gebhart/patrepeval huggingface dataset:
A Bayesian framework for semantic content characterization (2002)

Current systems for content filtering, browsing, and retrieval rely on low-level image descriptors which are unintuitive for most users. In this paper, we propose an alternative framework that exploits the structured nature of most content sources to achieve semantic content characterization, and lead to much more meaningful user interaction. Computationally, this framework is based on the principles of Bayesian inference and can be implemented efficiently with Bayesian networks. As an illustration of its potential we apply it to the domain of movie databases.
Crystal structure of the α1β1 integrin I‐domain: insights into integrin I‐domain function (1999)

The alpha1beta1 integrin is a major cell surface receptor for collagen. Ligand binding is mediated, in part, through a 200 amino acid inserted 'I'-domain contained in the extracellular part of the integrin alpha chain. Integrin I-domains contain a divalent cation binding (MIDAS) site and require cations to interact with integrin ligands. We have determined the crystal structure of recombinant I-domain from the rat alpha1beta1 integrin at 2.2 A resolution in the absence of divalent cations. The alpha1 I-domain adopts the dinucleotide binding fold that is characteristic of all I-domain structures that have been solved to date and has a structure very similar to that of the closely related alpha2beta1 I-domain which also mediates collagen binding. A unique feature of the alpha1 I-domain crystal structure is that the MIDAS site is occupied by an arginine side chain from another I-domain molecule in the crystal, in place of a metal ion. This interaction supports a proposed model for ligand-induced displacement of metal ions. Circular dichroism spectra determined in the presence of Ca2+, Mg2+ and Mn2+ indicate that no changes in the structure of the I-domain occur upon metal ion binding in solution. Metal ion binding induces small changes in UV absorption spectra, indicating a change in the polarity of the MIDAS site environment.
Recombinant human osteogenic protein-1 (hOP-1) induces new bone formation in vivo with a specific activity comparable with natural bovine osteogenic protein and stimulates osteoblast proliferation and differentiation in vitro. (1992)

We reported previously that a 32-36-kDa osteogenic protein purified from bovine bone matrix is composed of dimers of two members of the transforming growth factor (TGF)-beta superfamily: the bovine equivalent of human osteogenic protein-1 (OP-1) and bone morphogenetic protein-2a, BMP-2a (BMP-2). In the present study, we produced the recombinant human OP-1 (hOP-1) in mammalian cells as a processed mature disulfide-linked homodimer with an apparent molecular weight of 36,000. Examination of hOP-1 in the rat subcutaneous bone induction model demonstrated that hOP-1 was capable of inducing new bone formation with a specific activity comparable with that exhibited by highly purified bovine osteogenic protein preparations. The half-maximal bone-inducing activity of hOP-1 in combination with a rat collagen matrix preparation was 50-100 ng/25 mg of matrix as determined by the calcium content of day 12 implants. Evaluation of hOP-1 effects on cell growth and collagen synthesis in rat osteoblast-enriched bone cell cultures showed that both cell proliferation and collagen synthesis were stimulated in a dose-dependent manner and increased 3-fold in response to 40 ng of hOP-1/ml. Examination of the expression of markers characteristic of the osteoblast phenotype showed that hOP-1 specifically stimulated the induction of alkaline phosphatase (4-fold increase at 40 ng of hOP-1/ml), parathyroid hormone-mediated intracellular cAMP production (4-fold increase at 40 ng of hOP-1/ml), and osteocalcin synthesis (5-fold increase at 25 ng of hOP-1/ml). In long-term (11-17 day) cultures of osteoblasts in the presence of beta-glycerophosphate and L(+)-ascorbate, hOP-1 markedly increased the rate of mineralization as measured by the number of mineral nodules per well (20-fold increase at 20 ng of hOP-1/ml). Direct comparison of TGF-beta 1 and hOP-1 in these bone cell cultures indicated that, although both hOP-1 and TGF-beta 1 promoted cell proliferation and collagen synthesis, only hOP-1 was effective in specifically stimulating markers of the osteoblast phenotype.
Structure and Function of Complement Activating Enzyme Complexes C1 and MBL-MASPs (2001)

The complement system is a major effector arm of the immune defense contributing to the destruction of invading pathogens. There are three possible routes of complement cascade activation: the classical, the alternative and the lectin pathways. The activation of the classical and lectin pathways is initiated by supramolecular complexes, which resemble each other. Each complex has a recognition subunit (C1q in the classical and mannose-binding lectin (MBL) in the lectin pathway), which associates with serine protease zymogens (C1q with C1r and C1s, and MBL with MBL-associated serine proteases: MASP-1, MASP-2) to form the C1 and MBL-MASPs complexes, respectively. As the recognition subunits bind to activator structures, subsequent activation of the serine protease zymogens occurs. The precise structure of the complexes and the exact mechanism of their activation have not been solved, yet. In this review we summarize the recent advances about the structure and function of the individual subcomponents of both complexes achieved by genetic engineering, molecular modeling, physico-chemical and functional studies. Special emphasis will be laid on the serine proteases: the role of the individual domains in the assembly of the C1s-C1r-C1r-C1s tetramer and in the control of the protease activity will be discussed. We will then focus on recent functional models of the supramolecular complexes. The question of how a non-enzymatic signal (the binding of C1q or MBL to activators) can be converted into enzymatic events (activation of serine protease zymogens) will be addressed. The similarities and differences between C1 and MBL-MASPs will also be discussed.
Fas ligand expression by astrocytoma in vivo: maintaining immune privilege in the brain? (1997)

Astrocytomas are among the most common brain tumors that are usually fatal in their malignant form. They appear to progress without significant impedance from the immune system, despite the presence of intratumoral T cell infiltration. To date, this has been thought to be the result of T cell immunosuppression induced by astrocytoma-derived cytokines. Here, we propose that cell contact-mediated events also play a role, since we demonstrate the in vivo expression of Fas ligand (FasL/CD95L) by human astrocytoma and the efficient killing of Fas-bearing cells by astrocytoma lines in vitro and by tumor cells ex vivo. Functional FasL is expressed by human, mouse, and rat astrocytoma and hence may be a general feature of this nonlymphoid tumor. In the brain, astrocytoma cells can potentially deliver a death signal to Fas+ cells which include infiltrating leukocytes and, paradoxically, astrocytoma cells themselves. The expression of FasL by astrocytoma cells may extend the processes that are postulated to occur in normal brain to maintain immune privilege, since we also show FasL expression by neurons. Overall, our findings suggest that FasL-induced apoptosis by astrocytoma cells may play a significant role in both immunosuppression and the regulation of tumor growth within the central nervous system.
Renal dysfunction associated with infection of Leptospira interrogans in a horse (1992)

Renal failure associated with infection of Leptospira interrogans was detected in a horse. Fever, leukocytosis, pyuria, isosthenuria, and azotemia were suggestive of an inflammatory urinary tract disease. Despite persistent pyuria, no bacteria were found during routine microscopic examinations or bacteriologic culturing of urine. A fluorescent antibody examination of the urine was positive for L interrogans. Serologic testing during a 6-month period, supported an acute infection with L interrogans serovar pomona. Treatment with intravenously administered fluids and antimicrobials resulted in clinical recovery. Leptospira interrogans serovar pomona has been reported as causing fever, uveitis, or abortion in horses.
Emerging drugs to reduce abnormal β-amyloid protein in Alzheimer’s disease patients (2016)

Introduction: Currently available drugs against Alzheimer’s disease (AD) target cholinergic and glutamatergic neurotransmissions without affecting the underlying disease process. Putative disease-modifying drugs are in development and target β-amyloid (Aβ) peptide and tau protein, the principal neurophatological hallmarks of the disease.Areas covered: Phase III clinical studies of emerging anti-Aβ drugs for the treatment of AD were searched in US and EU clinical trial registries and in the medical literature until May 2016.Expert opinion: Drugs in Phase III clinical development for AD include one inhibitor of the β-secretase cleaving enzyme (BACE) (verubecestat), three anti-Aβ monoclonal antibodies (solanezumab, gantenerumab, and aducanumab), an inhibitor of receptor for advanced glycation end products (RAGE) (azeliragon) and the combination of cromolyn sodium and ibuprofen (ALZT-OP1). These drugs are mainly being tested in subjects during early phases of AD or in subjects at preclinical stage of familial AD or even in asymptomatic subjects at high risk of developing AD. The hope is to intervene in the disease process when it is not too late. However, previous clinical failures with anti-Aβ drugs and the lack of fully understanding of the pathophysiological role of Aβ in the development of AD, put the new drugs at substantial risk of failure.
Improving the Design of Existing Code (2000)

class Price { abstract int getPriceCode(); // 取得價格代號 } class ChildrensPrice extends Price { int getPriceCode() { return Movie.CHILDRENS; } } class NewReleasePrice extends Price { int getPriceCode() { return Movie.NEW_RELEASE; } } class RegularPrice extends Price { int getPriceCode() { return Movie.REGULAR; } } 現在我可以編譯這些新 classes了。
Dosing With 5% Imiquimod Cream 3 Times per Week for the Treatment of Actinic Keratosis (2005)

The 5% imiquimod cream dosed 3 times weekly for 16 weeks is safe and effective for the treatment of AK.
The natural history of epilepsy in tuberous sclerosis complex (2009)

Most patients with TSC develop epilepsy and most develop multiple seizure types. Onset typically occurs in the first year of life; however, adults remain at risk. Although refractory epilepsy is common, many patients achieve seizure control. Many features of seizure history are predictive of cognitive and epilepsy outcome.
N.D.德朗斯抽水蓄能电站建设概况 (2012)

由于N.D.德朗斯抽水蓄能电站能够在短短几分钟内实现抽水和发电模式的双向转换,因此,该电站在增强国际互联电网稳定性方面将发挥重要作用。对该工程的建设背景、设计方案研究、设计理念及目的、施工状况及进展,以及工程建成后的环境影响等方面作了介绍。
Incorporation of the factor IX Padua mutation into FIX-Triple improves clotting activity in vitro and in vivo (2013)

Using gain-of-function factor IX (FIX) for replacement therapy for haemophilia B (HB) is an attractive strategy. We previously reported a high-activity FIX, FIX-Triple (FIX-V86A/E277A/R338A) as a good substitute for FIX-WT (wild-type) in protein replacement therapy, gene therapy, and cell therapy. Here we generated a new recombinant FIX-TripleL (FIX-V86A/E277A/R338L) by replacing the alanine at residue 338 of FIX-Triple with leucine as in FIX-Padua (FIX-R338L). Purified FIX-TripleL exhibited 22-fold higher specific clotting activity and 15-fold increased binding affinity to activated FVIII compared to FIX-WT. FIX-TripleL increased the therapeutic potential of FIX-Triple by nearly 100% as demonstrated with calibrated automated thrombogram and thromboelastography. FIX-TripleL demonstrated a normal clearance rate in HB mice. The clotting activity of FIX-TripleL was consistently 2- to 3-fold higher in these mice than that of FIX-Triple or FIX-R338L. Gene delivery of adeno-associated virus (AAV) in HB mice showed that FIX-TripleL had 15-fold higher specific clotting activity than FIX-WT, and this activity was significantly better than FIX-Triple (10-fold) or FIX-R338L (6-fold). At a lower viral dose, FIX-TripleL improved FIX activity from sub-therapeutic to therapeutic levels. Under physiological conditions, no signs of adverse thrombotic events were observed in long-term AAV-FIX-treated C57Bl/6 mice. Hepatocellular adenomas were observed in the high- but not the medium- or the low-dose AAV-treated mice expressing FIX-WT or FIX-Triple, indicating the advantages of using hyperfunctional FIX variants to reduce viral doses while maintaining therapeutic clotting activity. Thus, incorporation of the FIX Padua mutation significantly improves the clotting function of FIX-Triple so as to optimise protein replacement therapy and gene therapy.
Ubiquitination of α-synuclein and autophagy in Parkinson's disease (2008)

alpha-Synuclein is mutated in Parkinson's disease (PD) and is found in cytosolic inclusions, called Lewy bodies, in sporadic forms of the disease. A fraction of alpha-synuclein purified from Lewy bodies is monoubiquitinated, but the role of this monoubiquitination has been obscure. We now review recent data indicating a role of alpha-synuclein monoubiquitination in Lewy body formation and implicating the autophagic pathway in regulating these processes. The E3 ubiquitin-ligase SIAH is present in Lewy bodies and monoubiquitinates alpha-synuclein at the same lysines that are monoubiquitinated in Lewy bodies. Monoubiquitination by SIAH promotes the aggregation of alpha-synuclein into amorphous aggregates and increases the formation of inclusions within dopaminergic cells. Such effect is observed even at low monoubiquitination levels, suggesting that monoubiquitinated alpha-synuclein may work as a seed for aggregation. Accumulation of monoubiquitinated alpha-synuclein and formation of cytosolic inclusions is promoted by autophagy inhibition and to a lesser extent by proteasomal and lysosomal inhibition. Monoubiquitinated alpha-synuclein inclusions are toxic to cells and recruit PD-related proteins, such as synphilin-1 and UCH-L1. Altogether, the new data indicate that monoubiquitination might play an important role in Lewy body formation. Decreasing alpha- synuclein monoubiquitination, by preventing SIAH function or by stimulating autophagy, constitutes a new therapeutic strategy for Parkinson's disease.
Measles Virus Structural Components Are Enriched into Lipid Raft Microdomains: a Potential Cellular Location for Virus Assembly (2000)

The process of measles virus (MV) assembly and subsequent budding is thought to occur in localized regions of the plasma membrane, to favor specific incorporation of viral components, and to facilitate the exclusion of host proteins. We demonstrate that during the course of virus replication, a significant proportion of MV structural proteins were selectively enriched in the detergent-resistant glycosphingolipids and cholesterol-rich membranes (rafts). Isolated rafts could infect the cell through a membrane fusion step and thus contained all of the components required to create a functional virion. However, they could be distinguished from the mature virions with regards to density and Triton X-100 resistance behavior. We further show that raft localization of the viral internal nucleoprotein and matrix protein was independent of the envelope glycoproteins, indicating that raft membranes could provide a platform for MV assembly. Finally, at least part of the raft MV components were included in the viral particle during the budding process. Taken together, these results strongly suggest a role for raft membranes in the processes of MV assembly and budding.
Neural encoding of single-formant stimuli in the cat. I. Responses of auditory nerve fibers (1993)

1. We have studied auditory responses to a set of speech-related narrowband sounds, single-formant stimuli (SFSs), in populations of auditory nerve fibers (ANFs). An analytic method was developed to extract the envelope of temporal discharge patterns of the ANF responses to nonsinusoidally modulated stimuli, whose spectra have multiple clusters of components. Such responses are often encountered in the auditory system when complex stimuli are used and have traditionally been studied by analyzing the fundamental component of the responses. 2. The envelope modulation in the SFSs is shown to be represented by the response patterns of ANFs. When the whole ANF population is considered, the information on modulation in stimulus envelope does not disappear at the highest sound level tested at all best frequencies (BFs) we studied (1-10 kHz). The representation is the best at medium sound levels and degrades at high sound levels. Low/medium-spontaneous rate (SR) ANFs showed greater envelope modulation in their responses at high sound levels than do high-SR ANFs. The quality of the representation at high sound levels is, on average, proportional to BF threshold of an ANF. On the basis of populations of ANFs with all SRs, the envelope modulation in the SFSs is represented over a wide range of sound levels. 3. We found that low-BF ANFs differ from high-BF ANFs in representing envelope modulation in the SFSs. For ANFs with BFs less than approximately 6 kHz, information on stimulus envelope is not only contained in spectral components near direct current but also in components at the vicinities of frequencies equal to BF and its multiples. In fact, for ANFs with BFs < 3 kHz, the contribution from spectral components centered at BF to overall response modulation is greater than that from spectral components near direct current. These findings indicate that, by using measures solely based on the fundamental component, the amount of modulation in the responses to narrowband stimuli is underestimated for low-BF ANFs. 4. Off-BF stimulation of ANFs with SFSs was found to result in increased envelope modulation in responses at high sound levels. The further away the stimulus is centered relative to unit BF, the greater the modulation it induces, provided that the stimulus is capable of exciting the unit. An SFS centered as close as 15% off unit BF can produce a significant increase in the modulation of responses at very high sound levels.(ABSTRACT TRUNCATED AT 400 WORDS)
Development of a lysis-filtration blood culture technique (1977)

A lysed-blood culture system that quickly lyses patients' blood near neutrality and is relatively noninjurious to more delicate pathogens such as Haemophilus influenzae and Bacteroides fragilis is reported. The lysing solution includes culture medium, 0.004 M sodium carbonate and bicarbonate, 0.04% Triton X-100,and 0.6% Rhozyme (a mixture of proteases). Most of the pathogens tested multiplied in the lysing solution. The lysed blood normally is immediately filtered. The membrane is transferred to culture broth. The greatest advantage realized from this blood culture technique is separation of pathogens from antibiotics, bactericidal antibodies, complement, opsonins, and phagocytic systems. Another advantage is the concentration of organisms into a small volume of clear medium for faster growth and visualization of growth. It was observed that both gram-negative and -positive organisms were attracted during filtration to the filter material and were not removed from it by backwashing with buffer. Thus, filter membranes with porosities much larger than would nominally be expected to retain bacteria retained all or part of light and heavy Escherichia coli and Staphylococcus aureus suspensions. Advantage may be taken of this phenomenon to use filters with larger pore sizes and avoid filter clogging by poorly lysed specimens. Porr lysis may result from addition of too much blood to the lysing solution, blood with elevated numbers of erythrocytes or leukocytes, or blood from some people whose blood is naturally more resistant to lysis.
Enhanced spread spectrum watermarking of MPEG-2 AAC audio (2002)

A novel AAC watermarking scheme with low structural and computational complexity is proposed to achieve real-time AAC audio watermark embedding capability. In this scheme, an enhanced spread spectrum watermarking method that increases the robustness and information hiding capacity of the watermarking channel is developed and employed. Furthermore, this scheme improves the speed of the encoding process in that we directly use the quantized indices rather than the dequantized coefficients, thus no explicit dequantization and requantization are performed. Our embedded watermark is tested to be robust against AAC/MP3 transcoding at a rate of 10 bps. The scheme is suitable for speedy encoding and decoding of watermark with low cost hardware.
Novel Single Chain cAMP Sensors for Receptor-induced Signal Propagation (2004)

cAMP is a universal second messenger of many G-protein-coupled receptors and regulates a wide variety of cellular events. cAMP exerts its effects via cAMP-dependent protein kinase (PKA), cAMP-gated ion channels, and two isoforms of exchange protein directly activated by cAMP (Epac). Here we report the development of novel fluorescent indicators for cAMP based on the cAMP-binding domains of Epac and PKA. Fluorescence resonance energy transfer between variants of green fluorescent protein (enhanced cyan fluorescent protein and enhanced yellow fluorescent protein) fused directly to the cAMP-binding domains was used to analyze spatial and temporal aspects of cAMP-signaling in different cells. In contrast to previously developed PKA-based indicators, these probes are comprised of only a single binding site lacking cooperativity, catalytic properties, and interactions with other proteins and thereby allow us to easily image free intracellular cAMP and rapid signaling events. Rapid beta-adrenergic receptor-induced cAMP signals were observed to travel with high speed ( approximately 40 microm/s) throughout the entire cell body of hippocampal neurons and peritoneal macrophages. The developed indicators could be ubiquitously applied to studying cAMP, its physiological role and spatio-temporal regulation.
Macroporous Hydrogel Scaffolds and Their Characterization By Optical Coherence Tomography (2010)

A simple porogen-leaching method to fabricate macroporous cyclic acetal hydrogel cell scaffolds is presented. Optical coherence tomography (OCT) was applied for nondestructive imaging and quantitative characterization of the scaffold structures. High-resolution OCT reveals the microstructures of the engineered tissue scaffolds in three dimensions. It also enables subsequent image processing to investigate quantitatively several key morphological design parameters for macroporous scaffolds, including the volume porosity, pore interconnectivity, and pore size. Two image-processing algorithms were adapted: three-dimensional labeling was applied to assess the interconnectivity, and erosion was applied to assess the pore size. Scaffolds with different design parameters were imaged, characterized, and compared. OCT imaging and image processing successfully discriminated scaffolds made from different formulations in terms of volume porosity, interconnectivity, and pore size. The cell viability and their spread across the scaffolds were confirmed by the fluorescence microscopy co-registered with OCT.