-specific massive diversification of the transcriptome is utilized.
Regulation of Metabolism by Hypoxia-Inducible Factor 1 (2011)

The maintenance of oxygen homeostasis is critical for survival, and the master regulator of this process in metazoan species is hypoxia-inducible factor 1 (HIF-1), which controls both O(2) delivery and utilization. Under conditions of reduced O(2) availability, HIF-1 activates the transcription of genes, whose protein products mediate a switch from oxidative to glycolytic metabolism. HIF-1 is activated in cancer cells as a result of intratumoral hypoxia and/or genetic alterations. In cancer cells, metabolism is reprogrammed to favor glycolysis even under aerobic conditions. Pyruvate kinase M2 (PKM2) has been implicated in cancer growth and metabolism, although the mechanism by which it exerts these effects is unclear. Recent studies indicate that PKM2 interacts with HIF-1α physically and functionally to stimulate the binding of HIF-1 at target genes, the recruitment of coactivators, histone acetylation, and gene transcription. Interaction with HIF-1α is facilitated by hydroxylation of PKM2 at proline-403 and -408 by PHD3. Knockdown of PHD3 decreases glucose transporter 1, lactate dehydrogenase A, and pyruvate dehydrogenase kinase 1 expression; decreases glucose uptake and lactate production; and increases O(2) consumption. The effect of PKM2/PHD3 is not limited to genes encoding metabolic enzymes because VEGF is similarly regulated. These results provide a mechanism by which PKM2 promotes metabolic reprogramming and suggest that it plays a broader role in cancer progression than has previously been appreciated.
Selective Excision of AZTMP by Drug-Resistant Human Immunodeficiency Virus Reverse Transcriptase (2001)

Two distinct mechanisms can be envisioned for resistance of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) to nucleoside analogs: one in which the mutations interfere with the ability of HIV-1 RT to incorporate the analog, and the other in which the mutations enhance the excision of the analog after it has been incorporated. It has been clear for some time that there are mutations that selectively interfere with the incorporation of nucleoside analogs; however, it has only recently been proposed that zidovudine (AZT) resistance can involve the excision of the nucleoside analog after it has been incorporated into viral DNA. Although this proposal resolves some important issues, it leaves some questions unanswered. In particular, how do the AZT resistance mutations enhance excision, and what mechanism(s) causes the excision reaction to be relatively specific for AZT? We have used both structural and biochemical data to develop a model. In this model, several of the mutations associated with AZT resistance act primarily to enhance the binding of ATP, which is the most likely pyrophosphate donor in the in vivo excision reaction. The AZT resistance mutations serve to increase the affinity of RT for ATP so that, at physiological ATP concentrations, excision is reasonably efficient. So far as we can determine, the specificity of the excision reaction for an AZT-terminated primer is not due to the mutations that confer resistance, but depends instead on the structure of the region around the HIV-1 RT polymerase active site and on its interactions with the azido group of AZT. Steric constraints involving the azido group cause the end of an AZT 5'-monophosphate-terminated primer to preferentially reside at the nucleotide binding site, which favors excision.
SYNTHESIS, MOLECULAR STRUCTURE AND TAUTOMERISM OF 1(2)H-DIHYDROPYRAZOLO[3,4-b]PYRIDIN-6-ONES (1999)

Six l(2)//-3-aryl-4-/?-chlorophenyl-dihydropyrazolo [3,4-b]pyridin-6-ones have been prepared from the corresponding arylaminopyrazoles. The NMR study of these compounds reveals that all of them exist as 2//-tautomers in solution (DMSO-dg) as well and in the solid state.
Giga-Pixel Lensfree Holographic Microscopy and Tomography Using Color Image Sensors (2012)

We report Giga-pixel lensfree holographic microscopy and tomography using color sensor-arrays such as CMOS imagers that exhibit Bayer color filter patterns. Without physically removing these color filters coated on the sensor chip, we synthesize pixel super-resolved lensfree holograms, which are then reconstructed to achieve ~350 nm lateral resolution, corresponding to a numerical aperture of ~0.8, across a field-of-view of ~20.5 mm(2). This constitutes a digital image with ~0.7 Billion effective pixels in both amplitude and phase channels (i.e., ~1.4 Giga-pixels total). Furthermore, by changing the illumination angle (e.g., ± 50°) and scanning a partially-coherent light source across two orthogonal axes, super-resolved images of the same specimen from different viewing angles are created, which are then digitally combined to synthesize tomographic images of the object. Using this dual-axis lensfree tomographic imager running on a color sensor-chip, we achieve a 3D spatial resolution of ~0.35 µm × 0.35 µm × ~2 µm, in x, y and z, respectively, creating an effective voxel size of ~0.03 µm(3) across a sample volume of ~5 mm(3), which is equivalent to >150 Billion voxels. We demonstrate the proof-of-concept of this lensfree optical tomographic microscopy platform on a color CMOS image sensor by creating tomograms of micro-particles as well as a wild-type C. elegans nematode.
Automatic cough detection based on airflow signals for portable spirometry system (2020)

We give a short introduction to cough detection efforts that were undertaken during the last decade and we describe the solution for automatic cough detection developed for the AioCare portable spirometry system. In contrast to more popular analysis of sound and audio recordings, we fully based our approach on airflow signals only. As the system is intended to be used in a large variety of environments and different patients, we trained and validated the algorithm using AioCare-collected data and the large database of spirometry curves from the NHANES database by the American National Center for Health Statistics. We trained different classifiers, such as logistic regression, feed-forward artificial neural network, support vector machine, and random forest to choose the one with the best performance. The ANN solution was selected as the final classifier. The classification results on the test set (AioCare data) are: 0.86 (sensitivity), 0.91 (specificity), 0.91 (accuracy) and 0.88 (F1 score). The classification methodology developed in this study is robust for detecting cough events during spirometry measurements. As far as we know, the solution presented in this work is the first fully reproducible description of the automatic cough detection algorithm based totally on airflow signals and the first cough detection implemented in a commercial spirometry system that is published.
Thyroid hormone administration enhances remyelination in chronic demyelinating inflammatory disease (2004)

Chronic disabilities in multiple sclerosis are believed to be due to neuron damage and degeneration, which follow remyelination failure. Due to the presence of numerous oligodendrocyte precursors inside demyelination plaques, one reason for demyelination failure could be the inability of oligodendrocyte precursor cells to turn into myelinating oligodendrocytes. In this study, we show that thyroid hormone enhances and accelerates remyelination in an experimental model of chronic demyelination, i.e., experimental allergic encephalomyelitis in congenic female Dark Agouti rats immunized with complete guinea pig spinal cord. Thyroid hormone, when administered during the acute phase of the disease, increases expression of platelet-derived growth factor alpha receptor, restores normal levels of myelin basic protein mRNA and protein, and allows an early and morphologically competent reassembly of myelin sheaths. Moreover, thyroid hormone exerts a neuroprotective effect with respect to axonal pathology.