Miracle-dz/UniFAR-FTUs huggingface dataset:
Post-translational Modifications of Integral Membrane Proteins Resolved by Top-down Fourier Transform Mass Spectrometry with Collisionally Activated Dissociation*

Integral membrane proteins remain a challenge to proteomics because they contain domains with physicochemical properties poorly suited to today's bottom-up protocols. These transmembrane regions may potentially contain post-translational modifications of functional significance, and thus development of protocols for improved coverage in these domains is important. One way to achieve this goal is by using top-down mass spectrometry whereby the intact protein is subjected to mass spectrometry and dissociation. Here we describe top-down high resolution Fourier transform mass spectrometry with collisionally activated dissociation to study post-translationally modified integral membrane proteins with polyhelix bundle and transmembrane porin motifs and molecular masses up to 35 kDa. On-line LC-MS analysis of the bacteriorhodopsin holoprotein yielded b- and y-ions that covered the full sequence of the protein and cleaved 79 of 247 peptide bonds (32%). The experiment proved that the mature sequence consists of residues 14–261, confirming N-terminal propeptide cleavage and conversion of N-terminal Gln-14 to pyrrolidone carboxylic acid (−17.02 Da) and C-terminal removal of Asp-262. Collisionally activated dissociation fragments localized the N6-(retinylidene) modification (266.20 Da) between residues 225–248 at Lys-229, the sole available amine in this stretch. Off-line nanospray of all eight subunits of the cytochrome b6f complex from the cyanobacterium Nostoc PCC 7120 defined various post-translational modifications, including covalently attached c-hemes (615.17 Da) on cytochromes f and b. Analysis of murine mitochondrial voltage-dependent anion channel established the amenability of the transmembrane β-barrel to top-down MS and localized a modification site of the inhibitor Ro 68-3400 at Cys-232. Where neutral loss of the modification is a factor, only product ions that carry the modification should be used to assign its position. Although bond cleavage in some transmembrane α-helical domains was efficient, other regions were refractory such that their primary structure could only be inferred from the coincidence of genomic translation with precursor and product ions that spanned them.
Prevalence of rheumatoid factor and parameters associated with rheumatoid factor positivity in Korean health screening subjects and subjects with hepatitis B surface antigen

ObjectivesThe purpose of this study is to assess the prevalence and titer of rheumatoid factor (RF) in Korean health screening subjects and consecutive subjects with hepatitis B surface antigen (HBsAg) and to examine the factors influencing RF positivity.MethodsThis study was performed in 37,660 patients (23,269 men, 14,391 women) without arthralgia, who participated in a health checkup program in 2009.ResultsApproximately 3.7% of health screening subjects (3.3% of males and 4.4% of females) were positive for RF. Among subjects with HBsAg (n = 1,494) and antibody for hepatitis C virus (HCV) (n = 132), 11.8 and 10.6% were RF positive, respectively. There was a significant difference in the RF-positive rate between males and females. The RF-positive rate had a significant linear-by-linear association with aging, but there was no significant relationship between RF positivity and aging among subjects with HBsAg or anti-HCV antibody. Presence of HBsAg and anti-HCV antibody, positive C-reactive protein (CRP), and female sex were factors strongly associated with RF positivity.ConclusionsThe rate of RF positivity in health screening adults and subjects with HBsAg in Korea can be estimated to be 3.7 and 11.8%, respectively. Clinicians should consider hepatitis B or C virus infection status, CRP positivity, and sex when interpreting RF-positive results.
Price Transmission along the Supply Chain of Strawberries in Mexico

By combining data from multiple sources, we model supply and demand of strawberry in Mexico for the 1970-2013 period. The main purpose of the study is to measure transmission of prices in this sector. Producer prices, wholesaler prices, exporter prices, and consumer prices are components of the model. Our three-stage least squares regression results show, consistent with the literature, that the pass-through of price changes is imperfect; that is, a price change at the producer level is not fully transmitted to domestic consumers and exporters. (Dickey-Fuller Augmented and Ljung-Box tests were performed to ensure efficiency of estimators.) Furthermore, a change in producer prices has a higher impact on the domestic market than in the exports market, in percentage basis. However, higher price mark-ups in the export market compared to domestic market’s make exporting more attractive to Mexican strawberry producers. Results of this study may have important implications as both supply and exports of strawberry from Mexico have experienced high growth in the last decade, with more than 90% of strawberry being exported to the U.S. According the Mexican Department of Agriculture, volume harvested of strawberry grew 2.14 times from 2003 to 2014 while exports did 2.88 times.
Simplified calculation of coverage area for MF AM broadcast stations

It is shown that the coverage area of medium- and high-frequency stations using ground-wave propagation beyond the horizon, especially MF AM stations, can be calculated by a simplified method. Recent field measurements have shown that the cumbersome FCC and CCIR calculations for estimating service area can be simplified to allow calculations with a PC, or even a programmable pocket calculator. The ground-wave electrical field intensity calculations are simplified by the introduction of a shadow or diffraction factor in the Norton planar earth expression. This factor permits the ground E field to be calculated well beyond the geometric and radio horizon, where E-field values are close to the atmospheric noise level. The approach permits engineers or technicians to calculate their own E=field curves for any frequency and any kind of soil. <<ETX>>
Characterization of Novel Microelectrode Geometries for Detection of Neurotransmitters

In this paper, a microelectrode array is introduced and characterized using differential pulse voltammetry (DPV), amperometry and fast scan cyclic voltammetry with norepinephrine as a model neurotransmitter. Twenty-one sensor geometries were evaluated with DPV to determine optimal electrode configurations. Next, electrode responses were characterized for the best electrode geometry using an onboard platinum pseudo-reference electrode, whose reliability is established.
BURGELIJK WETBOEK (Menelusuri Sejarah Hukum Pemberlakuannya di Indonesia)

Burgelijk Wetboek or the book of civil law is historically derived from Dutch. It has been applied on the basis of concordancy principle; in fact, the legislative institution has not published civil laws that being coded and unified yet. It is urgent to apply new laws that exclusively manage law of contract (in particular or general) as a part of civil laws, in order to support the economic activity of nation. Dutch has already revised their own Burgelijk Weboek that has been applied in Indonesia.
Beneficial Effect of Immunosuppressive Drugs on Parry-Romberg Syndrome: A Case Report and Review of the Literature

Progressive facial hemiatrophy, also known as Parry-Romberg syndrome (PRS), is characterized by slowly progressive atrophy of one side of the face, primarily involving the subcutaneous tissues and fat. Involvement of the central nervous system with impairment of neurologic function occurs infrequently. At present, there is no agreement as to whether PRS is a distinct entity or a clinical variant of linear scleroderma en coup de sabre. The exact reason for PRS has not yet been determined; therefore, no suitable treatment exists. We observed beneficial effects of immunosuppressive agents on neurologic lesions in particular in a patient with PRS who presented with immunoinflammatory findings and neurologic involvement, apart from cutaneous manifestations.
An alternative approach to dissipative particle dynamics

We describe a simulation method based on combining the ideas behind Andersen's thermostat and dissipative particle dynamics (DPD). The result is a Galilean invariant thermostat that conserves momentum and enhances viscosity. It therefore displays the same characteristics as DPD. Our method differs primarily in that it satisfies detailed balance by construction. If a simple scheme is used to solve the equations of motion the thermostat does not disturb the equilibrium properties of the system, regardless of the time step. We illustrate the properties of the model by describing the results of various tests on the analogous system to the dissipative ideal gas. We show that with an appropriate choice of parameters it is practical to make the viscosity orders of magnitude greater than the diffusion coefficient. This is a criterion that should be satisfied if one is interested in studying the dynamics of mesoscopic systems.
State Policies on School Climate and Bully Prevention Efforts: Challenges and Opportunities for Deepening State Policy Support for Safe and Civil Schools.

The National School Climate Center (NSCC) recently completed a 50-state policy scan on state school climate and anti-bullying policies to better understand the current state policy infrastructure supporting the development of positive school climates. This policy brief examines the current status of school climate and anti-bullying policies in each state, and provides policy examples and recommendations for policymakers, districts, schools and school climate advocates to consider. In conducting the policy scan, we defined policies as a state’s statutes, administrative code, state education standards and rules/regulations.
High relative abundance of the stable fly Stomoxys calcitrans is associated with lumpy skin disease outbreaks in Israeli dairy farms

The vector of lumpy skin disease (LSD), a viral disease affecting Bovidae, is currently unknown. To evaluate the possible vector of LSD virus (LSDV) under field conditions, a yearlong trapping of dipterans was conducted in dairy farms that had been affected by LSD, 1‐2 years previously. This was done in order to calculate monthly relative abundances of each dipteran in each farm throughout the year. The relative abundances of Stomoxys calcitrans (Diptera: Muscidae) in the months parallel to the outbreaks (December and April) were significantly higher than those of other dipterans. A stable fly population model based on weather parameters for the affected area was used to validate these findings. Its results were significantly correlated with S. calcitrans abundance. This model, based on weather parameters during the epidemic years showed that S. calcitrans populations peaked in the months of LSD onset in the studied farms. These observations and model predictions revealed a lower abundance of stable flies during October and November, when LSD affected adjacent grazing beef herds. These findings therefore suggest that S. calcitrans is a potential vector of LSD in dairy farms and that another vector is probably involved in LSDV transmission in grazing herds. These findings should be followed up with vector competence studies.
In vitro activities of 39 antimicrobial agents for Branhamella catarrhalis and comparison of results with different quantitative susceptibility test methods

The in vitro activities of 39 antimicrobial agents were assessed versus 74 clinical isolates of Branhamella catarrhalis. Resistance was observed only with penicillin and ampicillin and then only with beta-lactamase-producing strains. The results of in vitro susceptibility tests with agar dilution and broth microdilution procedures were found to be comparable. The results of broth tube macrodilution tests were, in general, one twofold-concentration increment higher.
Molecular Cloning, Sequence, and Expression of Mouse Flavin‐Containing Monooxygenases 1 and 5 (FMO1 and FMO5)

Full‐length cDNA clones encoding FMO1 and FMO5 have been isolated from a library constructed with mRNA from the liver of a female CD‐1 mouse. The derived sequence of FMO1 contains 2310 bases: 1596 in the coding region, 301 in the 5′‐flanking region, and 413 in the 3′‐flanking region. The sequence for FMO5 consists of 3168 bases; 1599 in the coding region, 812 in the 5′‐flanking region, and 757 in the 3′‐flanking region. The sequence of FMO1 encodes a protein of 532 amino acids with a predicted molecular weight of 59.9 kDa and shows 83.3% identity to human FMO1 and 83–94% identity to other FMO1 homologs. FMO5 encodes a protein of 533 amino acids with a predicted molecular weight of 60.0 kDa and 84.1% identity to human FMO5 and 83–84% identity to other FMO5 orthologs. Two GxGxxG putative pyrophosphate binding domains exist beginning at positions 9 and 191 for FMO1, and 10 and 192 for FMO5. Mouse FMO1 and FMO5 were expressed in E. coli and show similar mobility to the native proteins as determined by SDS‐PAGE. The expressed FMO1 protein showed activity toward methimazole, and FMO5 was active toward n ‐octylamine. In addition, FMO1 was shown to metabolize radiolabeled phorate, whereas FMO5 showed no activity toward phorate. © 1998 John Wiley & Sons, Inc. J Biochem Toxicol 12: 205–212, 1998
Thromboxane A2 receptors in equine monocytes: identification of a new subclass of TXA2 receptors

Abstract: Thromboxane (TX) A2 has been implicated as an important pathophysiologic mediator of a variety of cardiovascular diseases. Monocytes synthesize TXA2 and it modulates their function. This study sought to characterize monocyte TXA2 receptors. Radioligand binding studies were performed on membranes prepared from equine peripheral blood monocytes using [*25I]BOP, a TXA2 receptor agonist. [125I]BOP bound to a single class of binding sites (Kd ‐ 1.0 ± 0.3 nM and Bmax = 389 ± 191 fmol/mg protein; n = 5). Several TXA2 receptor agonists and antagonists competed for binding with [125I]BOP. I‐ BOP produced a concentration‐dependent inhibition of endotoxin‐induced tumor necrosis factor (TNF) activity (IC50 = 9.6 ± 2.5 nM; n = 5). In contrast to its effects in platelets and vascular smooth muscle, I‐BOP significantly increased cAMP formation in monocytes (EC50 = 22 ± 3.6 nM; n = 4). The TXA2 receptor antagonists SQ29548 (5.6 nM) and L657925 (0.13 μM) significantly blocked I‐BOP‐ stimulated cAMP formation but did not block 250 nM prostaglandin E2‐stimulated cAMP formation. These data support the presence of a TXA2 receptor in equine peripheral blood monocytes. Activation of this receptor results in suppression of endotoxin‐induced TNF formation and stimulation of cAMP production. Increased cAMP production after receptor activation suggests that this receptor may represent a unique subclass of TXA2 receptors.
Inhibition of Stabilin-2 elevates circulating hyaluronic acid levels and prevents tumor metastasis

Hyaluronic acid (HA) has been implicated in the proliferation and metastasis of tumor cells. However, most previous studies were conducted on extracellular matrix or pericellular HA, and the role of circulating HA in vivo has not been studied. HA is rapidly cleared from the bloodstream. The scavenger receptor Stabilin-2 (Stab2) is considered a major clearance receptor for HA. Here we report a dramatic elevation in circulating HA levels in Stab2-deficient mice without any overt phenotype. Surprisingly, the metastasis of B16F10 melanoma cells to the lungs was markedly suppressed in the Stab2-deficient mice, whereas cell proliferation was not affected. Furthermore, administration of an anti-Stab2 antibody in Stab2+ mice elevated serum HA levels and prevented the metastasis of melanoma to the lung, and also suppressed spontaneous metastasis of mammary tumor and human breast tumor cells inoculated in the mammary gland. Administration of the antibody or high-dose HA in mice blocked the lodging of melanoma cells to the lungs. Furthermore, HA at high concentrations inhibited the rolling/tethering of B16 cells to lung endothelial cells. These results suggest that blocking Stab2 function prevents tumor metastasis by elevating circulating HA levels. Stab2 may be a potential target in antitumor therapy.
The Risk-Return Trade-Off Among Equity Factors

We examine the risk-return trade-off among several long-short equity factors. We obtain a positive trade-off for the operating profitability (RMW) and investment (CMA) factors, and a negative relationship for the market (RM) and momentum factors. The estimated trade-off subsists by accounting for the covariance with RM, and tends to be stronger in recessions. The out-of-sample forecasting power (of factor variances for own returns) is economically significant for both RMW and CMA. This suggests that the risk-return trade-off is stronger within segments of the stock market than for the whole. The factor risk-return trade-off is weaker among most international stock markets.
Essays on Internet economics: customer reviews, advertising, and technology adoption

This dissertation consists of three chapters on the economics of the Internet. The first chapter begins with presenting the advertising spending patterns of US local restaurants that have different ratings on Yelp.com. Rating information on Yelp includes display ratings and review distributions. The Yelp’s rounding algorithm creates a discontinuity in display ratings. Therefore, I use a regression discontinuity design to identify the effect of a higher display rating on local restaurants’ advertising spendings. I find a significantly negative effect of display rating for highly-rated restaurants on advertising. However, when the display rating is constant between two steps, the relationship between local restaurant advertising spending and average rating is significantly positive. The second chapter uses a game-theoretic model to analyze competing firms’ advertising and pricing decisions. Here customer reviews are available and firms may build up loyal customer bases. I find that highly-rated firms are more likely to advertise more, i.e., online reviews complement advertising. Comparative static results can explain the results found in the first chapter. Intuitively, when the capacity of a local business becomes limited, a jump in the display rating will reduce the complementary effect of online reviews on advertising. I also analyze an extension of the model, where an entrant and an incumbent interact. I find that customer reviews undo the “fat-cat” effect of a large incumbent with lots of loyal customers. The third chapter proposes a new explanation for adoption failure or delay in markets with network effects. In the model, consumers and software providers play a dynamic adoption game.
Achieving sustainable performance in natural monopolies - the role of strategic planning in the European air navigation services

Air transport is a major enabler for growth. The European economy needs an air transport system technologically advanced, safe, cost efficient and environmentally friendly. These attributes are often conceived by the public as part of the airlines' realm. However there is the important business of the air navigation services (ANS) dealing with its air traffic services (ATS) part with the safe, orderly and expeditious flow of the air traffic (Regulation (EC) No 549/2004 of the European Parliament and of the Council). The paper tests and confirms that the business of air traffic services (ATS) is a natural monopoly. Its performance affects considerably the overall air transport sector and as all monopolies needs to be regulated appropriately. The current situation in Europe, the related developments in improving the performance of the service as well as the risks associated with designed top-down measures are briefly analyzed. The paper proposes a novel approach to achieving and securing the sustainability of the "right" performance and avoiding the risks of over-regulation. The proposed novel approach has been tried in a number of cases.
Overlapped Handwriting Input on Mobile Phones

In this paper, we propose an overlapped handwriting input method on handheld devices, which allows users to write continuously without breaks on a single size-restricted writing area. 2 issues have been considered during the implementation of the overlapped input method: previous characters on the background may obstruct the clear viewing of current character and the messy overlapped handwriting is difficult to be segmented and recognized. In our method, a quick segmentation method based on an artificial neural network is used to tackle the first problem and a novel system is implemented to recognize the messy handwriting based on the output of an isolated character recognition engine and a language model. The recognition rate for Chinese characters is about 92.5\% for a testing database containing GB2312 Chinese characters and other frequently used symbols. The positive feedbacks from testers have also confirmed the validity of the proposed method.
Technological Advance and the Labour Share of National Income in the European Union

This article tests the hypothesis that member states of the EU have been experiencing a declining share of labour income due to technological advance. It discusses factors that lead to the fall in the labour share, including technological advance, which is a tendency found in the capitalist system. We also identify the undesirable effects of a fall in the labour shares. The results of an econometric test conducted in our study, based on a labour demand equation that was derived from the CES production function, confirm the hypothesis that technological progress negatively affected the labour share of income, everything else remaining constant. This finding has important implications for EU Member States, namely that some form of policy intervention would seem to be necessary, as technological progress could lead to a continuing fall in the share of labour income if left to its own devices.
Platelet concentrations and platelet-associated IgG in greyhounds.

BACKGROUND Greyhounds have lower platelet concentrations (PC) than dogs of other breeds have. No underlying cause has been investigated. HYPOTHESIS We hypothesized that Greyhounds have lower mean PC because of breed variation, not immune-mediated causes. Our secondary hypothesis was that PC is dependent on the method of analysis. ANIMALS Sixty privately owned Greyhounds in Kansas. METHODS Blood samples were collected into evacuated glass tubes containing ethylenediamine tetraacetic acid (EDTA). Blood smears were evaluated for platelet clumps. All 60 samples had PC determined by manual, impedance, and buffy coat analyzer methods. Results of the 60 samples were compared with results of samples with (n = 25) and without (n = 35) clumps, and with control dogs. Platelets were assayed for the presence of surface-associated antigen (PSAIgG) by direct immunofluorescence. RESULTS The mean PC was below that of the control dogs for the impedance method (P < .001). No significant difference in PC was detected between analysis methods or between samples with or without platelet clumps. Three of 60 (5%) of the Greyhounds had PC between 50,000 and 100,000/microL with impedance analysis; no samples had < 100,000/microL via buffy coat analysis. PSAIgG was not identified in any samples. CONCLUSIONS AND CLINICAL IMPORTANCE The mean Greyhound PC for the impedance method was below the reference interval for control dogs but was not significantly different from PC determined by other methods. An immune-mediated cause for the lower PC was unlikely because no samples had PSAIgG. The decreased PC is most consistent with breed variation. As only 0-5% of samples, depending on analysis method, had PC < 100,000/microL, a Greyhound with a PC < 100,000/microL is not necessarily consistent with breed variation, thus diagnostic testing is indicated.