gebhart/patrepeval huggingface dataset:
Structural characterization of a mutant peptide derived from ubiquitin: Implications for protein folding (2000)

The formation of the N-terminal beta-hairpin of ubiquitin is thought to be an early event in the folding of this small protein. Previously, we have shown that a peptide corresponding to residues 1-17 of ubiquitin folds autonomously and is likely to have a native-like hairpin register. To investigate the causes of the stability of this fold, we have made mutations in the amino acids at the apex of the turn. We find that in a peptide where Thr9 is replaced by Asp, U(1-17)T9D, the native conformation is stabilized with respect to the wild-type sequence, so much so that we are able to characterize the structure of the mutant peptide fully by NMR spectroscopy. The data indicate that U(1-17)T9D peptide does indeed form a hairpin with a native-like register and a type I turn with a G1 beta-bulge, as in the full-length protein. The reason for the greater stability of the U(1-17)T9D mutant remains uncertain, but there are nuclear Overhauser effects between the side chains of Asp9 and Lys 11, which may indicate that a charge-charge interaction between these residues is responsible.
Discovery of a Nitric Oxide Responsive Quorum Sensing Circuit inVibrio harveyi (2012)

Bacteria use small molecules to assess the density and identity of nearby organisms and formulate a response. This process, called quorum sensing (QS), commonly regulates bioluminescence, biofilm formation, and virulence. Vibrio harveyi have three described QS circuits. Each involves the synthesis of a molecule that regulates phosphorylation of its cognate receptor kinase. Each receptor exchanges phosphate with a common phosphorelay protein, LuxU, which ultimately regulates bioluminescence. Here, we show that another small molecule, nitric oxide (NO), participates in QS through LuxU. V. harveyi display a NO concentration-dependent increase in bioluminescence that is regulated by an hnoX gene. We demonstrate that H-NOX is a NO sensor and NO/H-NOX regulates phosphorylation of a kinase that transfers phosphate to LuxU. This study reveals the discovery of a fourth QS pathway in V. harveyi and suggests that bacteria use QS to integrate not only the density of bacteria but also other diverse information about their environment into decisions about gene expression.
Transverse Sphere and Texture of Carbon Fibers Prepared through Cross Shaped Nozzles of Different Lobe Dimensions (1999)

Methylnaphthalene derived mesophase pitch was spun through Y- and cross- shaped nozzles of different lobe dimensions in temperature range of 280 to 295℃ by fixing the spinning rate to evaluate die-swelling phenomena which deformed cross-sectional shape and domain alignment of the carbon fiber. The higher temperature of spinning enhanced the deformation through the lower viscosity. The thinner lobe emphasized the die-swelling through the larger shear rate, which reduces the viscosity, although the nozzles of the present study had the same cross-sectional area Shape factors of the nozzle and fiber describe the extents of cause and results of die-swelling, respectively. Die-swelling is found to change the radial type alignment of the constituent domains to random order. The degrees of preferred orientation along the fiber axis were slightly influenced by die-swelling. The pressure in spinning and the nozzle shape were correlated to the deformation extent of the resultant fiber.
bdrmap (2016)

We tackle the tedious and unsolved problem of automatically and correctly inferring network boundaries in traceroute. We explain why such a conceptually simple task is so hard in the real world, and how lack of progress has impeded a wide range of research and development efforts for decades. We develop and validate a method that uses targeted traceroutes, knowledge of traceroute idiosyncrasies, and codification of topological constraints in a structured set of heuristics, to correctly identify interdomain links at the granularity of individual border routers. In this study we focus on the network boundaries we have most confidence we can accurately infer in the presence of sampling bias: interdomain links attached to the network launching the traceroute. We develop a scalable implementation of our algorithm and validate it against ground truth information provided by four networks on 3,277 links, which showed 96.3% -- 98.9% of our inferences were correct.
Impact of LOCOS techniques on photonic wire waveguides (2012)

We use the LOCal oxidation of silicon (LOCOS) method as a fabrication technique to define submicrometer photonic waveguides. We attempted fabricating the wire waveguides with two different masking processes, one with a stack of pad oxide and silicon nitride layers, and the other with a single silicon nitride layer. The smallest waveguide we achieved had a cross-section profile of 280 nm×650 nm. The propagation loss of the waveguides was measured by the cut-back method, and the bending loss was measured by employing the serpentine pattern. The minimum propagation loss achieved was 8.78 dB/cm and the bending loss was 0.0089 dB/90° bend for a 5 μm bending radius.
[A study on the mechanism of damage to DNA in rats by ethylene oxide]. (1997)

DNA in the liver, kidney, testes, etc. was amplified with semi-random polymerase chain reaction (PCR) in Wistar male rats exposed to ethylene oxide (EtO) for various times and in control rats with hemoglobin gene-specific primer to study the damage effects of EtO on DNA molecule. Results showed that inhalation of 800 mg/m3 of EtO for six to nine weeks could cause damage to DNA in the liver, kidney and testes, etc. to various extent, with the most serious damage to DNA in the testes.
Neural activities classification of left and right finger gestures during motor execution and motor imagery (2020)

In this study, a new paradigm containing motor observation, motor execution, and motor imagery was designed to investigate whether motor imagery (MI) and motor execution (ME) of finger gestures can be used to extend commands of practical mBCIs. The subjects were instructed to perform or imagine 30 left and right finger gestures. Hierarchical support vector machine (hSVM) method was applied to classify four tasks (i.e., ME and MI tasks between left and right gestures). The average classification accuracies of motor imagery and execution tasks using fivefold cross-validation were 90.89 ± 9.87% and 74.08 ± 13.42% in first layer and second layer, respectively. The average accuracy of classification of four classes is 83.06 ± 7.29% overall. These results show that performing or imaging finger movements have the potential to extend the commands of the existing BCI, especially for healthy elderly living.
Biochemical and radiological inflammatory markers in oesophageal squamous cell carcinoma treated with radical chemoradiation (2018)

Introduction: Inflammatory markers have been shown to be associated with poor prognosis in various solid tumours. We aimed to evaluate the role of biochemical and radiological inflammatory markers in oesophageal SCC treated with radical chemoradiation (CRT). Methods: We retrospectively evaluated 48 patients with primary oesophageal SCC who completed radical CRT in a single tertiary institution between 2006-2015. Baseline and post-CRT serum inflammatory markers (neutrophil-to-lymphocyte (NLR) and platelet-to-lymphocyte ratios (PLR)) and baseline 18F-FDG PET parameters (SUV max, SUV mean, metabolic tumour volume (MTV) and total lesion glycolysis (TLG)) were derived and dichotomised using median values. Clinical parameters such as age and RT dose were obtained from medical notes. Univariate and multivariate overall survival (OS) analyses were performed using Cox regression model. Kaplan-Meier survival analysis was performed using dichotomised variables. A p-value Results: All patients (median age 65; 44 males) received radical radiotherapy (RT) with platinum-based chemotherapy. Total RT doses ranged between 41.4-70Gy. Sixteen patients had baseline PET scans available for analysis. Median follow-up was 21.5 months (range 3.0-113.8 months). Median OS for all patients was 21.2 months. Baseline PLR (HR 1.007, 95% CI 1.003-1.010, p < 0.001), post-CRT PLR (HR 1.002, 95% CI 1.001-1.003, p < 0.001) and RT dose (HR 0.938, 95% CI 0.892-0.986, p = 0.012) were significant univariate parameters. Patients with lower baseline (median OS 31.3 vs. 13.3 months, p = 0.007) and post-CRT PLRs (median OS 32.7 vs. 14.4 months, p = 0.001), and who received RT doses >50.4Gy (median OS 32.0 vs. 10.0 months, p < 0.001) had improved OS. An elevated post-CRT PLR (HR 1.002, 95% CI 1.001-1.003, p = 0.003) was associated with inferior OS in multivariate analysis. Age (HR 1.010, 95% CI 0.978-1.042, p = 0.556), NLR (baseline: HR 1.083, 95% CI 0.861-1.362, p = 0.495; post-CRT: HR 1.016, 95% CI 0.977-1.055, p = 0.432) and PET parameters (SUVmax: HR 1.051, 95% CI 0.967-1.144, p = 0.242; SUVmean: HR 1.213, 95% CI 0.977-1.508, p = 0.081; MTV: HR 1.003, 95% CI 0.987-1.019, p = 0.746; TLG: HR 1.000, 95% CI 0.999-1.002, p = 0.666) were not associated with OS. Conclusion: PLR, particularly in the post-CRT setting is a significant prognostic marker in oesophageal SCC but NLR and PET parameters are not associated with OS. Although the study is limited by the small sample size and retrospective bias, these results warrant larger confirmatory studies.
Collaboration Between Public Health and Law Enforcement: New Paradigms and Partnerships for Bioterrorism Planning and Response (2002)

The biological attacks with powders containing Bacillus anthracis sent through the mail during September and October 2001 led to unprecedented public health and law enforcement investigations, which involved thousands of investigators from federal, state, and local agencies. Following recognition of the first cases of anthrax in Florida in early October 2001, investigators from the Centers for Disease Control and Prevention (CDC) and the Federal Bureau of Investigation (FBI) were mobilized to assist investigators from state and local public health and law enforcement agencies. Although public health and criminal investigations have been conducted in concert in the past, the response to the anthrax attacks required close collaboration because of the immediate and ongoing threat to public safety. We describe the collaborations between CDC and FBI during the investigation of the 2001 anthrax attacks and highlight the challenges and successes of public health and law enforcement collaborations in general.
Anomalous Epithelial Variations and Ectopic Inflammatory Response in Chronic Obstructive Pulmonary Disease (2022)

Phenotypic alterations in the lung epithelium have been widely implicated in chronic obstructive pulmonary disease (COPD) pathogenesis, but the precise mechanisms orchestrating this persistent inflammatory process remain unknown because of the complexity of lung parenchymal and mesenchymal architecture. To identify cell type-specific mechanisms and cell-cell interactions among the multiple lung resident cell types and inflammatory cells that contribute to COPD progression, we profiled 57,918 cells from lungs of patients with COPD, smokers without COPD, and never-smokers using single-cell RNA sequencing technology. We predicted pseudotime of cell differentiation and cell-to-cell interaction networks in COPD. Although epithelial components in never-smokers were relatively uniform, smoker groups represent extensive heterogeneity in epithelial cells, particularly in alveolar type 2 (AT2) clusters. Among AT2 cells, which are generally regarded as alveolar progenitors, we identified a unique subset that increased in patients with COPD and specifically expressed a series of chemokines including CXCL1 and CXCL8. A trajectory analysis revealed that the inflammatory AT2 cell subpopulation followed a unique differentiation path, and a prediction model of cell-to-cell interactions inferred significantly increased intercellular networks of inflammatory AT2 cells. Our results identify previously unidentified cell subsets and provide an insight into the biological and clinical characteristics of COPD pathogenesis.
Design of Hybrid Distillation−Vapor Membrane Separation Systems (2009)

Currently the separation of olefins (ethylene, propylene) from (ethane, propane) on a commercial scale is performed almost exclusively by cryogenic distillation in petrochemical industries. Since this technology is highly energy intensive, there is a strong economic incentive to explore alternative separation technologies with lower energy consumption. In this work, using the separation of ethylene and ethane as a representative case, a mathematical programming approach is proposed to optimize and retrofit a hybrid separation system consisting of a distillation column and a parallel membrane separation unit. A two-stage approach is used. First, a shortcut model is introduced that allows determining whether the hybrid system could be of interest and the order of magnitude of the energy savings that can be expected. Second, a superstructure optimization approach is proposed that uses rigorous models for both the column and the membrane using a process simulator and state of the art MINLP solvers. The results presented in the case study show that significant savings in total costs and energy (up to 30%) can be obtained with the hybrid system.
Zinc citrate/Triclosan: a new anti‐plaque system for the control of plaque and the prevention of gingivitis: short‐term clinical and mode of action studies (1991)

Abstract. A dentifrice based upon the additive anti‐plaque effects of zinc citrate and Triclosan has been developed and optimised for clinical activity. In 16‐h and 4‐day plaque growth inhibition studies, zinc citrate/Triclosan inhibited plaque accumulation significantly more than either agent alone. The effect on the development of gingivitis has been demonstrated in a 21‐day experimental gingivitis study. ZCT/Triclosan reduced the development of gingival bleeding sites by significantly more than ZCT alone, suggesting that the system has the potential to give a gingival health benefit in a 6‐month unsupervised brushing study. Zinc and Triclosan employ multiple modes of antimicrobial action and these result in reduced growth, inhibition of glucose uptake and metabolism and modified virulence of periodontal pathogens. Importantly, the effects of zinc and Triclosan are additive and complementary. Oral substantivity is a pre‐requisite of any agent for anti‐plaque activity in vivo. Pharmacokinetic data demonstrate that ~30% of the zinc and Triclosan dosed is retained immediately after brushing. Saliva decay curves indicate that Triclosan is cleared more quickly from the mouth than zinc, consistent with the physicochemical properties of these agents. Triclosan is present in plaque for at least 8 h and in the oral mucosa for at least 3 h after brushing.
633 Field Performance of “Transgenic” Potato, with Resistance to Colorado Potato Beetle and Viruses (1999)

After more than 10 years of research, Monsanto scientists have developed improved seed potatoes that are protected from serious pests, including insects and disease. The first commercial products resulting from this effort were NewLeaf ® potatoes derived from `Russet Burbank' and `Atlantic' parents. The NewLeaf® product was commercialized in 1995 and contains a gene from Bacillus thuringiensis (variety tenebrionis ) (B.t.t.). for the production of the Cry3A protein. Potatoes expressing this gene are completely protected from the Colorado potato beetle (CPB) and need no additional chemical protection for this insect pest. The U.S. Food and Drug Administration (FDA), U.S. Dept. of Agriculture (USDA), and U.S. Environmental Protection Agency (EPA) have all determined that these potatoes are the same in safety and nutritional composition as any other `Russet Burbank' and `Atlantic' potatoes. These potatoes have also been approved by Health Canada, Agri-Food Canada and Agriculture Canada and by Japan and Mexico for food use. Commercial growers across North America have experienced outstanding performance while growing NewLeaf® potatoes 3 years in a row. This level of performance is the result of stable, nonsignificant differences in expression of the Cry3A gene. The stable performance, also, is a result of an effective insect resistance management program based on maintaining CPB refuges near NewLeaf ® fields, reducing CPB populations, and monitoring for CPB surviving exposure to NewLeaf® potatoes. In 1998 NewLeaf Y®), conferring resistance to both CPB and potato virus Y, and NewLeaf Plus®, conferring resistance to CPB and potato leafroll virus will be commercially released.
Progress in clinical diagnosis and treatment of Ramsay-Hunt syndrome (2018)

Ramsay-Hunt syndromeis the second most common cause of peripheral facial paralysis. This article systematically reviews the relevant literatures in the field of Ramsay-Hunt syndrome at home and abroad, summarizes the clinical manifestations and complications of Ramsay-Hunt syndrome, and discuss the diagnosis and treatment of new progress. Our objective is to improve the clinical understanding and treatment of Ramsay-Hunt syndrome. At the same time, we should pay attention to the Ramsay-Hunt syndrome presenting as cranial poly neuropathy and reduce misdiagnosis in clinical. As soon as possible to give a reasonable treatment to improve the cure rate.


Key words: 
Herpes Zoster; Antiviral Agents; Ramsay-Hunt syndrome
Communication. Limit of detection in analysis with ion-selective electrodes (1980)

D. Midgley, Analyst, 1980, 105, 1002 DOI: 10.1039/AN9800501002
HLA (Class I) antigens on platelets are involved in platelet function (1988)

HLA (Class I) antigens are ubiquitous in their cellular distribution and, while their function in major histocompatibility complex (MHC)-restricted phenomena are clear, their function on other cells, such as platelets, is not so obvious. We now report that several anti-HLA monoclonal antibodies (including an anti-beta 2 microglobulin antibody) selectively affect platelet function in that three different anti-HLA monoclonal antibodies caused not only the aggregation of human platelets, but also caused the release of 14C-serotonin. In addition, the anti-HLA antibodies could selectively block the binding of several platelet agonists such as collagen, adrenalin, ADP, but not the binding of others such as thrombin and arachidonic acid. In blocking studies there also appeared to be an association between platelet glycoprotein IIb-IIIa and HLA Class I antigens. We propose that both heavy and light chains of Class I HLA antigens on platelets may be involved in platelet aggregation and release and suggest an additional role for HLA antigens on platelets.
Functional Connectivity Magnetic Resonance Imaging Reveals Rapid and Reversible Changes in the Brain Following Induction of Psoriasiform Dermatitis in Mice (2018)

Functional connectivity magnetic resonance imaging (fcMRI), a specific form of MRI imaging, quantitatively assesses connectivity between brain regions that share functional properties. Functional connectivity magnetic resonance imaging has already provided unique insights into changes in the brain in patients with conditions such as depression and pain and symptoms that have been reported by patients with psoriasis and are known to impact quality of life. To identify the central neurological impact of psoriasiform inflammation of the skin, we applied fcMRI analysis to mice that had been topically treated with the Toll-like receptor agonist, imiquimod (IMQ) to induce psoriasiform dermatitis. Brain insula regions, due to their suggested role in stress, were chosen as seed regions for fcMRI analysis. Mouse ear and head skin developed psoriasiform epidermal thickening (up to 4-fold, P &lt; .05) and dermal inflammation after 4 days of topical treatment with IMQ. After fcMRI analysis, IMQ-treated mice showed significantly increased insula fc with wide areas throughout the brain, including, but not limited to, the somatosensory cortex, anterior cingulate cortex, and caudate putamen ( P &lt; .005). This reflects a potential central neurological impact of IMQ-induced psoriasis-like skin inflammation. These data indicate that fcMRI may be valuable tool to quantitatively assess the neurological impact of skin inflammation in patients with psoriasis.
Evaluation Of Performance Requirements For Seismic Design Of Piping System (2013)

The cost of damage to the non-structural systems in critical facilities like nuclear power plants and hospitals can exceed 80% of the total cost of damage during an earthquake. The failure of nonstructural components, especially, piping systems led to leakage of water and subsequent shut-down of hospitals immediately after the event. Consequently, the evaluation of performance of these types of structural configurations has become necessary to mitigate the risk and to achieve reliable designs. This paper focuses on a methodology to evaluate the static and dynamic characteristics of complex actual piping system based on NFPA-13 and SMACNA guidelines. The result of this study revealed that current piping system subjected to design lateral force and design spectrum based on UBC-97 was failed in both cases and mode shapes between piping system and building structure were very different
Clinical and genetic studies of muscular dystrophy in young girls (1986)

During the years 1971-81, we treated 7 girls with clinical features suggestive of Duchenne dystrophy. Muscle weakness developed at 1.5 or at 5-8 years and progressed rapidly. Two girls were in wheel-chairs in their teens. Muscle atrophy began in the proximal parts of the lower extremities and pseudohypertrophy of the calf occurred in all patients. Serum creatine phosphokinase (CPK) activity was moderately to highly elevated in all cases and EMG showed a moderate to marked myopathic pattern. Chromosomal studies showed normal finding in the five examined. Mental retardation (IQ 37-73) was present in four. Consanguinity was present in 3 out of the 7 cases. Two mothers showed elevated levels of CPK and myopathic patterns on EMG. In addition, one mother had slight muscle weakness at the age of 42 and another had prominent pseudohypertrophy of the calf. Sex-linked recessive inheritance might be considered here, because carriers of autosomal recessive type never showed elevated levels of CPK or mild myopathic symptoms. The other five of our seven might be cases of autosomal recessive inheritance, because the mothers had normal serum CPK levels and in 2 families there was a consanguinity.
Operating manual for the RRL 8 channel data logger (1979)

A data collection device which takes measurements from external sensors at user specified time intervals is described. Three sensor ports are dedicated to temperature, air pressure, and dew point. Five general purpose sensor ports are provided. The user specifies when the measurements are recorded as well as when the information is read or stored in a minicomputer or a paper tape.