gebhart/patrepeval huggingface dataset:
Slow and Steady Feature Analysis: Higher Order Temporal Coherence in Video (2016)

How can unlabeled video augment visual learning? Existing methods perform "slow" feature analysis, encouraging the representations of temporally close frames to exhibit only small differences. While this standard approach captures the fact that high-level visual signals change slowly over time, it fails to capture how the visual content changes. We propose to generalize slow feature analysis to "steady" feature analysis. The key idea is to impose a prior that higher order derivatives in the learned feature space must be small. To this end, we train a convolutional neural network with a regularizer on tuples of sequential frames from unlabeled video. It encourages feature changes over time to be smooth, i.e., similar to the most recent changes. Using five diverse datasets, including unlabeled YouTube and KITTI videos, we demonstrate our method's impact on object, scene, and action recognition tasks. We further show that our features learned from unlabeled video can even surpass a standard heavily supervised pretraining approach.
Fibril formation by primate, rodent, and Dutch-hemorrhagic analogs of Alzheimer amyloid .beta.-protein (1992)

Deposition of extraneuronal fibrils that assemble from the 39-43 residue beta/A4 amyloid protein is one of the earliest histopathological features of Alzheimer's disease. We have used negative-stain electron microscopy, Fourier-transform infrared (FT-IR) spectroscopy, and fiber X-ray diffraction to examine the structure and properties of synthetic peptides corresponding to residues 1-40 of the beta/A4 protein of primate [Pm(1-40); human and monkey], rodent [Ro(1-40); with Arg5-->Gly, Tyr10-->Phe, and His13-->Arg], and hereditary cerebral hemorrhage with amyloidosis of the Dutch type (HCHWA-D) [Du(1-40); with Glu22-->Gln]. As controls, we examined a reverse primate sequence [Pm*(40-1)] and an extensively substituted primate peptide [C(1-40); with Glu3-->Arg, Arg5-->Glu, Asp7-->Val, His13-->Lys, Lys16-->His, Val18-->Asp, Phe19-->Ser, Phe20-->Tyr, Ser26-->Pro, Ala30-->Val, Ile31-->Ala, Met35-->norLeu, Gly38-->Ile, Val39-->Ala, and Val40-->Gly]. The assembly of these peptides was studied to understand the relationship between species-dependent amyloid formation and beta/A4 sequence and the effect of a naturally occurring point mutation of fibrillogenesis. The three N-terminal amino acid differences between Pm(1-40) and Ro(1-40) had virtually no effect on the morphology or organization of the fibrils formed by these peptides, indicating that the lack of amyloid deposits in rodent brain is not due directly to specific changes in its beta/A4 sequence. beta-Sheet and fibril formation, judged by FT-IR, was maximal within the pH range 5-8 for Pm(1-40), pH 5-10.5 for Du(1-40), and pH 2.5-8 for Ro(1-40).(ABSTRACT TRUNCATED AT 250 WORDS)
Simultaneous measurement of angular and spectral properties of light scattering for characterization of tissue microarchitecture and its alteration in early precancer (2003)

We present a novel instrument to measure the spectral, angular, azimuthal, and polarization dependence of light backscattered by living biological tissues, thus providing the most comprehensive description of the light scattering to obtain unique quantitative information about the microarchitecture of living cells and tissues. We show the potential of this technique to characterize and diagnose early premalignant changes in the epithelia. In studies with a rodent model of colon carcinogenesis, we show that several parameters obtained using this technique, such as the number density of red blood cells in the capillary network immediately underlying the epithelium, the fractal dimension of the tissue, and the average roundness of subcellular structures, are significant for detection of precancerous changes at a very early stage of the carcinogenic process, at which no other histological or molecular markers have been identified.
Bacteriology of Moderate-to-Severe Diabetic Foot Infections and In Vitro Activity of Antimicrobial Agents (2007)

As part of a United States-based multicenter clinical trial, conducted from 2001 to 2004, that compared ertapenem to piperacillin-tazobactam for the treatment of moderate-to-severe diabetic foot infections (DFIs), we obtained 454 pretreatment specimens from 433 patients. After debridement, the investigators collected wound specimens, mostly by curettage or biopsy, and sent them to the R. M. Alden Research Laboratory for aerobic and anaerobic culture. Among the 427 positive cultures, 83.8% were polymicrobial, 48% grew only aerobes, 43.7% had both aerobes and anaerobes, and 1.3% had only anaerobes. Cultures yielded a total of 1,145 aerobic strains and 462 anaerobic strains, with an average of 2.7 organisms per culture (range, 1 to 8) for aerobes and 2.3 organisms per culture (range, 1 to 9) for anaerobes. The predominant aerobic organisms were oxacillin-susceptible Staphylococcus aureus (14.3%), oxacillin-resistant Staphylococcus aureus (4.4%), coagulase-negative Staphylococcus species (15.3%), Streptococcus species (15.5%), Enterococcus species (13.5%), Corynebacterium species (10.1%), members of the family Enterobacteriaceae (12.8%), and Pseudomonas aeruginosa (3.5%). The predominant anaerobes were gram-positive cocci (45.2%), Prevotella species (13.6%), Porphyromonas species (11.3%), and the Bacteroides fragilis group (10.2%). Pure cultures were noted for 20% of oxacillin-resistant Staphylococcus aureus cultures, 9.2% of Staphylococcus epidermidis cultures, and 2.5% of P. aeruginosa cultures. Two or more species of Staphylococcus were present in 13.1% of the patients. Ertapenem and piperacillin-tazobactam were each active against >98% of the enteric gram-negative rods, methicillin-sensitive S. aureus, and anaerobes. Among the fluoroquinolones, 24% of anaerobes, especially the gram-positive cocci, were resistant to moxifloxacin; 27% of the gram-positive aerobes but only 6% of the members of the family Enterobacteriaceae were resistant to levofloxacin. Moderate-to-severe DFIs are typically polymicrobial, and almost half include anaerobes. Our antibiotic susceptibility results can help to inform therapeutic choices.
Immunologic Control of HIV-1 (2002)

By destroying CD4+ T cells, human immunodeficiency virus-1 (HIV-1) infection results in immunodeficiency and the inability of the immune system to contain the virus in most individuals. Although treatment of HIV-1 infection with potent antiretroviral medications has resulted in enormous clinical benefit, there is a growing recognition of the limitations of this therapy. As a result, novel approaches to treating HIV-1 infection are being considered. One such strategy is immunotherapy, which seeks to boost immune responses against HIV-1 and control the virus. This approach is based on studies of other viruses in which a coordinated immune response contains the chronic infection. Recent studies show that CD4+ helper responses, CD8+ T cell activity, and antibodies may contribute to control of the virus without antiretroviral therapy in some HIV-positive individuals. Based on this understanding of the immunologic correlates of control of HIV-1, exciting new immunotherapeutic strategies for HIV-1 infection are being designed and tested.
RNA-Mediated Virus Resistance in Transgenic Plants: Exploitation of a Cellular Pathway Possibly Involved in RNA Degradation (1994)

Transgenic Nicotiana tabacum cv. Burley 49 plants were generated that express the 5' untranslated region of the tobacco etch potyvirus (TEV) genome ligated to a mutated version of the TEV coat protein gene sequence that rendered it untranslatable. Eight different transgenic plant lines were analyzed for transgene expression and for resistance to TEV. Three different responses were noted when the transgenic plant lines were inoculated with TEV: 1) some were highly resistant, and no virus replication occurred; 2) some were susceptible but able to recover from systemic TEV infection; and 3) some were susceptible to TEV infection. Plant tissue displaying the recovery phenotype was analyzed for virus replication and transgene expression. Recovered tissue could not be infected with TEV and had steady-state transgene RNA levels which were five- to eightfold lower than those of unchallenged transgenic plant tissue. Nuclear runoff assays suggested a post-transcriptional reduction in specific RNA levels. The highly resistant and recovery phenotypes associated with TEV challenge inoculation and the reduction of steady-state RNA levels in recovered transgenic leaf tissue may be manifestations of a common mechanism.
A Convenient Preparation of MonosubstitutedN,N′-di(Boc)-Protected Guanidines (1994)

1-H-Pyrazole-1-[N,N′-bis(tert-butoxycarbonyl)] carboxamidine (1) reacts under mild conditions with a number of amines and amino acids to give the respective protected guanidines in moderate to high isolated yields.
Laser welding of large diameter arteries and veins. (1987)

Based on our preliminary studies and the results of this study, we conclude that argon laser welding of 4-8 mm internal diameter veins, arteries, and arteriovenous fistulas may have several potential advantages compared to conventional suture techniques. The benefits of laser repairs may include improved mechanical properties, and absence of the foreign body response related to sutures. Laser welding is sterile, nontactile and possibly time conserving, and the wounds heal rapidly without aneurysms or excess tissue proliferation.
Substitution of Alanine for Serine 250 in the Murine Fatty Acid Transport Protein Inhibits Long Chain Fatty Acid Transport (1998)

The murine fatty acid transport protein (FATP) was identified on the basis of its ability to facilitate uptake of long chain fatty acids (LCFAs) when expressed in mammalian cells. To delineate FATP domains important for transport function, we cloned the human heart FATP ortholog. Comparison of the human, murine, and yeast amino acid sequences identified a highly conserved motif, IYTSGTTGXPK, also found in a number of proteins that form adenylated intermediates. We demonstrate that depletion of intracellular ATP dramatically reduces FATP-mediated LCFA uptake. Furthermore, wild-type FATP specifically binds [alpha-32P]azido-ATP. Introduction of a serine to alanine substitution (S250A) in the IYTSGTTGXPK motif produces an appropriately expressed and metabolized mutant FATP that demonstrates diminished LCFA transport function and decreased [alpha-32P]azido-ATP binding. These results are consistent with a mechanism of action for FATP involving ATP binding that is dependent on serine 250 of the IYTSGTTGXPK motif.
Alexa Dyes, a Series of New Fluorescent Dyes that Yield Exceptionally Bright, Photostable Conjugates (1999)

Alexa 350, Alexa 430, Alexa 488, Alexa 532, Alexa 546, Alexa 568, and Alexa 594 dyes are a new series of fluorescent dyes with emission/excitation spectra similar to those of AMCA, Lucifer Yellow, fluorescein, rhodamine 6G, tetramethylrhodamine or Cy3, lissamine rhodamine B, and Texas Red, respectively (the numbers in the Alexa names indicate the approximate excitation wavelength maximum in nm). All Alexa dyes and their conjugates are more fluorescent and more photostable than their commonly used spectral analogues listed above. In addition, Alexa dyes are insensitive to pH in the 4-10 range. We evaluated Alexa dyes compared with conventional dyes in applications using various conjugates, including those of goat anti-mouse IgG (GAM), streptavidin, wheat germ agglutinin (WGA), and concanavalin A (ConA). Conjugates of Alexa 546 are at least twofold more fluorescent than Cy3 conjugates. Proteins labeled with the Alexa 568 or Alexa 594 dyes are several-fold brighter than the same proteins labeled with lissamine rhodamine B or Texas Red dyes, respectively. Alexa dye derivatives of phalloidin stain F-actin with high specificity. Hydrazide forms of the Alexa dyes are very bright, formaldehyde-fixable polar tracers. Conjugates of the Alexa 430 (ex 430 nm/em 520 nm) and Alexa 532 (ex 530 nm/em 548 nm) fluorochromes are spectrally unique fluorescent probes, with relatively high quantum yields in their excitation and emission wavelength ranges.
Immune deficiency enhances expression of recombinant human antibody in mice after nonviral in vivo gene transfer. (2005)

A cDNA encoding human antibody against hepatitis B virus was expressed in normal and severe combined immune deficiency (SCID) mice to clarify whether or not host immune status affects circulating levels of the recombinant human antibody (RhAb) after nonviral in vivo gene transfer. For transferring genes, either electroporation (EP) or hydrodynamics-based transfection (HD) was employed. The former was applied to the leg muscle to express the gene, while the latter primarily targeted foreign gene expression in the liver. The expressed RhAb was secreted into the blood circulation, and its existence was assayed by ELISA. Prior to the investigation of host immune status, suitable forms of plasmid expression vectors and types of electrodes were determined in normal mice. Results showed that the vector encoding both the light and heavy chains driven by the CMV promoter had the highest plasma RhAb concentrations, and a pair of pincette-type electrodes conferred the best performance. In both EP and HD, the SCID state showed an increased and prolonged RhAb production in the blood circulation due probably to suppressed recognition of RhAb as a foreign protein to the host animal. The difference in gene transfer methods demonstrated a characteristic pattern: an early and sharp rise followed by a relatively rapid decrease in HD, in contrast to a gradual rise followed by a plateau level maintained in EP. As a result, with the same amount of gene transferred, the plasma RhAb concentrations for the first 7 or 8 weeks were higher in HD than EP, while the reverse was true for the latter period. Multiple gene transfer contributed to maintaining and prolonging high RhAb concentrations in plasma by both methods with similar characteristic patterns accompanying the respective gene transfer method. These results suggest the importance of host immunological potency for maintaining plasma RhAb concentrations if these gene transfer technologies are used for clinical and therapeutic purposes.
Profiling cytochrome P450 CYP1 enzyme expression in primary melanoma and disseminated disease utilizing spectral imaging microscopy (SIM) (2007)

8556 Background: The aim of this study was to profile cytochrome CYP1 family (CYP1A1/1A2, and CYP1B1) mono-oxygenase enzymes during the malignant progression of primary melanoma and metastatic disease. Methods: Tissue microarrays of primary (n = 75), and metastatic (n = 104) melanoma were constructed with the patient demographics: (1) primary melanoma; age 22 to 93 (median 59); sex M/F 36/44; Breslow thickness 0.4 to 15 mm (median 2.5 mm); ulceration 25/80, and (2) metastatic melanoma; age 26 to 92 (median 60 mm); sex M/F 54/49; ulceration 30/104; number of nodes 1 to 15 (median 2); extra-capsular spread 20/95. CYP1 protein was detected by IHC using validated selective poly- and monoclonal antibodies. Vector SG (grey) stain for CYP1 was used with nuclear fast red counterstain to aid spectral resolution from background melanin. Staining intensity was scored visually (negative 0, weak 1, moderate 2, strong 3) and using SIM at every pixel of a captured image of each melanoma core. Reference spectra of individual chromophores were used to spectrally ‘un-mix’ CYP1 staining before the mean normalised absorbance intensity was determined. Grading was by the 2002 AJCC classification system: primary stage I n = 27 (1A 8, 1B 19), and stage II n = 48 (2A 22, 2B 16, 2C 10), lymph node metastasis stage III n = 98 (3B 53, 3C 45), visceral metastasis stage IV n = 6. Normal skin (n = 27), benign naevi (n = 14), and dysplastic naevi (n = 21) were also included. Results: CYP1B1 was not in normal skin but was over-expressed in both primary and metastatic melanoma (visual: 71% &amp; 65%, SIM: 91% &amp; 83%). Primary melanoma (stage I &amp; II) was significantly greater (p = 0.004) than metastasis (stage III &amp; IV). CYP1B1 did not correlate with ulceration or Breslow thickness but did correlate with N stage lymph node metastasis (p = 0.005). CYP1B1 expression in dysplastic naevi indicated up-regulation at an early stage of melanoma progression. CYP1A1/1A2 was not expressed in normal skin nor primary/metastatic melanoma. Conclusions: CYP1B1 protein expression is maintained with advancing AJCC stage from primary through to visceral metastasis. Future work will seek to correlate protein expression with functionality with a view to exploiting CYP1B1 in the enzyme/prodrug therapy of malignant melanoma. No significant financial relationships to disclose.
An Extensible Simulation Framework Supporting Physically-based Interactive Painting (2006)

Since the introduction of computers, a lot of effort has gone into the research on applications that enable a user to create images for their artistic value. In case of interactive systems that try to provide a digital equivalent of the traditional painting process, however, most still produce images that appear too artificial and lack the \\natural look" and complexity that can be found in real paintings. Especially capturing the ambient behavior of watery paints like watercolor, gouache and Oriental ink, which run, drip and diffuse, is a challenging task to perform in real-time. For this reason, artists still prefer to use traditional methods. The advantages of such a paint system are numerous, however, as it allows to fully exploit the exibility of the digital domain, and perform all sorts of "non-physical" operations. In this dissertation we present a physically-based, interactive paint system that supports the creation of images with watery paint. We mainly target watercolor paint medium, but the model is general enough to simulate also related media like gouache and Oriental ink. In order to create a software system that is easy to maintain, change and extend, we first outline a component-based framework that is able to curb the complexity of building physically-based applications. The framework uses XML to provide a uniform description of the system's composition out of components. The cornerstone of the paint system is embodied by the canvas model, which adopts specialized algorithms, both physically-based and empiricallybased, on three different layers for the purpose of simulating paint behavior. Two implementations of the canvas model are presented: the first relies on a high-performance cluster (HPC) to perform a parallel simulation, while the second uses programmable graphics hardware. The second implementation is extended to a full virtual paint environment: \\WaterVerve", which features the Kubelka-Munk diffuse reflectance algorithm for rendering paint, a deformable 3D brush model and a set of artistic tools that fully exploit the physically based nature of the system.
Biological Formation of Molecular Hydrogen (1965)

From a general standpoint, the formation of molecular hydrogen can be considered a device for disposal of electrons released in metabolic oxidations. We presume that this means of performing anaerobic oxidations is of ancient origin and that the hydrogen-evolving system of strict anaerobes represents a primitive form of cytochrome oxidase, which in aerobes effects the terminal step of respiration, namely the disposal of electrons by combination with molecular oxygen. We further assume that the original pattern of reactions leading to H(2) production has become modified in various ways (with respect to both mechanisms and functions) during the course of biochemical evolution, and we believe that this point of view suggests profitable approaches for clarifying a number of problems in the intermediary metabolism of microorganisms which produce or utilize H(2). Of special general importance in this connection is the basic problem of defining more precisely the fundamental elements in the regulatory control of anaerobic energy metabolism. Among the more specific aspects awaiting further elucidation are: the relations between formation of H(2) and use of H(2) as a primary reductant for biosynthetic purposes; the various forms of direct and indirect interactions between hydrogenase and N(2) reduction systems; and the transitional stages between anaerobic and aerobic energy-metabolism patterns of facultative organisms.
Characteristics of an MM 22 medical microtron 6-MV photon beam (1984)

Instrument AB Scanditronix offers a 6-MV therapeutic photon beam as an option with the 22-MeV medical microtron (MM 22). The method of acceleration, target assembly, and use of two flattening filters produce beams having several characteristics (e.g., field flatness, penetration, and intensity) that are superior to many 6-MV Linac beams. Characteristics of the microtron's 6-MV photon beams including quality, surface dose, depth of maximum dose, peak dose rates, peak scatter factors, central axis percentage depth doses, tissue maximum ratios, and beam profiles are described.
Thymidine as a kinetic and biochemical modulator of 1-beta-D-arabinofuranosylcytosine in human acute nonlymphocytic leukemia. (1984)

We have carried out a clinical trial in which patients with relapsed leukemia were treated with thymidine (dThd) prior to and concomitantly with the administration of 1-beta-D-arabinofuranosylcytosine (ara-C) in an effort to kinetically and biochemically modulate the leukemic cells with two objectives: (a) to increase the S-phase fraction before giving ara-C; and (b) to increase the uptake and phosphorylation of ara-C. Six patients with acute nonlymphocytic leukemia who had relapsed after conventional or experimental therapy were given continuous i.v. infusions of dThd in conjunction with ara-C. dThd was started at 75 g/sq m/day (producing 1 mM plasma levels) and was given for 5 to 8 days until the proportion of bone marrow cells in S-phase (measured by autoradiography and flow cytometry) had increased and/or stabilized; then ara-C at 200 mg/sq m/day was begun. Twenty-four hr after initiation of ara-C therapy, the dThd dose was reduced to 30 g/sq m/day (plasma dThd, 0.1 to 0.6 mM). Both drugs were continued for 6 to 12 days until marrow aplasia or unacceptable toxicity occurred. Four patients with a base-line labeling index lower than 30% experienced a sustained increase in the S-phase fraction; two patients with a base-line labeling index higher than 30% experienced a reduction in the S-phase compartment during dThd infusion, in one case followed by an increase. The degree of S-phase arrest did not correlate with remission induction. In 5 patients, the flash incorporation of labeled ara-C into nucleoside triphosphate and deoxycytidine into DNA of bone marrow cells was measured. Three patients had a significant increase in the incorporation of deoxycytidine into DNA. Two of them achieved a complete remission. Increases in ara-C uptake were less impressive. A new technique was used to measure the absolute number of blasts present in the bone marrow. A decrease in leukemic cells between 0.9 and 2.6 logs10/mm was found at the end of the infusions. Three patients experienced greater than 2-log reduction. Two of them entered complete remission that lasted 6 weeks and 3 months, respectively. These correlations should be interpreted with caution because of the small number of patients treated. This study suggests that dThd, although of very limited therapeutic value by itself, may have potentiated the antitumor activity of ara-C to some extent. Whether this effect is of significance can only be determined by further studies.