gebhart/patrepeval huggingface dataset:
Material recognition in the wild with the Materials in Context Database (2015)

Recognizing materials in real-world images is a challenging task. Real-world materials have rich surface texture, geometry, lighting conditions, and clutter, which combine to make the problem particularly difficult. In this paper, we introduce a new, large-scale, open dataset of materials in the wild, the Materials in Context Database (MINC), and combine this dataset with deep learning to achieve material recognition and segmentation of images in the wild. MINC is an order of magnitude larger than previous material databases, while being more diverse and well-sampled across its 23 categories. Using MINC, we train convolutional neural networks (CNNs) for two tasks: classifying materials from patches, and simultaneous material recognition and segmentation in full images. For patch-based classification on MINC we found that the best performing CNN architectures can achieve 85.2% mean class accuracy. We convert these trained CNN classifiers into an efficient fully convolutional framework combined with a fully connected conditional random field (CRF) to predict the material at every pixel in an image, achieving 73.1% mean class accuracy. Our experiments demonstrate that having a large, well-sampled dataset such as MINC is crucial for real-world material recognition and segmentation.
Congestion Control using Pacing in a Packet Radio Network (1982)

Protocol design is a critical factor in achieving throughput and reliability goals in a packet radio network. Here we examine the details of a hop transport protocol algorithm, called "pacing", which operates in a CSMA packet radio network. The pacing algorithm provides adaptive flow control in order to accommodate changing traffic flow patterns and rates. In addition, pacing seeks to time packet transmissions to ameliorate the classical "hidden terminal" problem encountered in multi-hop CSMA networks. We found that the pacing algorithm considerably improves throughput and packet delivery reliability, compared to an earlier algorithm using a fixed-parameter flow control mechanism.
Is there a role for lactobacilli in prevention of urogenital and intestinal infections? (1990)

This review describes the importance of microbial adhesion in the ecology of the urogenital and intestinal tracts and the influence of host and microbial factors in bacterial interference. In a recent revival of interest in bacterial interference, lactobacillus administration has been studied as a means of treating and preventing disease. Although evidence is conflicting, Lactobacillus acidophilus appears to be involved in beneficial antagonistic and cooperative reactions that interfere with establishment of pathogens in the gastrointestinal tract. The mechanisms of action are believed to involve competitive exclusion and production of inhibitory substances, including bacteriocins. These characteristics, as well as demonstrated adherence abilities in vitro, led to selection of certain Lactobacillus strains for clinical studies of cystitis. Weekly intravaginal Lactobacillus therapy reduced the recurrence rate of uncomplicated lower urinary tract infections in women. Use of Lactobacillus strains resistant to Nonoxynol-9, a spermicide that kills members of the protective normal vaginal flora, may have potential for use in women with recurrent cystitis using this contraceptive agent. In veterinary studies, bacterial interference by administration of probiotics has also been beneficial in disease prevention in animals. Carefully selected bacterial mixtures integrate with the gastrointestinal flora of the animals and can confer disease resistance and improve physiological function. Additional human and animal trials are needed to determine the practical, long-term usefulness of bacterial interference as a protective mechanism against infectious diseases.
The thermosome: archetype of group II chaperonins (1998)

The thermosome, the chaperonin of the archaea, and its homologue from the cytosol of eukaryotes, known as TRiC or CCT, form a distinct subfamily of the chaperonins that does not depend on a co-chaperonin for protein folding activity. Recent structural data obtained by cryo- electron microscopy and X-ray crystallography provide the first insights into a novel mechanism remarkably different from that of the bacterial GroEL-GroES system.
Increased expression of cholesterol 24S‐hydroxylase results in disruption of glial glutamate transporter EAAT2 association with lipid rafts: a potential role in Alzheimer’s disease (2010)

The glial glutamate transporter EAAT2 (excitatory amino acid transporter 2) is the major mediator of glutamate clearance that terminates glutamate-mediated neurotransmission. Loss of EAAT2 and associated glutamate uptake function has been reported in the brains of patients with Alzheimer's disease (AD). We previously reported that EAAT2 is associated with lipid raft microdomains of the plasma membrane. In the present study, we demonstrated that association of EAAT2 with lipid rafts is disrupted in AD brains. This abnormality is not a consequence of neuron degeneration, oxidative stress, or amyloid beta toxicity. In AD brains, cholesterol 24S-hydroxylase (CYP46), a key enzyme in maintenance of cholesterol homeostasis in the brain, is markedly increased in astrocytes but decreased in neurons. We demonstrated that increased expression of CYP46 in primary astrocytes results in a reduction of membrane cholesterol levels and leads to the dissociation of EAAT2 from lipid rafts and the loss of EAAT2 and associated glutamate uptake function. These results suggest that a disturbance of cholesterol metabolism may contribute to loss of EAAT2 in AD.
Compressed sensing based UWB receiver: Hardware compressing and FPGA reconstruction (2009)

A low sampling rate approach for recovering ultra wide band (UWB) signals is proposed, using distributed amplifiers (DAs) and low speed analog-to-digital converters (ADCs) and based on the theory of compressed sensing. A microwave circuit consisting of a bank of DAs, followed by a bank of ADCs, is designed to implement analog compressing, where the elements of measurement matrix are realized by picosecond delay tap and flexible gain coefficients in DAs. Numerical simulation shows that a bank of eight DAs and ADCs with 500MHz sampling rate can almost perfectly recover a 100ps-resolution UWB echo signal in the noiseless case. For recovering the UWB signals in a real-time way, issues in field programmable gate array (FPGA) implementation are discussed.
A Critical Role of SHP-1 in Regulation of Type 2 Inflammation in the Lung (2008)

Asthma is a chronic inflammatory disorder of the airways. Type 2 T helper (Th) cell-dominated inflammation in the lung is a hallmark of asthma. Src homology 2 domain-containing protein tyrosine phosphatase (SHP)-1 is a negative regulator in the signaling pathways of many growth factor and cytokine receptors. However, a direct role of SHP-1 in the IL-4/IL-13 signaling pathway has not been established. In this study, we sought to define the function of SHP-1 in the lung by characterizing the pulmonary inflammation of viable motheaten (mev) mice, and to investigate the molecular mechanisms involved. Pulmonary histology, physiology, and cytokine expression of mev mice were analyzed to define the nature of the inflammation, and the gene-deletion approach was used to identify critical molecules involved. In mev mice, we observed spontaneous Th2-like inflammatory responses in the lung, including eosinophilia, mucus metaplasia, airway epithelial hypertrophy, pulmonary fibrosis, and increased airway resistance and airway hyperresponsiveness. The pulmonary phenotype was accompanied by up-regulation of Th2 cytokines and chemokines. Selective deletion of IL-13 or signal transducer and activator of transcription 6, key genes in the Th2 signaling pathway, significantly reduced, but did not completely eliminate, the inflammation in the lung. These findings suggest that SHP-1 plays a critical role in regulating the IL-4/IL-13 signaling pathway and in maintaining lung homeostasis.
Tuning Cell Adhesion by Incorporation of Charged Silicate Nanoparticles as Cross‐Linkers to Polyethylene Oxide (2010)

Controlling cell adhesion on a biomaterial surface is associated with the long-term efficacy of an implanted material. Here we connect the material properties of nanocomposite films made from PEO physically cross-linked with layered silicate nanoparticles (Laponite) to cellular adhesion. Fibroblast cells do not adhere to pure PEO, but they attach to silicate containing nanocomposites. Under aqueous conditions, the films swell and the degree of swelling depends on the nanocomposite composition and film structure. Higher PEO compositions do not support cell proliferation due to little exposed silicate surfaces. Higher silicate compositions do allow significant cell proliferation and spreading. These bio-nanocomposites have potential for the development of biomedical materials that can control cellular adhesion.
Molecular imaging of macrophages in atherosclerotic plaques using bimodal PEG‐micelles (2007)

Pegylated, fluorescent, and paramagnetic micelles were developed. The micelles were conjugated with macrophage scavenger receptor (MSR)-specific antibodies. The abdominal aortas of atherosclerotic apoE-KO mice were imaged with T(1)-weighted high-resolution MRI before and 24 h after intravenous administration of the contrast agent (CA). Pronounced signal enhancement (SE) (up to 200%) was observed for apolipoprotein E knockout (apoE-KO) mice that were injected with MSR-targeted micelles, while the aortic vessel wall of mice injected with nontargeted micelles showed little SE. To allow fluorescence microscopy and optical imaging of the excised aorta, the micelles were made fluorescent by incorporating either a quantum dot (QD) in the micelle corona or rhodamine lipids in the micelle. Ultraviolet (UV) illumination of the aorta allowed the identification of regions with high macrophage content, while MSR-targeted rhodamine micelles could be detected with fluorescence microscopy and were found to be associated with macrophages. In conclusion, this study demonstrates that macrophages in apoE-KO mice can be effectively and specifically detected by molecular MRI and optical methods upon administration of a pegylated micellar CA.
Structural insights into the production of 3-hydroxypropionic acid by aldehyde dehydrogenase from Azospirillum brasilense (2017)

3-Hydroxypropionic acid (3-HP) is an important platform chemical to be converted to acrylic acid and acrylamide. Aldehyde dehydrogenase (ALDH), an enzyme that catalyzes the reaction of 3-hydroxypropionaldehyde (3-HPA) to 3-HP, determines 3-HP production rate during the conversion of glycerol to 3-HP. To elucidate molecular mechanism of 3-HP production, we determined the first crystal structure of a 3-HP producing ALDH, α-ketoglutarate-semialdehyde dehydrogenase from Azospirillum basilensis (AbKGSADH), in its apo-form and in complex with NAD<sup>+</sup>. Although showing an overall structure similar to other ALDHs, the AbKGSADH enzyme had an optimal substrate binding site for accepting 3-HPA as a substrate. Molecular docking simulation of 3-HPA into the AbKGSADH structure revealed that the residues Asn159, Gln160 and Arg163 stabilize the aldehyde- and the hydroxyl-groups of 3-HPA through hydrogen bonds, and several hydrophobic residues, such as Phe156, Val286, Ile288, and Phe450, provide the optimal size and shape for 3-HPA binding. We also compared AbKGSADH with other reported 3-HP producing ALDHs for the crucial amino acid residues for enzyme catalysis and substrate binding, which provides structural implications on how these enzymes utilize 3-HPA as a substrate.
Dynamics of the Cellular Metabolome during Human Cytomegalovirus Infection (2006)

Viral replication requires energy and macromolecular precursors derived from the metabolic network of the host cell. Despite this reliance, the effect of viral infection on host cell metabolic composition remains poorly understood. Here we applied liquid chromatography-tandem mass spectrometry to measure the levels of 63 different intracellular metabolites at multiple times after human cytomegalovirus (HCMV) infection of human fibroblasts. Parallel microarray analysis provided complementary data on transcriptional regulation of metabolic pathways. As the infection progressed, the levels of metabolites involved in glycolysis, the citric acid cycle, and pyrimidine nucleotide biosynthesis markedly increased. HCMV-induced transcriptional upregulation of specific glycolytic and citric acid cycle enzymes mirrored the increases in metabolite levels. The peak levels of numerous metabolites during infection far exceeded those observed during normal fibroblast growth or quiescence, demonstrating that HCMV markedly disrupts cellular metabolic homeostasis and institutes its own specific metabolic program.
Autoregulation of glucose production in men with a glycerol load during rest and exercise (2001)

Related to hepatic autoregulation we evaluated hypotheses that 1) glucose production would be altered as a result of a glycerol load, 2) decreased glucose recycling rate (Rr) would result from increased glycerol uptake, and 3) the absolute rate of gluconeogenesis (GNG) from glycerol would be positively correlated to glycerol rate of disappearance (R d ) during a glycerol load. For these purposes, glucose and glycerol kinetics were determined in eight men during rest and during 90 min of leg cycle ergometry at 45 and 65% of peak O 2 consumption (V˙o 2 peak ). Trials were conducted after an overnight fast, with exercise commencing 12 h after the last meal. Subjects received a continuous infusion of [6,6- 2 H 2 ]glucose, [1- 13 C]glucose, and [1,1,2,3,3- 2 H 5 ]glycerol without (CON) or with an additional 1,000 mg (rest: 20 mg/min; exercise: 40 mg/min) of [2- 13 C]- or unlabeled glycerol added to the infusate (GLY). Infusion of glycerol dampened glucose Rr, calculated as the difference between [6,6- 2 H 2 ]- and [1- 13 C]glucose rates of appearance (R a ), at rest [0.35 ± 0.12 (CON) vs. 0.12 ± 0.10 mg · kg −1 · min −1 (GLY), P &lt; 0.05] and during exercise at both intensities [45%: 0.63 ± 0.14 (CON) vs. 0.04 ± 0.12 (GLY); 65%: 0.73 ± 0.14 (CON) vs. 0.04 ± 0.17 mg · kg −1 · min −1 (GLY), P &lt; 0.05]. Glucose R a and oxidation were not affected by glycerol infusion at rest or during exercise. Throughout rest and both exercise intensities, glycerol R d was greater in GLY vs. CON conditions (rest: 0.30 ± 0.04 vs. 0.58 ± 0.04; 45%: 0.57 ± 0.07 vs. 1.19 ± 0.04; 65%: 0.73 ± 0.06 vs. 1.27 ± 0.05 mg · kg −1 · min −1 , CON vs. GLY, respectively). Differences in glycerol R d (ΔR d ) between protocols equaled the unlabeled glycerol infusion rate and correlated with plasma glycerol concentration ( r = 0.97). We conclude that infusion of a glycerol load during rest and exercise at 45 and 65% ofV˙o 2 peak 1) does not affect glucose R a or R d , 2) blocks glucose Rr, 3) increases whole body glycerol R d in a dose-dependent manner, and 4) results in gluconeogenic rates from glycerol equivalent to CON glucose recycling rates.
Tyk2/STAT3 Signaling Mediates β-Amyloid-Induced Neuronal Cell Death: Implications in Alzheimer's Disease (2010)

One of the pathological hallmarks of Alzheimer's disease (AD) is deposition of extracellular amyloid-beta (Abeta) peptide, which is generated from the cleavage of amyloid precursor protein (APP). Accumulation of Abeta is thought to associate with the progressive neuronal death observed in AD. However, the precise signaling mechanisms underlying the action of Abeta in AD pathophysiology are not completely understood. Here, we report the involvement of the transcription factor signal transducer and activator of transcription 3 (STAT3) in mediating Abeta-induced neuronal death. We find that tyrosine phosphorylation of STAT3 is elevated in the cortex and hippocampus of APP/PS1 transgenic mice. Treatment of cultured rat neurons with Abeta or intrahippocampal injection of mice with Abeta both induces tyrosine phosphorylation of STAT3 in neurons. Importantly, reduction of either the expression or activation of STAT3 markedly attenuates Abeta-induced neuronal apoptosis, suggesting that STAT3 activation contributes to neuronal death after Abeta exposure. We further identify Tyk2 as the tyrosine kinase that acts upstream of STAT3, as Abeta-induced activation of STAT3 and caspase-3-dependent neuronal death can be inhibited in tyk2(-/-) neurons. Finally, increased tyrosine phosphorylation of STAT3 is also observed in postmortem brains of AD patients. Our observations collectively reveal a novel role of STAT3 in Abeta-induced neuronal death and suggest the potential involvement of Tyk2/STAT3 signaling in AD pathophysiology.
KCNQ1 Gain-of-Function Mutation in Familial Atrial Fibrillation (2003)

Atrial fibrillation (AF) is a common cardiac arrhythmia whose molecular etiology is poorly understood. We studied a family with hereditary persistent AF and identified the causative mutation (S140G) in the KCNQ1 (KvLQT1) gene on chromosome 11p15.5. The KCNQ1 gene encodes the pore-forming alpha subunit of the cardiac I(Ks) channel (KCNQ1/KCNE1), the KCNQ1/KCNE2 and the KCNQ1/KCNE3 potassium channels. Functional analysis of the S140G mutant revealed a gain-of-function effect on the KCNQ1/KCNE1 and the KCNQ1/KCNE2 currents, which contrasts with the dominant negative or loss-of-function effects of the KCNQ1 mutations previously identified in patients with long QT syndrome. Thus, the S140G mutation is likely to initiate and maintain AF by reducing action potential duration and effective refractory period in atrial myocytes.
Pulmonary drug delivery strategies: A concise, systematic review (2012)

Because of limitations associated with the conventional treatment of various chronic diseases a growing attention has been given to the development of targeted drug delivery systems. Pulmonary route of drug delivery gaining much importance in the present day research field as it enables to target the drug delivery directly to lung both for local and systemic treatment. Over the last 2 decades, the systemic absorption of a broad range of therapeutics after pulmonary application has been demonstrated in animals as well as in humans. This review was prepared with an aim to discuss the technical, physiological, and efficacy aspects of the novel pulmonary route of drug targeting. The review also focuses on the mechanisms of pulmonary drug administration along with compatibility of the excipients employed, devices used, and techniques of particulate dosage production. This review was prepared based on the method of extensive literature survey on the topics covering all the aspects discussed in the present subject. Hence, the better understanding of complexes and challenges facing the development of pulmonary drug delivery system offer an opportunity to the pharmaceutical scientist in minimizing the clinical and technical gaps.
Preparative and quantitative isolation of plasma lipoproteins: rapid, single discontinuous density gradient ultracentrifugation in a vertical rotor. (1980)

A rapid method has been developed for separation of the major plasma lipoproteins from up to 96 ml of plasma by a single ultracentrifugation step. This separation was achieved by a discontinuous density gradient centrifugation between the density range of 1.006 and 1.30 g/ml in Sorvall vertical rotors. Each lipoprotein fraction was sharply banded with VLDL at the top, LDL in the upper middle, and HDL in the lower middle portion of the tube. Use of authentic 125I-labeled lipoproteins showed that complete separation of the three major classes and partial separation of HDL2 and HDL3 was achieved. The lipoprotein fractions prepared by this technique have properties indistinguishable from those isolated by the sequential flotation method in regard to their equilibrium banding density, electrophoretic mobility, and apolipoprotein composition. This method is suitable for the preparative isolation of lipoproteins as well as for quantitative clinical determinations of cholesterol and triglycerides in VLDL, LDL and HDL fractions of plasma. Used as an analytical tool this method allows samples as small as 1 ml of plasma and spin times as short as 45 min. Cholesterol levels in HDL fractions separated by this method have significantly lower values (P less than 0.05) than those estimated by the heparin-manganese chloride precipitation method.
Formation of magnetite by bacteria and its application (2008)

Magnetic particles offer high technological potential since they can be conveniently collected with an external magnetic field. Magnetotactic bacteria synthesize bacterial magnetic particles (BacMPs) with well-controlled size and morphology. BacMPs are individually covered with thin organic membrane, which confers high and even dispersion in aqueous solutions compared with artificial magnetites, making them ideal biotechnological materials. Recent molecular studies including genome sequence, mutagenesis, gene expression and proteome analyses indicated a number of genes and proteins which play important roles for BacMP biomineralization. Some of the genes and proteins identified from these studies have allowed us to express functional proteins efficiently onto BacMPs, through genetic engineering, permitting the preservation of the protein activity, leading to a simple preparation of functional protein-magnetic particle complexes. They were applicable to high-sensitivity immunoassay, drug screening and cell separation. Furthermore, fully automated single nucleotide polymorphism discrimination and DNA recovery systems have been developed to use these functionalized BacMPs. The nano-sized fine magnetic particles offer vast potential in new nano-techniques.
Complications of femoral artery closure devices (2001)

We have examined our prospectively collected experience with femoral artery closure devices. Vasoseal (n = 937), Angioseal (N-742), and Techstar (n = 1001) were utilized consecutively in our laboratory for diagnostic and interventional femoral artery closures. Complications were compared to a similar number of closures with manual compression (MC; n = 1019) before closure devices were utilized. The incidence of surgical repair, acute femoral closure, transfusion due to groin complications, readmission for groin complications, infection, and total complications were examined. We found that the Vasoseal and Angioseal devices were associated with higher rates of total complications than manual compression. The Techstar and manual compression had similar total complication rates. Acute femoral artery occlusion was a potentially serious complication with the Angioseal device. Groin infection occurred with each of the closure devices but not with manual compression. Cathet Cardiovasc Intervent 2001;52:3–7. © 2001 Wiley-Liss, Inc.
Effects of sildenafil, a type‐5 cGMP phosphodiesterase inhibitor, and papaverine on cyclic GMP and cyclic AMP levels in the rabbit corpus cavernosum in vitro (1997)

Sildenafil specifically increases cGMP levels in rabbit corpora cavernosa; the increase is greater in the presence of SNP indicating that, in vivo, sildenafil may enhance erection by the augmentation of nitric oxide-mediated relaxation pathways. The erectogenic effect of sildenafil is mediated by a specific enhancement of cGMP accumulation in the corpus cavernosum, consistent with the known activity of sildenafil as a potent and highly selective inhibitor of cGMP-specific PDE.