gebhart/patrepeval huggingface dataset:
Identification of kinase fusion oncogenes in post-Chernobyl radiation-induced thyroid cancers (2013)

Exposure to ionizing radiation during childhood markedly increases the risk of developing papillary thyroid cancer. We examined tissues from 26 Ukrainian patients with thyroid cancer who were younger than 10 years of age and living in contaminated areas during the time of the Chernobyl nuclear reactor accident. We identified nonoverlapping somatic driver mutations in all 26 cases through candidate gene assays and next-generation RNA sequencing. We found that 22 tumors harbored fusion oncogenes that arose primarily through intrachromosomal rearrangements. Altogether, 23 of the oncogenic drivers identified in this cohort aberrantly activate MAPK signaling, including the 2 somatic rearrangements resulting in fusion of transcription factor ETS variant 6 (ETV6) with neurotrophic tyrosine kinase receptor, type 3 (NTRK3) and fusion of acylglycerol kinase (AGK) with BRAF. Two other tumors harbored distinct fusions leading to overexpression of the nuclear receptor PPARγ. Fusion oncogenes were less prevalent in tumors from a cohort of children with pediatric thyroid cancers that had not been exposed to radiation but were from the same geographical regions. Radiation-induced thyroid cancers provide a paradigm of tumorigenesis driven by fusion oncogenes that activate MAPK signaling or, less frequently, a PPARγ-driven transcriptional program.
Synthesis of Novel Derivatives of Pyridine‐2,6‐dicarboxylic Acid (2006)

Abstract Two series of novel derivatives of pyridine‐2,6‐dicarboxylic acid with potential as polydentate ligands were synthesized from pyridine‐2,6‐dicarboxylic acid. All new compounds were characterized by NMR, MS, IR, and EA.
The effect of source based rate adaptation extension in AMR-WB speech codec (2003)

This paper presents a source based rate adaptation concept for AMR wideband speech codec. The source based rate adaptation algorithm selects the multi rate codec mode based on the input speech characteristics and coding parameters to minimise the average bit rate. The presented concept introduces up to 50% reduction in average bit rate without any degradation in speech quality. The benefit of source based adaptation is in increasing the system capacity in conversational services as well as storage size in messaging type of applications.
Corneal (Lymph)angiogenesis—From Bedside to Bench and Back: A Tribute to Judah Folkman (2008)

The normal cornea, the transparent "windscreen" of the eye, is devoid of both blood and lymphatic vessels. Nevertheless, both hem- and lymphangiogenesis can occur in response to severe corneal inflammation and can lead to blindness. Judah Folkman and co-workers exceedingly used the normally avascular cornea as the in vivo model system to study the mechanisms of angiogenesis and to test activators and inhibitors of angiogenesis in the last 3 decades. Recently, the cornea also became a successful model to study especially inflammatory lymphangiogenesis. As the last step in the circle from bedside to bench and back, we now are seeing the first (usually off-label) use of specific novel angiogenesis inhibitors in the diseased and pathologically vascularized human cornea to treat sight-threatening corneal angiogenesis and to promote graft survival after corneal transplantation by inhibiting lymphangiogenesis.
Partial Resistance to Bacterial Wilt in Transgenic Tomato Plants Expressing Antibacterial Lactoferrin Gene (2002)

Expression of lactoferrin ( LF ) gene, a cationic iron-binding glycoprotein, was investigated in transgenic tomato plants ( Lycopersicon esculentum Mill.). Resistance of the transgenic tomato plants to the pathogen ( Ralstonia solanacearum Smith) causing bacterial wilt was also determined. Tomato line F7926-96, susceptible to bacterial wilt, was transformed with Agrobacterium strain C58C1 containing a plasmid construction carrying a modified LF cDNA. The introgression of LF cDNA into the susceptible tomato line was confirmed by Southern blot and the expression of full-length lactoferrin transcript and protein was also detected by northern and western blots, respectively. Based on resistance to kanamycin, a Mendelian segregation for a single locus insertion was observed in the T 1 and T 2 generations and all T 1 and T 2 plants resistant to kanamycin showed the single corresponding band of LF cDNA in Southern blot analysis. Two transgenic tomato lines inoculated with 1 × 10 7 and 1 × 10 8 colony-forming units (CFU)/mL with Rs isolate NC251 (K60, race 1) exhibited early resistance and subsequent susceptibility, while 44% to 55% of plants survived until maturity (fruit ripening) when inoculated with 1 × 10 5 CFU/mL in comparison with the fully susceptible tomato line. The latter resistance to bacterial wilt in transgenic tomatoes with the stable Mendelian segregation patterns for the LF gene suggests a potential new approach to consider for control of bacterial wilt of tomato. The possible value of this gene along with other plant genes to control bacterial pathogens is discussed.
A nonpetide integrin antagonist can inhibit epithelial cell ingestion of Streptococcus pyogenes by blocking formation of integrin α5β1-fibronectin-M1 protein complexes (2000)

Streptococcus pyogenes can be efficiently internalized by a variety of human epithelial cells. beta-lactam antibiotics, commonly used to treat S. pyogenes infections, do not readily permeate mammalian cells. There is growing evidence that the ability of streptococci to enter host cells contributes to the frequent failure of antibiotics to eradicate the organism from infected individuals. Recent studies have suggested that host cell entry requires the formation of a complex of a bacterial fibronectin (Fn) binding protein (e.g., M1 protein or protein F1/SfbI), human Fn, and the epithelial cell Fn receptor, integrin alpha5beta1. We report here that a low molecular weight, nonpeptide antagonist of integrin alpha5beta1, SJ755, can inhibit internalization of streptococci by primary human tonsillar epithelial cells and immortalized human epithelial (A549) cells, thus increasing the extent of bacterial killing by antibiotics. SJ755 blocked Fn binding by human tonsillar epithelial and A549 cells, suggesting that integrin alpha5beta1 is the major Fn receptor expressed by both cell types. SJ755 did not affect Fn binding by purified M1 protein or M1(+) bacteria. Purified M1 protein failed to associate with integrin alpha5beta1 unless the integrin had been prebound by Fn. Also, SJ755 blocked formation of alpha5beta1-Fn-M1 complexes in vitro. These results support the previous proposal that Fn functions as a molecular bridge between M1 protein and integrin alpha5beta1. Furthermore, these results suggest that integrin antagonists may enhance the efficacy of antibiotics in treatment of S. pyogenes infections.
First-Line Herceptin<sup>®</sup> Monotherapy in Metastatic Breast Cancer (2001)

The pivotal phase II and III Herceptin trials proved the efficacy and safety of second- or third-line single-agent Herceptin and first-line Herceptin in combination with chemotherapy, respectively. In the current trial, 114 patients were randomized to one of two dose groups of first-line Herceptin monotherapy: standard dose of 4 mg/ kg initial dose followed by 2 mg/kg intravenous (i.v.) weekly; or high dose of 8 mg/kg initial dose followed by 4 mg/kg i.v. weekly. The regimen was generally well tolerated. A similar incidence of adverse events was demonstrated in the two dose groups with the possible exception of acute infusion-related events such as fever and chills as well as rash and dyspnea, which appear to be more prevalent in the higher dose group. The overall response rate was 26% and response rates were similar between the two dose groups (24% for the standard Herceptin dose group and 28% for the high Herceptin dose group). Subgroup analysis determined a higher response rate in IHC 3+ patients (35%) and FISH-positive patients (41%). When women with stable disease for > or =6 months were included with responders, the clinical benefit rate in IHC 3+ patients was 47%. Median survival was 24.4 months, which is comparable with the survival rate seen in the pivotal phase III combination trial (25 months). Therefore, single-agent Herceptin is an important new option for the first-line treatment of HER2-positive metastatic breast cancer patients.
SH U 508, A Transpulmonary Echocontrast Agent Initial Experience (1990)

FRITZSCH, THOMAS DVM, PHD; HILMANN, JÜRGEN PHD; KÄMPFE, MICHAEL PHD; MÜLLER, NIKOLAUS DVM, PHD; SCHÖBEL, CHRISTEL DVM, PHD; SIEGERT, JOACHIM MD, PHD Author Information
Laying out and visualizing large trees using a hyperbolic space (1994)

We present a new focus+context (fisheye) scheme for visualizing and manipulating large hierarchies. The essence of our approach is to lay out the hierarchy uniformly on the hyperbolic plane and map this plane onto a circular display region. The projection onto the disk provides a natural mechanism for assigning more space to a portion of the hierarchy while still embedding it in a much larger context. Change of focus is accomplished by translating the structure on the hyperbolic plane, which allows a smooth transition without compromising the presentation of the context.
Diversity of Fibroblasts – A Review on Implications for Skin Tissue Engineering (2007)

Enormous advances in the development of skin substitutes have occurred in the past 3 decades. Major obstacles yet to be overcome in the quest for an optimal skin substitute include controlling scar formation, contraction and the loss of adnexal structures. Mesenchyme-derived signals are essential for epithelial proliferation, skin morphogenesis, homeostasis and differentiation. Having previously shown that fibroblasts differentiate along a lineage from highly proliferative progenitor fibroblasts with characteristic spindle-shaped appearance to differentiated postmitotic polygonal fibrocytes, we have now established that the different subsets of fibroblasts exert significantly different patterns of cytokine release and that the highest levels of keratinocyte growth factor and transforming growth factor-beta1 expression result from differentiated fibroblasts. Coculture studies with keratinocytes reveal that postmitotic fibroblasts stimulate keratinocyte proliferation to a greater extent than progenitor fibroblasts. Acellular and fibroblast-seeded dermal substitutes have been shown to improve scarring and contraction in animal studies, the latter substitutes yielding the most favorable results. Fibroblasts from different body sites display different functional properties which may affect their suitability for dermal substitutes. Future in vivo human studies in tissue-engineered dermal substitutes will likely focus on fibroblast-seeded lattices and the impact of fibroblast subpopulations and bone marrow-derived mesenchymal stem cells on dermal regeneration.
Human β‐defensin 4: a novel inducible peptide with a specific salt‐sensitive spectrum of antimicrobial activity (2001)

ABSTRACT β‐Defensins are antibiotic peptides involved in host defense at the epithelial surface. Three human β‐defensins (hBDs)‐‐hBD‐1, hBD‐2, and hBD‐3‐‐have been identified so far. We have characterized a new member of the β‐defensin family, hBD‐4, based on screening of genomic sequences and subsequent functional analysis. In contrast to hBD‐1, hBD‐2, and hBD‐3, which are diffusely expressed throughout many organs, hBD‐4 mRNA expression is confined to testis, stomach, uterus, neutrophils, thyroid, lung, and kidney. hBD‐4 expression was up‐regulated by infection with gram‐positive and gram‐negative bacteria in human respiratory epithelial cells, and in response to phorbol 12‐myristate 13‐acetate, but not in response to other inflammatory factors that up‐regulate the expression of hBD‐2 or hBD‐3. Synthetic hBD‐4 exhibits a selective, salt‐sensitive spectrum of antimicrobial activity, and it represents one of the most active antimicrobial peptides against Pseudomonas aeruginosa (minimal inhibitory concentration: 4.1 μg/ml) known to date. This new defensin is chemotactic for human blood monocytes, but it is inactive on neutrophils and eosinophils. These findings demonstrate the existence of a family of β‐defensin genes with different functions against diverse classes of microorganisms, regulated by different stimuli, and specific signal pathways, and confirm the relevance of antimicrobial peptides in host defense.
Tracking of Fingertips and Centers of Palm Using KINECT (2011)

Hand Gesture is a popular way to interact or control machines and it has been implemented in many applications. The geometry of hand is such that it is hard to construct in virtual environment and control the joints but the functionality and DOF encourage researchers to make a hand like instrument. This paper presents a novel method for fingertips detection and centres of palms detection distinctly for both hands using MS KINECT in 3D from the input image. KINECT facilitates us by providing the depth information of foreground objects. The hands were segmented using the depth vector and centres of palms were detected using distance transformation on inverse image. This result would be used to feed the inputs to the robotic hands to emulate human hands operation.
Production of the Isoflavones Genistein and Daidzein in Non-Legume Dicot and Monocot Tissues (2000)

Metabolic engineering for production of isoflavones in non-legume plants may provide the health benefits of these phytoestrogens from consumption of more widely used grains. In legumes, isoflavones function in both the symbiotic relationship with rhizobial bacteria and the plant defense response. Expression of a soybean isoflavone synthase (IFS) gene in Arabidopsis plants was previously shown to result in the synthesis and accumulation of the isoflavone genistein in leaf and stem tissue (Jung et al., 2000). Here we further investigate the ability of the heterologous IFS enzyme to interact with the endogenous phenylpropanoid pathway, which provides the substrate for IFS, and produces genistein in several plant tissue systems. In tobacco (Nicotiana tabacum) floral tissue that synthesizes anthocyanins, genistein production was increased relative to leaves. Induction of the flavonoid/anthocyanin branch of the phenylpropanoid pathway through UV-B treatment also enhanced genistein production in Arabidopsis. In a monocot cell system, introduced expression of a transcription factor regulating genes of the anthocyanin pathway was effective in conferring the ability to produce genistein in the presence of the IFS gene. Introduction of a third gene, chalcone reductase, provided the ability to synthesize an additional substrate of IFS resulting in production of the isoflavone daidzein in this system. The genistein produced in tobacco, Arabidopsis, and maize (Zea mays) cells was present in conjugated forms, indicating that endogenous enzymes were capable of recognizing genistein as a substrate. This study provides insight into requirements for metabolic engineering for isoflavone production in non-legume dicot and monocot tissues.
Sequence specificity in the binding of anti-tumour anthracyclines to DNA: a success of theory. (1991)

Up to 1985 apparent contradictions in the results of experimental investigations on the possible sequence specificity in the interaction of the two fundamental antitumour anthracyclines, daunomycin and Adriamycin, with DNA have led to an intellectually confused situation and serious doubts about the existence of any such specificity. Theoretical studies carried out in our laboratory in 1985 demonstrated that these failures were due to the attempt to relate the specificity exclusively to the nature of the two base pairs of the intercalation site. We have shown that a definite specificity can in fact be established but only at the level of triplets of base pairs, comprising in addition to the base pairs of the intercalation site, the neighbouring base pair at the 5' side. Our explicit predictions indicate the preferred triplets G-C, C-G, T-A or G-C, C-G, A-T with the intercalation site between the two GC base pairs, followed relatively closely by the A-T, C-G, T-A triplet with the intercalation site between the AT and CG base pairs. Subsequent extensive experimentation carried out in a number of laboratories confirmed the validity of our concept and the exactitude of our predictions, although some controversy persists among experimentalists as to the nature of the most preferred triplet.
In Vivo Production and Release of Acetylcholine from Primary Fibroblasts Genetically Modified to Express Choline Acetyltransferase (1993)

Primary rat fibroblasts genetically modified to express Drosophila choline acetyltransferase (dChAT) synthesize and release acetylcholine (ACh) in vitro. The ACh produced from the transduced fibroblasts was found to be enhanced by increasing amounts of choline chloride in the culture media. These dChAT-expressing cells were then implanted into the intact hippocampus of adult rats and in vivo microdialysis was performed 7-10 days after grafting to assess the ability of the cells to produce ACh and respond to exogenous choline in vivo. Samples collected from anesthetized rats revealed fourfold higher levels of ACh around dChAT grafts than from either non-grafted or control-grafted hippocampi. Localized choline infusion (200 microM) through the dialysis probes was found to induce a selective twofold increase in ACh release only from the dChAT-expressing fibroblasts. These results indicate not only that dChAT-expressing fibroblasts continue to synthesize and secrete ACh for at least 10 days after intracerebral grafting, but that the levels of ACh can be manipulated in vivo. The ability to regulate products within genetically modified cells in vivo may provide a powerful avenue for exploring the role of discrete substances within the CNS.
ChemInform Abstract: SYNTHESIS OF DIPHOSPHORUS‐SUBSTITUTED ESTERS OF ACETIC ACID (1976)

Abstract Aus den Natriumenolaten von monophosphorylierten Essigestern (I), (V), (VIII) und Chloriden bzw. Amiden von Säuren des dreiwertigen Phosphors (II), (IX) bilden sich diphosphorylierte Essigester (III), (VI), (X), die aber auch als O‐Isomere (IV), (VII), (XI) vorliegen können.
FastLSM (2007)

We introduce a simple technique that enables robust approximation of volumetric, large-deformation dynamics for real-time or large-scale offline simulations. We propose Lattice Shape Matching , an extension of deformable shape matching to regular lattices with embedded geometry; lattice vertices are smoothed by convolution of rigid shape matching operators on local lattice regions, with the effective mechanical stiffness specified by the amount of smoothing via region width. Since the naïve method can be very slow for stiff models - per-vertex costs scale cubically with region width - we provide a fast summation algorithm, Fast Lattice Shape Matching (FastLSM) , that exploits the inherent summation redundancy of shape matching and can provide large-region matching at constant per-vertex cost. With this approach, large lattices can be simulated in linear time. We present several examples and benchmarks of an efficient CPU implementation, including many dozens of soft bodies simulated at real-time rates on a typical desktop machine.
Strain‐Promoted Azide–Alkyne Cycloaddition with Ruthenium(II)–Azido Complexes (2013)

The reactivity of an exemplary ruthenium(II)-azido complex towards non-activated, electron-deficient, and towards strain-activated alkynes at room temperature and low millimolar azide and alkyne concentrations has been investigated. Non-activated terminal and internal alkynes failed to react under such conditions, even under copper(I) catalysis conditions. In contrast, as expected, rapid cycloaddition was observed with electron-deficient dimethyl acetylenedicarboxylate (DMAD) as the dipolarophile. Since DMAD and related propargylic esters are excellent Michael acceptors and thus unsuitable for biological applications, we investigated the reactivity of the azido complex towards cycloaddition with derivatives of cyclooctyne (OCT), bicyclo[6.1.0]non-4-yne (BCN), and azadibenzocyclooctyne (ADIBO). While no reaction could be observed in the case of the less strained cyclooctyne OCT, the highly strained cyclooctynes BCN and ADIBO readily reacted with the azido complex, providing the corresponding stable triazolato complexes, which were amenable to purification by conventional silica gel column chromatography. An X-ray crystal structure of an ADIBO cycloadduct was obtained and verified that the formed 1,2,3-triazolato ligand coordinates the metal center through the central N2 atom. Importantly, the determined second-order rate constant for the ADIBO cycloaddition with the azido complex (k2=6.9 × 10(-2) M(-1) s(-1)) is comparable to the rate determined for the ADIBO cycloaddition with organic benzyl azide (k2=4.0 × 10(-1) M(-1) s(-1)). Our results demonstrate that it is possible to transfer the concept of strain-promoted azide-alkyne cycloaddition (SPAAC) from purely organic azides to metal-coordinated azido ligands. The favorable reaction kinetics for the ADIBO-azido-ligand cycloaddition and the well-proven bioorthogonality of strain-activated alkynes should pave the way for applications in living biological systems.
Development of a Functional Measure for Persons With Alzheimer’s Disease: The Disability Assessment for Dementia (1999)

This instrument may help clinicians and caregivers of the population with Alzheimer's disease make decisions regarding the choice of suitable interventions.
Implementation issues for an interactive evolutionary computation system (2007)

The design and development of an Interactive Evolutionary Computation (IEC) system needs to take into account the implementation issues found when delivering the system to "Real World" users. This paper reports and reflects on the implementation issues found when rolling-out an IEC-based Programme Management system [1]. Although the system under discussion was for a specific application, it is felt that the issues and their resolution are generally applicable to a wide range of IEC systems.
The patella as an unusual site of renal cell carcinoma metastasis. (2007)

We report a rare case of renal cell carcinoma with metastasis to the patella in a 49-year-old man, who presented with seven months of left knee pain after a fall. Only two similar cases have been reported. Patellar metastasis is rare because it has a relatively poor blood supply and microemboli would have been sieved out by the pulmonary circulation. Patellectomy is the usual treatment for such cases. We suspect that the preferential metastasis in our patient is a result of tropism. Our treatment for this patient is unique. We opted for a patella-preserving operation involving the use of cryotherapy, as this treatment modality preserved the quality of life. An opportunistic biopsy one year later confirmed the absence of active disease within the patella. This case uniquely provides human in vivo histological confirmation that an intralesional procedure with local and systemic adjuvant therapy effectively controls local disease.
The Continuing Epidemics of Obesity and Diabetes in the United States (2001)

The prevalence of obesity and diabetes continues to increase among US adults. Interventions are needed to improve physical activity and diet in communities nationwide.
Definitions in hemophilia. Recommendation of the scientific subcommittee on factor VIII and factor IX of the scientific and standardization committee of the International Society on Thrombosis and Haemostasis. (2001)

Definitions in Hemophilia - Recommendation of the Scientific Subcommittee on Factor VIII and Factor IX of the Scientific and Standardization Committee of the International Society on Thrombosis and Haemostasis