Miracle-dz/UniFAR-FTUs huggingface dataset:
What Evidence Is There for the Homology of Protein-Protein Interactions?

The notion that sequence homology implies functional similarity underlies much of computational biology. In the case of protein-protein interactions, an interaction can be inferred between two proteins on the basis that sequence-similar proteins have been observed to interact. The use of transferred interactions is common, but the legitimacy of such inferred interactions is not clear. Here we investigate transferred interactions and whether data incompleteness explains the lack of evidence found for them. Using definitions of homology associated with functional annotation transfer, we estimate that conservation rates of interactions are low even after taking interactome incompleteness into account. For example, at a blastp -value threshold of , we estimate the conservation rate to be about between S. cerevisiae and H. sapiens. Our method also produces estimates of interactome sizes (which are similar to those previously proposed). Using our estimates of interaction conservation we estimate the rate at which protein-protein interactions are lost across species. To our knowledge, this is the first such study based on large-scale data. Previous work has suggested that interactions transferred within species are more reliable than interactions transferred across species. By controlling for factors that are specific to within-species interaction prediction, we propose that the transfer of interactions within species might be less reliable than transfers between species. Protein-protein interactions appear to be very rarely conserved unless very high sequence similarity is observed. Consequently, inferred interactions should be used with care.
Characteristics of Early Oropharyngeal Dysphagia in Patients with Multiple System Atrophy

Background/Aims: Dysphagia, a symptom of multiple system atrophy (MSA), is a major clinical concern. In this study, we investigate the characteristics of early oropharyngeal dysphagia (OD) in patients with MSA, and the differences between MSA subtypes. Methods: Patients enrolled in the study had previously been diagnosed with MSA at the clinic of the Department of Neurology, and had been referred for a videofluoroscopic swallowing study (VFSS), between 2005 and 2014, to check for dysphagia. The clinical characteristics and VFSS findings were analyzed and compared between the MSA subtypes. Results: This study enrolled 59 patients with MSA (24 men; 31 with MSA-P, 21 with MSA-C, and 7 with MSA-PC). Dysphagia symptoms were mostly limited to aspiration symptoms (90.48%) in patients with MSA-C, while difficulty in swallowing, increased mealtime, and drooling were frequent in those with MSA-P. The most common VFSS finding amongst patients was vallecular residue (n = 53, 89.8%), followed by penetration/aspiration (n = 40, 67.8%), and coating of the pharyngeal wall (n = 39, 66.1%). Comparison analysis between subtypes showed that apraxia and vallecular residue were more frequent and severe in MSA-P than in MSA-C (p = 0.033 and p = 0.010, respectively). Conclusion: Understanding early OD characteristics in patients with MSA and the differences between MSA subtypes could be helpful in managing dysphagia in patients with MSA. Several dysphagia symptoms similar to those of Parkinson disease were frequently observed in MSA-P, but not in MSA-C. A follow-up study is needed to elucidate the natural course of OD in MSA patients and the difference between MSA subtypes.
Effect of capsaicin on substrate oxidation and weight maintenance after modest body-weight loss in human subjects

The aim of the present study was to investigate whether capsaicin assists weight maintenance by limiting weight regain after weight loss of 5 to 10%. In this randomized double-blind placebo-controlled study, ninety-one moderately overweight subjects were randomly assigned to an intensive group that underwent all the measurements, and an extensive group that underwent the same measurements except the metabolism measurements. After a 4-week very-low-energy diet (VLED) intervention, a 3-month weight-maintenance period followed. During weight maintenance, subjects were divided into a capsaicin (135 mg capsaicin/d) and a placebo group. Body mass was measured before and after the VLED and after 1, 2 and 3 months of weight maintenance. The mean body-mass loss during the VLED was 6·6 (sd 2·0) kg (7·8 (sd 1·8)% initial body mass), and was not different between the subsequent treatment and placebo group. During weight maintenance, mean % regain during treatment was not significantly different compared with placebo (33·3 (sd 35·7) v. 19·2 (sd 41·8)%, P=0·09). RQ was significantly less increased during weight maintenance in the treatment group compared with placebo (0·04 (sd 0·06) v. 0·07 (sd 0·05), P < 0·05), indicating a relatively more sustained fat oxidation. Fat oxidation (g/h) after weight maintenance was higher in the capsaicin group compared with placebo (4·2 (sd 1·1) v. 3·5 (sd 0·9), P < 0·05). These results indicate that capsaicin treatment caused sustained fat oxidation during weight maintenance compared with placebo. However, capsaicin treatment has no limiting effect on 3-month weight regain after modest weight loss.
Nicarbazin OvoControl G Bait Reduces Hatchability of Eggs Laid by Resident Canada Geese in Oregon

Abstract Expanding populations of resident Canada geese (Branta canadensis) are resulting in increased conflicts with humans. Nonlethal and humane means are needed for managing Canada goose flocks at a variety of sites, including golf courses, industrial parks, government sites, and city parks. Decreased egg production and hatching are side effects of nicarbazin, a veterinary drug used to treat coccidiosis in chickens. Capitalizing on these effects, we developed nicarbazin as a reproductive inhibitor for Canada geese and conducted a field efficacy study. We recruited study sites in 2002 and 2003. Following laboratory testing, we conducted a field efficacy trial of nicarbazin for reducing the hatchability of Canada goose eggs in spring 2004 in Oregon, USA. The study began in February 2004 at 10 sites in Oregon, with 2 control and 3 treated sites on each side of the Cascades. We fed bait daily to resident Canada geese for approximately 6 weeks. We located and monitored nests until hatching or ≥5 days beyond the expected hatching date to determine hatchability. We completed data collection in May 2004. Geese consumed 8,000 kg of bait, with 5,100 kg of OvoControl G® (Innolytics, LLC, Rancho Santa Fe, CA) 2,500-ppm nicarbazin bait consumed among 6 treated sites and 2,900 kg of untreated bait consumed among 4 control sites. We monitored 63 nests at treated sites and 46 nests at control sites to determine hatching success of eggs. There was a 62% reduction in the percentage of nests with 100% hatchability at treated sites as compared to controls. There was a 93% increase in the percentage of nests at treated sites with 0% hatchability as compared to nests with no eggs hatching at control sites. Hatchability from treated sites versus control sites was reduced 36% (F = 5.72, P = 0.0622). We submitted results from this study to support Environmental Protection Agency registration of nicarbazin as a reproductive inhibitor for use in Canada geese. We have shown that treatment of resident Canada geese with OvoControl G 2,500-ppm nicarbazin bait by licensed, trained applicators immediately prior to and during the breeding season can reduce hatchability of eggs laid by treated geese, thereby reducing recruitment of goslings into problem resident Canada goose populations.
The default mode network and salience network in schizophrenia

The default mode network (DMN) is a network in the brain associated with activity during the so-called resting state, also called a “task negative” network. This network has been shown to decrease in activity when engaged in a task (i.e. cognitive task), and increases when at rest. Recent studies have found that the DMN in patients with schizophrenia have shown tendency for a failure of deactivation of the DMN when engaging in various tasks in the scanner. We wanted to explore if the DMN in fact has a tendency for failure of deactivation. In addition to this, we wanted to investigate whether the salience network (SN) has a role in regulating the “switching” between the DMN and task positive networks. Here, data from n= 129 controls and n= 89 patients with DSMIV schizophrenia which had undergone a working memory paradigm, were analysed with independent component analysis and dual regression approach. We compared the two wm conditions in all three components across groups, followed by comparing components between the HC and SZ groups. We found no significant group differences in the wm conditions when comparing components across groups. However, an interesting pattern of correlation was found within groups between the ADMN and PDMN. We could not confirm a SN contribution to DMN dysfunction, but our findings did not dismiss this possibility.
Food Consumption Tracker with Health Advises by Food Photos and Labels

Obesity, overweight, allergy and additives related disease are common health problems worldwide nowadays. Many of these problems directly relate to food consumption and dietary habits. Hence keep tracking food intake and knowing the consumed food ingredients are essential for a healthy life. However, tracking daily consumption is tedious, and seldom be kept for long. This paper presented a mobile solution to leverage these problems and provide health advices on food consumption adaptively. Users can simply take photos of their meals as they usually do for dietary record. Our system then automatically recognizes the food type and provides useful statistics for analysis. We can know the packaged food better with barcode scanning and text recognition of food labels. All captured information provide basis for proper alert on allergen, suggestions to achieve health and balanced dietary. A preliminary study reveals that this is welcomed by most users who care about their dietary.
Mutational Analysis of Eggplant Latent Viroid RNA Circularization by the Eggplant tRNA Ligase in Escherichia coli

Eggplant latent viroid (ELVd) is a relatively small non-coding circular RNA that induces asymptomatic infections in eggplants (Solanum melongena L.). Like other viroid species that belong to the family Avsunviroidae, ELVd contains hammerhead ribozymes in the strands of both polarities that self-cleave RNAs producing terminal 5′-hydroxyl and 2′,3′-cyclic phosphodiester groups. Available experimental data indicate that ELVd replicates in the chloroplasts of infected cells through a symmetric rolling-circle mechanism, in which RNA circularization is catalyzed by the chloroplastic isoform of the tRNA ligase. In this work, a mutational analysis was performed to gain insight into the sequence and structural requirements of the tRNA ligase-mediated circularization of ELVd RNAs. In the predicted minimum free energy conformation of the monomeric linear ELVd RNA intermediate of plus (+) polarity, the ligation site is located in the lower part of an opened internal loop, which is present in a quasi-rod-like structure that occupies the center of the molecule. The mutations analyzed herein consisted of punctual nucleotide substitutions and deletions surrounding the ligation site on the upper and lower strands of the ELVd quasi-double-stranded structure. Computational predictions of the mutated ELVd conformations indicated different degrees of distortions compared to the minimum free energy conformation of the wild-type ELVd linear monomer of + polarity. When these mutant RNAs were expressed in Escherichia coli, they were all circularized by the eggplant tRNA ligase with approximately the same efficiency as the wild-type ELVd, except for those that directly affected the ribozyme domain. These results suggest that the viroid ribozyme domains, in addition to self-cleavage, are also involved in the tRNA ligase-mediated circularization of the monomeric linear replication intermediates.
Chip-Integrated Geometric Metasurface As a Novel Platform for Directional Coupling and Polarization Sorting by Spin–Orbit Interaction

The focus of the research in metasurfaces has mainly been on the manipulation of the electromagnetic waves in free space during the past few years, which generally require thousands of subwavelength meta-atoms or even more. In this paper, we propose a conceptually new approach that chip-integrated metasurface can behave as a promising compact platform to control the propagation of guided waves when it is integrated with optical waveguide. As a proof of the concept, geometric metasurfaces consisting of only seven rotating anisotropic antennas, both metallic and dielectric, are integrated with silicon-on-insulator waveguide. Benefiting from the geometric phase shift stemming from spin–orbit interaction in metasurfaces, linearly gradient wavefront is generated along the waveguide, which is equivalent to introduce a unidirectional effective wavevector and thus leads to directional coupling. Inspired by the spin dependent gradient wavefront, opposite light flow is excited in the integrated waveguide by switching the handedness of incidence, which may provide a potential pathway to integrated polarization sorters and switchers.
Effects of the direct thrombin inhibitor dabigatran and its orally active prodrug, dabigatran etexilate, on thrombus formation and bleeding time in rats

Summary Dabigatran is a reversible direct, selective thrombin inhibitor, undergoing clinical development as its orally active prodrug, dabigatran etexilate. The objective of this trial was to assess the antithrombotic and anticoagulant effects of dabigatran and dabigatran etexilate in a rat model of venous thrombosis. In order to do this a modifiedWessler model was used to assess the antithrombotic and anticoagulant effects of intravenous (i.v.) dabigatran and oral dabigatran etexilate administration. In addition, a rat tail bleeding time model was used to investigate the antihemostatic effect of dabigatran.The study demonstrated that bolus administration of dabigatran (0.01–0.1 mg/kg) reduced thrombus formation dose-dependently,with an ED50 (50% of the effective dose) of 0.033 mg/kg and complete inhibition at 0.1 mg/kg. By comparison,ED50 values for heparin (0.03–0.3 mg/kg),hirudin (0.01–0.5 mg/kg) and melagatran (0.1–0.5 mg/kg) were 0.07, 0.15 and 0.12 mg/kg, respectively. Oral administration of dabigatran etexilate (5–30 mg/kg) inhibited thrombus formation in a dose- and time-dependent manner, with maximum inhibition within 30 min of pretreatment, suggesting a rapid onset of action. Following i.v. administration of dabigatran (0.1–1.0 mg/kg), a statistically significant prolongation of bleeding time was observed at doses at least 15- and 5-fold greater than ED50 and ED100 (100% of the effective dose) doses, respectively; there was no significant increase in bleeding tendency at the maximum therapeutically effective dose (0.1 mg/kg). It can be concluded that dabigatran and its oral prodrug, dabigatran etexilate, show promise in the management of thromboembolic disease.
Antimicrobial Photodynamic Therapy: Antimicrobial Efficacy in a Periodontal Biofilm Model and Flow Cytometric Evaluation of Cytoplasmic Membrane Damage

Citation: Cieplik F, Steinwachs V-S, Muehler D, Hiller K-A, Thurnheer T, Belibasakis GN, Buchalla W and Maisch T (2018) Phenalen-1-one-Mediated Antimicrobial Photodynamic Therapy: Antimicrobial Efficacy in a Periodontal Biofilm Model and Flow Cytometric Evaluation of Cytoplasmic Membrane Damage. Front. Microbiol. 9:688. doi: 10.3389/fmicb.2018. 00688 Phenalen-1-one-Mediated Antimicrobial Photodynamic Therapy: Antimicrobial Efficacy in a Periodontal Biofilm Model and Flow Cytometric Evaluation of Cytoplasmic Membrane Damage
Measurement of photoluminescence from a twisted-nematic liquid crystal/dye cell for an application in an energy-harvesting display

One can convert a Luminescent Solar Concentrator (LSC) to an energy-harvesting display by scanning a laser beam on it. By incorporating a guest-host system of liquid crystal (LC) and dye materials in an LSC, the power of photoluminescence (PL) utilized for either display or energy-harvesting can be adjusted to the changes in ambient lighting conditions. We have measured basic characteristics of an LC/dye cell with twisted-nematic (TN) alignment. These are absorption of the laser light, PL radiation pattern, contrast of luminance, spreading of the PL generated by a narrow laser beam, and their dependencies on the bias. The results are similar to those of the LC/dye cell with antiparallel (AP) alignment with the following exceptions. First, absorption by the TN cell depends on the bias for both polarization components of the excitation light, while the AP cell exhibits a bias dependency only for the component polarized along the alignment direction. Second, the PL from the TN cell is mostly polarized along the alignment direction on the exit side of the cell while the PL from the AP cell is mostly polarized along its alignment direction. These observations can be attributed to the fact that the polarization plane of a linearly polarized light rotates as it propagated the TN-LC layer. For both AP and TN cells, low-intensity PL is observed from the whole cell surfaces. This can degrade the contrast of a displayed image. Bias application to the cell suppresses this effect.
A Traditional Herbal Formula Xianlinggubao for Pain Control and Function Improvement in Patients with Knee and Hand Osteoarthritis: A Multicenter, Randomized, Open-Label, Controlled Trial

Evidence of efficacy of a traditional herbal formula Xianlinggubao (XLGB) for treatment of osteoarthritis (OA) is limited. The present study was designed to evaluate the efficacy of XLGB in the management of patients with knee and hand OA. This was a multicenter, stratified, open-label, randomized controlled trial conducted at six centers in China. People aged 40 or above, diagnosed with OA of the knee or hand, were randomly assigned to the XLGB treatment group or watchful waiting control group. Main outcome measures were the changes in the numeric pain rating scales (NPRS) and the Western Ontario and McMaster Universities Arthritis Index (WOMAC) or the Australian/Canadian Osteoarthritis Hand Index (AUSCAN) scores, from baseline to 6 months. In total 534 patients (272 to XLGB and 262 to control group) received interventions. Participants in the XLGB group exhibited significant improvement in NPRS (P < 0.001) and WOMAC score (P < 0.001) or AUSCAN score (P < 0.001) compared to control group. Treatment with XLGB at current regime significantly reduced pain and improved function of the knee and hand in patients with OA over a 6-month period, implying that XLGB could be suggested as an alternative treatment for patients with knee or hand OA.
Young Adult Gay and Bisexual Men’s Stigma Experiences and Mental Health: An 8-Year Longitudinal Study

This study investigated longitudinal trajectories of stigma (i.e., enacted, anticipated, internalized, concealed); stress-sensitive mental health disorder symptoms (i.e., depression, social anxiety); and their associations across 8 annual assessments in a sample of 128 young gay and bisexual U.S. university students. All forms of stigma significantly decreased over time, while depressive symptoms remained stable and social anxiety symptoms significantly increased. Men from higher socioeconomic backgrounds experienced quicker reductions in anticipated stigma, compared to men from lower socioeconomic backgrounds. More self-described feminine men experienced quicker reductions in concealment, compared to more self-described masculine men. Enacted stigma demonstrated contemporaneous associations with depression and social anxiety across 8 years; and anticipated stigma and internalized stigma demonstrated contemporaneous associations with social anxiety across 8 years. Enacted stigma was more strongly associated with depressive symptoms among men who reported greater masculinity compared to those who reported greater femininity. Findings are discussed in terms of common developmental influences across early sexual orientation identity formation, including gay and bisexual young men’s resilience to stigma-based stress; the transition from college; and the rapidly changing social climate surrounding sexual minority individuals. Findings suggest the need for future longitudinal examinations of stigma and mental health among sexual minorities that utilize multiple age cohorts to determine the relative contribution of cohort-specific versus common maturational factors influencing the mental health of this population.
Influence of Corn Hybrid Traits and Processing Method on Nutrient Digestibility1

ABSTRACT Two experiments were conducted to determine the effects of corn hybrid and processing method on the site and extent of nutrient digestibility and ruminal fermentation. Treatments consisted of 2 processing methods, dry-rolled corn (DRC) and high-moisture corn (HMC), and 3 hybrids, H-8562 (1), 33P67 (2), and H-9230 (3), in a 2 × 3 factorial arrangement. In Exp. 1, six ruminally cannulated crossbred steers (436 ± 8 kg) were used in a 6 × 6 Latin square design. Total tract DM, OM, and starch digestibility (STD) were greater ( P P P = 0.14) among hybrids but was greater ( P P P P
Effect of retrograded rice on weight control, gut function, and lipid concentrations in rats

The effects of retrograded rice on body weight gain, gut functions, and hypolipidemic actions in rats were examined. When the retrograded rice was produced by repetitive heating and cooling cycles, it contained significantly higher amounts of resistant starch (13.9 ± 0.98%) than is found in common rice (9.1 ± 1.02%) (P < 0.05). Sprague-Dawley rats were fed either common rice powder or retrograded rice powder, and mean body weight gain was significantly lower in the retrograded rice group (P < 0.05). The liver weight of the retrograded rice group (14.5 ± 0.5 g) was significantly lower than that of the common rice group (17.1 ± 0.3 g, P < 0.05). However, the weights of other organs, such as the kidney, spleen, thymus, and epididymal fat pad were not significantly affected by rice feeding. Intestinal transit time tended to be lower in rats fed retrograded rice when compared to rats fed the common rice, but the difference was not significant. The retrograded rice diet significantly increased stool output when compared to that in the common rice powder diet (P < 0.05), whereas fecal moisture content (%) was significantly higher in the retrograded rice group (23.3 ± 1.2) than that in the common rice group (19.1 ± 1.2) (P < 0.05). The retrograded rice group had significantly lower plasma cholesterol (P < 0.05), liver cholesterol (P < 0.05), and triacylglycerol contents in adipose tissue (P < 0.05) when compared to those in the common rice group. In conclusion, retrograded rice had higher resistant starch levels compared with those of common rice powder, and it lowered body weight gain and improved lipid profiles and gut function in rats.