gebhart/patrepeval huggingface dataset:
WORLD: A Vocoder-Based High-Quality Speech Synthesis System for Real-Time Applications (2016)

A vocoder-based speech synthesis system, named WORLD, was developed in an effort to improve the sound quality of real-time applications using speech. Speech analysis, manipulation, and synthesis on the basis of vocoders are used in various kinds of speech research. Although several high-quality speech synthesis systems have been developed, real-time processing has been difficult with them because of their high computational costs. This new speech synthesis system has not only sound quality but also quick processing. It consists of three analysis algorithms and one synthesis algorithm proposed in our previous research. The effectiveness of the system was evaluated by comparing its output with against natural speech including consonants. Its processing speed was also compared with those of conventional systems. The results showed that WORLD was superior to the other systems in terms of both sound quality and processing speed. In particular, it was over ten times faster than the conventional systems, and the real time factor (RTF) indicated that it was fast enough for real-time processing.
A Language and Protocol to Support Intelligent Agent Interoperability (1992)

We describe a language and protocol intended to support interoperability among intelligent agents in a distributed application. Examples of applications envisioned include intelligent multi-agent design systems as well as intelligent planning, scheduling and replanning agents supporting distributed transportation and scheduling applications. The language, KQML, for Knowledge Query and Manipulation Language, is part of a larger DARPA
Ground-state interpretation of x-ray emission spectroscopy on adsorbates: CO adsorbed on Cu(100) (2000)

The application of resonant inelastic x-ray scattering and resonantly excited x-ray emission to adsorbates has evolved into a powerful technique to investigate the valence electronic structure of adsorbates in an atom-specific and orbital-symmetry-selective way. A surprisingly simple interpretation of spectral features in a one-electron ground-state interpretation has been found empirically. In this work $c(2\ifmmode\times\else\texttimes\fi{}2)\mathrm{C}\mathrm{O}/\mathrm{C}\mathrm{u}(100)$ is used as a prototypical system to investigate and rationalize the ground-state interpretation for adsorbates on metal surfaces, employing experimental data and ab initio calculations in different approximations. We conclude that the observed agreement between experiment and the one-electron ground-state interpretation could be due to a cancellation of dynamic core-hole effects and valence-hole relaxation. This hypothesis should be tested further by improving theoretical techniques to include the fully relaxed valence-hole final states, not possible for adsorbate systems at present. An alternative interpretation is that the inelastic x-ray scattering process is a true one-step process without the formation of a relaxed core-hole intermediate state and small differential final-state effects. In any case, resonant inelastic x-ray scattering and resonantly excited x-ray emission applied to adsorbates can be interpreted as an atom-specific and orbital-symmetry-selective projection of the ground-state electronic structure.
Retinal Stem Cells in the Adult Mammalian Eye (2000)

The mature mammalian retina is thought to lack regenerative capacity. Here, we report the identification of a stem cell in the adult mouse eye, which represents a possible substrate for retinal regeneration. Single pigmented ciliary margin cells clonally proliferate in vitro to form sphere colonies of cells that can differentiate into retinal-specific cell types, including rod photoreceptors, bipolar neurons, and Müller glia. Adult retinal stem cells are localized to the pigmented ciliary margin and not to the central and peripheral retinal pigmented epithelium, indicating that these cells may be homologous to those found in the eye germinal zone of other nonmammalian vertebrates.
Bile salt-dependent lipase biosynthesis in rat pancreatic AR 4-2 J cells. Essential requirement of N-linked oligosaccharide for secretion and expression of a fully active enzyme. (1993)

This study used the rat pancreatic AR 4-2 J cell line as a model system to investigate the role of glycosylation in bile salt-dependent lipase (BSDL) secretion and esterolytic activity. Results indicated that AR 4-2 J cells synthesized BSDL, the esterolytic activity of which was the greater part of the cell activity toward 4-nitrophenylcaproate. The protein thus expressed was glycosylated and had a molecular mass approximately 74 kDa. Exposure of these cells to tunicamycin significantly decreased [3H]mannose incorporation, while [35S]methionine incorporation in trichloroacetic acid-precipitable material was not modified. Tunicamycin treatment of AR 4-2 J cells lead to a lower molecular mass form (approximately 70 kDa) of BSDL which did not incorporate [3H]mannose. The nonglycosylated low M(r) form of the enzyme was not secreted as shown by the decreasing activity in cell-free medium which paralleled the time-dependent secretion of the enzyme. Tunicamycin had no effect on BSDL synthesis. Nevertheless, the nonglycosylated BSDL was apparently not degraded in any cell compartment as shown in part by the enzyme activity accumulation within cells upon brefeldin A treatment. The BSDL expressed by AR 4-2 J cells was characterized by a Km of 68 +/- 30 microM and a kcat of 106 +/- 19 min-1. The sequestrated BSDL due to tunicamycin treatment of cells presents a significant increase of Km of over 10 times to 757 +/- 303 microM. kcat was affected by a factor of approximately 4-445 +/- 22 min-1. These data correlated with an approximately 2.5-fold decrease of the esterolytic activity following inhibition of the N-glycosylation of the protein. The nonglycosylated BSDL was less stable to temperature than the native form. Processing inhibitors (castanospermine, 1-deoxymannojirimycin, and swainsonine) had no effect either on the enzyme activity or on its secretion. Results suggested first that the transfer of the oligosaccharide precursor to the nascent BSDL is essential for the folding of the fully active BSDL. Second that the glycan structure is required for the enzyme secretion.
RAVEN - active learning of link specifications (2011)

Abstract. With the growth of the Linked Data Web, time-efficient ap-proaches for computing links between data sources have become indis-pensable. Yet, in many cases, determining the right specification for a link discovery problem is a tedious task that must still be carried out manually. We present RAVEN, an approach for the semi-automatic de-termination of link specifications. Our approach is based on the com-bination of stable solutions of matching problems and active learning with the time-efficient link discovery framework LIMES. RAVEN aims at requiring a small number of interactions with the user to generate classifiers of high accuracy. We focus on using RAVEN to compute and configure boolean and weighted classifiers, which we evaluate in three experiments against link specifications created manually. Our evaluation shows that we can compute linking configurations that achieve more than 90 % F-score by asking the user to verify at most twelve potential links.
A &#x00394;&#x003A3;-Digitized RF Transmitter (2007)

This paper demonstrates a new transmitter architecture digitizing an envelope to control a power amplifier. The transmitter employs a low-pass ΔΣ-modulator for constant envelope modulation and noise shaping. It enables the use of highly efficient switching amplifier with high linearity. For demonstration, the overall transmitter is implemented and tested with code-division multiple access (CDMA) IS-95A signal. The transmitter delivered the expected efficiency and linearity. The performances are maintained across the broad output power range. The results clearly show the controllability of highly efficient switching power amplifier in digital domain with simple envelope modulation technique.
ST viewer: a tool for analysis and visualization of spatial transcriptomics datasets (2018)

Supplementary data are available at Bioinformatics online.
Replacement Therapy for Alpha1-Antitrypsin Deficiency Associated with Emphysema (1987)

In patients with alpha 1-antitrypsin deficiency, the development of emphysema is believed to be caused by the unchecked action of proteases on lung tissue. We evaluated the feasibility, safety, and biochemical efficacy of intermittent infusions of alpha 1-antitrypsin in the treatment of patients with alpha 1-antitrypsin deficiency. Twenty-one patients were given 60 mg of active plasma-derived alpha 1-antitrypsin per kilogram of body weight, once a week for up to six months. After a steady state had been reached, the group had trough serum levels of alpha 1-antitrypsin of 126 +/- 1 mg per deciliter as compared with 30 +/- 1 mg per deciliter before treatment, and serum anti-neutrophil elastase capacities of 13.3 +/- 0.1 microM as compared with 5.4 +/- 0.1 microM. The alpha 1-antitrypsin level in the epithelial-lining fluid of the lungs was 0.46 +/- 0.16 microM before treatment, and the anti-neutrophil elastase capacity was 0.81 +/- 0.13 microM. Six days after infusion, alpha 1-antitrypsin levels (1.89 +/- 0.17 microM) and anti-neutrophil elastase capacities (1.65 +/- 0.13 microM) in the lining fluid were significantly increased (P less than 0.0001). Because of the chronicity of the disorder and the lack of sensitive measures of lung destruction, the clinical efficacy of this therapy could not be studied rigorously. No changes in lung function were observed in our patients over six months of treatment. The only important adverse reactions to the 507 infusions were four episodes of self-limited fever. This study demonstrates that infusions of alpha 1-antitrypsin derived from plasma are safe and can reverse the biochemical abnormalities in serum and lung fluid that characterize this disorder. Together with lifetime avoidance of cigarette smoking, replacement therapy with alpha 1-antitrypsin may be a logical approach to long-term medical treatment.
Intracellular delivery of therapeutic antibodies into specific cells using antibody-peptide fusions (2019)

Because of their favorable properties as macromolecular drugs, antibodies are a very successful therapeutic modality for interfering with disease-relevant targets in the extracellular space or at the cell membrane. However, a large number of diseases involve cytosolic targets and designing antibodies able to efficiently reach intracellular compartments would expand the antibody-tractable conditions. Here, we genetically fused cell penetrating peptides (CPPs) at various positions to an antibody targeting cancer cells, evaluated the developability features of the resulting antibody-peptide fusions and the ability of selected constructs to reach the cytosol. We first determined positions in the IgG structure that were permissive to CPP incorporation without destabilizing the antibody. Fusing CPPs to the C-terminus of the light chain and either before or after the hinge had the least effect on antibody developability features. These constructs were further evaluated for cell penetration efficiency. Two out of five tested CPPs significantly enhanced antibody penetration into the cytosol, in particular when fused before or after the hinge. Finally, we demonstrate that specific antibody binding to the cell surface target is necessary for efficient cell penetration of the CPP-antibody fusions. This study provides a solid basis for further exploration of therapeutic antibodies for intracellular targets.
C-reactive protein: a critical update (2003)

In the mid 1990s, immunoassays for C-reactive protein (CRP), with greater sensitivity than those previously in routine use, revealed that increased CRP values, even within the range previously considered normal, strongly predict future coronary events. These findings triggered widespread interest, especially, remarkably, in the US, where the clinical use of CRP measurement had been largely ignored for about 30 years. CRP production is part of the nonspecific acute-phase response to most forms of inflammation, infection, and tissue damage and was therefore considered not to provide clinically useful information. Indeed, CRP values can never be diagnostic on their own and can only be interpreted at the bedside, in full knowledge of all other clinical and pathological results. However, they can then contribute powerfully to management, just as universal recording of the patient’s temperature, an equally nonspecific parameter, is of great clinical utility.

The present torrent of studies of CRP in cardiovascular disease and associated conditions is facilitated by the ready commercial availability of automated CRP assays and of CRP itself as a research reagent. However, unlike the earlier rejection in the US of CRP as an empirical test because of its perceived lack of specificity, the current enthusiasm over CRP in cardiovascular disease is widely characterized by failure to recognize appropriately the nonspecific nature of the acute-phase response, and by lack of critical biological judgment. Quality control of the source, purity, and structural and functional integrity of the CRP, and the relevance of experimental design before ascribing pathophysiological functions, are also often ignored.

This article provides information about CRP as a protein and an acute-phase reactant, and a knowledge-based framework for interpretation and analysis of clinical observations of CRP in relation to cardiovascular and other diseases. We also review the properties of CRP, its possible role in pathogenesis of disease, and our own observations that identify it as a possible therapeutic target.
Cytokines in the pathogenesis of systemic lupus erythematosus. (1999)

Cytokines, chemokines, and growth factors are overexpressed by renal parenchymal cells and by infiltrating mononuclear cells in human and experimental lupus nephritis. The importance of cytokines in the pathogenesis of lupus nephritis has been established using spontaneous mouse models of systemic lupus erythematosus (SLE). The actions of these cytokines are complex. There is a growing appreciation that the cytokine level and stage of kidney disease determines whether cytokine protects or promotes further tissue injury. This article identifies potential therapeutic targets and strategies that might halt progressive renal injury in patients with SLE.
Acid phosphatase in human breast cancer tissue (1984)

When the total acid phosphatase (AP) activity of mammary carcinoma was compared with those of benign pathology and normal mammary tissue the results showed statistically significant differences (P less than 0.05) when expressed per milligram of protein: 358 +/- 42 nmoles per hour (mean +/- standard error) in the malignant tumor, 216 +/- 30 in the benign pathology, and 96 +/- 45 in normal tissue and when expressed per milligram of DNA: 1858 +/- 234, 1227 +/- 140, 695 +/- 345 nmoles per hour, respectively. The polyacrylamide gel electrophoretic profiles showed different levels of isoenzymes 3 and 4 in the three tissue groups. The appearance of isoenzyme 1 is reported after treatment of the homogenates with 5% Triton X-100. It was also found by counterimmunoelectrophoresis that the 28,000 Xg mammary tumor supernatant cross reacts with an antiserum raised against AP isoenzyme 2 although the mammary tissue does not contain such an isoenzyme. To elucidate this point, isoenzymes 1, 3 and 4 were separated by columns of Sephadex G-200 and DEAE-Sephadex. By counterimmunoelectrophoresis, it was observed that only the fraction containing isoenzyme 4 cross-reacted with the antiserum anti-AP isoenzyme 2 maintaining the catalytic activity.
Prevention of progression of dental erosion by professional and individual prophylactic measures (1996)

The key elements for the establishment of a preventive program for patients suffering from erosion are described on pathophysiologic grounds. These elements aim 1) to diminish frequency and severity of acid challenge, 2) enhance salivary flow, 3) to enhance acid resistance, remineralization and rehardening by fluoride application, 4) to offer chemical protection by buffering substances, 5) to minimize abrasion, 6) to offer mechanical protection. Recommendations for prophylactic measures are made as a conclusion and summarized in the form of check-lists.
Isoflurane protects cardiomyocytes and mitochondria by immediate and cytosol‐independent action at reperfusion (2010)

At reperfusion, APoC inhibited mitochondrial respiration, depolarized mitochondria and acidified pH(m). These events may lead to inhibition of mPTP opening and, consequently, to preserved DeltaPsi(m) and ATP synthesis. This reduces intracellular Ca(2+) overload and cell death.
Biomaterials Used in Urology: Current Issues of Biocompatibility, Infection, and Encrustation* (1998)

This review focuses on the biomaterials used in urology, in particular, the properties of urethral catheters and ureteral stents currently being used in clinical practice. The importance of biomaterial type, biocompatibility, and encrustations are discussed and explained. Current management of bacterial infection and the importance of biofilms are presented, with recommendations based on published information.
Targeting genes in living mammals by RNA interference (2011)

More than a decade has passed since the discovery of RNA interference (RNAi), an eukaryotic sequence-specific degradation of mRNA induced by complementary double-stranded RNA (dsRNA). RNAi became a common tool for controlled down-regulation of gene expression in cultured cells, as well as in various model organisms. This review summarizes RNAi-based tools for silencing genes in living mammals, which include: (i) transgenic RNAi strategies, where RNAi is triggered by a transgene transmitted through the germline and (ii) approaches, where an RNAi trigger is delivered into an adult animal.
The Effect of Implants Loaded with Autologous Mesenchymal Stem Cells on the Healing of Canine Segmental Bone Defects* (1998)

Bone marrow has been shown to contain a population of rare mesenchymal stem cells that are capable of forming bone, cartilage, and other connective tissues. We examined the effect of cultured autologous mesenchymal stem cells on the healing of critical-sized (twenty-one-millimeter-long) segmental defects in the femora of adult female dogs. Autologous mesenchymal stem cells were isolated from bone marrow, grown in culture, and loaded onto porous ceramic cylinders consisting of hydroxyapatite (65 per cent) and beta-tricalcium phosphate ceramic (35 per cent). The animals were randomly assigned to one of three groups. In Group A (six dogs), a porous ceramic cylinder that had been loaded with autologous mesenchymal stem cells was implanted in the defect. In Group B (six dogs), a ceramic cylinder that had not been loaded with cells was placed in the defect. In Group C (three dogs), the defect was left untreated (no ceramic cylinder was implanted). Radiographs were made immediately after the operation and at four-week intervals. At sixteen weeks, the animals were killed, the involved femora were removed, and undecalcified histological sections from the defects and adjacent bone were prepared. Histological and histomorphometric studies were carried out to examine the healing of the defects and the formation of bone in and around the ceramic implants. Atrophic non-union occurred in all of the femora that had untreated defects, and only a small amount of trabecular bone formed at the cut ends of the cortex of the host bone in this group. In contrast, radiographic union was established rapidly at the interface between the host bone and the implants that had been loaded with mesenchymal stem cells. Numerous fractures, which became more pronounced with time, developed in the implants that had not been loaded with cells. Histological and morphometric analyses demonstrated that both woven and lamellar bone had filled the pores of the implants that had been loaded with mesenchymal stem cells; the amount of bone was significantly greater (p < 0.05) than that found in the pores of the implants that had not been loaded with cells. In addition, a large collar of bone (mean maximum thickness, 3.14 millimeters) formed around the implants that had been loaded with cells; this collar became integrated and contiguous with callus that formed in the region of the periosteum of the host bone. The collar of bone remodeled during the sixteen-week period of study, resulting in a size and shape that were comparable with those of the segment of bone that had been resected. Callus did not develop around the cortex of the host bone or around the defect in any of the specimens in the other two groups.
CREB Activation Induces Adipogenesis in 3T3-L1 Cells (2000)

Obesity is the result of numerous, interacting behavioral, physiological, and biochemical factors. One increasingly important factor is the generation of additional fat cells, or adipocytes, in response to excess feeding and/or large increases in body fat composition. The generation of new adipocytes is controlled by several "adipocyte-specific" transcription factors that regulate preadipocyte proliferation and adipogenesis. Generally these adipocyte-specific factors are expressed only following the induction of adipogenesis. The transcription factor(s) that are involved in initiating adipocyte differentiation have not been identified. Here we demonstrate that the transcription factor, CREB, is constitutively expressed in preadipocytes and throughout the differentiation process and that CREB is stimulated by conventional differentiation-inducing agents such as insulin, dexamethasone, and dibutyryl cAMP. Stably transfected 3T3-L1 preadipocytes were generated in which we could induce the expression of either a constitutively active CREB (VP16-CREB) or a dominant-negative CREB (KCREB). Inducible expression of VP16-CREB alone was sufficient to initiate adipogenesis as determined by triacylglycerol storage, cell morphology, and the expression of two adipocyte marker genes, peroxisome proliferator activated receptor gamma 2, and fatty acid binding protein. Alternatively, KCREB alone blocked adipogenesis in cells treated with conventional differentiation-inducing agents. These data indicate that activation of CREB was necessary and sufficient to induce adipogenesis. Finally, CREB was shown to bind to putative CRE sequences in the promoters of several adipocyte-specific genes. These data firmly establish CREB as a primary regulator of adipogenesis and suggest that CREB may play similar roles in other cells and tissues.
WePS-3 Evaluation Campaign: Overview of the Web People Search Clustering and Attribute Extraction Tasks. (2010)

Abstract. The third WePS (Web People Search) Evaluation campaign took place in 2009-2010 and attracted the participation of 13 research groups from Europe, Asia and North America. Given the top web search results for a person name, two tasks were addressed: a clustering task, which consists of grouping together web pages referring to the same person, and an extraction task, which consists of extracting salient attributes for each of the persons sharing the same name. Continuing the path of previous campaigns, this third evaluation aimed at merging both problems into one single task, where the system must return both the documents and the attributes for each of the different people sharing a given name. This is not a trivial step from the point of view of evaluation: a system may correctly extract attribute profiles from different URLs but then incorrectly merge profiles. This campaign also featured a larger testbed and the participation of a state-of-the-art commercial WePS system in the attribute extraction task. This paper presents the definition, resources, evaluation methodology and results for the clustering and attribute extraction tasks.