gebhart/patrepeval huggingface dataset:
An absolute bound on limit cycles due to roundoff errors in digital filters (1973)

An absolute bound on limit cycle oscillations in fixed-point digital filter implementations due to roundoff errors is presented. Periodicity of the limit cycles is assumed in the derivation. Useful design results are explicitly given for the case of second-order filter sections. In addition it is shown that this bound is equal to the rms bound of Sandberg and Kaiser for real roots, and is never more than a factor of two greater than the rms bound for complex roots for second-order filters.
The use of oxygen uptake rate to optimise air feed rate to a continuous ethanol fermentation (1994)

In a continous ethanol fermentation in a stirred tank reactor, the effect of oxygen transfer rate on the biomass concentration, specific activity and overall ethanol productivity of a thermo-tolerant yeast Kluyveromyces marxianus was investigated. The dissolved oxygen concentration was maintained at zero. Although an increased oxygen transfer rate led to an increase in biomass concentration, the reduction in specific activity led to a reduction in overall ethanol productivity. The optimum oxygen transfer rate was zero. The maximum ethanol productivity was 1.3 mL/L h. The ethanol productivity in the stirred tank reactor was compared with two alternative fermenter configurations: - two fermenters in series - poorly mixed aerated fermenter An ethanol productivity of 3.9 mL/L h was achieved in both these systems.
Interdependent SMAD and JNK Signaling in Transforming Growth Factor-β-mediated Transcription (1999)

SMAD and JNK cascades are essential components of the transforming growth factor-beta (TGF-beta) signaling machinery and are implicated in common transcriptional responses. However, the relationship of these pathways to one another downstream of the TGF-beta receptor complex is unknown. We show that JNK is rapidly activated by TGF-beta in a SMAD-independent manner and phosphorylates Smad3 outside its -SSXS motif. Smad3 phosphorylation by JNK facilitates both its activation by the TGF-beta receptor complex and its nuclear accumulation. JNK regulates SMAD- and TGF-beta-mediated transcriptional responses, yet JNK activators only partially stimulate transcriptional responses characteristic of TGF-beta without coincident SMAD pathway activation. These results suggest an interdependent relationship between the JNK and SMAD pathways in TGF-beta-mediated transcription.
Principal axis extracting vector excitation coding: high quality speech at 8 kb/s (2002)

Principal axis extracting vector excitation coding (PAVXC) is proposed in which an efficient codebook search method and an improved excitation modeling technique are used. A two-step codebook search using a small-size codebook of 20 dimensions (half the conventional size) can reduce the computational complexity by a factor of 64, maintaining the reproduced speech quality within a slight degradation of 0.9 dB in SNR seg. Multiple vector excitation using an impulse vector jointly with the conventional stochastic code vector can provide more precise representation of the excitation. The impulse vector is extracted from each code vector by principal axis extraction, and its gain is jointly optimized with the gain for the code vector. The improvement in SNR seg is 1.2 dB, which compensates for the degradation caused by the two-step codebook search. The quality of the reproduced speech using PAVXC is subjectively much better than that of conventional VXC, thanks especially to the improvement in voiced regions.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Dual-Continuum Design Approach for Intuitive and Low-Cost Upper Gastrointestinal Endoscopy (2018)

Target mapping was achieved with an average error of 5° in bending angle. Simulated endoscopies were performed by an expert user successfully, within a time comparable to conventional endoscopy (<1 minute difference). Non-experts using the proposed device achieved visualization of the stomach in a shorter time (9s faster on average) than with a conventional endoscope. The estimated cost is <10 USD and <30 USD for disposable and reusable parts, respectively. Significance and Conclusions: Flexible endoscopes are complex and expensive devices, actuated via non-intuitive cable-driven mechanisms. They frequently break, requiring costly repair, and necessitate a dedicated reprocessing facility to prevent cross contamination. The proposed solution is portable, inexpensive, and easy to use, thus lending itself to disposable use by personnel without formal training in flexible endoscopy.
A long-lasting, plasmin-activatable thrombin inhibitor aids clot lysis in vitro and does not promote bleeding in vivo (2009)

Summary The leech protein hirudin is a potent inhibitor of thrombin, but clinical use of recombinant hirudin is restricted by haemorrhagic risks, and complicated by hirudin’s rapid clearance from the circulation. We previously employed albumin fusion to slow hirudin variant 3 (HV3) clearance. In this study, we hypothesized that reconfiguration of the chimera, appending human serum albumin (HSA) to the N-terminus of HV3, with an intervening plasmin cleavage site, would create a slowly cleared, plasmin-activatable HV3. Potential plasmin cleavage sites were screened by expression in Escherichia coli, interposed between glutathione sulfotransferase and HV3 domains. The most reactive sequence (GSGIYR-ITY) was recreated in C-terminally His-tagged albumin fusion protein HSACHV3, expressed in Pichia pastoris yeast and purified by nickel-chelate affinity chromatography. HSACHV3 showed no thrombin inhibitory activity in the absence of plasmin, but liberated active HV3 in a time- and concentration-dependent manner in its presence. In a discontinuous clot assay involving clot-bound thrombin, HSACHV3 assisted clot lysis by limiting clot extension in a tPA- and concentration-dependent manner. Similar results were obtained in plasma at higher concentrations of HSACHV3. The chimeric protein exhibited much slower clearance in mice than unfused HV3, and indistinguishable pharmacokinetics from unfused recombinant HSA. In a mouse tail transection bleeding model, doses of HSACHV3 identical to those of HV3 that elicited a four-fold increase in the volume of shed blood were without effect. Our results suggest that HSACHV3 is a fully latent, plasmin activatable, long-lasting hirudin, of potential benefit in thrombotic disorders resistant to natural or pharmacological clot lysis.
PubMeth: a cancer methylation database combining text-mining and expert annotation (2007)

Epigenetics, and more specifically DNA methylation is a fast evolving research area. In almost every cancer type, each month new publications confirm the differentiated regulation of specific genes due to methylation and mention the discovery of novel methylation markers. Therefore, it would be extremely useful to have an annotated, reviewed, sorted and summarized overview of all available data. PubMeth is a cancer methylation database that includes genes that are reported to be methylated in various cancer types. A query can be based either on genes (to check in which cancer types the genes are reported as being methylated) or on cancer types (which genes are reported to be methylated in the cancer (sub) types of interest). The database is freely accessible at http://www.pubmeth.org. PubMeth is based on text-mining of Medline/PubMed abstracts, combined with manual reading and annotation of preselected abstracts. The text-mining approach results in increased speed and selectivity (as for instance many different aliases of a gene are searched at once), while the manual screening significantly raises the specificity and quality of the database. The summarized overview of the results is very useful in case more genes or cancer types are searched at the same time.
NUCLEAR REACTORS FOR RESEARCH (1955)

Maintaining a constant number and ratio of immune cells is one critical aspect of the tight regulation of immune homeostasis. Breakdown of this balance will lead to autoimmune diseases such as multiple sclerosis (MS). The antiepileptic drug valproic acid (VPA) was reported to regulate the growth, survival, and differentiation of many cells. However, its function in T cell homeostasis and MS treatment remains unknown. In this study, VPA was found to reduce spinal cord inflammation, demyelination, and disease scores in experimental autoimmune encephalomyelitis, a mouse model of MS. Further study indicated that VPA induces apoptosis in activated T cells and maintains the immune homeostasis. This effect was found to be mainly mediated by the caspase-8/caspase-3 pathway. Interestingly, this phenomenon was also confirmed in T cells from normal human subjects and MS patients. Considering the long history of clinical use and our new findings, we believe VPA might be a safe and effective therapy for autoimmune diseases, such as multiple sclerosis.
Localization of the binding site of tissue-type plasminogen activator to fibrin. (1986)

Functionally active A and B chains were separated from a two-chain form of recombinant tissue-type plasminogen activator after mild reduction and alkylation. The A chain was found to be responsible for the binding to lysine-Sepharose or fibrin and the B chain contained the catalytic activity of tissue-type plasminogen activator. An extensive reduction of two-chain tissue-type plasminogen activator, however, destroyed both the binding and catalytic activities. A thermolytic fragment, Fr. 1, of tissue-type plasminogen activator that contained a growth factor and two kringle segments retained its lysine binding activity. Additional thermolytic cleavages in the kringle-2 segment of Fr. 1 caused a total loss of the binding activity. These results indicated that the binding site of tissue-type plasminogen activator to fibrin was located in the kringle-2 segment.
110 channels x 2.35 Gb/s from a single femtosecond laser (1999)

We demonstrate the feasibility of a wavelength-division-multiplexed transmitter using a single femtosecond laser and generating 110 channels at 2.35 Gb/s. Chirped-pulse wavelength-division multiplexing is used to carve channels spaced by about 0.3 nm out of the broad spectrum of the laser. A 64-fold increase in bit rate per channel is accomplished through optical time-division multiplexing.
Super-resolution for everybody: An image processing workflow to obtain high-resolution images with a standard confocal microscope (2016)

In the presented work we aimed at improving confocal imaging to obtain highest possible resolution in thick biological samples, such as the mouse oocyte. We therefore developed an image processing workflow that allows improving the lateral and axial resolution of a standard confocal microscope. Our workflow comprises refractive index matching, the optimization of microscope hardware parameters and image restoration by deconvolution. We compare two different deconvolution algorithms, evaluate the necessity of denoising and establish the optimal image restoration procedure. We validate our workflow by imaging sub resolution fluorescent beads and measuring the maximum lateral and axial resolution of the confocal system. Subsequently, we apply the parameters to the imaging and data restoration of fluorescently labelled meiotic spindles of mouse oocytes. We measure a resolution increase of approximately 2-fold in the lateral and 3-fold in the axial direction throughout a depth of 60μm. This demonstrates that with our optimized workflow we reach a resolution that is comparable to 3D-SIM-imaging, but with better depth penetration for confocal images of beads and the biological sample.
Cycloheptatriene dimers: New precursors of diamantane (1981)

Dimerization of cycloheptatriene, catalyzed by titanium complexes, afforded pentacyclo[8.4.0.0 3,7 .0 4,14 .0 6,11 ]tetradeca-8,12-diene ( I ) (10%) and pentacyclo[7.5.0.0 2,8 .0 5,14 .0 7,11 ]tetradeca-3,12-diene ( II ) (90%). Structure of both dimers and their derivatives was determined by means of 1 H NMR, 13 C NMR and mass spectra. On heating, the diene II was converted into the more stable isomer I . On hydrogenation and further catalytic isomerization, both I and II gave diamantane in high yield.
ChemInform Abstract: Combining Gold(I)/Gold(III) Catalysis and C—H Functionalization: A Formal Intramolecular [3 + 2] Annulation Towards Tricyclic Indolines and Mechanistic Studies. (2011)

Abstract Tricyclic indolines are obtained by the present new intramolecular [3+2] annulation between a vinyl group and an aniline moiety using Selectfluor as oxidant.
Font recognition based on global texture analysis (2001)

We describe a novel texture analysis-based approach toward font recognition. Existing methods are typically based on local typographical features that often require connected components analysis. In our method, we take the document as an image containing some specific textures and regard font recognition as texture identification. The method is content-independent and involves no detailed local feature analysis. Experiments are carried out by using 14000 samples of 24 frequently used Chinese fonts (six typefaces combined with four styles), as well as 32 frequently used English fonts (eight typefaces combined with four styles). An average recognition rate of 99.1 percent is achieved. Experimental results are also included on the robustness of the method against image degradation (e.g., pepper and salt noise) and on the comparison with existing methods.
Acute Liver Failure (2001)

Acute liver failure (ALF) is defined as hepatic encephalopathy complicating acute liver injury. The most common etiologies are acute viral hepatitis A and B, medication overdose (e.g., acetaminophen), idiosyncratic drug reactions, ingestion of other toxins (e.g., amanita mushroom poisoning), and metabolic disorders (e.g., Reye's syndrome). Despite advances in intensive care management, mortality continues to be high (40-80%) and is partly related to ALF's complications, such as cerebral edema, sepsis, hypoglycemia, gastrointestinal bleeding, and acute renal failure. Several prognostic models have been developed to determine which patients will spontaneously recover. Treatment is directed at early recognition of the complications and general supportive measures. The only proven therapy for those who are unlikely to recover is liver transplantation. Therefore, recognition of ALF is paramount, and urgent referral to a transplant center is critical to assess transplantation status.
Efficient maximum likelihood decoding of linear block codes using a trellis (1978)

It is shown that soft decision maximum likelihood decoding of any <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">(n,k)</tex> linear block code over <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">GF(q)</tex> can be accomplished using the Viterbi algorithm applied to a trellis with no more than <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">q^{(n-k)}</tex> states. For cyclic codes, the trellis is periodic. When this technique is applied to the decoding of product codes, the number of states in the trellis can be much fewer than <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">q^{n-k}</tex> . For a binary <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">(n,n - 1)</tex> single parity check code, the Viterbi algorithm is equivalent to the Wagner decoding algorithm.
Tunneling spectroscopy of an electron waveguide (1991)

On an AlGaAs/GaAs heterostructure, we have implemented a unique ``leaky'' electron waveguide with a thin tunneling barrier as one of its confining boundaries. The current flowing through the waveguide as well as the 1D to 2D tunneling current leaking out the thin side barrier were independently measured as the electron density in the waveguide was modulated. The tunneling current shows very strong oscillations lined up with the 2${\mathit{e}}^{2}$/h conductance steps for the waveguide current. A proposed explanation is that the oscillations are a result of the 1D density of states sweeping through the Fermi level.
Feasibility of agarose microbeads with xenogeneic islets as a bioartificial pancreas (1994)

A bioartificial pancreas, that is, transplantation of islets of Langerhans (islets) which are enclosed in a semipermeable membrane, has been proposed as a treatment for type I diabetes. The islets are immuno-isolated from the host by the semipermeable membrane preventing rejection while maintaining control of glucose metabolism for an extended period. The purpose of the current research is to evaluate the feasibility of preparing agarose microbeads with xenogeneic hamster islets as a bioartificial pancreas in streptozotocin induced diabetic mice. In the recipients with a low level of anti-hamster antibodies, the combination of encapsulation of hamster islets in 5% agarose microbeads and in vitro culture of them prolonged xenograft survivals. Four of 6 recipients were still normoglycemic at 100 days after implantation. However, the same procedure was not effective in the recipients which were sensitized in advance by transplantation of free hamster islets and thus had high levels of anti-hamster antibodies. The average normoglycemic period was 32 days. Antibodies permeated through the microbeads and activated complement on the cell surfaces. The network of agarose microbeads was rendered dense by increasing the concentration of agarose to restrict the diffusion of antibodies. Graft survivals were prolonged with increasing concentrations of agarose. As an analysis using diffusion equations predicted, the survivals were inversely proportional to the diffusion coefficient of IgG in each agarose gel. Islet xenotransplantation was enabled by the combination of the microbeads with a concentration of agarose higher than 7.5% and in vitro culture even in recipients having a high level of preformed antibodies.
Plant genomic instability detected by microsatellite-primers (2000)

This report describes a new application of the Inter-Simple Sequence Repeat (ISSR) technique. This technology based on the amplification of regions between microsatellites was applied to different calli from the same cauliflower mother plant. One of the tested ISSR primers, (GATA) 4 , generated great polymorphism. Twelve different markers were detected on polyacrylamide gels. After sequencing, one sequence showed homology with a predicated A. thaliana gene closely related to genes involved in the regulation of cell proliferation in mammalians. This marker is characterised by three microsatellites and a palindromic sequence. Possible causes of mutations in this marker are discussed and will be investigated. ISSR amplification appears as a reliable method in the determination of genetic instability at early stages in in vitro culture.
Alternating copolymerization of propylene oxide and carbon dioxide with highly efficient and selective (salen)Co(III) catalysts: Effect of ligand and cocatalyst variation (2006)

Abstract Synthetic routes to a series of new (salen)CoX (salen = N , N ′‐bis(salicylidene)‐1,2‐diaminoalkane; X = Br or pentafluorobenzoate (OBzF 5 )) species are described. Several of these complexes are active for the copolymerization of propylene oxide (PO) and CO 2 , yielding regioregular poly(propylene carbonate) (PPC) without the generation of propylene carbonate byproduct. Variation of the salen ligand, as well as the inclusion of organic‐based ionic or Lewis basic cocatalysts, has dramatic effects on the resultant (salen) CoX catalytic activity. Highly active ( R , R )‐(salen‐ 1 )CoOBzF 5 (salen‐ 1 = N , N ′‐bis(3,5‐ di‐ tert ‐butylsalicylidene)‐1,2‐diaminocyclohexane) catalysts with [Ph 4 P]Cl or [PPN]Y ([PPN] = bis(triphenylphosphine)iminium; Y = Cl or OBzF 5 ) cocatalysts exhibited turnover frequencies up to 720 h − 1 for rac ‐PO/CO 2 copolymerization, yielding PPC with greater than 90% head‐to‐tail connectivity. Additionally, the ( R , R )‐(salen‐ 1 )CoOBzF 5 /[PPN]Cl catalyst system demonstrated a k rel of 9.7 for the enchainment of ( S )‐ over ( R )‐PO when the copolymerization was carried out at low temperatures. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 5182–5191, 2006
Neuron splitting for efficient feature map formation (2002)

Kohonen's Self Organising Feature Map (SOFM) produces an ordered mapping from one space to another. The paper describes an algorithm inspired by the splitting initialisation for the classical LBG method or generalised Lloyd algorithm (Y. Linde et al., 1980) for vector quantiser design, which allows the efficient generation of maps with various topologies and with high local and global ordering.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Comparisons of Ultrafine and Fine Particles in Their Associations with Biomarkers Reflecting Physiological Pathways (2014)

Using a quasi-experimental opportunity offered by greatly restricted air pollution emissions during the Beijing Olympics compared to before and after the Olympics, we conducted the current study to compare ultrafine particles (UFPs) and fine particles (PM2.5) in their associations with biomarkers reflecting multiple pathophysiological pathways linking exposure and cardiorespiratory events. Number concentrations of particles (13.0-764.7 nm) and mass concentrations of PM2.5 were measured at two locations within 9 km from the residence and workplace of 125 participating Beijing residents. Each participant was measured 6 times for biomarkers of autonomic function (heart rate, systolic and diastolic blood pressures), hemostasis (von Willebrand factor, soluble CD40 ligand, and P-selectin), pulmonary inflammation and oxidative stress (exhaled nitric oxide and exhaled breath condensate pH, malondialdehyde, and nitrite), and systemic inflammation and oxidative stress (urinary malondialdehyde and 8-hydroxy-2'-deoxyguanosine, plasma fibrinogen, and white blood cells). Linear mixed models were used to estimate associations of biomarkers with UFPs and PM2.5 measured 1-7 days prior to biomarker measurements (lags). We found that the correlation coefficient for UFPs at two locations (∼ 9 km apart) was 0.45, and at the same location, the correlation coefficient for PM2.5 vs UFPs was -0.18. Changes in biomarker levels associated with increases in UFPs and PM2.5 were comparable in magnitude. However, associations of certain biomarkers with UFPs had different lag patterns compared to those with PM2.5, suggesting that the ultrafine size fraction (≤ 100 nm) and the fine size fraction (∼ 100 nm to 2.5 μm) of PM2.5 are likely to affect PM-induced pathophysiological pathways independently.
5‐Isopropyliden‐1,2‐oxathiole 2‐Oxide by Photoisomerization of 2,2‐Dimethyl‐3(2<i>H</i>)‐thiophenone 1‐Oxide (1988)

The cyclic s-trans-1,3-dienes 3 are novel, highly promising synthetic intermediates. They may be obtained easily and selectively from the cyclic ketovinyl sulfoxides 2. This photoreaction is surprising, for the compounds 1 react completely differently upon irradiation. The photoisomerization of 2 presumably occurs via the diradical 4 as intermediate.