gebhart/patrepeval huggingface dataset:
The stretch-activation response may be critical to the proper functioning of the mammalian heart (1999)

The "stretch-activation" response is essential to the generation of the oscillatory power required for the beating of insect wings. It has been conjectured but not previously shown that a stretch-activation response contributes to the performance of a beating heart. Here, we generated transgenic mice that express a human mutant myosin essential light chain derived from a family with an inherited cardiac hypertrophy. These mice faithfully replicate the cardiac disease of the patients with this mutant allele. They provide the opportunity to study the stretch-activation response before the hearts are distorted by the hypertrophic process. Studies disclose a mismatch between the physiologic heart rate and resonant frequency of the cardiac papillary muscles expressing the mutant essential light chain. This discordance reduces oscillatory power at frequencies that correspond to physiologic heart-rates and is followed by subsequent hypertrophy. It appears, therefore, that the stretch-activation response, first described in insect flight muscle, may play a role in the mammalian heart, and its further study may suggest a new way to modulate human cardiac function.
248: Ureteral Replacement with Intestine: A Viable and Safe Option for Complex Ureteral Reconstruction (2004)

You have accessJournal of UrologyPodium, Saturday, May 8, 2004, 3:30 - 5:30 pm1 Apr 2004248: Ureteral Replacement with Intestine: A Viable and Safe Option for Complex Ureteral Reconstruction Benjamin I. Chung, Karim J. Hamawy, John J. Smith, Leonard N. Zinman, and John A. Libertino Benjamin I. ChungBenjamin I. Chung More articles by this author , Karim J. HamawyKarim J. Hamawy More articles by this author , John J. SmithJohn J. Smith More articles by this author , Leonard N. ZinmanLeonard N. Zinman More articles by this author , and John A. LibertinoJohn A. Libertino More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(18)37510-4AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "248: Ureteral Replacement with Intestine: A Viable and Safe Option for Complex Ureteral Reconstruction." The Journal of Urology, 171(4S), p. 65 © 2016 by American Urological AssociationFiguresReferencesRelatedDetails Volume 171Issue 4SApril 2004Page: 65 Advertisement Copyright & Permissions© 2016 by American Urological AssociationMetricsAuthor Information Benjamin I. Chung More articles by this author Karim J. Hamawy More articles by this author John J. Smith More articles by this author Leonard N. Zinman More articles by this author John A. Libertino More articles by this author Expand All Advertisement PDF DownloadLoading ...
Scalable training ofL1-regularized log-linear models (2007)

The L-BFGS limited-memory quasi-Newton method is the algorithm of choice for optimizing the parameters of large-scale log-linear models with L2 regularization, but it cannot be used for an L1-regularized loss due to its non-differentiability whenever some parameter is zero. Efficient algorithms have been proposed for this task, but they are impractical when the number of parameters is very large. We present an algorithm Orthant-Wise Limited-memory Quasi-Newton (OWL-QN), based on L-BFGS, that can efficiently optimize the L1-regularized log-likelihood of log-linear models with millions of parameters. In our experiments on a parse reranking task, our algorithm was several orders of magnitude faster than an alternative algorithm, and substantially faster than L-BFGS on the analogous L2-regularized problem. We also present a proof that OWL-QN is guaranteed to converge to a globally optimal parameter vector.
Photodynamic Therapy for Corneal Neovascularization (1998)

Photodynamic therapy appears to be safe and effective for eliciting prolonged (> 28 days) occlusion of corneal neovascularization in the rat model with minimal side effects and good clinical outcomes.
Mutational analysis of a conserved tetraloop in the 5′ untranslated region of hepatitis C virus identifies a novel RNA element essential for the internal ribosome entry site function (1999)

The 5' untranslated region of hepatitis C virus RNA forms an extensive secondary structure including several hairpin motifs and mediates translation initiation by an internal ribosome entry site-dependent pathway. We report, here, an extensive mutagenesis analysis of a highly conserved tetraloop in the 5' untranslated region of hepatitis C virus, namely hairpin IIIe (295'-GAUA-298'). Our results demonstrate that hairpin IIIe is essential for the internal ribosome entry site function. Moreover, they indicate the importance of the primary structure of this motif because mutations in all four nucleotides of the loop caused a severe loss of internal ribosome entry site activity. These data represent the first experimental evidence for the functional significance of tetraloops in internal ribosome entry site-driven translation of hepatitis C virus.
[Significance of MMP2 and MMP9 expression in prostate cancer]. (2005)

The expression of MMP2 and MMP9 may play an important role in the development and metastasis of PCa.
An SMA-based flexible active endoscope for minimal invasive surgery (1995)

In this paper we describe the design, fabrication and testing of an active endoscope for minimal invasive surgery (MIS). The device has a silicone rubber body with 8 mm outer diameter and 40 mm length. This configuration has two bending degrees of freedom. The device is actuated by three miniature SMA springs, which are heated by Joule effect and cooled by a forced air flow. The actuators are located in three lumina (1.5 mm diameter) of the endoscope. The active endoscope incorporates a fibre optic bundle for visual inspection which has been used in the current experiments to measure the performance of the endoscope tip in terms of bending angles and directivity.
Risk of Sequelae afterChlamydia trachomatisGenital Infection in Women (2010)

Chlamydia trachomatis infection, the most common reportable disease in the United States, can lead to pelvic inflammatory disease (PID), infertility, ectopic pregnancy, and chronic pelvic pain. Although C. trachomatis is identified among many women who receive a diagnosis of PID, the incidence and timing of PID and long-term sequelae from an untreated chlamydial infection have not been fully determined. This article examines evidence reviewed as part of the Centers for Disease Control and Prevention Chlamydia Immunology and Control Expert Advisory Meeting; 24 reports were included. We found no prospective studies directly assessing risk of long-term reproductive sequelae, such as infertility, after untreated C. trachomatis infection. Several studies assessed PID diagnosis after untreated chlamydial infection, but rates varied widely, making it difficult to determine an overall estimate. In high-risk settings, 2%-5% of untreated women developed PID within the approximately 2-week period between testing positive for C. trachomatis and returning for treatment. However, the rate of PID progression in the general, asymptomatic population followed up for longer periods appeared to be low. According to the largest studies, after symptomatic PID of any cause has occurred, up to 18% of women may develop infertility. In several studies, repeated chlamydial infection was associated with PID and other reproductive sequelae, although it was difficult to determine whether the risk per infection increased with each recurrent episode. The present review critically evaluates this body of literature and suggests future research directions. Specifically, prospective studies assessing rates of symptomatic PID, subclinical tubal damage, and long-term reproductive sequelae after C. trachomatis infection; better tools to measure PID and tubal damage; and studies on the natural history of repeated chlamydial infections are needed.
Advances in atomic force microscopy (2003)

This article reviews the progress of atomic force microscopy in ultrahigh vacuum, starting with its invention and covering most of the recent developments. Today, dynamic force microscopy allows us to image surfaces of conductors and insulators in vacuum with atomic resolution. The most widely used technique for atomic-resolution force microscopy in vacuum is frequency-modulation atomic force microscopy (FM-AFM). This technique, as well as other dynamic methods, is explained in detail in this article. In the last few years many groups have expanded the empirical knowledge and deepened our theoretical understanding of frequency-modulation atomic force microscopy. Consequently spatial resolution and ease of use have been increased dramatically. Vacuum atomic force microscopy opens up new classes of experiments, ranging from imaging of insulators with true atomic resolution to the measurement of forces between individual atoms.
Interaction techniques in large display environments using hand-held devices (2006)

Hand-held devices possess a large potential as an interaction device for their today's ubiquity, and present us with an opportunity to devise new and unique ways of interaction as a smart device with multi-modal sensing and display capabilities. This paper introduces user interaction techniques (for selection, translation, scaling and rotation of objects) using a camera-equipped hand-held device such as a mobile phone or a PDA for large shared environments. We propose three intuitive interaction techniques for 2D and 3D objects in such an environment. The first approach uses the motion flow information to estimate the relative motion of the hand-held device and interact with the large display. The marker-object and marker-cursor approaches both use software markers on the interaction object or on the cursor for the various interactive tasks. The proposed interaction techniques can be further combined with many auxiliary functions and wireless services (of the hand-held devices) for seamless information sharing and exchange among multiple users. A formal usability analysis is currently on-going.
Proliferating cell nuclear antigen (PCNA): a key factor in DNA replication and cell cycle regulation (2010)

Most plant PCNAs exhibit features similar to those found for PCNAs of other eukaryotes. Similarities include: (1) a trimeric ring structure of the PCNA sliding clamp, (2) the involvement of PCNA in DNA replication and repair, (3) the ability to stimulate the activity of DNA polymerase δ and (4) the ability to interact with p21, a regulator of the cell cycle. However, many plant genomes seem to contain the second, probably functional, copy of the PCNA gene, in contrast to PCNA pseudogenes that are found in mammalian genomes.
A minimum mean-squared error interpretation of residual ISI channel shortening for discrete multitone transceivers (2002)

P.J.W. Melsa et al. (see IEEE Transactions on Communications, vol.44, p.1662-72, 1996) presented a channel shortening technique for discrete multitone transceivers that reduces intersymbol interference (ISI) by forcing the effective channel's impulse response to lie within a window of v+1 consecutive samples. G. Arslan et al. (see IEEE International Conference on Acoustic Speech and Signal Processing (ICASSP), p.2965-8, 2000) claim that although this method is intuitive, no previous study has been made on its optimality. They comment on its optimality by simulation. We demonstrate that Melsa's approach is in fact theoretically equivalent to a minimum mean-squared error (MMSE) solution to the channel-shortening problem. As a corollary to this we are afforded an insight into MMSE channel shortening as originally proposed by D.D. Falconer and F.R. Magee (see Bell Systems Technical Journal, p.1541-62, 1973). Previously, it has not been intuitive as to why the desired impulse response (DIR) should be made adaptive in this approach. Our result demonstrates that allowing DIR adaptation achieves a minimisation of the effective impulse response energy outside the desired window of v samples.
14. Genome Assembly and Annotation Process (2003)

The primary data produced by genome sequencing projects are often highly fragmented and sparsely annotated. This is especially true for the Human Genome Project [http://www.genome.gov/ page.cfm?pageID=10001772] as a result of its policy of releasing sequence data to the public sequence databases every day (1, 2). So that individual researchers do not have to piece together extended segments of a genome and then relate the sequence to genetic maps and known genes, NCBI provides annotated assemblies of public genome sequence data. NCBI assimilates data of various types, from numerous sources, to provide an integrated view of a genome, making it easier for researchers to spot informative relationships that might not have been apparent from looking at the primary data. The annotated genomes can be explored using Map Viewer (Chapter 20) to display different types of data side-by-side and to follow links between related pieces of data. This chapter describes the series of steps, the “pipeline”, that produces NCBI's annotated genome assembly from data deposited in the public sequence databases. A variant of the annotation process developed for the human genome is used to annotate the mouse genome, and similar procedures will be applied to other genomes (Box 1). NCBI constantly strives to improve the accuracy of its human genome assembly and annotation, to make the data displays more informative, and to enhance the utility of our access tools. Each run through the assembly and annotation procedure, together with feedback from outside groups and individual users, is used to improve the process, refine the parameters for individual steps, and add new features. Consequently, the details of the assembly and annotation process change from one run to the next. This chapter, therefore, describes the overall human genome assembly and annotation process and provides short descriptions of the key steps, but it does not detail specific procedures or parameters. However, sufficient detail is provided to enable users of our assembly and annotations to become familiar with the complexities and possible limitations of the data we provide.
The unexpected discovery of a novel low-oxygen-activated locus for the anoxic persistence of Burkholderia cenocepacia (2013)

Burkholderia cenocepacia is a Gram-negative aerobic bacterium that belongs to a group of opportunistic pathogens displaying diverse environmental and pathogenic lifestyles. B. cenocepacia is known for its ability to cause lung infections in people with cystic fibrosis and it possesses a large 8 Mb multireplicon genome encoding a wide array of pathogenicity and fitness genes. Transcriptomic profiling across nine growth conditions was performed to identify the global gene expression changes made when B. cenocepacia changes niches from an environmental lifestyle to infection. In comparison to exponential growth, the results demonstrated that B. cenocepacia changes expression of over one-quarter of its genome during conditions of growth arrest, stationary phase and surprisingly, under reduced oxygen concentrations (6% instead of 20.9% normal atmospheric conditions). Multiple virulence factors are upregulated during these growth arrest conditions. A unique discovery from the comparative expression analysis was the identification of a distinct, co-regulated 50-gene cluster that was significantly upregulated during growth under low oxygen conditions. This gene cluster was designated the low-oxygen-activated (lxa) locus and encodes six universal stress proteins and proteins predicted to be involved in metabolism, transport, electron transfer and regulation. Deletion of the lxa locus resulted in B. cenocepacia mutants with aerobic growth deficiencies in minimal medium and compromised viability after prolonged incubation in the absence of oxygen. In summary, transcriptomic profiling of B. cenocepacia revealed an unexpected ability of aerobic Burkholderia to persist in the absence of oxygen and identified the novel lxa locus as key determinant of this important ecophysiological trait.
Model Predicting Survival in Stage I Melanoma Based on Tumor Progression (1989)

We used the lesional steps in tumor progression and multivariable logistic regression to develop a prognostic model for primary, clinical stage I cutaneous melanoma. This model is 89% accurate in predicting survival. Using histologic criteria, we assigned melanomas to tumor progression steps by ascertaining their particular growth phase. These phases were the in situ and invasive radial growth phase and the vertical growth phase (the focal formation of a dermal tumor nodule or dermal tumor plaque within the radial growth phase or such dermal growth without an evident radial growth phase). After a minimum follow-up of 100.6 months and a median follow-up of 150.2 months, 122 invasive radial-growth-phase tumors were found to be without metastases. Eight-year survival among the 264 patients whose tumors had entered the vertical growth phase was 71.2%. Survival prediction in these patients was enhanced by the use of a multivariable logistic regression model. Twenty-three attributes were tested for entry into this model. Six had independently predictive prognostic information: (a) mitotic rate per square millimeter, (b) tumor-infiltrating lymphocytes, (c) tumor thickness, (d) anatomic site of primary melanoma, (e) sex of the patient, and (f) histologic regression. When mitotic rate per square millimeter, tumor-infiltrating lymphocytes, primary site, sex, and histologic regression are added to a logistic regression model containing tumor thickness alone, they are independent predictors of 8-year survival (P less than .0005).
Altered pattern of Cul‐1 protein expression and neddylation in human lung tumours: relationships with CAND1 and cyclin E protein levels (2007)

The Cul-1 protein is the scaffold element of SCF complexes that are involved in the proteasomal degradation of numerous proteins regulating cell cycle progression. Owing to this central role in cell growth control, aberrant expression of the components of SCF is thought to play a role during tumourigenesis. Nothing is known about Cul-1 expression in human tumours. In this study, we have analysed its status in a series of 128 human lung carcinomas, comprising 50 non-small cell lung cancers (NSCLCs; 29 squamous cell carcinomas and 21 adenocarcinomas) and 78 neuroendocrine (NE) lung tumours (24 typical and atypical carcinoids, 19 large cell NE carcinomas and 35 small cell lung carcinomas), using immunohistochemistry. We report for the first time an altered pattern of Cul-1 expression in human tumours; indeed, we show that Cul-1 expression is up-regulated in 40% (51/128) of all lung tumours as compared to normal lung tissues, including 34% (17/50), 75% (18/24) and 30% (16/54) of NSCLCs, carcinoids and high grade neuroendocrine lung carcinomas, respectively. Furthermore, we demonstrate that high levels of Cul-1 protein are associated with a low KI67 proliferative index (p = 0.005) and with a decrease in the cyclin E oncoprotein (p = 0.0003), one of the major targets of SCF complexes. These data suggest that up-regulation of Cul-1 could protect cells from hyperproliferative signals through cyclin E down-regulation. Cul-1 is modified by neddylation, a post-translational modification that grafts ubiquitin-like Nedd8/Rub1 residues and controls Cul-1 activity. We also provide evidence that neddylated forms of Cul-1 are specifically expressed in high-grade NE lung tumours and are associated with down-regulation of the Cul-1 inhibitor CAND1 (p = 0.03) and a high level of cyclin E (p = 0.0002). These data support the notion that alterations in the Cul-1 neddylation/deneddylation pathway could contribute to the development of these highly aggressive lung tumours.
A soluble transforming growth factor beta type III receptor suppresses tumorigenicity and metastasis of human breast cancer MDA-MB-231 cells. (1999)

Transforming growth factor beta (TGF-beta) can promote late stage tumor progression in a number of model systems. In the present study, we have examined whether expression of a truncated soluble extracellular domain of TGF-beta type III receptor (sRIII) in human breast cancer MDA-MB-231 cells can antagonize the tumor-promoting activity of TGF-beta by sequestering active TGF-beta isoforms that are produced by the cancer cells. The secretion of sRIII reduced the amount of active TGF-beta1 and TGF-beta2 in the conditioned medium. This led to a significant reduction of the growth-inhibitory activity of the medium conditioned by sRIII-expressing cells on the growth of mink lung epithelial CCL64 cells in comparison with the medium conditioned by the control cells. The tumor incidence and growth rate of all of the three sRIII-expressing clones studied were significantly lower than those of the control cells in athymic nude mice. Four of five control cell-inoculated mice showed spontaneous metastasis in the lung, whereas none of the sRIII-expressing cell-inoculated mice had any lung metastasis. Thus, our results suggest that the sRIII may be used to antagonize the tumor-promoting activity of TGF-beta.
Improving Solubility ofShewanellaoneidensisMR-1 andClostridiumthermocellumJW-20 Proteins Expressed intoEsherichiacoli (2005)

Low solubility of proteins overexpressed in E. coli is a frequent problem in high-throughput structural genomics. To improve solubility of proteins from mesophilic Shewanella oneidensis MR-1 and thermophilic Clostridium thermocellum JW20, an approach was attempted that included a fusion of the target protein to a maltose-binding protein (MBP) and a decrease of induction temperature. The MBP was selected as the most efficient solubilizing carrier when compared to a glutathione S-transferase and a Nus A protein. A tobacco etch virus (TEV) protease recognition site was introduced between fused proteins using a double polymerase-chain reaction and four primers. In this way, 79 S. oneidensis proteins have been expressed in one case with an N-terminal 30-residue tag and in another case as a fusion protein with MBP. A foreign tag might significantly affect the properties of the target polypeptide. At 37 degrees C and 18 degrees C induction temperatures, only 5 and 17 tagged proteins were soluble, respectively. In fusion with MBP 4, 34, and 38 proteins were soluble upon induction at 37 degrees, 28 degrees, and 18 degrees C, respectively. The MBP is assumed to increase stability and solubility of a target protein by changing both the mechanism and the cooperativity of folding/unfolding. The 66 C. thermocellum proteins were expressed as fusion proteins with MBP. Induction at 37 degrees, 28 degrees, and 18 degrees C produced 34, 57, and 60 soluble proteins, respectively. The higher solubility of C. thermocellum proteins in comparison with the S. oneidensis proteins under similar conditions of induction correlates with the thermophilicity of the host. The two-factor Wilkinson-Harrison statistical model was used to identify soluble and insoluble proteins. Theoretical and experimental data showed good agreement for S. oneidensis proteins; however, the model failed to identify soluble/insoluble Clostridium proteins. A suggestion has been made that the Wilkinson-Harrison model is not applicable to C. thermocellum proteins because it did not account for the peculiarities of protein sequences from thermophiles.