gebhart/patrepeval huggingface dataset:
Expression of fibronectin-binding protein FbpA modulates adhesion in Streptococcus gordonii The GenBank accession number for the sequence reported in this paper is X65164. (2002)

Fibronectin binding is considered to be an important virulence factor in streptococcal infections. Adhesion of the oral bacterium Streptococcus gordonii to immobilized forms of fibronectin is mediated, in part, by a high molecular mass wall-anchored protein designated CshA. In this study, a second fibronectin-binding protein of S. gordonii is described that has been designated as FbpA (62.7 kDa). This protein, which is encoded by a gene located immediately downstream of the cshA gene, shows 85 and 81% identity to the fibronectin-binding proteins PavA, of Streptococcus pneumoniae, and FBP54, of Streptococcus pyogenes, respectively. Purified recombinant FbpA bound to immobilized human fibronectin in a dose-dependant manner, and isogenic mutants in which the fbpA gene was inactivated were impaired in their binding to fibronectin. This effect was apparent only for cells in the exponential phase of growth, and was associated with reduced surface hydrophobicity and the surface expression of CshA. Cells in the stationary phase of growth were unaffected in their ability to bind to fibronectin. By utilizing gene promoter fusions with cat (encoding chloramphenicol O-acetyltransferase), it was demonstrated that cshA expression was down-regulated during the exponential phase of growth in the fbpA mutant. Expression of fbpA, but not cshA, was sensitive to atmospheric O2 levels, and was found to be up-regulated in the presence of elevated O2 levels. The results suggest that FbpA plays a regulatory role in the modulation of CshA expression and, thus, affects the adhesion of S. gordonii to fibronectin.
Folate deficiency causes uracil misincorporation into human DNA and chromosome breakage: Implications for cancer and neuronal damage (1997)

Folate deficiency causes massive incorporation of uracil into human DNA (4 million per cell) and chromosome breaks. The likely mechanism is the deficient methylation of dUMP to dTMP and subsequent incorporation of uracil into DNA by DNA polymerase. During repair of uracil in DNA, transient nicks are formed; two opposing nicks could lead to chromosome breaks. Both high DNA uracil levels and elevated micronucleus frequency (a measure of chromosome breaks) are reversed by folate administration. A significant proportion of the U.S. population has low folate levels, in the range associated with elevated uracil misincorporation and chromosome breaks. Such breaks could contribute to the increased risk of cancer and cognitive defects associated with folate deficiency in humans.
Alignment and statistical difference analysis of complex peptide data sets generated by multidimensional LC‐MS (2005)

A method for high-resolution proteomics analyses of complex protein mixtures is presented using multidimensional HPLC coupled to MS (MDLC-MS). The method was applied to identify proteins that are differentially expressed during fruit ripening of tomato. Protein extracts from red and green tomato fruits were digested by trypsin. The resulting highly complex peptide mixtures were separated by strong cation exchange chromatography (SCX), and subsequently analyzed by RP nano-LC coupled to quadrupole-TOF MS. For detailed quantitative comparison, triplicate RP-LC-MS runs were performed for each SCX fraction. The resulting data sets were analyzed using MetAlign software for noise and data reduction, multiple alignment and statistical variance analysis. For each RP-LC-MS chromatogram, up to 7000 mass components were detected. Peak intensity data were compared by multivariate and statistical analysis. This revealed a clear separation between the green and red tomato samples, and a clear separation of the different SCX fractions. MS/MS spectra were collected using the data-dependent acquisition mode from a selected set of differentially detected peptide masses, enabling the identification of proteins that were differentially expressed during ripening of tomato fruits. Our approach is a highly sensitive method to analyze proteins in complex mixtures without the need of isotope labeling.
A neural network based real-time robot tracking controller using position sensitive detectors (2002)

A real-time visual servo tracking system for an industrial robot has been developed. The position sensitive detector or PSD, instead of the CCD, is used as a real time vision sensor due to its fast response (The position is converted to analog current). A neural network learns the complex association between the object position and its sensor reading and uses it to track that object. It also turns out that this scheme lends itself to a convenient way to teach a workpath for the robot. Furthermore, for real-time use of the neural net, a novel architecture has been developed based on the concept of input space partitioning and local learning. It exhibits characteristics of fast processing and learning as well as optimal usage of hidden neurons.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Proton nuclear magnetic resonance studies on methylthiohydantoins, thiohydantoins, and hydantoins of amino acids (1977)

Proton magnetic resonance spectra of methylthiohydantoin (3-methyl-2-thiohydantoin), thiohydantoin (2-thiohydantoin), and hydantoin derivatives of amino acids were studied in dimethyl sulfoxide-d6. Their parent amino acids could be identified by the spectra. An application to the N- and C-terminal amino acid analysis of a tripeptide was examined.
Prosthetic anterior cruciate ligaments in the rabbit. A comparison of four types of replacement (1987)

Four types of prosthetic replacement for the anterior cruciate ligament (carbon fibre, carbon fibre and Dacron composite, Dacron alone and bovine xenograft) were assessed at three, six and 12 months after implantation in the knees of New Zealand white rabbits. The synovium and both intra-articular and intra-osseous portions of the ligaments were examined macroscopically, by light microscopy and by scanning electron microscopy. All the knees showed mild synovitis, and there was no significant growth into the intra-articular part of any ligament. Carbon fibre and xenograft did not appear to be suitable materials in this animal model. The composite ligament showed short-term ingrowth of fibrous tissue only into the periphery of the sheath in its intra-osseous portion, whereas the Dacron ligament showed progressive fibrous tissue ingrowth with some bony incorporation of its outer fibres.
Do all roads lead to Rome? Routes to metastasis development (2011)

Metastasis, the life-threatening aspect of cancer, is a systemic disease process. Considerable progress has been made in recent years regarding how tumor cells circulating in the blood and lymphatic systems interact with and extravasate into secondary sites, and what determines whether these disseminated tumors cells survive, remain dormant or go on to form macrometastases. New insights into the routes that tumor cells take once leaving the primary tumor have emerged. Novel concepts regarding early seeding of metastases coupled to parallel progression, self-seeding of primary tumors by circulating tumor cells and the induction of premetastatic niches in distant organs by primary tumors have come to the fore. The perceived role of the lymphatic system in determining patterns of metastasis formation in distant organs has been reassessed. Together these new insights have the potential to offer new therapeutic options. In particular, the regulation of tumor cell dormancy emerges as a key event in metastasis formation, and therapeutic control of dormancy holds the promise of rendering cancer a chronic rather than life-threatening disease.
Irrigation Treatment in Split-Thickness Skin Grafting of Intractable Leg Ulcers (1985)

Continuous irrigation with saline through a felt dressing was used following mesh split-skin grafting of intractable leg ulcers. Antibiotics were added to the irrigation fluid in certain cases. Effective drainage of the grafted area was achieved and no signs of infection were seen.
Fast and accurate automatic structure prediction with HHpred (2009)

Automated protein structure prediction is becoming a mainstream tool for biological research. This has been fueled by steady improvements of publicly available automated servers over the last decade, in particular their ability to build good homology models for an increasing number of targets by reliably detecting and aligning more and more remotely homologous templates. Here, we describe the three fully automated versions of the HHpred server that participated in the community-wide blind protein structure prediction competition CASP8. What makes HHpred unique is the combination of usability, short response times (typically under 15 min) and a model accuracy that is competitive with those of the best servers in CASP8.
La santé : histoire d’un droit (2014)

Le petit ouvrage que Véronique Harouel-Bureloup vient de publier est particulièrement bienvenu. Rares sont les livres traitant du droit international de la santé et cette grande spécialiste du droit international humanitaire en général et du Comité international de la Croix-Rouge en particulier nous en livre ici une vision particulièrement intéressante. Trop souvent les ouvrages traitant de droit international de la santé se résument à l’histoire de la santé au travers de l’OMS et des organis...
Parathyroid hormone improves contractile performance of adult rat ventricular cardiomyocytes at low concentrations in a non-acute way (2009)

Low concentrations of PTH improve cell shortening by increasing calcium load at rest. By this mechanism cardiomyocytes compensate reduced extracellular calcium levels as they occur in patients with heart failure.
Evolutionary Dynamics of GII.4 Noroviruses over a 34-Year Period (2009)

Noroviruses are a major cause of epidemic gastroenteritis in children and adults, and GII.4 has been the predominant genotype since its first documented occurrence in 1987. This study examined the evolutionary dynamics of GII.4 noroviruses over more than three decades to investigate possible mechanisms by which these viruses have emerged to become predominant. Stool samples (n = 5,424) from children hospitalized at the Children's Hospital in Washington, DC, between 1974 and 1991 were screened for the presence of noroviruses by a custom multiplex real-time reverse transcription-PCR. The complete genome sequences of five GII.4 noroviruses (three of which predate 1987 by more than a decade) in this archival collection were determined and compared to the sequences of contemporary strains. Evolutionary analysis determined that the GII.4 VP1 capsid gene evolved at a rate of 4.3 x 10(-3) nucleotide substitutions/site/year. Only six sites in the VP1 capsid protein were found to evolve under positive selection, most of them located in the shell domain. No unique mutations were observed in or around the two histoblood group antigen (HBGA) binding sites in the P region, indicating that this site has been conserved since the 1970s. The VP1 proteins from the 1974 to 1977 noroviruses contained a unique sequence of four consecutive amino acids in the P2 region, which formed an exposed protrusion on the modeled capsid structure. This protrusion and other observed sequence variations did not affect the HBGA binding profiles of recombinant virus-like particles derived from representative 1974 and 1977 noroviruses compared with more recent noroviruses. Our analysis of archival GII.4 norovirus strains suggests that this genotype has been circulating for more than three decades and provides new ancestral strain sequences for the analysis of GII.4 evolution.
Sorting out signature schemes (1993)

Digital signature schemes are a fundamental tool for secure distributed systems. It is important to have a formal notion of what a secure digital signature scheme is, so that there is a clear interface between designers and users of such schemes. A definition that seemed final was given by Goldwasser, Micali, and Rivest in 1988, and although most signature schemes used in practice cannot be proved secure with respect to it, they are all built so that they hopefully fulfil it, e.g., by the inclusion of hash functions or redundancy to counter active attacks.
Gaussian Mixture Generative Adversarial Networks for Diverse Datasets, and the Unsupervised Clustering of Images (2018)

Generative Adversarial Networks (GANs) have been shown to produce realistically looking synthetic images with remarkable success, yet their performance seems less impressive when the training set is highly diverse. In order to provide a better fit to the target data distribution when the dataset includes many different classes, we propose a variant of the basic GAN model, called Gaussian Mixture GAN (GM-GAN), where the probability distribution over the latent space is a mixture of Gaussians. We also propose a supervised variant which is capable of conditional sample synthesis. In order to evaluate the model's performance, we propose a new scoring method which separately takes into account two (typically conflicting) measures - diversity vs. quality of the generated data. Through a series of empirical experiments, using both synthetic and real-world datasets, we quantitatively show that GM-GANs outperform baselines, both when evaluated using the commonly used Inception Score, and when evaluated using our own alternative scoring method. In addition, we qualitatively demonstrate how the \textit{unsupervised} variant of GM-GAN tends to map latent vectors sampled from different Gaussians in the latent space to samples of different classes in the data space. We show how this phenomenon can be exploited for the task of unsupervised clustering, and provide quantitative evaluation showing the superiority of our method for the unsupervised clustering of image datasets. Finally, we demonstrate a feature which further sets our model apart from other GAN models: the option to control the quality-diversity trade-off by altering, post-training, the probability distribution of the latent space. This allows one to sample higher quality and lower diversity samples, or vice versa, according to one's needs.
Interrelation of the renin system and erythropoietin in rats. (1980)

Evidence is presented implicating the renin-angiotensin system in the regulation of plasma erythropoietin concentration. Male and female rats were exposed to hypoxia at 0.43 atm for 8 hr. In male rats, individual erythropoietin values showed a positive correlation with renin, renin substrate, and angiotensin I after 8 hr of hypoxia. In female rats, renin was not elevated during hypoxia. However, after renin was injected subcutaneously, plasma renin values became similar to those in male rats and erythropoietin doubled. Individual erythropoietin values of the combined groups showed a positive correlation with plasma renin. A single oral dose of SQ 14225, an angiotensin I-converting enzyme inhibitor, reduced erythropoietin to undetectable levels in renin-injected female rats. Angiotensin II, in subpressor amounts, prevented the suppression of erythropoietin by SQ 14225. SQ 14225 also reduced renin substrate concentration at ambient pressure and during hypoxic exposure. The correlation coefficient between renin substrate and erythropoietin in rats given SQ 14225 to lower substrate or angiotensin II to increase substrate was 0.85; p < 0.0005. The increase in renin substrate that occurred during hypoxia in female rats given angiotensin II correlated positively with erythropoietin, r = 0.86; p < 0.0005.
Expression and Iron Loading of Recombinant Ferritin Homopolymers (2021)

Ferritin is an iron storage protein consisting of H and L chains to form a 24-subunit heropolymer. Ceruloplamin oxidizes Fe(II) and then loads the iron into ferritin. This research was conducted to determine which ferritin subunit is involved and whether a proposed iron-loading channel is required for iron loading by ceruloplasmin. Recombinant rat liver H and L chain ferritin homopolymers, designated as rH-Ft and rL-Ft, respectively, were produced using insect cell-baculovirus and Escherichia coli expression systems. The expressed rH-Ft strongly suppressed the growth of the host. The rH-Ft expressed in the E. coli contained approximately 150 iron atoms/ferritin and was observed to have protein damage, which was found to affect iron-loading by ceruloplasmin. The ferritin expressed in the E. coli system apparently was not proper for this iron loading study. Alternatively, the ferritins expressed in the insect cell-baculovirus system were utilized for this purpose . Ceruloplasmin was able to load iron into the rH-Ft, but not the rL-Ft. The initial rate of loading iron into the rH-Ft by ceruloplasmin was similar to that of native rat liver ferritin heteropolymer. Both the rH-Ft and the native rat liver ferritin could be maximally loaded with iron by ceruloplasmin up to 2,500 iron atoms/ferritin. When the rH-Ft or the native ferritin was present, the ferroxidase activity of ceruloplasmin was enhanced. No such enhancement was observed in the presence of the rL-Ft. This suggests that ceruloplasmin only associates with the ferritin H, but not L, chain during iron loading. The role of an a-helix bundle channel in iron loading by ceruloplasmin was investigated by using sitedirected mutagenesis. The channel in the rH-Ft was closed by mutation E62K and H65G to form a K62 to El07 salt bridge, which is thought to exist in the L chain. Conversely, the salt bridge in the channel of the L chain was removed by mutation K58E and G61H to form a channel similar to that in the four-a-helix bundle of the H chain. The initial rate of loading iron into the rL-FT mutant by ceruloplasmin was 50% of that for loading iron into the rH-Ft. When 500 atoms of iron per ferritin were used for loading, 98% loaded into the rH-Ft by ceruloplasmin in 5 minutes, but only 30% loaded into the rL-Ft mutant in the same time. The ferroxidase activity of ceruloplasmin was enhanced in the presence of the rHFt and its mutant, but not in the presence of the rL-Ft or its mutant. These results indicate that the association of ceruloplasmin and ferritin is required and the a-helix bundle channel is a channel for iron loading.
Management of incidental durotomy in minimally invasive spine surgery (2011)

In the authors' consecutive series of patients undergoing MISS, an unintended durotomy was associated with fewer complications than previously reported for open spinal surgery. The authors propose a simple management algorithm that includes early mobilization and results in excellent clinical outcomes with no incidence of postoperative cutaneous CSF fistula or other complications.
Identification of Two Ikaros‐like Transcription Factors in Lamprey (2002)

The jawless Agnatha (lampreys and hagfishes) represent the phylogenetically oldest order of vertebrates that are believed to lack the adaptive immune system of jawed vertebrates. In order to search for molecular markers specific for cellular components of the adaptive immune system in lampreys, we used the polymerase chain reaction (PCR) to identify genes for transcription factors of the Ikaros family in genomic DNA and cDNA libraries from two species of lampreys, Petromyzon marinus and Lampetra fluviatilis. The mammalian Ikaros-like family of transcription factors consists of five members, Ikaros, Helios, Aiolos, Eos and Pegasus, of which the first three appear to be essential for lymphocyte development. Two different Ikaros-like genes, named IKLF1 and IKLF2, were identified in lamprey. They both have the conserved exon-intron structure of seven exons and show alternative splicing like their counterparts in jawed vertebrates. The genes code for predicted proteins of 589 and 513 amino acid residues, respectively. The proteins contain six highly conserved zinc finger motifs that are 83-91% identical to the mammalian members of the Ikaros-like family. The remaining parts of the sequences are, however, mostly unalignable. Phylogenetic analysis based on the alignable segments of the sequences does not identify the orthologous gene in jawed vertebrates but rather shows equidistance of the lamprey Ikaros-like factors to each other and to Ikaros, Helios, Aiolos and Eos. Expression studies by reverse transcription (RT)-PCR and in situ hybridization (ISH), however, provide evidence for moderate expression in presumed lymphoid tissues like the gut epithelium and for high levels of expression in the gonads, especially in the ovary.
Preparation and Hydration Control of Corneal Tissue Strips for Experimental Use (2003)

The hydration of corneal tissue strips is maintained at normal values when the strips are immersed in 25% Dextran solution. Corneal strips swell to thicknesses above normal values in solutions with lower molecular weights.
Two denoising methods by wavelet transform (1999)

To wavelet-based noise reduction methods are discussed. First, we improve the traditional spatially selective noise filtration technique proposed by Xu et al. (1994). Second, we introduce a new threshold-based denoising algorithm based on undecimated discrete wavelet transform. Simulations and comparisons are given.
Integrated fuel alcohol production systems. Phase III. Experimental facility design report (1985)

An overall objective is to develop and demonstrate ethanol production technology for small-scale production systems. The low-temperature, low-pressure, two-stage sulfuric acid process was selected because of its adaptability to small-scale production systems and because of the availability of research data for major process operations. Many processes require very large production facilities before they can be operated economically. The selected process (1) is batch operated requiring relatively simple control procedures and instrumentation, (2) operates at atmospheric pressure eliminating the need for pressure vessels and elaborate safety procedures, (3) requires relatively common process and materials handling equipment, and (4) is economical to construct and operate at the 10-gph scale. The low-temperature and pressure conditions allow widespread use of inexpensive fiberglass or plastic materials. 14 refs., 22 figs., 8 tabs.
Visualizing the Loss Landscape of Neural Nets (2017)

Neural network training relies on our ability to find "good" minimizers of highly non-convex loss functions. It is well-known that certain network architecture designs (e.g., skip connections) produce loss functions that train easier, and well-chosen training parameters (batch size, learning rate, optimizer) produce minimizers that generalize better. However, the reasons for these differences, and their effects on the underlying loss landscape, are not well understood. In this paper, we explore the structure of neural loss functions, and the effect of loss landscapes on generalization, using a range of visualization methods. First, we introduce a simple "filter normalization" method that helps us visualize loss function curvature and make meaningful side-by-side comparisons between loss functions. Then, using a variety of visualizations, we explore how network architecture affects the loss landscape, and how training parameters affect the shape of minimizers.