gebhart/patrepeval huggingface dataset:
Structural Basis of Toll-Like Receptor 3 Signaling with Double-Stranded RNA (2008)

Toll-like receptor 3 (TLR3) recognizes double-stranded RNA (dsRNA), a molecular signature of most viruses, and triggers inflammatory responses that prevent viral spread. TLR3 ectodomains (ECDs) dimerize on oligonucleotides of at least 40 to 50 base pairs in length, the minimal length required for signal transduction. To establish the molecular basis for ligand binding and signaling, we determined the crystal structure of a complex between two mouse TLR3-ECDs and dsRNA at 3.4 angstrom resolution. Each TLR3-ECD binds dsRNA at two sites located at opposite ends of the TLR3 horseshoe, and an intermolecular contact between the two TLR3-ECD C-terminal domains coordinates and stabilizes the dimer. This juxtaposition could mediate downstream signaling by dimerizing the cytoplasmic Toll interleukin-1 receptor (TIR) domains. The overall shape of the TLR3-ECD does not change upon binding to dsRNA.
Decreased Synaptic Activity Shifts the Calcium Dependence of Release at the Mammalian Neuromuscular JunctionIn Vivo (2004)

We examined the mechanism underlying increased quantal content after block of activity at the mouse neuromuscular junction in vivo. We found that, when quantal content was measured in solution containing normal extracellular calcium, block of activity had no effect on either quantal content or the response to repetitive stimulation. However, when quantal content was measured in low extracellular calcium, there was a large increase in quantal content after block of activity. The increase in quantal content was accompanied by increased depression during repetitive stimulation. The explanation for these findings was that there was a shift in the calcium dependence of release after block of activity that manifested as an increase in probability of release in low extracellular calcium. Block of presynaptic P/Q channels eliminated the increase in probability of release. We propose that activity-dependent regulation of presynaptic calcium entry may contribute to homeostatic regulation of quantal content.
Repeat application of microneedles does not alter skin appearance or barrier function and causes no measurable disturbance of serum biomarkers of infection, inflammation or immunity in mice in vivo (2017)

We address, for the first time, the impact of skin insertion on multiple occasions of polymeric microneedle arrays in an animal model in vivo. Dissolving microneedle arrays prepared from aqueous blends of 20% w/w Gantrez® S-97 BF and 40% w/w poly(vinyl pyrrolidone) 58kDa and hydrogel-forming microneedle arrays prepared from aqueous blends of and poly(ethyleneglycol) 10kDa were repeatedly applied to the skin of hairless mice in vivo. Skin appearance and skin barrier function, as illustrated by measurement of transepidermal water loss, were not measurably altered during the entire study period. Biomarkers of infection, immunity and inflammation/irritation were also statistically unchanged, regardless of the microneedle formulation, needle density or number of applications. Mice remained healthy throughout and continued to gain weight during the study. For example, transepidermal water loss values were typically in the range 10-15gm<sup>-2</sup>h<sup>-1</sup> immediately prior to microneedle insertion and 15-25gm<sup>-2</sup>h<sup>-1</sup> immediately following microneedle removal, regardless of when they were measured during the study periods. Serum biomarker levels, measured immediately post-mortem were always in the range 10-20µgml<sup>-1</sup> for C-reactive protein, 0.5-1.5mgml<sup>-1</sup> for Immunoglobulin G and 1000-2500pgml<sup>-1</sup> for interleukin 1-β and were never statistically different from untreated controls. No measurable levels of tumour necrosis factor-α were found in any animals. These findings are encouraging for the formulations investigated, suggesting that their repeated use by patients will not cause undesirable side-effects. By beginning to address potential regulatory questions at an early stage, the microneedles field will be ideally-placed to take advantage of the potential market. This work illustrates a potential pre-clinical strategy for development of regulatory dossiers on microneedle technologies.
Histochemical and molecular analyses of distraction osteogenesis in a mouse model (1998)

Abstract A tibial lengthening scheme in the mouse was used to study the molecular and cellular events regulating tissue regeneration during distraction osteogenesis. Here, we report on the surgical technique and frame design and describe the histochemical and molecular aspects of distraction during different phases of treatment. A total of 26 mice were used in this study. The treatment protocol was divided into a latency period of 7 days, a phase of active distraction that lasted 10 days with a distraction rate of 0.42 mm/day, and a maturation phase of 9 days. During latency, the distraction site resembled a stabilized fracture callus bn both a histochemical and a molecular level. During active distraction, the gap was characterized by a central fibrous interzone bordered by primary matrix fronts, regenerate bone aligned with the distraction force, parallel columns of vascular sinusoids, and a medullary cavity. Alkaline phosphatase activity was detectedin the endosteal and periosteal surfaces of the bone ends. Tartrate resistant acid phosphatase staining revealed that osteoclasts remodeled the bone regenerate as it formed. Collagen type I was expressed in the periosteum and the primary matrix front during distraction, whereas collagen type‐II transcripts were localizedto discrete regions on the periosteal surfaces, immediately adjacent to the osteotomy ends. Collagen type‐II transcripts were not detected in the fibrous interzone. During the maturation phase, cells within the fibrous interzone expressed collagen type I and exhibited abundant alkaline phosphatase activity, suggesting that they had begun to terminally differentiate. Collectively, these data demonstrate the utility of a mouse model to study the molecular and cellular bases for the regeneration and remodeling of tissue.
Management of Graves’ Ophthalmopathy: Reality and Perspectives* (2000)

Graves' ophthalmopathy is an debilitating disease impairing the quality of life of affected individuals. Despite recent progress in the understanding of its pathogenesis, treatment is often not satisfactory. In mild cases, local therapeutic measures (artificial tears and ointments, sunglasses, nocturnal taping of the eyes, prisms) can control symptoms and signs. In severe forms of the disease (3-5%), aggressive measures are required. If the disease is active, high-dose glucocorticoids and/or orbital radiotherapy, or orbital decompression represent the mainstay of treatment. If the disease is severe but inactive, orbital decompression is preferred. Novel treatments such as somatostatin analogs or intravenous immunoglobulins are under evaluation. Rehabilitative (extraocular muscle or eyelid) surgery is often needed after treatment and inactivation of eye disease. Correction of both hyper- and hypothyroidism is crucial for the ophthalmopathy. Antithyroid drugs and thyroidectomy do not influence the course of the ophthalmopathy, whereas radioiodine treatment may cause the progression of preexisting ophthalmopathy, especially in smokers. The exacerbation, however, is prevented by glucocorticoids. In addition, thyroid ablation may prove beneficial for the ophthalmopathy in view of the pathogenetic model relating eye disease to autoimmune reactions directed against antigens shared by the thyroid and the orbit.
COLONY-LEVEL IMPACTS OF IMMUNE RESPONSIVENESS IN HONEY BEES, APIS MELLIFERA (2005)

Social insects have evolved both communal and individual traits that reduce the impacts of their numerous parasites and pathogens. Among the individual traits, innate-immune responses have the potential to reduce both individual mortality and the spread of pathogens among colony members. An understanding of the costs and benefits of such responses can provide a more complete understanding of a primary risk of social life, horizontal disease transmission among colony members. Here we assess the impacts of individual immunity on colony-level disease in honey bee (Apis mellifera) colonies following exposure to an important bacterial pathogen (Paenibacillus larvae subsp. larvae, cause of the disease American foulbrood). Colony-level disease rates were negatively correlated with the immune responsiveness of colony members, as assessed by larval transcript levels for the gene encoding the antibacterial peptide abaecin. Concomitantly, colonies whose members mounted a stronger abaecin response showed significantly lower productivity, indicating a colony-level cost to this immune response. The results show considerable variation across colonies in an immune trait important for survival, and point toward a significant trade-off between this trait and colony productivity.
Reduced Incidence of Preterm Delivery with Metronidazole and Erythromycin in Women with Bacterial Vaginosis (1995)

Treatment with metronidazole and erythromycin reduced rates of premature delivery in women with bacterial vaginosis and an increased risk for preterm delivery.
Optical frequency-selective amplification in a distributed feedback type semiconductor laser amplifier (1987)

Optical frequency-selective amplification of an injected optical signal in a distributed feedback type semiconductor laser amplifier is studied. Based on this mechanism an optical demultiplexer with optical gain for optical frequency-division multiplexing is developed. A 9 GHz spectrum selectivity and a 11 dB extinction ratio are observed.
FDA Perspective on Peptide Formulation and Stability Issues (1998)

Traditionally, peptide drugs are prepared as sterile solutions and administered to patients by daily injection. However, this form of drug delivery causes pain and inconvenience to patients and thus has been poorly accepted. In addition to improving patient compliance, many novel delivery systems have been developed to address the need for prolonged, localized (targeted), or pulsatile drug action. Examples include, but are not limited to oral, nasal, or long-acting controlled release injectable dosage forms; a number of them have been approved by FDA recently. The unique characteristics and the relevant regulatory issues with respect to each type of delivery system are presented.
Silicon-Based Photonic Crystals (2001)

Photonic crystals can be thought of as optical analogues of semiconductors. Here recent advances in photonic crystals based on silicon are reviewed. After summarizing the theory of photonic bandgap materials, the preparation and linear optical properties of 1D, 2D, and 3D silicon-based photonic crystals are discussed. Laterally structured porous silicon with a defect line is shown in the Figure.
Measurement and modeling of transient effects in partially-depleted SOI MOSFETs (1996)

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1996.
High-Tc Superconductivity in New Oxide Systems (1987)

Superconducting transitions have been observed by resistivity measurements for several specimens of L-M-Cu-O system with L being Yb, Lu, Y, La and the mixture of Yb and La, and M being Ba and mixture of Ba and Sr. The onset transition temperature T c becomes very close to 100 K. Since Yb-Ba-Cu-O and Lu-Ba-Cu-O have almost the same transition temperatures ( T c &gt;90 K), the magnetic moment of Yb atoms does not seem to destroy the superconductivity in the present system. This suggests that the superconductivity occurs in certain parts of the system which are, at least, far from the Yb atom sites. Therefore M-Cu-O or Cu-O system may have an essential role in the occurrence of the superconductivity.
Interaction of cytosol fractions containing activated glucocorticoid‐receptor complexes from rat liver and thymus with heterologous nuclei: effects on transcription (1989)

Two rat liver cytosol fractions containing activated glucocorticoid-receptor complexes are able to stimulate the transcriptional activity of rat liver nuclei; the respective fractions from the cytosol of thymocytes inhibit the capacity of thymus nuclei for RNA synthesis. A similar inhibitory effect on thymus nuclei is exerted by the presence of rat liver cytosol fractions. Spot hybridization using a tyrosine aminotransferase (TAT) probe demonstrates that TAT gene expression is stimulated by the liver cytosol fractions acting on homologous nuclei whereas it is inhibited, in thymus nuclei, by the addition of thymus cytosol fractions. No effect on transcription is observed if the liver or thymus cytosol is heat activated in the presence of the glucocorticoid antagonist, cortexolone. Treatment of liver nuclei, previously subjected to the action of thymus cytosol fractions with the respective liver ones, restores transcriptional activity to control or higher levels. We conclude that rat thymocyte nuclei and cytosol contain transcriptional factors, which in the presence of the glucocorticoid-receptor complex, irrespective of its source, inhibit gene expression, whereas in the absence of such factors, the glucocorticoid-receptor complex positively regulates the respective genes.
Dampak Fluktuasi Barga Minyak Indonesia terhadap Indikator Makroekonomi Indonesia Peri ode 2005:Ml - 2008:M8 (2008)

Abstraksi\nDalam beberapa dekade terakhir, kenaikan harga minyak terjadi tak hanya di dunia internasional namun\njuga di Indonesia. Kenaikan harga minyak membuat pemerintah menaikkan harga BBM sebesar 28,7% pada 24 Mei 2008. Ini membuat subsidi pemerintah membengkak, yang implikasi negatifnya sangat luas bagi seluruh pelaku ekonomi, seperti kenaikan harga jual barang dan jasa, penurunan kegiatan produksi yang mengakibatkan pengangguran. Mengingat Indonesia sekarang adalah negara importir minyak maka pengaruh varia bel-varia bel makroekonomi seperti pertumbuhan\nekonomi, injlasi, jub dan kurs tentu menarik untuk dicermati.\nDalam paper ini akan dibahas\nmengenai bagaimana harga minyak mempengaruhi variabel-variabel makroekonomi seperti pertumbuhan ekonomi, inflasi, jub dan kurs. Metodologi yang dipakai adalah dengan menggunakan Model Vector Autoregressive Model (VAR) dengan analisis Impulse Response Function\n(IRF) dan Variance Decomposition (VD) untuk melihat bagaimana respon antar variabel dan seberapa besar variasi harga minyak dalam\nmempengaruhi varia bel makroekonomi.
Sparse Convolutional Neural Networks (2015)

Deep neural networks have achieved remarkable performance in both image classification and object detection problems, at the cost of a large number of parameters and computational complexity. In this work, we show how to reduce the redundancy in these parameters using a sparse decomposition. Maximum sparsity is obtained by exploiting both inter-channel and intra-channel redundancy, with a fine-tuning step that minimize the recognition loss caused by maximizing sparsity. This procedure zeros out more than 90% of parameters, with a drop of accuracy that is less than 1% on the ILSVRC2012 dataset. We also propose an efficient sparse matrix multiplication algorithm on CPU for Sparse Convolutional Neural Networks (SCNN) models. Our CPU implementation demonstrates much higher efficiency than the off-the-shelf sparse matrix libraries, with a significant speedup realized over the original dense network. In addition, we apply the SCNN model to the object detection problem, in conjunction with a cascade model and sparse fully connected layers, to achieve significant speedups.
ADAM10 mediates E-cadherin shedding and regulates epithelial cell-cell adhesion, migration, and β-catenin translocation (2005)

E-cadherin controls a wide array of cellular behaviors, including cell-cell adhesion, differentiation, and tissue development. We show here that E-cadherin is cleaved specifically by ADAM (a disintegrin and metalloprotease) 10 in its ectodomain. Analysis of ADAM10-deficient fibroblasts, inhibitor studies, and RNA interference-mediated down-regulation of ADAM10 demonstrated that ADAM10 is responsible not only for the constitutive shedding but also for the regulated shedding of this adhesion molecule in fibroblasts and keratinocytes. ADAM10-mediated E-cadherin shedding affects epithelial cell-cell adhesion as well as cell migration. Furthermore, the shedding of E-cadherin by ADAM10 modulates the beta-catenin subcellular localization and downstream signaling. ADAM10 overexpression in epithelial cells increased the expression of the beta-catenin downstream gene cyclin D1 dose-dependently and enhanced cell proliferation. In ADAM10-deficient mouse embryos, the C-terminal E-cadherin fragment is not generated, and the full-length protein accumulates, highlighting the in vivo relevance for ADAM10 in E-cadherin shedding. Our data strongly suggest that this protease constitutes a major regulatory element for the multiple functions of E-cadherin under physiological as well as pathological conditions.
Metalloproteinases in Drosophila to Humans That Are Central Players in Developmental Processes (2011)

Many secreted proteins are synthesized as precursors with propeptides that must be cleaved to yield the mature functional form of the molecule. In addition, various growth factors occur in extracellular latent complexes with protein antagonists and are activated upon cleavage of such antagonists. Research in the separate fields of embryonic patterning and extracellular matrix formation has identified members of the BMP1/Tolloid-like family of metalloproteinases as key players in these types of biosynthetic processing events in species ranging from Drosophila to humans.
Decreased Expression of the Aryl Hydrocarbon Receptor in Ocular Behcet’s Disease (2014)

Recent studies show that the aryl hydrocarbon receptor (AhR) is involved in immune responses. AhR is activated following interaction with its ligands, such as 6-formylindolo[3,2-b]carbazole (FICZ) and 2-(1'H-indole-3'-carbonyl)-thiazole-4-carboxylic acid methyl ester (ITE). In this study, we investigated the role of AhR activation by its endogenous ligands in the pathogenesis of ocular Behcet's disease (BD). The expression of AhR was significantly decreased in active BD patients as compared to inactive BD patients and normal controls. Both FICZ and ITE inhibited Th1 and Th17 polarization and induced the expression of IL-22 by PBMCs and by CD4(+)T cells in active BD patients and normal controls. Stimulation of purified CD4(+)T cells with FICZ or ITE caused a decreased expression of RORC, IL-17, IL-23R, and CCR6 and an increased phosphorylation of STAT3 and STAT5. The present study suggests that a decreased AhR expression is associated with disease activity in BD patients. The activation of AhR by either FICZ or ITE was able to inhibit Th1 and Th17 cell polarization. Further studies are needed to investigate whether modulation of AhR might be used in the treatment of BD.
Synthesis of marine adhesive proteins secreted from chilean mussel. (1991)

アミノ酸の一次構造がすでに決められている海洋接着タンパク質にはバイオ接着剤としての関心が寄せられている. その中でいちばん短い繰り返しヘプタペプチド配列を有するチリ産い貝の接着タンパク質 (Ala-Gly-Tyr-Gly-Gly-X-Lys) n (XはAla及びIle) をフラグメント縮合を経て活性エステル法で合成した. 天然物の繰り返しヘプタペプチドの繰り返し数 (n) は天然物では約160であり, 合成物では17～24であった. 3-残基目のTyrは酵素によりDopaへの変換が可能である.
ChemInform Abstract: Properties of Organolithium Reagents at Low Temperature (2011)

Abstract Review: 13 refs.
[Polymorphism in Helicobacter pylori--a key function in recurrence of infection?]. (1992)

Despite the fact that Helicobacter (H.) pylori is ubiquitous throughout the world, little is known at present about the source of infection and mode of transmission. Person-to-person transmission may be of importance. The fact that Helicobacter pylori can revert to a coccoid form stimulated speculation about its role in transmission and as a possible cause of reinfection in duodenal ulcer disease. Various antibacterial agents (bismuth subcitrate 32 mg/l bismuth subsalicylate 64 mg/l, amoxicillin 0.05 mg/l, ampicillin 2 mg/l, erythromycin 4 mg/l, glycochenodeoxycholic acid 423 mg/l, ursodeoxycholic acid 540 mg/l) inhibit the growth of H. pylori and stimulate the formation of coccoid structures. Ultrastructural and biochemical results show that the coccoid form meets the necessary criteria for survival. Thus, to be successful, treatment must aim not only at eliminating the vegetative form, but also at preventing the development of the coccoid form.
Neural and connective tissue response to long-term implantation of multiple contact nerve cuff electrodes (2000)

The objective of this study was to characterize the tissue response to multiple contact spiral nerve cuff electrodes implanted on the sciatic nerve of seven cats for 28-34 weeks. The cuffs were surrounded by fibrous tissue encapsulation consisting of foreign body cells, collagen, and fibroblasts. Focal areas of abnormal neural morphology including perineurial thickening, endoneurial fibrosis, thinly myelinated axons, and focal reduction in the density of myelinated axons were noted in five of seven nerves. In three implants, the percutaneous lead cable was destroyed by the animal pulling on the external leads. Morphological changes were observed in two of three nerves from implants sustaining no known animal induced trauma (group A), and in three of four nerves from implants damaged by the animal pulling at the leads (group B). All nerves appeared normal 2 cm proximal to the cuff. At the cuff level, small regions of one fascicle in each of two nerves (both group B) exhibited abnormalities, while the proximal and distal sections of both nerves were normal. Distal to the cuff, small regions of seven fascicles distributed among three nerves (two group A, one group B) exhibited abnormalities. These nerves were normal at the cuff level but exhibited abnormalities in individual nerve branches distal to the cuff. The incidence and characteristics of the morphological abnormalities at the cuff level are consistent with those observed in previous studies of nerve cuff electrodes, and support the hypothesis that spiral cuff electrodes can be implanted with an internal diameter less than that of the nerve and expand to accommodate the nerve without compression The pattern of morphological abnormalities indicated that mechanical trauma had occurred at some time in the past, and the distribution suggested animal intervention and the lead cable as possible causes.
Industrial media and fermentation processes for improved growth and protease production by Tetrahymena thermophila BIII (2000)

Tetrahymena thermophila was cultivated on industrial by-product media. The composition of the best medium (with milk proteins) was optimised by a central composite design for growth and protease secretion. The optimal combination [1.07% (w/v) of yeast extract and 0.99% (w/v) of skimmed milk] improved biomass production by 46%. In a fermentation strategy, the pH must be regulated to produce no cell damage, lengthening the stationary phase and resulting in a more abundant protease production. To increase cell concentration and protease secretion, a continuous culture with cell recycling by microfiltration was successfully tested on ciliated protozoa.