gebhart/patrepeval huggingface dataset:
A new paradigm in the treatment of osteoporosis: Wnt pathway proteins and their antagonists. (2007)

The need to develop novel drugs that stimulate bone formation and thereby elevate bone mass (anabolics), as opposed to preventing bone loss (anti-resorptives), has opened new research areas for therapeutic intervention in the treatment of osteoporosis. One of these areas is the Wnt/beta-catenin (canonical) pathway that plays an important role in regulating osteoblast proliferation and differentiation. Alterations in this pathway have been associated with bone disorders characterized by either low or high bone mass. However, as the Wnt/beta-catenin pathway is a ubiquitous mechanism not just exclusively involved in bone formation, targeting Wnts may be a challenge (eg, targeting Wnt activity may induce cancer). Nevertheless, specific pharmacological targets to influence bone formation have been identified in this pathway; these include the Wnt-lipoprotein receptor-related protein 5/6-frizzled complex and Wnt antagonists such as sclerostin. Since sclerostin expression is highly restricted to osteocytes, this specific target may be ideal for anabolic drug therapy.
In silico prototyping of wetlab experiments (2002)

The background, implementation, and graphical interface of the Cybermouse simulation-dynamic information system are outlined. It is believed that simulation-dynamic information systems are the next steps in managing complex information through semi-autonomous software. In particular, by making available simulation methods based on nonlinear, event-driven dynamics, such systems show emergent behaviors derived from self-organization and are therefore useful tools in education and research.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Heparin Potentiates the in Vivo Ectopic Bone Formation Induced by Bone Morphogenetic Protein-2 (2006)

Although bone morphogenetic proteins (BMPs) are clinically useful for bone regeneration, large amounts are required to induce new bone formation in monkeys and humans. We found recently that heparin stimulates BMP activity in vitro (Takada, T., Katagiri, T., Ifuku, M., Morimura, N., Kobayashi, M., Hasegawa, K., Ogamo, A., and Kamijo, R. (2003) J. Biol. Chem. 278, 43229-43235). In the present study, we examined whether heparin enhances bone formation induced by BMPs in vivo and attempted to determine the molecular mechanism by which heparin stimulates BMP activity using C2C12 myoblasts. Heparin enhanced BMP-2-induced gene expression and Smad1/5/8 phosphorylation at 24 h and thereafter, although not within 12 h. Heparitinase treatment did not affect the response of cells to BMP-2. In the presence of heparin, degradation of BMP-2 was blocked, and the half-life of BMP-2 in the culture medium was prolonged by nearly 20-fold. Although noggin mRNA was induced by BMP-2 within 1 h regardless of the presence of heparin, noggin failed to inhibit BMP-2 activity in the presence of heparin. Furthermore, simultaneous administration of BMP-2 and heparin in vivo dose-dependently induced larger amounts of mineralized bone tissue compared with BMP-2 alone. These findings clearly indicate that heparin enhances BMP-induced osteoblast differentiation not only in vitro but also in vivo. This study indicates that heparin enhances BMP-induced osteoblast differentiation in vitro and in vivo by protecting BMPs from degradation and inhibition by BMP antagonists.
Plant breeding: principles and prospects. (1993)

Introduction. Genetic systems and population structure. Genetic systems, recombination and variability. Population structure and variability. Sources variation. Plant genetic resources. Induced mutations. Interspecific hybridization by sexual means. Chromosome manipulation and polyploidy. Somatic hybridization. Gene cloning and identification. Gene transfer to plants: approaches and available techniques. The role of gene technology in plant breeding. Assessment of variation. Biometrical genetics in breeding. Biochemical characterization of populations. Manipulation of genetic systems. Self- and cross-incompatibility systems. Male sterility. Apomixis. Micropropagation and somatic embryogenesis. Andro- and parthenogenesis. Selection methods. Selection strategies and choice of breeding methods. Marker-assisted selection. Gametophytic and sporophytic selection. In vitro selection. Adaptation. Genotype x environment interaction and adaptation. Augmenting yield-based selection. Resistance to abiotic stresses. Resistance to parasites. Specific trait breeding. Breeding for improved symbiotic nitrogen fixation. Photosynthetic and respiratory efficiency. Breeding for efficient root systems. On the utilization of renewable plant resources. Epilogue. The need for comprehensive plant breeding strategy.
SIR2004: an improved tool for crystal structure determination and refinement (2005)

SIR2004 is the evolution of the SIR2002 program [Burla, Camalli, Carrozzini, Cascarano, Giacovazzo, Polidori &amp; Spagna (2003). J. Appl. Cryst. 36 , 1103]. It is devoted to the solution of crystal structures by direct and Patterson methods. Several new features implemented in SIR2004 make this program efficient: it is able to solve ab initio both small/medium-size structures as well as macromolecules (up to 2000 atoms in the asymmetric unit). In favourable circumstances, the program is also able to solve protein structures with data resolution up to 1.4–1.5 Å, and to provide interpretable electron density maps. A powerful user-friendly graphical interface is provided.
The effects of gp100 and tyrosinase peptide vaccinations on nevi in melanoma patients (2006)

The primary goal of peptide vaccinations with gp100 and tyrosinase is to activate melanoma-specific T cells in order to prevent melanoma recurrence. Nevi were studied in order to assess the effects on benign melanocytes. No significant changes in lymphocytes, langerhans cells, expression of MHC antigens, or melanocytic markers were found. The increase in p53 and bcl-2 raises the possibility that vaccination with melanocytic antigens stimulates a response in benign melanocytes.
Wespen en mieren: Vespidae – plooivleugelwespen (2004)

Plooivleugelwespen zijn, althans in Nederland, direct herkenbaar aan de in rust overlangs dubbelgevouwen voorvleugels (fig. 57). Hierdoor lijken de vleugels erg smal. In het buitenland is dit wat minder eenvoudig, omdat daar ook plooivleugelwespen zonder gevouwen voorvleugels voorkomen, en er ook andere Hymenoptera bestaan met dit kenmerk. Iedereen kent de sociale vertegenwoordigers van deze groep, zoals de ‘limonadewespen’ van het genus Vespula. Dit is echter slechts een klein gedeelte van deze wespenfamilie. Over de voordelen van het hebben van geplooide vleugels wordt in de literatuur slechts gespeculeerd. Misschien zijn lange, ongevouwen vleugels hinderlijk bij de bewegingen van de dieren in smalle nestgangen en broedcellen en raken ze sneller versleten.
Characterization of functional neurotensin receptors on human lymphocytes. (1994)

Using a combination of molecular techniques and Scatchard analysis, we have demonstrated the presence of a cell surface NTR with a high affinity for neurotensin on human PBLS and the MOLT-4 cell line. The functional role of NTR has been established by enhanced proliferation with addition of neurotensin. These data provide further evidence for a link between neurotensin and the immune system and suggest that neurotensin may play an important regulatory role in gut mucosal immune responses in vivo.
Parametric blends for shape modeling (2003)

Blends are surfaces that arise in manufacturing and do not usually appear on blue-prints. Methods are presented for modelling them in CAD/CAM systems. Modelling of two types of blends for parametric surfaces is considered; rolling sphere blends and general cross-section blends. The blend surface design task is split into two subtasks: identification of the normal cross section as well as the path followed by it. The path is identified as the intersection of the offsets of the given two surfaces. The offsetting technique establishes a natural parametric correspondence between the two blend boundary curves. The design of the shape of the cross section curve is left to the user. This provides the flexibility demanded by the application at hand.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Infection, autoimmunity and autoimmune disease (1996)

Studies of the immune response of mammals to infectious agents have revealed that members of the hsp60 and hsp 70 family are highly immunodominant. Given their high conservation during evolution this was surprising, because of the apparent risk of triggering of autoimmunity and autoimmune disease during the defense of a mammal against infection. However, detailed studies of the immune responses to HSP in models of autoimmune diseases in animals resulted in a change of the view that autoimmunity necessarily leads to autoimmune disease. It has been found that modulation of autoimmunity to HSP is one way to prevent autoimmune disease. At least in some cases even treatment of autoimmune diseases by immunization with heat shock protein appears feasible. This was shown in adjuvant arthritis in Lewis rats and insulin dependent diabetes in NOD mice. Hsp60 and hsp70 are ubiquitous proteins. Their involvement in regulatory loops of autoimmunity may serve as basis for the development of strategies, to prevent and/or treat autoimmune diseases even without knowledge of the causative (auto-)antigen.
Interaction primitives for human-robot cooperation tasks (2014)

To engage in cooperative activities with human partners, robots have to possess basic interactive abilities and skills. However, programming such interactive skills is a challenging task, as each interaction partner can have different timing or an alternative way of executing movements. In this paper, we propose to learn interaction skills by observing how two humans engage in a similar task. To this end, we introduce a new representation called Interaction Primitives. Interaction primitives build on the framework of dynamic motor primitives (DMPs) by maintaining a distribution over the parameters of the DMP. With this distribution, we can learn the inherent correlations of cooperative activities which allow us to infer the behavior of the partner and to participate in the cooperation. We will provide algorithms for synchronizing and adapting the behavior of humans and robots during joint physical activities.
High Levels of Cathepsin B Predict Poor Outcome in Patients with Breast Cancer (1998)

Cathepsin B (CB) is a thiol-stimulated protease implicated in cancer invasion and metastasis. Other proteases involved in cancer spread such as urokinase-type plasminogen activator (uPA) and cathepsin D have previously been shown to be prognostic markers in breast cancer. CB was assayed by ELISA in 193 patients with primary breast cancer. CB levels were significantly higher in both primary and metastatic breast tumors than in fibroadenomas (p = 0.0001). In the primary carcinomas, CB levels showed no significant correlation with either nodal status, tumor size or estrogen receptor (ER) status. Patients with primary breast cancers containing high levels of CB had a significantly shorter disease-free interval (p = 0.01, chi-square = 6.61) and overall survival (p = 0.014, chi-square = 6.08) than patients with low levels of the protease. However, in multivariate analysis, using nodal status, tumor size, ER status and urokinase plasminogen activator (uPA), CB was not an independent prognostic marker. In contrast, nodal status, ER status and uPA were prognostic in multivariate analysis. In conclusion, CB, like certain other proteases implicated in cancer metastasis, correlates with poor outcome in patients with breast cancer. These results thus support the evidence from model systems linking CB to cancer spread. Inhibition of CB expression or activity might therefore be exploited for anti-metastatic therapies.
Simulation of Application Strategies for Local Drug Delivery to the Inner Ear (2006)

Local, rather than systemic, drug delivery to the inner ear is becoming more widely used to treat inner ear disorders. While many substances are undergoing preclinical and clinical studies, it is equally important to develop appropriate drug delivery systems. Pharmacokinetic studies are technically demanding in animals and almost impossible in humans. Computer simulations have helped establish the basic principles of drug distribution in the inner ear. The distribution of methylprednisolone in the guinea pig cochlea has been simulated for different drug delivery systems based on kinetic parameters established in prior studies. Results were compared for different rates of drug clearance from the middle ear. Absolute and relative drug levels in the perilymph were highly dependent on how long the drug remained in the middle ear. For a brief (30 min) application, the basal to apical drug gradient was higher than for longer delivery times. These findings show that controlling middle ear drug clearance is of critical importance.
Strong Influence of Hole Shape on Extraordinary Transmission through Periodic Arrays of Subwavelength Holes (2004)

We show that extraordinary light transmission of periodic subwavelength hole arrays, generally attributed to surface-plasmon resonances, is strongly influenced by the hole shape. Both experiments and calculations, based on a Fourier modal method, demonstrate that a shape change from circular to rectangular increases the normalized transmission by an order of magnitude while the hole area decreases. Moreover, the spectra exhibit large redshifts (approximately 2500 cm(-1)). A comparison with the transmission of isolated holes shows that shape resonances of the rectangular holes play a dominant role.
Cognitive Decline in Prodromal Alzheimer Disease and Mild Cognitive Impairment (2011)

Dementia due to Alzheimer disease is preceded by about 5 to 6 years of accelerated decline in multiple cognitive functions. By contrast, little decline is evident in persons who do not develop Alzheimer disease.
Effectiveness of Inactivated Influenza Vaccines Varied Substantially with Antigenic Match from the 2004–2005 Season to the 2006–2007 Season (2008)

Influenza VE varied substantially across 3 seasons and was highest when antigenic match was optimal. VE estimates that used data from test-negative control subjects were consistently higher than those that used data from traditional control subjects.
Epac Mediates a cAMP-to-PKC Signaling in Inflammatory Pain: An Isolectin B4(+) Neuron-Specific Mechanism (2005)

The epsilon isoform of protein kinase C (PKCepsilon) has emerged as a critical second messenger in sensitization toward mechanical stimulation in models of neuropathic (diabetes, alcoholism, and cancer therapy) as well as acute and chronic inflammatory pain. Signaling pathways leading to activation of PKCepsilon remain unknown. Recent results indicate signaling from cAMP to PKC. A mechanism connecting cAMP and PKC, two ubiquitous, commonly considered separate pathways, remains elusive. We found that, in cultured DRG neurons, signaling from cAMP to PKCepsilon is not mediated by PKA but by the recently identified cAMP-activated guanine exchange factor Epac. Epac, in turn, was upstream of phospholipase C (PLC) and PLD, both of which were necessary for translocation and activation of PKCepsilon. This signaling pathway was specific to isolectin B4-positive [IB4(+)] nociceptors. Also, in a behavioral model, cAMP produced mechanical hyperalgesia (tenderness) through Epac, PLC/PLD, and PKCepsilon. By delineating this signaling pathway, we provide a mechanism for cAMP-to-PKC signaling, give proof of principle that the mitogen-activated protein kinase pathway-activating protein Epac also stimulates PKC, describe the first physiological function unique for the IB4(+) subpopulation of sensory neurons, and find proof of principle that G-protein-coupled receptors can activate PKC not only through the G-proteins alpha(q) and betagamma but also through alpha(s).
Genomic analysis I: inheritance units and genetic selection in the rapid discovery of locus linked DNA markers (1986)

We propose, and test using a Monte-Carlo analysis (a computer-based numerical analysis using a random number generator), a novel and efficient method to obtain sets of DNA markers linked to any inherited genetic locus. The method consists of a targeted search that is based on the common inheritance among members of an outbred pedigree, of discrete chromosome lengths, which we call inheritance units, to obtain DNA markers linked to the locus. In cases where two individuals inherit the same trait through two different lines of descent from a common ancestor, the set of inheritance units in each of the two genomes includes an inheritance unit that is identical in both individuals for a substantial distance on both sides of the DNA sequence which confers the trait. The power of the technique derives from the genetic selection that reduces the size and number of the inheritance units as the generational distance between the two individuals being compared increases.
Optimization of Retroviral Gene Transfer Protocol to Maintain the Lymphoid Potential of Progenitor Cells (2001)

We have attempted to improve retrovirus-mediated gene transfer efficacy into hematopoietic progenitor cells (HPCs) without causing them to lose their lymphoid potential. Highly purified CD34(+) cells on CH-296 fibronectin fragments have been transduced with three different cytokine combinations. Murine CD2 was used as a marker gene. Transgene expression was assayed by FACS analysis shortly after transduction of CD34(+) cells and after long-term culture (LTC) extended by differentiation of various lymphoid lineages: NK cells, B cells, and dendritic cells. Compared with the historical cytokine mix, i.e., SCF (stem cell factor) + IL-3 (interleukin 3) + IL-6, the combination SCF + FL (Flt-3 ligand) + M-GDF (megakaryocyte growth and differentiation factor) + IL-3 significantly improved the total number of viable cells and CD34(+) cells after transduction and the long term-cultured progenitors after 6 weeks. In addition, the combination of SCF + FL + M-GDF + IL-3 maintained more efficiently the lymphoid potential of the progeny of transduced long term-cultured CD34(+) cells, as attested by the significantly higher number of CD56(+), CD19(+), and CD1a(+) cells recovered when FL and M-GDF were added to SCF + IL-3. Thus, even though additional improvements may still be needed in transduction of HPCs, these conditions were adopted for a clinical trial of gene therapy for X-linked severe combined immunodeficiency.
Fractal Image Compression (1993)

The top-selling multimedia encyclopedia Encarta, published by Microsoft Corporation, includes on one CD-ROM seven thousand color photographs which may be viewed interactively on a computer screen. The images are diverse; they are of buildings, musical instruments, people’s faces, baseball bats, ferns, etc. What most users do not know is that all of these photographs are based on fractals and that they represent a (seemingly magical) practical success of mathematics. Research on fractal image compression evolved from the mathematical ferment on chaos and fractals in the years 1978–1985 and in particular on the resurgence of interest in Julia sets and dynamical systems. Here I describe briefly some of the underlying ideas. Following Hutchinson [7], see also [5], consider first a finite set of contraction mappings wi, each with contractivity factor s < 1, taking a compact metric space X into itself, i = 1,2, . . .N. Such a setup is called an iterated function system (IFS), [1]. Use this IFS to construct a mapping W from the space H of nonempty compact subsets of X into itself by defining, in the self-explanatory notation, W (B) = N ⋃
Amorphous silicon alloy solar cells and modules-opportunities and challenges (1996)

The low material cost and proven manufacturability of amorphous silicon (a-Si) alloy solar panels make them ideally suited for low-cost terrestrial application. a-Si alloy solar panels have been commercially available for more than a decade for applications ranging from small calculators to large-scale grid-connected power systems. Extensive R&D efforts have resulted in a significant improvement in stable cell and module efficiencies with the achievement of 11.8% cell efficiency and 10.2% module efficiency using a spectral-splitting triple-bandgap, triple-cell approach. Further gains in efficiency are expected through an improved understanding of plasma chemistry and growth kinetics. Large-scale commercialization programs are under way, with proposed expansion of annual production capacities exceeding 25 MW to take place within the next one year. This will make a-Si alloy the dominant photovoltaic technology. In this paper, the author discusses the progress in science, technology and commercialization of a-Si alloy photovoltaics with special emphasis on the opportunities and the challenges that exist.
Internalization of bacterial redox protein azurin in mammalian cells: entry domain and specificity (2005)

Azurin is a member of a group of copper-containing redox proteins called cupredoxins. Different cupredoxins are produced by different aerobic bacteria as agents of electron transfer. Recently, we demonstrated that azurin enters into J774 and several types of cancer cells leading to the induction of apoptosis. We now demonstrate that azurin is internalized in J774 or cancer cells in a temperature-dependent manner. Azurin shows preferential entry into cancer compared with normal cells. An 28-amino-acid fragment of azurin fused to glutathione S-transferase (GST) or the green fluorescent protein (GFP), which are incapable of entering mammalian cells by themselves, can be internalized in J774 or human melanoma or breast cancer cells at 37 degrees C, but not at 4 degrees C. Competition experiments as well as studies with inhibitors such as cytochalasin D suggest that azurin may enter cells, at least in part, by a receptor-mediated endocytic process. The 28-amino-acid peptide therefore acts as a potential protein transduction domain (PTD), and can be used as a vehicle to transport cargo proteins such as GST and GST-GFP fusion proteins. Another member of the cupredoxin family, rusticyanin, that has also been shown to enter J774 and human cancer cells and exert cytotoxicity, does not demonstrate preferential entry for cancer cells and lacks the structural features characteristic of the azurin PTD.
Learning moods and emotions from color combinations (2010)

In this paper, we tackle the problem of associating combinations of colors to abstract categories (e.g. capricious, classic, cool, delicate, etc.). It is evident that such concepts would be difficult to distinguish using single colors, therefore we consider combinations of colors or color palettes. We leverage two novel databases for color palettes and we learn categorization models using low and high level descriptors. Preliminary results show that Fisher representation based on GMMs is the most rewarding strategy in terms of classification performance over a baseline model. We also suggest a process for cleaning weakly annotated data, whilst preserving the visual coherence of categories. Finally, we demonstrate how learning abstract categories on color palettes can be used in the application of color transfer, personalization and image re-ranking.