gebhart/patrepeval huggingface dataset:
Comparative Analysis of Human Protein-Coding and Noncoding RNAs between Brain and 10 Mixed Cell Lines by RNA-Seq (2011)

In their expression process, different genes can generate diverse functional products, including various protein-coding or noncoding RNAs. Here, we investigated the protein-coding capacities and the expression levels of their isoforms for human known genes, the conservation and disease association of long noncoding RNAs (ncRNAs) with two transcriptome sequencing datasets from human brain tissues and 10 mixed cell lines. Comparative analysis revealed that about two-thirds of the genes expressed between brain and cell lines are the same, but less than one-third of their isoforms are identical. Besides those genes specially expressed in brain and cell lines, about 66% of genes expressed in common encoded different isoforms. Moreover, most genes dominantly expressed one isoform and some genes only generated protein-coding (or noncoding) RNAs in one sample but not in another. We found 282 human genes could encode both protein-coding and noncoding RNAs through alternative splicing in the two samples. We also identified more than 1,000 long ncRNAs, and most of those long ncRNAs contain conserved elements across either 46 vertebrates or 33 placental mammals or 10 primates. Further analysis showed that some long ncRNAs differentially expressed in human breast cancer or lung cancer, several of those differentially expressed long ncRNAs were validated by RT-PCR. In addition, those validated differentially expressed long ncRNAs were found significantly correlated with certain breast cancer or lung cancer related genes, indicating the important biological relevance between long ncRNAs and human cancers. Our findings reveal that the differences of gene expression profile between samples mainly result from the expressed gene isoforms, and highlight the importance of studying genes at the isoform level for completely illustrating the intricate transcriptome.
Continuous polymerization of lactam–lactone block copolymers in a twin‐screw extruder (2003)

Abstract Continuous copolymerizations of ϵ‐caprolactone with ϵ‐caprolactam and ω‐lauryl lactam were carried out in a modular intermeshing corotating twin‐screw extruder. Sodium hydride (initiator) and N ‐acetyl caprolactam (coinitiator) were used to synthesize lactam–lactone copolymers in a twin‐screw extruder. We consider the variables of feeding order and feed rate of comonomers on the reactive extrusion of lactam–lactone copolymers. It was observed that simultaneous feeding of both monomers with initiator and coinitiator in the first hopper produced a mixture of homopolymers. When we fed the lactam into the first hopper and caprolactone sequentially into the second hopper, we obtained the lactam–caprolactone block copolymers. However, when we fed caprolactone first into the first hopper and the lactam into the second hopper, the extruded product was a mixture of poly(ϵ‐caprolactone) and lactam monomer. We synthesized high molecular weight copolymers of poly(caprolactam‐ b ‐caprolactone) and poly(lauryl lactam‐ b ‐caprolactone) with different block lengths by sequential feeding of monomers. The block length of the block copolymer could be adjusted by controlling the feed rate of each monomer during reactive extrusion. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 88: 1429–1437, 2003
Location corrections through differential networks (LOCD-IN) (2018)

Many modern personal devices (cell phones, tablet computer, smart watches, etc.) contain embedded GNSS receivers capable of determining their position with a typical error of around 8-20 meters. Recent improvements to the software and hardware of these devices have given access to the raw GNSS data allowing developers the ability to manipulate and refine the computation of the position solution produced by the embedded GNSS receiver. This paper discusses the implementation of networked differential ground stations in an effort to reduce the error of a GNSS receiver on a mobile device and describe the improvement obtained.
Electrical precipitation: Theory of the removal of suspended matter from fluids (1915)

The frictional resistance of a small particle moving through a fluid is given by the law of Stokes. Knowing the density and size of the particles and the coefficient of viscosity of the medium, the amount of energy required to remove suspended matter from fluids can be calculated. From the formulas the relative efficiences of the different methods used to remove suspended matter from gases can be obtained. From these formulas the electrical method is shown to be especially adapted to fine suspended particles or to a mixture of gases that can be selectively ionized. In a practical case of electrical precipitation of smoke it is shown that approximately 4 per cent of the energy of the corona discharge is actually expended in the process of precipitation. The manner of the distribution of the energy of the corona discharge is discussed. The nature of the corona ionization and the “corona” rays is also briefly described. The application of the theory of electrical precipitation is given so that it is possible to determine the best working conditions for precipitating a given kind of suspended matter from a given fluid. The theory also indicates the limits of usefulness of the method of electrical precipitation.
A junction isolation technology for integrating silicon controlled rectifiers in crosspoint switching circuits (1976)

An integrated circuit technology has been developed to fabricate a matrix array of 32 junction isolated Silicon Controlled Rectifiers (SCR) for telephone switching systems. Other integrated SCR arrays have employed the more complicated dielectric or air isolation technologies to eliminate parasitic substrate leakages. This leakage in junction isolated structures results from the collection of minority carriers by the substrate. Our technology employs a vertical pnpn structure similar to collector diffusion isolation (1) with a p-substrate, n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> buried layer, p-epitaxy, wrap around n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> isolation diffusion, implanted n-gate and diffused p <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> anode regions. Through the use of gold recombination centers for carrier lifetime reduction, the structure achieves substrate leakages of less than one part in 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sup> . The SCRs also have adequately low leakages of typically 10 nA at 30V forward or reverse.
A Matched FIR Filter Bank for Audio Coding. (2006)

This paper describes a novel technique for audio coding, a lossy compression algorithm, that considers perceptual and rate-distortion criteria. It is based on matched finite impulse response (FIR) wavelet-packet-like filter banks, the filter coefficients being produced adoptively according to the input signal. This technique achieves perceptually transparent coding of high-quality audio, signals sampled at 44.1 KHz - 16 bits PCM, at bit rates of about 54 - 64 Kbps. The matched filter-bank makes a time-frequency-shape analysis, reducing the number of sub-bands requiring quantization. The decoder that implements this algorithm works effectively in real time. This reassures the efficacy of our technique.
DIGITAL CHAOTIC CODEC FOR DS-CDMA COMMUNICATION SYSTEMS (2006)

The potentialities of chaos to secure transmitted messages in digital communications has been proved. This by use Direct Sequence Code Division Multiple Access (DS- CDMA) system using chaotic spreading sequences. Two synchronization methods for Chua’s digital chaotic generator, are presented: the master-slave synchronization and the impulsive synchronization. In the first method, the driving signal is continuously transmitted from the driving to the driven system. In the second method, impulses from the driving system are transmitted to the driven one, by means of a time division scheme. A more robust digital chaotic codec is then developed to increase the complexity of the chaotic digital signal. The later is based on the general structure Penaud’s codec and Frey’s modified codec, associated with the technique of dead-beat chaos synchronisation developed by Angeli. Contrary to the others, the proposed codec is suitable to pass-band modulation. Comparison between these methods is achieved. The principle of the secure communication systems and the general chaotic QAM modem are presented.
Release of nitric oxide from endothelial cells stimulated by YC‐1, an activator of soluble guanylyl cyclase (1999)

1 In this study we examined the endothelium-dependent effect of YC-1 - a benzyl indazole derivative which directly activates soluble guanylyl cyclase (sGC) - on vascular relaxation and nitric oxide (NO) and guanosine-3',5'-cyclic monophosphate (cyclic GMP) in endothelial cells. 2 In preconstricted rat aortic rings with intact endothelium, YC-1 produced a concentration-dependent relaxation. However, the concentration response curve was shifted rightward to higher concentrations of YC-1, when (i) the aortas were pre-treated with L-NG-nitroarginine methylester (L-NAME) or (ii) the endothelium was removed. 3 Incubation of bovine aortic endothelial cells (BAEC) with YC-1 produced a concentration-dependent NO synthesis and release as assessed using a porphyrinic microsensor. Pre-incubating cells with L-NAME or with 8-bromo-cyclic GMP decreased this effect indicating that the YC-1 stimulation of NO synthesis is due to an activation of nitric oxide synthase, but not to an elevation of cyclic GMP. No direct effect of YC-1 on recombinant endothelial constitutive NO synthase activity was observed. 4 The YC-1 stimulated NO release was reduced by 90%, when extracellular free calcium was diminished. 5 In human umbilical vein endothelial cells (HUVEC), YC-1 stimulated intracellular cyclic GMP production in a concentration- and time-dependent manner. Stimulation of cyclic GMP was greater with a maximum concentration of YC-1 compared to calcium ionophore A23187. Similar effects were observed in BAEC and rat microvascular coronary endothelial cells (RMCEC). 6 When HUVEC and RMCEC were pre-treated with L-NG-nitroarginine (L-NOARG), the maximum YC-1 stimulated cyclic GMP increase was reduced by >/=50%. 7 These results indicate, that beside being a direct activator of sGC, YC-1 stimulates a NO-synthesis and release in endothelial cells which is independent of elevation of cyclic GMP but strictly dependent on extracellular calcium. The underlying mechanism needs to be determined further.
Plasma Signature of Neurological Disease in the Monogenetic Disorder Niemann-Pick Type C (2014)

Early diagnosis of neurological disorders would greatly improve their management and treatment. A major hurdle is that inflammatory products of cerebral disease are not easily detected in blood. Inflammation in multiple organs and heterogeneity in disease present additional challenges in distinguishing the extent to which a blood-based marker reflects disease in brain or other afflicted organs. Murine models of the monogenetic disorder Niemann-Pick Type C present aggressive forms of cerebral and liver inflammatory disease. Microarray analyses previously revealed age-dependent changes in innate immunity transcripts in the mouse brain. We have now validated four putative secretory inflammatory markers that are also elevated in mouse liver. We include limited, first time analysis of human Niemann-Pick Type C liver and cerebellum. Furthermore, we utilized 2-hydroxypropyl-β-cyclodextrin (HPβCD, an emerging therapeutic) administered intraperitoneally in mice, which abrogates inflammatory pathology in the liver but has limited effect on the brain. By analyzing the corresponding effects on inflammatory plasma proteins, we identified cathepsin S as a lead indicator of liver disease. In contrast, lysozyme was a marker of both brain and liver disease. 2-Hydroxypropyl-β-cyclodextrin had no effect on transcripts of neuron-specific 24-hydroxylase, and its product 24(S)-hydroxycholesterol was not a useful indicator in mouse plasma. Our data suggest that dual analysis of levels of the inflammatory markers lysozyme and cathepsin S may enable detection of multiple distinct states of neurodegeneration in plasma.
HPOSim: An R Package for Phenotypic Similarity Measure and Enrichment Analysis Based on the Human Phenotype Ontology (2015)

HPOSim can be used to predict disease genes and explore disease-related function of gene modules. HPOSim is open source and freely available at SourceForge (https://sourceforge.net/p/hposim/).
Deposition of Ti–Si–N films on Al substrates by magnetron sputtering (2013)

The objective of this work is to settle the problem of adhesion between hard films and soft metal substrates. Hard Ti–Si–N films were deposited onto soft Al substrates with a double target magnetron sputtering system. The composition, structure, surface morphologies and mechanical properties were characterised by electron probe microanalyser, X-ray diffraction, atomic force microscope, scratch test and nanoindentation respectively. The as-deposited films had good adhesion to the Al substrates and had a smooth and lustrous surface. The maximum hardness of the films achieved was as high as 27·2 GPa at the Si target power of 80 W.
Preconditioning the limited-memory bfgs algorithm (2006)

For large scale unconstrained optimization, truncated Newton methods and limited memory quasi-Newton methods are most effective choices. Often, the truncated Newton method adopts a preconditioner to speed up the convergence. However, very little previous study has explored the possibility of using a preconditioner in the limited memory quasi-Newton method. In this thesis, we focus on the LBFGS method, which belongs to the limited memory quasi-Newton methods, and we implement and study this preconditioned LBFGS algorithm (PLBFGS). 
We did experiments on protein structure prediction problems with three kinds of preconditioners constructed from the protein potential energy function. We also did experiments on a set of general test problems using a general preconditioner, the incomplete Cholesky factorization preconditioner. The results show that PLBFGS method has significant performance improvement over LBFGS algorithm by using the preconditioners, and has advantages over the standard preconditioned truncated Newton method. 
We also proposed a dynamic preconditioner update interval strategy, which benefits both preconditioned LBFGS method and preconditioned truncated Newton method.
Bimodal Paramagnetic and Fluorescent Liposomes for Cellular and Tumor Magnetic Resonance Imaging (2007)

A novel bimodal fluorescent and paramagnetic liposome is described for cellular labeling. In this study, we show the synthesis of a novel gadolinium lipid, Gd.DOTA.DSA, designed for liposomal cell labeling and tumor imaging. Liposome formulations consisting of this lipid were optimized in order to allow for maximum cellular entry, and the optimized formulation was used to label HeLa cells in vitro. The efficiency of this novel bimodal Gd-liposome formulation for cell labeling was demonstrated using both fluorescence microscopy and magnetic resonance imaging (MRI). The uptake of Gd-liposomes into cells induced a marked reduction in their MRI T 1 relaxation times. Fluorescence microscopy provided concomitant proof of uptake and revealed liposome internalization into the cell cytosol. The optimized formulation was also found to exhibit minimal cytotoxicity and was shown to have capacity for plasmid DNA (pDNA) transfection. A further second novel neutral bimodal Gd-liposome is described for the labeling of xenograft tumors in vivo utilizing the enhanced permeation and retention effect (EPR). Balb/c nude mice were inoculated with IGROV-1 cells, and the resulting tumor was imaged by MRI using these in vivo Gd-liposomes formulated with low charge and a poly(ethylene glycol) (PEG) calyx for long systemic circulation. These Gd-liposomes which were less than 100 nm in size were shown to accumulate in tumor tissue by MRI, and this was also verified by fluorescence microscopy of histology samples. Our in vivo tumor imaging results demonstrate the effectiveness of MRI to observe passive targeting of long-term circulating liposomes to tumors in real time, and allow for MRI directed therapy, wherein the delivery of therapeutic genes and drugs to tumor sites can be monitored while therapeutic effects on tumor mass and/or size may be simultaneously observed, quantitated, and correlated.
Muscle ultrasound in neuromuscular disorders (2008)

Muscle ultrasound is a useful tool in the diagnosis of neuromuscular disorders, as these disorders result in muscle atrophy and intramuscular fibrosis and fatty infiltration, which can be visualized with ultrasound. Several prospective studies have reported high sensitivities and specificities in the detection of neuromuscular disorders. Although not investigated in large series of patients, different neuromuscular disorders tend to show specific changes on muscle ultrasound, which can be helpful in differential diagnosis. For example, Duchenne muscular dystrophy results in a severe, homogeneous increase of muscle echo intensity with normal muscle thickness, whereas spinal muscular atrophy shows an inhomogeneous increase of echo intensity with severe atrophy. A major advantage of muscle ultrasound, compared to other imaging techniques, is its ability to visualize muscle movements, such as muscle contractions and fasciculations. This study reviews the possibilities and limitations of ultrasound in muscle imaging and its value as a diagnostic tool in neuromuscular disorders.
Differential Utilization of Alternate Initiation Sites in a Plant Defense Gene Responding to Environmental Stimuli (1994)

The upstream regulatory region of an efficiently expressed phenylalanine ammonia-lyase (PAL5) gene from tomato (Lycopersicon esculentum) was characterized by DNA sequencing and S1-nuclease-protection studies. Two transcription initiation sites giving rise to a long and a short transcript were identified, each corresponding to a different putative TATA sequence element with multiple conserved upstream regulatory motifs. When tomato plants were challenged with three different environmental stimuli, wounding, light and Verticillium infection, this gene was observed to utilize the alternate initiation sites differentially, in a tissue-dependent and stimulus-dependent manner. In general, basal levels of the shorter transcript were very low but preferentially and strongly stimulated by the environmental factors. In contrast, the longer transcript was less affected, essentially representing a constitutive expression of this gene. The results suggest that the multiple regulatory sites in the PAL5 gene promoter provide for both an essential constitutive expression of phenylalanine ammonia-lyase as well as an appropriate response to different environmental stresses.
Encoding plans in propositional logic (1996)

In recent work we showed that planning problems can be efficiently solved by general propositional satisfiability algorithms (Kautz and Selman 1996). A key issue in this approach is the development of practical reductions of planning to SAT. We introduce a series of different SAT encodings for STRIPS-style planning, which are sound and complete representations of the original STRIPS specification, and relate our encodings to the Graphplan system of Blum and Furst (1995). We analyze the size complexity of the various encodings, both in terms of number of variables and total length of the resulting formulas. This paper complements the empirical evaluation of several of the encodings reported in Kautz and Selman (1996). We also introduce a novel encoding based on the theory of causal planning, that exploits the notionof &quot;lifting&quot; from the theorem-proving community. This new encoding strictly dominates the others in terms of asymptotic complexity. Finally, we consider further reductions i...
Fc-Receptor-Mediated Intracellular Delivery of Cu/Zn-superoxide Dismutase (SOD1) Protects Against Redox-Induced Apoptosis Through a Nitric Oxide Dependent Mechanism (2000)

To define the pharmacologic mechanism of action of bovine SOD1, we attempted to identify the second messengers that are induced by SOD1 IC. In this work, we propose that Fc-mediated intracellular delivery of the SOD1 that reduced the production of superoxide anion and of peroxynitrite, promoted a NO-induced protective effect in inducing the antioxidant armature of the cells. Taken together, these data suggested that specific immune responses against antigenic SOD1 could promote the pharmacological properties of the antioxidant enzyme likely via a NO-dependent mechanism.
XCIX.—Formation of ethereal salts of polycarboxylic acids (1898)

S. Ruhemann and A. V. Cunnington, J. Chem. Soc., Trans., 1898, 73, 1006 DOI: 10.1039/CT8987301006
A Meta-analysis of the Significance of Granzyme B and Perforin in Noninvasive Diagnosis of Acute Rejection After Kidney Transplantation (2015)

Currently, neither GZMB nor PRF, if evaluated alone, could be a convincing noninvasive diagnostic marker for AR in clinical practice. Combined use of PRF and GZMB post-kidney transplant may be a better choice in AR evaluation to direct allograft biopsy execution and earlier therapeutic intervention.
Increased Serum Thymidine Kinase Activity in Acute Sarcoidosis. (2002)

This is the first case report of acute sarcoidosis with increased serum thymidine kinase (TK) activity. A 43-year-old male presented fever, swelling of parotid glands, lymphadenopathy, and peripheral neuropathy. Sarcoidosis was pathologically diagnosed by lung and parotid gland biopsy. His serum TK, which was increased to 11.2 U/l at diagnosis (normal <5 U/l), normalized after glucocorticoid therapy. Serum TK has been considered as a good marker of the proliferative activity of various types of neoplasms. Its rise in sarcoidosis has, however, not been described. Because acute sarcoidosis sometimes resembles malignant lymphoma, the possible rise of serum TK in sarcoidosis may be worthy of note.
A double blind study of metoclopramide in the treatment of migraine attacks. (1980)

One hundred and fifty patients with migraine attacks attending the Copenhagen acute migraine clinic were treated either with metoclopramide 10 mg i.m. metoclopramide 20 mg as suppository or placebo in a double blind trial. All patients simultaneously or 30 minutes later received paracetamol 1 g and diazepam 5 mg orally. The nausea was relieved in 71% of the patients by placebo and bed rest, but metoclopramide was significantly (p = 0.04) more effective and relieved nausea in 86% of the patients. Metoclopramide did not by itself reduce the pain, but enhanced the effect of the analgesic or sedative medication. This effect, however, just failed to be statistically significant (p = 0.06).
Random access three-dimensional two-photon microscopy (2007)

We propose a two-photon microscope scheme capable of real-time, three-dimensional investigation of the electric activity pattern of neural networks or signal summation rules of individual neurons in a 0.6 mm x 0.6 mm x 0.2 mm volume of the sample. The points of measurement are chosen according to a conventional scanning two-photon image, and they are addressed by separately adjustable optical fibers. This allows scanning at kilohertz repetition rates of as many as 100 data points. Submicrometer spatial resolution is maintained during the measurement similarly to conventional two-photon microscopy.