gebhart/patrepeval huggingface dataset:
Determination of the genetic diversity and microlabial adaptation of Aeromonas SPP. (2013)

The genus Aeromonas comprises ubiquitous bacteria which are known to play several roles in the environment. They were first described as fish pathogens, but their presence was also documented in other reservoirs, in animals and also in humans. To date, they are described as emerging pathogens, but their effective role in human pathogenicity is still controversial. At the same time, their taxonomy is a very debated issue, as inter- and intra-species relationships are often difficult to characterise.&#13;\nIn order to achieve a precise species definition, both between different clades and also at a strain level, a Multilocus Sequence Typing (MLST) scheme has been developed for the Aeromonas genus and applied to a total of 258 strains of different origins. The sampling and the inclusion of the strains in this study was a fundamental step as the main sources of Aeromonas have been considered: fish, food products and human cases of disease. The objective was to characterise all the strains and to find a potential association among them at different levels: species, sharing of virulence factors, source and adaptation to a particular habitat. In particular, the mode of evolution and the adaptation mechanisms were investigated. The MLST was identified and chosen as the best and most practical approach to conduct this work. &#13;\nAll the strains were characterised, demonstrating the exceptionally high nucleotide variability of the Aeromonas genus. A different distribution of the species were found among the sources, highlighting the occurrence of adaptation processes towards some specific habitats.&#13;\nFinally, the first Aeromonas MLST on-line database was opened (www.pubmlst.org/aeromonas) and it is available for collecting and sharing information about Aeromonas strains from different laboratories all over the world.&#13;\n
Chromatin modification by SUMO-1 stimulates the promoters of translation machinery genes (2012)

SUMOylation of transcription factors and chromatin proteins is in many cases a negative mark that recruits factors that repress gene expression. In this study, we determined the occupancy of Small Ubiquitin-like MOdifier (SUMO)-1 on chromatin in HeLa cells by use of chromatin affinity purification coupled with next-generation sequencing. We found SUMO-1 localization on chromatin was dynamic throughout the cell cycle. Surprisingly, we observed that from G1 through late S phase, but not during mitosis, SUMO-1 marks the chromatin just upstream of the transcription start site on many of the most active housekeeping genes, including genes encoding translation factors and ribosomal subunit proteins. Moreover, we found that SUMO-1 distribution on promoters was correlated with H3K4me3, another general chromatin activation mark. Depletion of SUMO-1 resulted in downregulation of the genes that were marked by SUMO-1 at their promoters during interphase, supporting the concept that the marking of promoters by SUMO-1 is associated with transcriptional activation of genes involved in ribosome biosynthesis and in the protein translation process.
[Positive effects of chenodeoxycholic acid (CDCA) on the biohumoral clinical aspect of cholesterin calculosis of the gallbladder]. (1978)

The efficacy and possible sideeffects of chenodeoxycholic acid have been studied in 35 patients with biliary calculosis lithiasis. In 53% of the cases treated for six months or more partial or complete gallstone dissolution was observed. The action of this drug on hematic triglyceride level and on severity and frequency of the hypostenic dyspeptic symptoms and biliary colic is interesting from the viewpoint of new therapeutic prospects. Diarrhea has been the only relevant side-effect.
A Micro System for Rigid Bony Fixation in Orbital Surgery (1991)

Plates and screws are effective for rigid internal fixation of bone fractures and osteotomies in the midface, orbit, and cranium. We describe our experience with the Luhr Micro System. This is the newest generation of Luhr Systems and is the smallest system available for rigid internal fixation. The self-tapping screws are 0.8 mm in diameter, with lengths of 2-8 mm. The plates have an extremely flat profile. We have used the Micro System for closure of elective osteotomies following resection of orbital neoplasm, bony orbital reconstruction, and repair of congenital craniofacial deformities. Because the orbital bones have minimal functional stress, the Micro System provides adequate support. The plates are not apparent through the thin periorbital skin. For bony fixation in the periorbital region, the Micro System appears superior to larger systems and to wire or nonabsorbable sutures.
Variability of Post-Cardiac Arrest Care Practices Among Cardiac Arrest Centers: United States and South Korean Dual Network Survey of Emergency Physician Research Principal Investigators (2016)

There is little consensus regarding many post-cardiac arrest care parameters. Variability in such practices could confound the results and generalizability of post-arrest care research. We sought to characterize the variability in post-cardiac arrest care practice in Korea and the United States. A 54-question survey was sent to investigators participating in one of two research groups in South Korea (Korean Hypothermia Network [KORHN]) and the United States (National Post-Arrest Research Consortium [NPARC]). Single investigators from each site were surveyed (N = 40). Participants answered questions based on local institutional protocols and practice. We calculated descriptive statistics for all variables. Forty surveys were completed during the study period with 30 having greater than 50% of questions completed (75% response rate; 24 KORHN and 6 NPARC). Most centers target either 33°C (N = 16) or vary the target based on patient characteristics (N = 13). Both bolus and continuous infusion dosing of sedation are employed. No single indication was unanimous for cardiac catheterization. Only six investigators reported having an institutional protocol for withdrawal of life-sustaining therapy (WLST). US patients with poor neurological prognosis tended to have WLST with subsequent expiration (N = 5), whereas Korean patients are transferred to a secondary care facility (N = 19). Both electroencephalography modality and duration vary between institutions. Serum biomarkers are commonly employed by Korean, but not US centers. We found significant variability in post-cardiac arrest care practices among US and Korean medical centers. These practice variations must be taken into account in future studies of post-arrest care.
Epidemiological features of Adamantiades-BehÇet's disease in Germany and in Europe (1997)

The German Registry of Adamantiades-Behçet's disease was founded in 1990 in Berlin and it provides current data on the epidemiology, the clinical manifestations and the course of the disease in Germany on a continuous basis. A total of 218 patients, including 89 German and 100 Turkish patients, had been reported to the German Registry until October 1997. One hundred and ninety-six patients fulfilled the criteria of the Behçet's disease classification tree. The prevalence of the disease evaluated in Berlin-West was 1.68/100,000 in 1989 and had risen to 2.26/100,000 by 1994. The median age of onset was 25 years (range 5 to 66 years; German-Turks, ns). Juvenile disease was recorded in 6.9% of patients. The complete clinical picture according to the criteria of the International Study Group of Behçet's Disease developed in 15.5 months. The interval between onset of the disease and diagnosis was 35 months, which was significantly longer than the duration of the development of the complete clinical picture (p < 0.0001). The disease was diagnosed later in German (48.5 months) than in Turkish patients (25.5 months, p = 0.003). While German patients presented an equal male-to-female ratio, a male predominance was shown in Turkish patients (M:F 2.1:1, p = 0.022). Familial occurrence was detected in 2.0% of German and 15.9% of Turkish patients (p = 0.013). The frequencies of major clinical manifestations were: oral ulcers 99%, skin lesions 76%, genital ulcers 75%, ocular manifestations 59%, arthritis 59%, and positive pathergy test 52%. Clinical differences between German and Turkish patients were only found in the frequency of ocular lesions (48% vs. 66%, p = 0.025). Oral ulcers were with 72% the most common onset symptom of the disease followed by erythema nodosum (9%), uveitis (7%), arthritis (7%), genital ulcers (3%), superficial thrombophlebitis (2%) and papules/sterile pustules (2%). Uveitis and erythema nodosum as onset symptoms shortened the median interval to diagnosis to 1.5 and 15 months, respectively, while arthritis delayed diagnosis (43.5 months; p = 0.029). A severe course developed in 25% of the patients; irreversible retinal vasculitis to blindness in 15%, sterile meningoencephalitis in 8%, severe arthritis in 5%, hemoptysis in 2%, lethal outcome in 2% and bowel perforation in 1%. The relative risk of HLA-B5 positive German natives developing the disease. HLA-B5 was confirmed as a marker of severe prognosis. Cardiolipin autoantibodies were associated with cutaneous vasculitis and superficial thrombophlebitis was correlated with systemic vessel involvement.
Growing Old Disgracefully: The Cosmetic Use of Botulinum Toxin (2003)

The explosive growth in the use of botulinum toxin for cosmetic purposes has undoubtedly had an impact on the number of animals used in the potency testing of this product. The test used is a classical LD50, a severe procedure during which animals experience increasing paralysis until the occurrence of death. The enthusiastic adoption by the general public of the use of botulinum toxin as an anti-wrinkle treatment has, at least in Europe, paradoxically taken place against a background of moves to stop animal testing of cosmetics and cosmetic ingredients. There appears to be a dearth of information aimed at the public concerning botulinum toxin testing. Botulinum toxin does have important medical applications; however, the question arises whether a blanket licence for the testing can be justified, when a large proportion of the product is being used cosmetically. A further question is why death continues to be the endpoint of the potency test, when a more-humane endpoint has been proposed. In addition, a number of alternative methods have been developed, which could have the potential to replace the lethal potency test altogether. These methods are discussed in this paper, and the importance of establishing a strategy for their validation is emphasised, a need that has become even more urgent in the light of the recently published draft monograph on botulinum toxin by the European Pharmacopoeia Commission.
Brain-Penetrant Tetrahydronaphthalene Thromboxane A2-Prostanoid (TP) Receptor Antagonists as Prototype Therapeutics for Alzheimer’s Disease (2012)

A hallmark pathological feature of the Alzheimer's disease (AD) brain is the presence of senile plaques, which comprise amyloid β (Aβ) peptides that are derived from the amyloid precursor protein (APP). The plaque-containing AD brain is thought to be under oxidative stress, as evidenced by increased lipid oxidation products that include isoprostane-F2αIII (iPF2αIII). IPF2αIII can bind to and activate the thromboxane A2-prostanoid (TP) receptor, and TP receptor activation causes increased Aβ production through enhancement of APP mRNA stability. Moreover, TP receptor antagonists have been shown to block iPF2αIII-induced increases of Aβ secretion. Thus, the TP receptor may be a potential drug target for AD therapy. However, here we show that existing TP receptor antagonists have poor blood-brain barrier (BBB) permeability, likely due to the presence of a carboxylic acid moiety that is believed to be important for receptor interaction, but which may hamper passive diffusion across the BBB. We now report selected analogues of a known tetrahydronaphthalene TP receptor antagonist, wherein the carboxylic acid moiety has been replaced by heterocyclic bioisosteres. These heterocyclic analogues retained relatively high affinity for the mouse and human TP receptors, and, unlike the parent carboxylic acid compound, several examples freely diffused across the BBB into the brain upon administration to mice. These results reveal that brain-penetrant tetrahydronaphthalene TP receptor antagonists can be developed by substituting the carboxylic acid moiety with a suitable nonacidic bioisostere. Compounds of this type hold promise as potential lead structures to develop drug candidates for the treatment of AD.
Hyperspectral Unmixing via $L_{1/2}$ Sparsity-Constrained Nonnegative Matrix Factorization (2011)

Hyperspectral unmixing is a crucial preprocessing step for material classification and recognition. In the last decade, nonnegative matrix factorization (NMF) and its extensions have been intensively studied to unmix hyperspectral imagery and recover the material end-members. As an important constraint for NMF, sparsity has been modeled making use of the <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$L_{1}$</tex></formula> regularizer. Unfortunately, the <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$L_{1}$</tex></formula> regularizer cannot enforce further sparsity when the full additivity constraint of material abundances is used, hence limiting the practical efficacy of NMF methods in hyperspectral unmixing. In this paper, we extend the NMF method by incorporating the <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex Notation="TeX">$L_{1/2}$</tex></formula> sparsity constraint, which we name <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$L_{1/2}$</tex> </formula> -NMF. The <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$L_{1/2}$</tex></formula> regularizer not only induces sparsity but is also a better choice among <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$L_{q}(0 &lt; q &lt; 1)$</tex> </formula> regularizers. We propose an iterative estimation algorithm for <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX"> $L_{1/2}$</tex></formula> -NMF, which provides sparser and more accurate results than those delivered using the <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$L_{1}$</tex></formula> norm. We illustrate the utility of our method on synthetic and real hyperspectral data and compare our results to those yielded by other state-of-the-art methods.
Continuous speech recognition using dynamic synapse neural network (2004)

The modified architecture of the dynamic synapse neural network (DSNN) is used to model windowed short time speech signal. The quasi-linearization algorithm is applied to train the network. The parameters of the trained network, which are representatives of the signal, are fed into the GMM/HMM based classifier. The performance of the modified architecture with GMM/HMM based classifier is demonstrated by recognition of continuous speech from unprocessed, noisy raw waveforms spoken by multiple speakers. Our results indicate that the features obtained from DSNN are robust in the presence of additive white Gaussian noise with respect to state-of-the-art Mel frequency features. [Work supported in part by DARPA, NASA and ONR.]
Effects of nimesulide and its reduced metabolite on mitochondria (2000)

1. We investigated the effects of nimesulide, a recently developed non-steroidal anti-inflammatory drug, and of a metabolite resulting from reduction of the nitro group to an amine derivative, on succinate-energized isolated rat liver mitochondria incubated in the absence or presence of 20 microM Ca(2+), 1 microM cyclosporin A (CsA) or 5 microM ruthenium red. 2. Nimesulide uncoupled mitochondria through a protonophoretic mechanism and oxidized mitochondrial NAD(P)H, both effects presenting an EC(50) of approximately 5 microM. 3. Within the same concentration range nimesulide induced mitochondrial Ca(2+) efflux in a partly ruthenium red-sensitive manner, and induced mitochondrial permeability transition (MPT) when ruthenium red was added after Ca(2+) uptake by mitochondria. Nimesulide induced MPT even in de-energized mitochondria incubated with 0.5 mM Ca(2+). 4. Both Ca(2+) efflux and MPT were prevented to a similar extent by CsA, Mg(2+), ADP, ATP and butylhydroxytoluene, whereas dithiothreitol and N-ethylmaleimide, which markedly prevented MPT, had only a partial or no effect on Ca(2+) efflux, respectively. 5. The reduction of the nitro group of nimesulide to an amine derivative completely suppressed the above mitochondrial responses, indicating that the nitro group determines both the protonophoretic and NAD(P)H oxidant properties of the drug. 6. The nimesulide reduction product demonstrated a partial protective effect against accumulation of reactive oxygen species derived from mitochondria under conditions of oxidative stress like those resulting from the presence of t-butyl hydroperoxide. 7. The main conclusion is that nimesulide, on account of its nitro group, acts as a potent protonophoretic uncoupler and NAD(P)H oxidant on isolated rat liver mitochondria, inducing Ca(2+) efflux or MPT within a concentration range which can be reached in vivo, thus presenting the potential ability to interfere with the energy and Ca(2+) homeostasis in the liver cell.
Cell surface antigens of murine leukemias induced by radiation leukemia virus. Recognition of individually distinct cell surface antigens by cytotoxic T cells on leukemias expressing crossreactive transplantation antigens. (1986)

The specificity of transplantation immunity and T cell cytotoxicity against leukemias induced by RadLV was examined. Subcutaneous inoculation of two RadLV leukemias induced in BALB/c mice, BALBRVB and BALBRVD, resulted in initial tumor growth in CB6F1 mice, followed by complete tumor regression. Mice that had rejected leukemias BALBRVB or BALBRVD were subsequently challenged with various tumors of BALB/c origin. The growth of all five RadLV leukemias tested, and of one radiation-induced leukemia, was significantly inhibited. Another radiation-induced leukemia, a methylcholanthrene-induced sarcoma, and a leukemia induced by the Moloney leukemia virus, were not inhibited. The results indicate that RadLV leukemias share cell surface antigens that induce transplantation immunity in vivo. Cytotoxic lymphocytes were generated by coculturing spleen cells from mice that had rejected leukemia BALBRVB or BALBRVD with the corresponding leukemia cells. Direct tests and inhibition tests showed that such cytotoxic cells recognized individually specific antigens on leukemias BALBRVB and BALBRVD, distinct from the shared antigens detected in transplantation experiments. The effector cells in cytotoxicity assays were Thy-1+, Lyt-1+,-, Lyt-2+, and Lyt-3+ T cells.
Spin-polarized electron energy-loss spectroscopy of metastable bcc cobalt films (abstract) (1988)

Recent developments now allow for the study of the spin dependence of electron energy-loss features for scattering from magnetized ferromagnetic materials. Particular interest in such studies has been focused on Stoner (or spin-flip) excitations1 because of their fundamental nature as well as their proposed role in the polarization enhancement for low energy secondary electron emission from ferromagnets.2 We have performed spin-polarized electron energy loss spectroscopy (SPEELS) on thin (∼40-Å) metastable bcc Co(110) films which have been grown by e-beam evaporation on atomically clean GaAs(110) substrates. Surface order and cleanliness of the substrate and grown film are monitored by LEED and AES. Details of the bcc Co deposition, growth, and characterization have been reported elsewhere.3 After growth, the thin ferromagnetic films are magnetized to near-saturation remanence magnetization along the in-plane [001] (magnetically easy) direction3 by placement in the center of a pulsed coil. The spin-polarized primary electron beam is obtained by photoemission from a negative electron affinity GaAs surface excited by circularly polarized light. The direction of polarization of the electron beam is easily reversed without changing the beam intensity or transport characteristics. The degree of polarization of the source is estimated to be 28–30%. The scattering geometry is chosen so that only the energy-loss spectrum of the specularly reflected beam is measured by a hemispherical energy analyzer. We obtain spin dependent loss spectra for specularly reflected electron beams for a range of primary beam energies. Two polarization dependent features are observed in the energy-loss spectra, a shoulder at 1.6 eV and a well-defined peak at 2.8 eV. The data obtained is normalized to the measured elastic peak intensity, which is assumed to be the same for both spin polarization directions. Polarization analysis shows both features to be due almost entirely to inelastic scattering of incident electrons polarized parallel to the spin-down (minority) direction. The FWHM of both features are quite narrow, suggesting a near rigid exchange splitting for the bcc Co bands. The magnetization reversal behavior and the energy dependence of these spin-dependent features are consistant with the behavior of Stoner excitations. We have tentatively identified the feature at 1.6 eV as the primary Stoner excitation which implies the exchange splitting for bcc Co is also 1.6 eV. The higher-energy peak is most likely a second peak in the Stoner density-of-states.4 Additional theoretical calculations are being performed to verify these identifications.5
Cylindrical vector beam generation from spun fiber (2008)

Recently there has been considerable interest in the generation of cylindrical vector beams for numerous possible applications in nano-biophotonics, optical imaging, the laser processing of materials and the generation of single photon sources among others. Cylindrical vector optical vortex beams are shown by propagating a fundamental laser mode through a spun ber. The polarization state of the output from the ber is characterized and the the process of this mode conversion will be discussed.
X-linked retinoschisis: an update (2006)

X-linked retinoschisis is the leading cause of macular degeneration in males and leads to splitting within the inner retinal layers leading to visual deterioration. Many missense and protein truncating mutations have now been identified in the causative retinoschisis gene (RS1) which encodes a 224 amino acid secretory retinal protein, retinoschisin. Retinoschisin octamerisation is implicated in cell-cell interactions and cell adhesion perhaps by interacting with beta2 laminin. Mutations cause loss of retinoschisin function by one of the three mechanisms: by interfering with protein secretion, by preventing its octamerisation or by reducing function in the secreted octamerised protein. The development of retinoschisis mouse models have provided a model system that closely resembles the human disease. Recent reports of RS1 gene transfer to these models and the sustained restoration of some retinal function and morphology suggest gene replacement may be a possible future therapy for patients.