gebhart/patrepeval huggingface dataset:
Splitting of a Liquid Jet (2007)

We demonstrate that a flowing liquid jet can be controllably split into two separate subfilaments through the application of a sufficiently strong tangential stress to the surface of the jet. In contrast, normal stresses can never split a liquid jet. We apply these results to observations of uncontrolled splitting of jets in electric fields. The experimental realization of controllable jet splitting would provide an entirely novel route for producing small polymeric fibers.
More on reconstructing strings from random traces: insertions and deletions (2005)

We are given a collection of m received strings or traces that have been independently generated by randomly inserting and deleting bits from a common string t of length n. Our goal is to reconstruct the string t from these observed traces. This paper considers both the algorithms for doing this reconstruction and seeks to understand the error rates at which reconstruction is possible. Note the difference from the typical coding theory scenario rather than trying to infer a codeword from a single received word, we are interested in inferring an arbitrary (or near arbitrary) word from multiple, independently generated received words. We present two main results. Firstly we show that for almost all transmitted strings, if the deletion/insertion error probability is O(1/log <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> n) then with m = O(log n) traces we can exactly reconstruct the transmitted string with high probability. Furthermore we can still reconstruct in the presence of additional noise that flips each bit with constant probability. Secondly, for arbitrary strings (with no run of length > n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">epsi</sup> ) we show that with a constant number of received strings we can reconstruct when the deletion/insertion probability is O(1/n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1/2+epsi</sup> ). This paper continues work initiated in Batu et. al. (2004) which considered only deletion errors. Our setting can be viewed as the study of an idealized biological evolutionary process where the DNA string undergoes point mutations, deletions and insertions. Our goal is to understand at what mutation rates, a small number of observed samples can be correctly aligned to reconstruct the parent string
Antithrombotic effects of some flavonoids alone and combined with acetylsalicylic acid. (1977)

In the rat, a selection of two experimental models of "prethrombotic states", one of venostatic thrombosis and one of arterial thrombosis was used to compare the antithrombotic of three flavonoid preparations: O,-(beta-hydroxyethyl)-rutosides (HR), an association of trihydroxyethylrutoside and coumarin (troxerutin) and 7-mono-hydroxyethylrutoside (7-Mono-HR), as well as acetylsalicylic acid (ASA). The flavonoids were very effective "protectors" on the prethrombotic models, but only ASA was active on the model of arterial thrombosis. No compound showed a clear protection on the venostatic model if direct activation by kaolin was used. However, if an indirect activation by vessel wall stimulation was used, 7-Mono-HR possessed a marked protective effect. The most favourable results were obtained with an association of 7-Mono-HR and ASA, which could be considered for investigation in clinical thrombosis prophylaxis.
Amino Acids Mixtures in Prevention of Acute Ammonia Intoxication in Dogs (1967)

HEPATIC encephalopathy continues to present a serious complication in patients following portasystemic shunt. It results from multiple metabolic derangements in patients with chronic liver disease and hepatocellular damage and is related to a disturbance of ammonia metabolism. It has been extensively studied by Sherlock and associates, 1 McDermott, 2 Zuidema and associates, 3 and others. Although other toxic substances have been implicated, the most commonly found metabolic product of protein metabolism that is indictable in its genesis is ammonia. Our current concepts of management are oriented in attempts to limit exogenous sources of proteins and inhibition of bacterial decomposition in the colon with antibiotics. In addition, other methods of treatment of encephalopathy and ammonia intoxication have consisted of use of cation exchange resin, amino acid therapy with glutamic acid, and arginine, hemodialysis, isolated liver perfusion, total blood exchange and replacement, and finally colectomy or colon exclusion. In spite of vigorous
Surface protein characterization of human adipose tissue‐derived stromal cells (2001)

Human bone marrow stromal cells are a multipotent population of cells capable of differentiating into a number of mesodermal lineages as well as supporting hematopoeisis. Their distinct protein and gene expression phenotype is well characterized in the literature. Human adipose tissue presents an alternative source of multipotent stromal cells. In this study, we have defined the phenotype of the human adipose tissue-derived stromal cells in both the differentiated and undifferentiated states. Flow cytometry and immunohistochemistry show that human adipose tissue-derived stromal cells have a protein expression phenotype that is similar to that of human bone marrow stromal cells. Expressed proteins include CD9, CD10, CD13, CD29, CD34, CD44, CD 49(d), CD 49(e), CD54, CD55, CD59, CD105, CD106, CD146, and CD166. Expression of some of these proteins was further confirmed by PCR and immunoblot detection. Unlike human bone marrow-derived stromal cells, we did not detect the STRO-1 antigen on human adipose tissue-derived stromal cells. Cells cultured under adipogenic conditions uniquely expressed C/EBPalpha and PPARdelta, two transcriptional regulators of adipogenesis. Cells cultured under osteogenic conditions were more likely to be in the proliferative phases of the cell cycle based on flow cytometric analysis of PCNA and Ki67. The similarities between the phenotypes of human adipose tissue-derived and human bone marrow-derived stromal cells could have broad implications for human tissue engineering.
Conversion of biomass to selected chemical products (2011)

This critical review provides a survey illustrated by recent references of different strategies to achieve a sustainable conversion of biomass to bioproducts. Because of the huge number of chemical products that can be potentially manufactured, a selection of starting materials and targeted chemicals has been done. Also, thermochemical conversion processes such as biomass pyrolysis or gasification as well as the synthesis of biofuels were not considered. The synthesis of chemicals by conversion of platform molecules obtained by depolymerisation and fermentation of biopolymers is presently the most widely envisioned approach. Successful catalytic conversion of these building blocks into intermediates, specialties and fine chemicals will be examined. However, the platform molecule value chain is in competition with well-optimised, cost-effective synthesis routes from fossil resources to produce chemicals that have already a market. The literature covering alternative value chains whereby biopolymers are converted in one or few steps to functional materials will be analysed. This approach which does not require the use of isolated, pure chemicals is well adapted to produce high tonnage products, such as paper additives, paints, resins, foams, surfactants, lubricants, and plasticisers. Another objective of the review was to examine critically the green character of conversion processes because using renewables as raw materials does not exempt from abiding by green chemistry principles (368 references).
Scopes Too Flexible...and Too Stiff (2010)

The article investigates how the difficulties caused by the flexibility of the endoscope shaft could be solved and to provide a categorized overview of designs that potentially provide a solution. The following are discussed: paradoxical problem of flexible endoscopy; NOTES or hybrid endoscopy surgery; design challenges; shaft-guidance: guiding principles; virtual track guidance; physical track guidance; shaft-guidance: rigidity control; material stiffening; structural stiffening; and hybrid stiffening.
Evaluation of Corrosion Fatigue Properties for Spring Steels and Its Application (1998)

In this paper, the, experimental method for evaluating a corrosive mode of spring steels to meet with the real usage of car, and the statistic approach for avaluating a corrosive pit characteristic, were studied.The studies were also extended to the influence of alloy elements and shot peering to corrosive fatigue strength.It was found that these approaches may have some possibility to predict corrosive fatigue strength, as described below.1) The corrosive pit characteristic can be improved by adding Cu, Ni and Cr to spring steels.2) The proposed statistic approach by using the estimated value of pit dimension can evaluate corrosive pit characteristic of spring steels quantitatively.3) The shot peering process can improve corrosive fatigue strength for the residual stress can restrain crack propagation at the bottom corrosive pit.4) It can be realized the prediction of corrosive fatigue strength may become possible by applying the estimated value of pit dimension to Murakami's ewuation.
World Bank GEF energy efficiency portfolio, review and practitioners' handbook (2005)

This report summarizes the main findings of this review, assesses some trends in project designs and program models, highlights emerging lessons learned, and attempts to offer some insights, suggestions and issues for continued discussion in the years ahead. The report has five chapters: introduction, summary of the project portfolio, discussion of program models and implementation experiences to date, energy efficiency (EE) financing programs and emerging good practices, and conclusion. Given the high number of EE financing programs in the pipeline, the report places a particular emphasis on this type of operation.
Imaging and therapy of malignant pleural mesothelioma using replication‐competent herpes simplex viruses (2006)

These findings support the continued investigation of oncolytic HSV as potential therapy for patients with therapy-resistant MPM.
Type I Interferon-Sensitive Recombinant Newcastle Disease Virus for Oncolytic Virotherapy (2010)

Newcastle disease virus (NDV), an avian paramyxovirus, is tumor selective and intrinsically oncolytic because of its potent ability to induce apoptosis. Several studies have demonstrated that NDV is selectively cytotoxic to tumor cells but not normal cells due to defects in the interferon (IFN) antiviral responses of tumor cells. Many naturally occurring strains of NDV have an intact IFN-antagonistic function and can still replicate in normal human cells. To avoid potential toxicity issues with NDV, especially in cancer patients with immunosuppression, safe NDV-oncolytic vectors are needed. We compared the cell killing abilities of (i) a recombinant NDV (rNDV) strain, Beaudette C, containing an IFN-antagonistic, wild-type V protein (rBC), (ii) an isogenic recombinant virus with a mutant V protein (rBC-Edit virus) that induces increased IFN in infected cells and whose replication is restricted in normal human cells, and (iii) a recombinant LaSota virus with a virulent F protein cleavage site that is as interferon sensitive as rBC-Edit virus (LaSota V.F. virus). Our results indicated that the tumor-selective replication of rNDV is determined by the differential regulation of IFN-alpha and downstream antiviral genes induced by IFN-alpha, especially through the IRF-7 pathway. In a nude mouse model of human fibrosarcoma, we show that the IFN-sensitive NDV variants are as effective as IFN-resistant rBC virus in clearing the tumor burden. In addition, mice treated with rNDV exhibited no signs of toxicity to the viruses. These findings indicate that augmentation of innate immune responses by NDV results in selective oncolysis and offer a novel and safe virotherapy platform.
Attenuation of Aβ deposition in the entorhinal cortex of normal elderly individuals associated with tobacco smoking (2005)

Investigating correlates of tobacco smoking provides the only currently available opportunity of examining effects of long-term exposure of nicotinic receptors on a specific nicotinic agonist in human. Alzheimer-type pathology (Abeta and abnormally phosphorylated tau assessed on the basis of AT8 immunoreactivity) together with vascular markers has been compared in age-matched groups of normal elderly smokers and non-smokers in the entorhinal cortex, an area of noted age-related pathology. The density of total Abeta and diffuse Abeta immunoreactivity, together with formic acid-extractable Abeta42 but not Abeta40, was reduced in smokers (n = 10-18) compared with non-smokers (n = 10-20) (P < 0.05). There was also a reduced percentage of cortical and leptomeningeal vessels with associated Abeta immunoreactivity in smokers (n = 13) compared with non-smokers (n = 14) (P < 0.005 and 0.05, respectively). There was a significant inverse correlation between formic acid-extractable Abeta42 and pack years (n = 34, r = -0.389, P = 0.025), with a similar trend for total Abeta immunoreactivity which did not reach statistical significance (n = 30, r = -0.323, P = 0.082). In contrast, there were no significant group differences for vascular markers (collagen IV, alpha-actin or glucose transporter 1), AT8 immunoreactivity or phosphate-buffered saline-soluble Abeta peptides, and no significant associations with gender for any of the measured parameters. These findings are consistent with previously reported reductions in histologically assessed amyloid plaques in aged human brain associated with tobacco use and dramatic lessening of Abeta deposits in APPsw mice after nicotine treatment. Development of nicotinic drugs to protect against beta-amyloidosis as one of the principal pathological hallmarks of brain ageing and Alzheimer's disease is indicated.
Recurrent inactivating mutations of ARID2 in non‐small cell lung carcinoma (2012)

In eukaryotic cells, DNA is packaged into chromatin and this compact storage in the nucleus promotes transcriptional repression of genes. Chromatin remodeling complexes such as the SWI/SNF complex are involved in making DNA accessible to transcription factors and thereby are implicated in the regulation of gene expression. Mutations and altered expression of chromatin remodeling complex genes have been described in cancer cells. Indeed, non-small cell lung cancer cell lines have been shown to harbor mutations in SMARCA4 (BRG1), a member of the SWI/SNF complex, but evidence has been less clear in primary tumors. Recently, inactivating mutations in AT-rich interaction domain 2 (ARID2) were found in liver cancer related to HCV infection and in melanoma. Here, we explored, using a genome-wide strategy and subsequent sequencing of targeted genes, whether chromatin remodeling is implicated in primary lung adenocarcinoma. Two genes were individualized from the genome screening as homozygously deleted in a set of samples: JARID2 and ARID2. Subsequent analysis of the entire coding sequences showed that ARID2 loss-of-function mutations were found in 5% of nonsmall cell lung cancers, thereby constituting one of the most frequently mutated genes in this cancer type after TP53, KRAS, EGFR, CDKN2A and STK11.
Self-Healing Circuits for Space-Applications (2007)

In particular for applications where no repair is possible, e.g. space missions, high reliability is usually an important requirement. Long mission times and harsh environment are a challenge for electronic circuits, and particular error mitigation techniques have to be implemented in order to be able to cope with the expected error effects. Our approach instead is based on delay-insensitive asynchronous logic, more precisely on the four state logic (FSL) design style and partial reconfiguration. Compared to synchronous circuits, FSL implies a considerable area overhead, but also provides some hidden and usually unused features. In this paper an overview is presented, how these features can be utilized in order to implement self-healing circuits in a very efficient way. As the FSL design style plays a central role in the presented concept, first an introduction to FSL is provided. Subsequently the self-healing approach will be explained showing how the above mentioned tasks to achieve self-healing are realized. The paper concludes with the current implementation status and open problems.
Mitochondria-targeted nitroxides exacerbate fluvastatin-mediated cytostatic and cytotoxic effects in breast cancer cells (2011)

Mito-CP11, a mitochondria-targeted nitroxide formed by conjugating a triphenylphosphonium cation to a five-membered nitroxide, carboxy-proxyl (CP), has been used as a superoxide dismutase (SOD) mimetic. In this study, we investigated the antiproliferative and cytotoxic properties of submicromolar levels of Mito-CP11 alone and in combination with fluvastatin, a well known cholesterol lowering drug, in breast cancer cells. Mito-CP11, but not CP or CP plus the cationic ligand, methyl triphenylphosphonium (Me-TPP+), inhibited MCF-7 breast cancer cell proliferation. Mito-CP11 had only minimal effect on MCF-10A, non-tumorigenic mammary epithelial cells. Mito-CP11, however, significantly enhanced fluvastatin-mediated cytotoxicity in MCF-7 cells. Mito-CP11 alone and in combination with fluvastatin inhibited nuclear factor kappa-B activity mainly in MCF-7 cells. We conclude that mitochondria-targeted nitroxide antioxidant molecules (such as Mito-CP11) that are non-toxic to non-tumorigenic cells could enhance the cytostatic and cytotoxic effects of statins in breast cancer cells. This strategy of combining mitochondria-targeted non-toxic molecules with cytotoxic chemotherapeutic drugs may be successfully used to enhance the efficacy of antitumor therapies in breast cancer treatment.
VHLinactivation in renal cell carcinoma: implications for diagnosis, prognosis and treatment (2007)

Clear cell renal cell carcinoma (ccRCC) provides a tumor paradigm for the integration of genetics, molecular biology, therapeutic target validation and the introduction of high-impact treatment strategies. Most cases of sporadic as well as familial ccRCC acquire somatic inactivating mutations of the von Hippel-Lindau tumor-suppressor gene, VHL. pVHL, VHL gene product and a protein member of the E3 ubiquitin ligase family, acts in normal cells to direct the degradation and clearance of the hypoxia inducible factor (HIF)alpha transcription factor family, such that in its absence, as in ccRCC, the HIF proteins stabilize, accumulate to supraphysiologic levels and activate the transcription of genes such as VEGF and PDGF, which contributes substantially to the physiology of the tumor, and has been assessed indirectly as a prognostic factor. Molecularly targeted therapy blocking components of this pathway has been successfully introduced to the clinic with a substantive impact on clinical parameters of RCC. This review will examine the regulation of these molecular pathways in RCC and discuss the impact on the clinical management of patients with RCC.
Impact of linker and conjugation chemistry on antigen binding, Fc receptor binding and thermal stability of model antibody-drug conjugates (2012)

Antibody-drug conjugates (ADCs) with biotin as a model cargo tethered to IgG1 mAbs via different linkers and conjugation methods were prepared and tested for thermostability and ability to bind target antigen and Fc receptor. Most conjugates demonstrated decreased thermostability relative to unconjugated antibody, based on DSC, with carbohydrate and amine coupled ADCs showing the least effect compared with thiol coupled conjugates. A strong correlation between biotin-load and loss of stability is observed with thiol conjugation to one IgG scaffold, but the stability of a second IgG scaffold is relatively insensitive to biotin load. The same correlation for amine coupling was less significant. Binding of antibody to antigen and Fc receptor was investigated using surface plasmon resonance. None of the conjugates exhibited altered antigen affinity. Fc receptor FcγIIb (CD32b) interactions were investigated using captured antibody conjugate. Protein G and Protein A, known inhibitors of Fc receptor (FcR) binding to IgG, were also used to extend the analysis of the impact of conjugation on Fc receptor binding. H10NPEG4 was the only conjugate to show significant negative impact to FcR binding, which is likely due to higher biotin-load compared with the other ADCs. The ADC aHISNLC and aHISTPEG8 demonstrated some loss in affinity for FcR, but to much lower extent. The general insensitivity of target binding and effector function of the IgG1 platform to conjugation highlight their utility. The observed changes in thermostability require consideration for the choice of conjugation chemistry, depending on the system being pursued and particular application of the conjugate.
A Robust Clustering Method for Chemical Structures (2005)

A clustering method based on finding the largest set of disconnected fragments that two chemical compounds have in common is shown to be able to group structures in a way that is ideally suited to medicinal chemistry programs. We describe how markedly improved results can be obtained by using a similarity metric that accounts not just for the size of the shared fragments but also on their relative arrangement in the two parent compounds. The use of a physiochemical atom typing scheme is also shown to provide significant contributions. Results from calculations using a test set consisting of actives from nine different important biological target proteins demonstrate the strengths of our clustering method and the advantages over other approaches that are widely used throughout the pharmaceutical industry.
<title>Prototype scanning fiber endoscope</title> (2002)

Commercial optical endoscopes rely on image transfer and acquisition based on an array of photon detectors, such as a coherent fiberoptic bundle, a video camera, and/or the human retina. An alternative approach uses a resonantly vibrating optical fiber that scans laser illumination. However, the limitation of laser-scanning endoscopic development has been the technological challenge of fabricating a small diameter, opto-mechanical scanner. A proof-of-concept micro-optical scanner has been built using a 2.3 mm diameter piezoelectric actuator and 4 mm diameter lenses. Images are generated using resonant spiral scanning of the fiber, projecting monochromatic laser light to an illumination plane. A single photodetector is used to acquire grayscale images one pixel at a time. In vitro, the acquired images of test targets have 10 to 20 micrometers maximum spatial resolution and a field-of-view that can be electronically varied.
Statics and Dynamics of Single DNA Molecules Confined in Nanochannels (2005)

The successful design of nanofluidic devices for the manipulation of biopolymers requires an understanding of how the predictions of soft condensed matter physics scale with device dimensions. Here we present measurements of DNA extended in nanochannels and show that below a critical width roughly twice the persistence length there is a crossover in the polymer physics.