gebhart/patrepeval huggingface dataset:
Using generative models for handwritten digit recognition (1996)

We describe a method of recognizing handwritten digits by fitting generative models that are built from deformable B-splines with Gaussian "ink generators" spaced along the length of the spline. The splines are adjusted using a novel elastic matching procedure based on the expectation maximization algorithm that maximizes the likelihood of the model generating the data. This approach has many advantages: 1) the system not only produces a classification of the digit but also a rich description of the instantiation parameters which can yield information such as the writing style; 2) the generative models can perform recognition driven segmentation; 3) the method involves a relatively small number of parameters and hence training is relatively easy and fast; and 4) unlike many other recognition schemes, it does not rely on some form of pre-normalization of input images, but can handle arbitrary scalings, translations and a limited degree of image rotation. We have demonstrated that our method of fitting models to images does not get trapped in poor local minima. The main disadvantage of the method is that it requires much more computation than more standard OCR techniques.
Degradation of endogenous bacterial cell wall polymers by the muralytic enzyme mutanolysin prevents hepatobiliary injury in genetically susceptible rats with experimental intestinal bacterial overgrowth. (1992)

Jejunal self-filling blind loops with subsequent small bowel bacterial overgrowth (SBBO) induce hepatobiliary injury in genetically susceptible Lewis rats. Lesions consist of portal tract inflammation, bile duct proliferation, and destruction. To determine the pathogenesis of SBBO-induced hepatobiliary injury, we treated Lewis rats with SBBO by using several agents with different mechanisms of activity. Buffer treatment, ursodeoxycholic acid, prednisone, methotrexate, and cyclosporin A failed to prevent SBBO-induced injury as demonstrated by increased plasma aspartate aminotransferase (AST) and elevated histology scores. However, hepatic injury was prevented by mutanolysin, a muralytic enzyme whose only known activity is to split the beta 1-4 N-acetylmuramyl-N-acetylglucosamine linkage of peptidoglycan-polysaccharide (PG-PS), a bacterial cell wall polymer with potent inflammatory and immunoregulatory properties. Mutanolysin therapy started on the day blind loops were surgically created and continued for 8 wk significantly diminished AST (101 +/- 37 U/liter) and liver histology scores (2.2 +/- 2.7) compared to buffer-treated rats (228 +/- 146 U/liter, P < 0.05, 8.2 +/- 1.9, P < 0.001 respectively). Mutanolysin treatment started during the early phase of hepatic injury, 16-21 d after surgery, decreased AST in 7 of 11 rats from 142 +/- 80 to 103 +/- 24 U/liter contrasted to increased AST in 9 of 11 buffer-treated rats from 108 +/- 52 to 247 +/- 142 U/liter, P < 0.05. Mutanolysin did not change total bacterial numbers within the loop, eliminate Bacteroides sp., have in vitro antibiotic effects, or diminish mucosal PG-PS transport. However, mutanolysin treatment prevented elevation of plasma anti-PG antibodies and tumor necrosis factor-alpha (TNF alpha) levels which occurred in buffer treated rats with SBBO and decreased TNF alpha production in isolated Kupffer cells stimulated in vitro with PG-PS. Based on the preventive and therapeutic activity of this highly specific muralytic enzyme, we conclude that systemic uptake of PG-PS derived from endogenous enteric bacteria contributes to hepatobiliary injury induced by SBBO in susceptible rat strains.
Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution (2019)

Spatial positions of cells in tissues strongly influence function, yet a high-throughput, genome-wide readout of gene expression with cellular resolution is lacking. We developed Slide-seq, a method for transferring RNA from tissue sections onto a surface covered in DNA-barcoded beads with known positions, allowing the locations of the RNA to be inferred by sequencing. Using Slide-seq, we localized cell types identified by single-cell RNA sequencing datasets within the cerebellum and hippocampus, characterized spatial gene expression patterns in the Purkinje layer of mouse cerebellum, and defined the temporal evolution of cell type-specific responses in a mouse model of traumatic brain injury. These studies highlight how Slide-seq provides a scalable method for obtaining spatially resolved gene expression data at resolutions comparable to the sizes of individual cells.
Safety and Toxicity of Catheter Gene Delivery to the Pulmonary Vasculature in a Patient with Metastatic Melanoma (1994)

One approach to gene therapy for human cancer is transcatheter injection of DNA liposomes into tumor masses. To determine the feasibility of selective delivery of recombinant genes by a catheter to the pulmonary vasculature in humans, a patient with melanoma received two treatments of HLA-B7 plasmid DNA complexed to cationic liposomes into a right posterior basal pulmonary artery associated with a mass lesion. The treatments were well tolerated. No adverse respiratory, cardiac, immunologic, or other organ toxicities were detected. The delivery of recombinant genes by catheter may be a useful modality to treat human malignancy and other diseases.
Location and Mobility in a Sensor Network of Mobile Phones (2007)

Mobile phones have two sensors: a camera and a microphone. Our goal in this position paper it to explore the use of these sensors for building an audio-visual sensor network that exploits the deployed base of millions of mobile phones worldwide. Among the several salient features of such a sensor network, we focus on mobility. Mo-bility is advantageous since it yields significant advantage in spatial coverage. However, due to the uncontrolled nature of device motion, it is difficult to sample a required region with a given device. We propose a data based abstraction to deal with this difficulty. Rather than treating the physical devices as our sensor nodes, we introduce a layer of static virtual sensor nodes corresponding to the sampled data locations. The virtual nodes corresponding to the required re-gion to be sensed can be queried directly to obtain data samples for that region. We discuss how the locations of the virtual sensor nodes can be enhanced, and sometimes derived, using the visual data con-tent itself. Experiments with real data are presented to expose some of the practical considerations for our design approach.
Fluoreszierende Stoffe aus Drosophila melanogaster. 14. Mitteilung [1]. Eine Synthese des Biopterins (1969)

Abstract 2,4,5‐Triamino‐6‐oxo‐1, 6‐dihydropyrimidin wird mit 1‐(Benzylphenylhydrazino)‐5‐desoxy‐ L ‐ribulose in wässrigem Methanol unter N 2 kondensiert. Die Mischung der gebildeten Tetrahydropterine wird zu den entsprechenden Pterinen oxydiert, wobei die polyhydroxyalkylierte Kette teilweise abgespalten wird. Diese Pterine stellen eine Mischung von Biopterin, wenig seines 7‐Isomeren und viel Pterin sensu stricto dar. Aus dieser Mischung lässt sich reines Biopterin durch Chromatographie an Dowex 1 × 8 gewinnen. Das synthetische und das aus Drosophila melanogaster isolierte Biopterin sind völlig identisch.
Assessment of Heat Resistance of Bacterial Spores from Food Product Isolates by Fluorescence Monitoring of Dipicolinic Acid Release (2005)

This study is aimed at the development and application of a convenient and rapid optical assay to monitor the wet-heat resistance of bacterial endospores occurring in food samples. We tested the feasibility of measuring the release of the abundant spore component dipicolinic acid (DPA) as a probe for heat inactivation. Spores were isolated from the laboratory type strain Bacillus subtilis 168 and from two food product isolates, Bacillus subtilis A163 and Bacillus sporothermodurans IC4. Spores from the lab strain appeared much less heat resistant than those from the two food product isolates. The decimal reduction times (D values) for spores from strains 168, A163, and IC4 recovered on Trypticase soy agar were 1.4, 0.7, and 0.3 min at 105 degrees C, 120 degrees C, and 131 degrees C, respectively. The estimated Z values were 6.3 degrees C, 6.1 degrees C, and 9.7 degrees C, respectively. The extent of DPA release from the three spore crops was monitored as a function of incubation time and temperature. DPA concentrations were determined by measuring the emission at 545 nm of the fluorescent terbium-DPA complex in a microtiter plate fluorometer. We defined spore heat resistance as the critical DPA release temperature (Tc), the temperature at which half the DPA content has been released within a fixed incubation time. We found Tc values for spores from Bacillus strains 168, A163, and IC4 of 108 degrees C, 121 degrees C, and 131 degrees C, respectively. On the basis of these observations, we developed a quantitative model that describes the time and temperature dependence of the experimentally determined extent of DPA release and spore inactivation. The model predicts a DPA release rate profile for each inactivated spore. In addition, it uncovers remarkable differences in the values for the temperature dependence parameters for the rate of spore inactivation, DPA release duration, and DPA release delay.
NB-CNN: Deep Learning-Based Crack Detection Using Convolutional Neural Network and Naïve Bayes Data Fusion (2017)

Regular inspection of nuclear power plant components is important to guarantee safe operations. However, current practice is time consuming, tedious, and subjective, which involves human technicians reviewing the inspection videos and identifying cracks on reactors. A few vision-based crack detection approaches have been developed for metallic surfaces, and they typically perform poorly when used for analyzing nuclear inspection videos. Detecting these cracks is a challenging task since they are tiny, and noisy patterns exist on the components' surfaces. This study proposes a deep learning framework, based on a convolutional neural network (CNN) and a Naïve Bayes data fusion scheme, called NB-CNN, to analyze individual video frames for crack detection while a novel data fusion scheme is proposed to aggregate the information extracted from each video frame to enhance the overall performance and robustness of the system. To this end, a CNN is proposed to detect crack patches in each video frame, while the proposed data fusion scheme maintains the spatiotemporal coherence of cracks in videos, and the Naïve Bayes decision making discards false positives effectively. The proposed framework achieves a 98.3% hit rate against 0.1 false positives per frame that is significantly higher than state-of-the-art approaches as presented in this paper.
Chemoprevention of asbestos-linked cancers: a systematic review. (2012)

Asbestos has been used extensively and, in spite of many countries having banned most of its uses, professional, domestic and environmental exposure has not ceased worldwide. Inhaled asbestos fibers can lead to malignant mesothelioma, lung cancer and non-cancerous conditions, while the substance persists indefinitely in the lung and pleural tissue, resulting in continuous damage. Exposed individuals may be offered medical surveillance or compensation, but nothing is currently being done to lower their specific cancer risk: chemoprevention seems a promising approach. A web search and a PubMed review of the literature on chemoprevention trials in individuals exposed to asbestos have been conducted. Forty-six articles on five projects were found and newly reviewed but, surprisingly, no novel trials have been set up for twenty years, although considerable advances have been gained in cancer chemoprevention. A re-consideration of possibilities offered by chemoprevention should be encouraged. New trials based on the most recently characterized molecules should be planned, taking into account specific issues such as the need for a very large number of participants and a long follow up or, alternatively, the use of biomarkers as surrogate endpoints. The long latency of asbestos related diseases may offer delayed intervention opportunities. The lack of chemoprevention trials for asbestos exposure highlights the urgent need for research in this field.
Expression of activated rat neu oncogene is sufficient to induce experimental metastasis in 3T3 cells. (1991)

Amplification or overexpression of the human neu oncogene has been shown to correlate with the number of lymph node metastases in breast cancer patients, suggesting that expression of the neu oncogene may be associated with increased metastatic potential. However, there has been no systematic study on the role of the neu oncogene in metastasis to support this correlation. In our study, mouse embryo fibroblast 3T3 cells transformed by the mutation-activated rat neu oncogene exhibited metastatic properties both in vitro and in vivo, while parental 3T3 cells did not. Monoclonal antibodies capable of inducing down-regulation of the neu-encoded p185 protein reduced the metastatic potential induced by neu. These data provide strong experimental evidence that neu oncogene expression is sufficient for the induction of metastasis in the 3T3 cell system and supply a molecular basis supporting the correlations found in clinical observation. The results also suggest that neu-specific monoclonal antibodies may have preventative or therapeutic potential for neu-induced metastasis.
Scalable Functional Group Engineering of Carbon Nanotubes by Improved One-Step Nitrene Chemistry (2008)

A facile, green, low cost and efficient one-step technology to synthesize highly dispersible functional single-walled and multiwalled carbon nanotubes (f-SWNTs and f-MWNTs) up to supergrams is reported. Large-scale (up to hundreds of grams) synthesis of functional azides was developed at first, and various reactive groups (i.e., −OH, −NH2, −COOH, and −Br) were then introduced onto the convex surfaces of CNTs in merely one reaction of nitrene addition under a relatively mild condition without causing significant damage to nanotubes. The contents of the functional moieties can be easily controlled by adjusting the feed ratio of the azide compounds to CNTs. In order to demonstrate the reactivity and functions of the immobilized organic moieties, different chemical reactions, including surface-initiated polymerizations, amidation, and reduction of metal ions, were performed on the functional CNTs, affording various CNT-polymer and CNT-Pt nanohybrids. The resulting materials were characterized by various measurements, such as TGA, Raman, XPS, FTIR, NMR, XRD, SEM, TEM, and HRTEM. The presented one-step methodology opens the avenue for industrial production of functional CNTs.
Structure-Function Analysis of the Human Sialyltransferase ST3Gal I (2004)

All eukaryotic sialyltransferases have in common the presence in their catalytic domain of several conserved peptide regions (sialylmotifs L, S, and VS). Functional analysis of sialylmotifs L and S previously demonstrated their involvement in the binding of donor and acceptor substrates. The region comprised between the sialylmotifs S and VS contains a stretch of four highly conserved residues, with the following consensus sequence (H/y)Y(Y/F/W/h)(E/D/q/g). (Capital letters and lowercase letters indicate a strong or low occurrence of the amino acid, respectively.) The functional importance of these residues and of the conserved residues of motif VS (HX(4)E) was assessed using as a template the human ST3Gal I. Mutational analysis showed that residues His(299) and Tyr(300) of the new motif, and His(316) of the VS motif, are essential for activity since their substitution by alanine yielded inactive enzymes. Our results suggest that the invariant Tyr residue (Tyr(300)) plays an important conformational role mainly attributable to the aromatic ring. In contrast, the mutants W301F, E302Q, and E321Q retained significant enzyme activity (25-80% of the wild type). Kinetic analyses and CDP binding assays showed that none of the mutants tested had any significant effect in nucleotide donor binding. Instead the mutant proteins were affected in their binding to the acceptor and/or demonstrated lower catalytic efficiency. Although the human ST3Gal I has four N-glycan attachment sites in its catalytic domain that are potentially glycosylated, none of them was shown to be necessary for enzyme activity. However, N-glycosylation appears to contribute to the proper folding and trafficking of the enzyme.
The A and B Subgroups of Human Respiratory Syncytial Virus: Comparison of Intergenic and Gene-overlap Sequences (1988)

Intergenic and flanking gene regions for the 1C-1B, 1B-N, N-P, M-1A, G-F and F-22K gene junctions of respiratory syncytial virus strain 18537, representing antigenic subgroup B, were determined by dideoxynucleotide sequencing of polycistronic cDNAs and mRNAs. Comparison with their counterparts from the subgroup A strain A2 showed that the intergenic sequences were not conserved within or between the strains. Flanking non-coding gene sequences also were generally not conserved except for the highly conserved gene-start and gene-end transcription signals. The sequence of the overlap between the 22K and L genes was conserved almost exactly between the two subgroups.
Medical Department, United States Army. Blood Program in World War War II. (1964)

Abstract : Medical officers who, like myself, served overseas in World War ll, and who observed the management of casualties with and without the use of whole blood, are peculiarly qualified to appreciate the achievements of the whole- blood program. Its results unfolded before our eyes. In forward hospitals, we saw men saved from death and sometimes, almost brought back from the dead. In fixed hospitals, we received wounded men who once would have died in forward hospitals, or even on the battlefield. We received casualties with the most serious wounds in good condition. With the aid of more blood, we performed radical surgery upon them, and we watched them withstand operation and, with still more blood, recover promptly from it. There are more than the usual reasons for the preparation and publication of this volume on the whole-blood program. A major reason, of course, is the impact this therapeutic advance has had upon medical care, civilian as well as military. Another reason is to keep faith with the multiple personnel who planned and operated the whole-blood program, and with the millions of American citizens whose gifts of their own blood saved the lives of so many American soldiers, who otherwise would have died.
Role of γδT Cells in the Inflammatory Response of Experimental Colitis Mice (2003)

We examined the severity of experimental colitis induced by dextran sulfate sodium (DSS) using immunologically manipulated mice. C57BL/6 mice showed more severe colitis than BALB/c mice, but mice of both strains recovered fully from the disease after the removal of DSS from their drinking water. The infiltrated cells at the lesions were mainly granulocytes in normal littermates. However, C.B-17 scid, IL-7Ralpha deficient, and TCR-Cbetadelta double-deficient mice showed severe colitis and did not recover from the disease even after the removal of DSS. It was found that the infiltrated cells at the lesions in the lethal strains were monocytes. Although both TCR-Cdelta(-/-) and TCR-Cbeta(-/-) mice showed severe colitis phenotypes, infiltration in the former is monocyte-dominant while that in the latter is granulocyte-dominant. Thus the type of cells that infiltrate at the lesions of DSS-induced experimental colitis may be controlled by functional T cell subsets. Immunohistological and RT-PCR analyses of the inflamed colon revealed that the murine homologue of human GROalpha released by some cells under the control of gammadeltaT cells is a possible candidate determining the severity of DSS-induced experimental colitis.
Spinal Cord Sodium, Potassium, Calcium, and Water Concentration Changes in Rats After Graded Contusion Injury (1989)

Spinal cord Na, K, Ca, and H2O changes were measured 6 h after graded contusion injuries in 40 Sprague-Dawley rats. A 10 g weight was dropped 1.25 cm (n = 6), 2.5 cm (n = 7), 5.0 cm (n = 6), or 7.5 cm (n = 7) onto the thoracic spinal cord of 26 rats. An additional 10 rats served as laminectomy controls and 4 rats were unoperated controls. At 6 h after surgery or injury, the spinal cords were rapidly cut into 4 mm segments, weighed to obtain tissue wet weights (W), dried for 14-16 h at 97 degrees C in a vacuum oven (30 mmHg), and reweighed for tissue dry weights (D). Water concentrations ([H2O]d) were estimated from (W-D)/D in units of ml/g D. Ionic concentrations ([Na]d, [K]d, and [Ca]d) of the tissue samples were measured by atomic absorption spectroscopy with units of mumol/g D. Ionic shifts (delta [Na]d, delta [K]d, delta [Ca]d) were calculated by subtracting laminectomy control values from those measured in injured cords. Laminectomy alone significantly increased [Na]d and [H2O]d compared to unoperated controls. Mean +/- standard deviations of [H2O]d, [Na]d, [K]d, and [Ca]d were, respectively, 1.95 +/- 0.07, 182.6 +/- 5.9, 277.2 +/- 11.8, and 12.1 +/- 1.4 in unoperated controls; 2.12 +/- 0.08, 238.6 +/- 9.2, 277.8 +/- 9.2, and 11.7 +/- 1.1 in laminectomy controls. At the impact site, [K]d fell by 14-37% and [H2O]d rose by 14-24%, [Na]d by 13-64%, and [Ca]d by 65-137% of laminectomy control values. delta [Na]d, delta [K]d, and delta [Ca]d correlated linearly with impact velocities; [Ca]d increased by 1.0% per cm/sec (r = 0.995, p less than 0.005), [Na]d increased 0.67% per cm/sec (r = 0.950, p less than 0.01), and [K]d decreased 0.34% per cm/sec (r = 0.964, p less than 0.01). Neither delta [H2O] nor delta [Na]d + delta [K]d consistently predicted impact velocity. [Na]d + [K]d correlated with [H2O]d with a slope of 177.4 mumol/ml (r = 0.697, p less than 0.005). Since Na and K constitute greater than 95% of tissue inorganic ions, the slope approximates net ionic shift per ml of water entry or the ionic osmolarity of edema fluid. These results indicate that increasing contusions produce graded ionic shifts and that edema does not predict contusion severity. These data support our hypothesis that net ionic shifts cause edema in injured spinal cords.
Identification and partial characterization of a cytolytic toxin produced by Gardnerella vaginalis (1990)

Generation and release into the culture medium of a cytolytic toxin by Gardnerella vaginalis has been demonstrated. Addition of starch and of the nonionic detergent Tween 80 to the culture medium was essential to recover cytolytic activity. A protein with an apparent molecular mass of 61 to 63 kDa was purified from the culture supernatants showing lytic activity towards erythrocytes and nucleated cells, such as human endothelial cells and human neutrophils. The protein had marked selectivity for human erythrocytes, while erythrocytes from other species were not lysed or were lysed at much higher concentrations of the protein than those needed for human erythrocytes. The cytolytic activity was remarkably unstable in polar media, but was stabilized by nonionic detergents, by binding, or by insertion into the target cell membrane, suggesting its amphiphilic nature.