gebhart/patrepeval huggingface dataset:
Mice lacking Nf1 in osteochondroprogenitor cells display skeletal dysplasia similar to patients with neurofibromatosis type I (2011)

Mutations in NF1 cause neurofibromatosis type I (NF1), a disorder characterized, among other clinical manifestations, by generalized and focal bony lesions. Dystrophic scoliosis and tibial pseudoarthrosis are the most severe skeletal manifestations for which treatment is not satisfactory, emphasizing the dearth of knowledge related to the biology of NF1 in bone cells. Using reporter mice, we report here that the mouse Col2α1-Cre promoter (collagen, type II, alpha 1) is active not only in chondrocytes but also in adult bone marrow osteoprogenitors giving rise to osteoblasts. Based on this finding, we crossed the Col2α1-Cre transgenic and Nf1(flox/flox) mice to determine whether loss of Nf1 in axial and appendicular osteochondroprogenitors recapitulates the skeletal abnormalities of NF1 patients. By microtomographic and X-rays studies, we show that Nf1(Col2)(-/-) mice display progressive scoliosis and kyphosis, tibial bowing and abnormalities in skull and anterior chest wall formation. These defects were accompanied by a low bone mass phenotype, high bone cortical porosity, osteoidosis, increased osteoclastogenesis and decreased osteoblast number, as quantified by histomorphometry and 3D-microtomography. Loss of Nf1 in osteochondroprogenitors also caused severe short stature and intervertebral disc defects. Blockade of the RAS/ERK activation characteristic of Nf1(-/-) osteoprogenitors by lovastatin during embryonic development could attenuate the increased cortical porosity observed in mutant pups. These data and the skeletal similarities between this mouse model and NF1 patients thus suggest that activation of the RAS/ERK pathway by Nf1 loss-of-function in osteochondroprogenitors is responsible for the vertebral and tibia lesions in NF1 patients, and that this molecular signature may represent a good therapeutic target.
Multi-Sensor Multi-Target Tracking - Strategies for Events that become Invisible. (1995)

Within the context of multi-sensor, multi-target tracking, this paper addresses the problems of dealing with objects in the world that, for various reasons, were being observed but are no longer. A modification to the usual Mahalanobis distance metric used for matching observations to Extended Kalman Filters is proposed, and also two strategies for terminating tracks and tracking objects through blind zones are described. Experimental results obtained from a sensor-equipped vehicle navigating in road traffic are presented. 1
Information Systems Opportunities in Brain–Machine Interface Decoders (2014)

Brain-machine interface (BMI) systems convert neural signals from motor regions of the brain into control signals to guide prosthetic devices. The ultimate goal of BMIs is to improve the quality of life for people with paralysis by providing direct neural control of prosthetic arms or computer cursors. While considerable research over the past 15 years has led to compelling BMI demonstrations, there remain several challenges to achieving clinically viable BMI systems. In this review, we focus on the challenge of increasing BMI performance and robustness. We review and highlight key aspects of intracortical BMI decoder design, which is central to the conversion of neural signals into prosthetic control signals, and discuss emerging opportunities to improve intracortical BMI decoders. This is one of the primary research opportunities where information systems engineering can directly impact the future success of BMIs.
Psoriatic Keratinocytes Express High Levels of Nerve Growth Factor (1998)

Many investigators have reported proliferation of terminal cutaneous nerves and upregulation of various neuropeptides (substance P, vasoactive intestinal polypeptide, calcitonin gene-related peptide) in psoriatic lesions. Nerve growth factor promotes growth of nerves and causes upregulation of neuropeptides like substance P and calcitonin gene-related peptide. In this study we investigated the expression of nerve growth factor in psoriatic lesions, non-lesional psoriatic skin, lichen planus and normal control skin. Immunoperoxidase staining was applied on cryosections prepared from snap-frozen biopsy specimens. The primary antibody used was a polyclonal anti-NGF-beta antibody. Nerve growth factor was detected only in the keratinocytes. In psoriatic tissue the number of keratinocytes per square millimeter of epidermis positive for nerve growth factor was 84.7 +/- 46.3 compared to 44.8 +/- 29.9, 18.9 +/- 11.8 and 7.5 +/- 16.9, respectively, in non-lesional psoriatic skin, normal skin and lichen planus. Increased expression of nerve growth factor substantiates larger numbers of terminal cutaneous nerves and upregulations of substance P and calcitonin gene-related peptide in psoriatic lesions. In addition, nerve growth factor is mitogenic to keratinocytes, activates T-lymphocytes and can induce migration of inflammatory cellular infiltrates, histological features characteristic of psoriasis.
Requirements for Transforming Growth Factor-β Regulation of the Pro-α2(I) Collagen and Plasminogen Activator Inhibitor-1 Promoters (1995)

Experiments were designed to clarify the role of several proteins, junB, retinoblastoma protein (RB), and the transforming growth factor-beta (TGF-beta) receptors that are potential intermediates in TGF-beta activation of the alpha 2(I) collagen promoter. Treatment of NIH-3T3 cells with TGF-beta increased the activity of a transiently transfected murine alpha 2(I) collagen promoter (nucleotides -350 to +54) fused to a luciferase reporter gene 9-fold. Cotransfection of a junB stimulated the basal activity of the alpha 2(I) collagen promoter 93-fold, respectively. Expression of antisense junB RNA attenuated the effect of TGF-beta. Simian virus 40 large T antigen, an inhibitor RB function, did not prevent TGF-beta effects on the alpha 2(I) collagen promoter. A chimeric receptor containing the extracellular domain of the colony-stimulating factor-1 receptor and the intracellular domain of the type I TGF-beta receptor enhanced alpha 2(I) collagen promoter activity 4.8-fold, whereas a similar chimera containing the type II receptor intracellular domain had much weaker effects. Similar results were obtained with a plasminogen activator inhibitor-1 promoter, previously shown to be activated by TGF-beta through AP-1 elements. We conclude that TGF-beta activates the alpha 2(I) collagen and plasminogen activator inhibitor-1 promoters in NIH-3T3 cells through junB and the type I TGF-beta receptor kinase domain.
Marinobufagenin, an Endogenous α-1 Sodium Pump Ligand, in Hypertensive Dahl Salt-Sensitive Rats (2001)

Dahl salt-sensitive rats (DS), which have a mutation in the alpha-1 subunit of Na(+)/K(+)-ATPase, exhibit impaired pressure natriuresis and on a high-salt diet, retain Na(+) and exhibit increased blood pressure. Recently, we have shown that mammalian tissues contain a bufadienolide Na(+)/K(+)-ATPase inhibitory factor, marinobufagenin (MBG), that exhibits greater affinity for the alpha-1 than alpha-3 sodium pump isoform. The present study investigated the possible role of MBG in hypertension in DS on a high NaCl intake. Eight DS and 8 Dahl salt-resistant rats (DR) were placed on an 8% NaCl diet. Within 2 weeks, systolic blood pressure increased in DS (162+/-9 mm Hg at week 2 versus 110+/-2 mm Hg in baseline, P<0.01), and increased less in DR (124+/-3 mm Hg at week 2 versus 112+/-2 mm Hg in baseline). Renal excretion of MBG increased 4-fold (38.9+/-7.6 pmol versus 9.1+/-1.3 pmol in baseline, P<0.01) in DS, but by only 25% in DR (13.2+/-0.9 pmol versus 10.3+/-0.7 pmol in baseline). Excretion of endogenous ouabain did not change in either strain. MBG-immunoreactive material was purified from the urine of hypertensive DS by means of 2 steps of reverse-phase high performance liquid chromatography (HPLC) and compared with plant ouabain and amphibian MBG for its ability to inhibit the Na(+)/K(+)-ATPase from rat kidney (which expresses only alpha-1 Na(+)/K(+)-ATPase isoform). Unlike ouabain (IC(50)=248 micromol/L), serially diluted, HPLC-purified MBG immunoreactivity from DS and authentic MBG potently inhibited rat kidney Na(+)/K(+)-ATPase (IC(50)=70 and 78 nmol/L, respectively). Our results suggest that an alpha-1 Na(+)/K(+)-ATPase ligand, MBG, is elaborated to promote natriuresis in hypertensive DS. MBG acts as a selective inhibitor of the ouabain-resistant alpha-1 Na(+)/K(+)-ATPase subunit, ie, the major sodium pump isoform of the kidneys, as would be expected of a putative natriuretic hormone.
Low-temperature proximity effect in clean metals with repulsive electron-electron interaction (2008)

Theories of proximity effect in layered superconductor--normal-metal (SN) structures usually deal with a hypothetic normal metal with no direct repulsive interaction between electrons and with finite temperatures often close to the superconductor critical temperature. We present an asymptotic solution of the Gor'kov equations in the opposite low-temperature limit for a clean normal metal with a repulsive interaction between electrons. The order parameter in the metal exhibits a power-law decay, $\ensuremath{\Delta}(x)\ensuremath{\propto}\ensuremath{\xi}/x$, as a function of the distance from the SN boundary, $x$, with a proximity length $\ensuremath{\xi}$ strongly depending on the repulsive interaction.
Shape specification in design using fuzzy logic (2003)

A shape specification system based on fuzzy logic is proposed, which aims to facilitate designers in the conceptual design stage by allowing them to specify and work with rough models in a more intuitive fashion. The system uses a 3D object representation called 'parametric geons' which provide both qualitative and quantitative descriptions, in addition to global shape constraints, via eight shape parameters. Geometric descriptors and aesthetic descriptors are introduced and their fuzzy membership functions are constructed. Inference rules are obtained to link these descriptors with shape parameters. The system which models after designers' behaviour, allows designers' own aesthetic terms and interpretation of shapes to be added, and a library of successful designs with appropriate fuzzy descriptions to be constructed for later use.
Robust SNP genotyping by multiplex PCR and arrayed primer extension (2008)

We have shown our methods to be effective for robust multiplex SNP genotyping using APEX, with 100% call rate and >99.9% accuracy. We believe that such methodology may be useful in future point-of-care clinical diagnostic applications where accuracy and call rate are both paramount.
Growth arrest‐specific gene 6 and Axl signaling enhances gastric cancer cell survival via Akt pathway (2006)

Activation of tyrosine kinases is an important factor during cancer development. Axl, one of the receptor tyrosine kinases, binds to the specific ligand growth arrest-specific gene 6 (Gas6), which encodes a vitamin K-dependent gamma-carboxyglutamyl protein. Although many receptor tyrosine kinases and their ligands are involved in gastric carcinogenesis, whether Gas6-Axl signaling is involved in gastric carcinogenesis has not been elucidated. The aim of this study was to investigate the expression of Gas6 and Axl in gastric cancer and also their roles during gastric carcinogenesis. mRNA and protein of Gas6 and Axl were highly expressed in a substantial proportion of human gastric cancer tissue and cell lines, and Gas6 expression was significantly associated with lymph node metastasis. With recombinant Gas6 and a decoy-receptor of Axl in vitro, we demonstrated that Gas6-Axl signaling pathway enhanced cellular survival and invasion and suppressed apoptosis via Akt pathway. Our results suggests that Gas6-Axl signaling plays a role during gastric carcinogenesis, and that targeting Gas6-Axl signaling could be a novel therapeutic for gastric cancer.
Titelbild: Single DNA Rotaxanes of a Transmembrane Pore Protein (Angew. Chem. 23/2004) (2004)

Eine isolierte Rotaxanstruktur die durch Auffädeln und Arretieren eines DNA‐Poly(ethylenglycol)‐Stranges in einem α‐Hämolysin(α‐HL)‐Transmembranprotein entsteht, stellen M. R. Ghadiri et al. in ihrer Zuschrift auf S. 3125 ff. vor. Abhängig vom angelegten Potential, von der Orientierung, der Synthesemethode und der Stoppergruppe können die DNA‐α‐HL‐Rotaxane reversibel zwischen zwei Zuständen geschaltet werden. Aus der Studie lässt sich eine direkte Methode zum Abfangen von DNA‐Strängen definierter Länge und Sequenz ableiten.
Noise and motion correction in dynamic contrast‐enhanced MRI for analysis of atherosclerotic lesions (2002)

Dynamic contrast-enhanced MRI of atherosclerotic vessels after contrast agent injection may provide unique information regarding lesion structure and vulnerability. The high-resolution images necessary for viewing lesion substructures, however, are often corrupted by patient motion and low signal-to-noise ratios, making pixel-level analyses difficult. This article presents a postprocessing method that enables pixel-level analysis of dynamic images by eliminating motion and enhancing image quality. Noise and motion correction are performed using optimal statistical methods under the assumption that noise and contrast agent dynamics are random processes. The method is demonstrated and validated on dynamic images of atherosclerotic plaques in human carotid arteries.
Direct Induction of Chondrogenic Cells from Human Dermal Fibroblast Culture by Defined Factors (2013)

The repair of large cartilage defects with hyaline cartilage continues to be a challenging clinical issue. We recently reported that the forced expression of two reprogramming factors (c-Myc and Klf4) and one chondrogenic factor (SOX9) can induce chondrogenic cells from mouse dermal fibroblast culture without going through a pluripotent state. We here generated induced chondrogenic (iChon) cells from human dermal fibroblast (HDF) culture with the same factors. We developed a chondrocyte-specific COL11A2 promoter/enhancer lentiviral reporter vector to select iChon cells. The human iChon cells expressed marker genes for chondrocytes but not fibroblasts, and were derived from non-chondrogenic COL11A2-negative cells. The human iChon cells formed cartilage but not tumors in nude mice. This approach could lead to the preparation of cartilage directly from skin in human, without going through pluripotent stem cells.
Stability of Levodopa/Carbidopa Rectal Suspensions (2016)

<b>Objective:</b> The combination of levodopa and carbidopa (L/C) is used as an effective therapy for treating Parkinson's disease; however when oropharyngeal dysphagia develops or when insertion of an nasogastric tube is not possible, then rectal administration could be used. To reduce compounding workload and establish a beyond use date, this study was conducted to determine the stability of 2 L/C rectal suspension formulations when stored at either 22°C or 5°C. <b>Methods:</b> Two formulations of L/C rectal suspension were compounded and then packaged in amber polypropylene bottles. Three bottles of each formulation were stored at either 22°C or 5°C and analyzed at 11 time periods. Physical parameters such as caking, ease of resuspending, and pH were also determined at each time period. A validated stability-indicating high-performance liquid chromatography (HPLC) method was used to analyze both active ingredients. <b>Results:</b> All solutions were easy to resuspend, there were no signs of caking, and there was no significant change in pH over the 35 days of storage at either temperature. The glycerin-based formulation (formulation 1) was less stable at 22°C (10 days) than formulation 2 (24 days). Both rectal suspensions were stable for 35 days when stored at 5°C. <b>Conclusions:</b> The physical compatibility and chemical stability of 2 formulations of L/C rectal suspension packaged in amber polypropylene bottles was determined to be either 10 or 24 days when stored at 22°C or 35 days at 5°C.
A General Theory of Phase Noise in Electrical Oscillators (2009)

A general model is introduced which is capable of making accurate, quantitative predictions about the phase noise of different types of electrical oscillators by acknowledging the true periodically time-varying nature of all oscillators. This new approach also elucidates several previously unknown design criteria for reducing close-in phase noise by identifying the mechanisms by which intrinsic device noise and external noise sources contribute to the total phase noise. In particular, it explains the details of how 1/f noise in a device upconverts into close-in phase noise and identifies methods to suppress this upconversion. The theory also naturally accommodates cyclostationary noise sources, leading to additional important design insights. The model reduces to previously available phase noise models as special cases. Excellent agreement among theory, simulations, and measurements is observed.
Computationally deconstructing movie narratives: An informatics approach (2015)

In general, popular films and screenplays follow a well defined storytelling paradigm that comprises three essential segments or acts: exposition (act I), conflict (act II) and resolution (act III). Deconstructing a movie into its narrative units can enrich semantic understanding of movies, and help in movie summarization, navigation and detection of the key events. A multimodal framework for detecting such three act narrative structure is developed in this paper. Various low-level features are designed and extracted from video, audio and text channels of a movie so as to capture the pace and excitement of the movie's narrative. Information from the three modalities is combined to compute a continuous dynamic measure of the movie's narrative flow, referred to as the story intensity of the movie in this paper. Guided by the knowledge of film grammar, the act boundaries are detected, and compared against annotations collected from human experts. Promising results are demonstrated for nine full-length Hollywood feature films of various genres.
Tau's role in the developing brain: implications for intellectual disability (2011)

Microdeletions encompassing the MAPT (Tau) locus resulting in intellectual disability raised the hypothesis that Tau may regulate early functions in the developing brain. Our results indicate that neuronal migration was inhibited in mouse brains following Tau reduction. In addition, the leading edge of radially migrating neurons was aberrant in spite of normal morphology of radial glia. Furthermore, intracellular mitochondrial transport and morphology were affected. In early postnatal brains, a portion of Tau knocked down neurons reached the cortical plate. Nevertheless, they exhibited far less developed dendrites and a striking reduction in connectivity evident by the size of boutons. Our novel results strongly implicate MAPT as a dosage-sensitive gene in this locus involved in intellectual disability. Furthermore, our results are likely to impact our understanding of other diseases involving Tau.
Process and formulation variables in the preparation of injectable and biodegradable magnetic microspheres (2007)

The aim of this study was to prepare biodegradable sustained release magnetite microspheres sized between 1 to 2 microm. The microspheres with or without magnetic materials were prepared by a W/O/W double emulsion solvent evaporation technique using poly(lactide-co-glycolide) (PLGA) as the biodegradable matrix forming polymer. Effects of manufacturing and formulation variables on particle size were investigated with non-magnetic microspheres. Microsphere size could be controlled by modification of homogenization speed, PLGA concentration in the oil phase, oil phase volume, solvent composition, and polyvinyl alcohol (PVA) concentration in the outer water phase. Most influential were the agitation velocity and all parameters that influence the kinematic viscosity of oil and outer water phase, specifically the type and concentration of the oil phase. The magnetic component yielding homogeneous magnetic microspheres consisted of magnetite nanoparticles of 8 nm diameter stabilized with a polyethylene glycole/polyacrylic acid (PEG/PAA) coating and a saturation magnetization of 47.8 emu/g. Non-magnetic and magnetic microspheres had very similar size, morphology, and size distribution, as shown by scanning electron microscopy. The optimized conditions yielded microspheres with 13.7 weight% of magnetite and an average diameter of 1.37 microm. Such biodegradable magnetic microspheres seem appropriate for vascular administration followed by magnetic drug targeting.
Immune and Clinical Outcomes in Patients with Stage IV Melanoma Vaccinated with Peptide-Pulsed Dendritic Cells Derived From CD34+ Progenitors and Activated with Type I Interferon (2005)

Twenty-two HLA A*0201 patients with stage IV melanoma were enrolled in a phase 1 safety and feasibility trial using a composite dendritic cell (DC) vaccine generated by culturing CD34 hematopoietic progenitors and activated with IFN-alpha. The DC vaccine was loaded with peptides derived from four melanoma tissue differentiation antigens (MART-1, tyrosinase, MAGE-3, and gp100) and influenza matrix peptide (Flu-MP). Twenty patients were evaluable, 14 of whom received vaccination with peptide-pulsed DCs without keyhole limpet hemocyanin (KLH) and 6 of whom received vaccination with KLH-loaded DCs. Patients were vaccinated until disease progression or until they had received eight vaccinations. None of the analyzed patients showed the expansion of melanoma-peptide-specific circulating effector memory T cells that secrete IFN-gamma in direct ELISPOT. Melanoma-peptide-specific recall memory CD8 T cells able to secrete IFN-gamma and to proliferate could be detected in six of the seven analyzed patients. There were no objective clinical responses. The estimated median overall survival was 12 months (range 2-38), and the median event-free survival was 4 months (range 1-12). There was no statistically significant survival advantage in patients who received KLH-loaded vaccines. As of March 2005, four patients remained alive, 26+, 28+, 28+, and 36+ months. Three of them had received KLH-loaded vaccines and all of them had had additional therapy. Overall, these results suggest that IFN-alpha-activated CD34-DCs are safe but elicit only limited immune responses, underscoring the need to test different DC maturation factors.
Topical Umbilical Cord Care for Prevention of Infection and Neonatal Mortality (2012)

Umbilical cord care varies often reflecting community or health-worker beliefs. We undertook a review of current evidence on topical umbilical cord care. Study quality was assessed using the Grading of Recommendations, Assessment, Development and Evaluation system, and a meta-analysis was conducted for comparable trials. Available moderate-quality to high-quality evidence indicate that cord cleansing with 4% chlorhexidine may reduce the risk of neonatal mortality and sepsis (omphalitis) in low-resource settings.
Analysing diet of small herbivores: the efficiency of DNA barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex plant mixtures (2009)

We conclude that DNA barcoding opens up for new possibilities in the study of plant-herbivore interactions, giving a detailed and relatively unbiased picture of food utilization of herbivores.
A Framework for Video Modeling (2000)

In recent years, research in video databases has increased greatly, but relatively little work has been done in the area of semantic content-based retrieval. In this paper, we present a framework for video modelling with emphasis on semantic content of video data. The video data model presented distinguishes four layers: the raw data layer, the feature layer, the object layer and the event layer. It supports automatic definition of high-level concepts, such as video objects and events, based on extracted features. We focus our attention on event descriptions in this paper and give two modelling examples in the medical and soccer domain to show that the proposed event grammar can be efficiently used in different domains.