Miracle-dz/UniFAR-FTUs huggingface dataset:
Oral administration of fermented wild ginseng ameliorates DSS-induced acute colitis by inhibiting NF-κB signaling and protects intestinal epithelial barrier

Ginseng has been widely used for therapeutic and preventive purposes for thousands of years. However, orally administered ginseng has very low bioavailability and absorption in the intestine. Therefore, fermented ginseng was developed to enhance the beneficial effects of ginseng in the intestine. In this study, we investigated the molecular mechanisms underlying the anti-inflammatory activity of fermented wild ginseng (FWG). We found that FWG significantly alleviated the severity of colitis in a dextran sodium sulfate (DSS)-induced colitis mouse model, and decreased expression level of pro-inflammatory cytokines in colonic tissue. Moreover, we observed that FWG suppressed the infiltration of macrophages in DSS-induced colitis. FWG also attenuated the transcriptional activity of nuclear factor-κB (NF-κB) by reducing the translocation of NF-κB into the nucleus. Our data indicate that FWG contains anti-inflammatory activity via NF-κB inactivation and could be useful for treating colitis. [BMB Reports 2015; 48(7): 419-425]
The role of interpersonal control and need thwarting in the prediction of ill-being in sport : a self-determination theory approach

Utilizing self-determination theory (SDT; Deci & Ryan, 1985; Ryan & Deci, 2002) as a framework, the current thesis aimed to explore the social conditions that satisfy versus thwart psychological needs and, in turn, impact upon psychological and physiological functioning and well/ill-being in the sport context. Although research guided by SDT has explored the conditions (i.e., autonomy support) and psychological processes (i.e., need satisfaction) that foster healthy development and effective functioning in athletes, very little research has considered the potential role of interpersonal control and psychological need thwarting in the development of athlete ill-being. To address these limitations, this thesis begins by outlining the development and initial validation of two new questionnaire measures: the Controlling Coach Behaviors Scale (Chapter 2) and the Psychological Need Thwarting Scale (Chapter 3). The new questionnaire measures were subsequently utilized in three studies, reported in Chapter 4. Across all three samples, need satisfaction was better predicted by autonomy-supportive behaviors, and need thwarting was better predicted by coach control. In turn, athletes’ perceptions of need satisfaction predicted positive outcomes (i.e., vitality and positive affect) whereas need thwarting consistently better predicted maladaptive outcomes (i.e., disordered eating, burnout, depression, negative affect, physical symptoms, and perturbed physiological functioning). Such novel findings indicate that controlling interpersonal behaviors and psychological need thwarting represent important aspects of the SDT framework which must be further researched (both in sport and in other life domains) if the development of diminished functioning and ill-being is to be properly understood.
The joint effects of kin, multilevel selection and indirect genetic effects on response to genetic selection

Kin and levels‐of‐selection models are common approaches for modelling social evolution. Indirect genetic effect (IGE) models represent a different approach, specifying social effects on trait values rather than fitness. We investigate the joint effect of relatedness, multilevel selection and IGEs on response to selection. We present a measure for the degree of multilevel selection, which is the natural partner of relatedness in expressions for response. Response depends on both relatedness and the degree of multilevel selection, rather than only one or the other factor. Moreover, response is symmetric in relatedness and the degree of multilevel selection, indicating that both factors have exactly the same effect. Without IGEs, the key parameter is the product of relatedness and the degree of multilevel selection. With IGEs, however, multilevel selection without relatedness can explain evolution of social traits. Thus, next to relatedness and multilevel selection, IGEs are a key element in the genetical theory of social evolution.
Measures of maturation in early fossil hominins: events at the first transition from australopiths to early Homo

An important question in palaeoanthropology is whether, among the australopiths and the first fossil hominins attributed to early Homo, there was a shift towards a more prolonged period of growth that can be distinguished from that of the living great apes and whether between the end of weaning and the beginning of puberty there was a slow period of growth as there is in modern humans. Evidence for the pace of growth in early fossil hominins comes from preserved tooth microstructure. A record of incremental growth in enamel and dentine persists, which allows us to reconstruct tooth growth and compare key measures of dental maturation with modern humans and living great apes. Despite their diverse diets and way of life, it is currently difficult to identify any clear differences in the timing of dental development among living great apes, australopiths and the earliest hominins attributed to the genus Homo. There is, however, limited evidence that some early hominins may have attained a greater proportion of their body mass and stature relatively earlier in the growth period than is typical of modern humans today. This article is part of the themed issue ‘Major transitions in human evolution’.
Condensation patterns of prophase/prometaphase chromosome are correlated with H4K5 histone acetylation and genomic DNA contents in plants

Mitotic prophase chromosome condensation plays an essential role in nuclear division being therefore regulated by highly conserved mechanisms. However, degrees of chromatin condensation in prophase-prometaphase cells may vary along the chromosomes resulting in specific condensation patterns. We examined different condensation patterns (CPs) of prophase and prometaphase chromosomes and investigated their relationship with genome size and distribution of histone H4 acetylated at lysine 5 (H4K5ac) in 17 plant species. Our results showed that most species with small genomes (2C < 5 pg) (Arachis pusilla, Bixa orellana, Costus spiralis, Eleutherine bulbosa, Indigofera campestris, Phaseolus lunatus, P. vulgaris, Poncirus trifoliata, and Solanum lycopersicum) displayed prophase chromosomes with late condensing terminal regions that were highly enriched in H4K5ac, and early condensing regions with apparently non-acetylated proximal chromatin. The species with large genomes (Allium cepa, Callisia repens, Araucaria angustifolia and Nothoscordum pulchellum) displayed uniformly condensed and acetylated prophase/prometaphase chromosomes. Three species with small genomes (Eleocharis geniculata, Rhynchospora pubera, and R. tenuis) displayed CP and H4K5ac labeling patterns similar to species with large genomes, whereas a forth species (Emilia sonchifolia) exhibited a gradual chromosome labeling, being more acetylated in the terminal regions and less acetylated in the proximal ones. The nucleolus organizer chromatin was the only chromosomal region that in prometaphase or metaphase could be hyperacetylated, hypoacetylated or non-acetylated, depending on the species. Our data indicate that the CP of a plant chromosome complement is influenced but not exclusively determined by nuclear and chromosomal DNA contents, whereas the CP of individual chromosomes is clearly correlated with H4K5ac distribution.
Direct versus indirect comparisons: A summary of the evidence

Objectives: The aim of this study was to provide a comprehensive summary and interpretation of the current evidence on the use and validity of statistical methods to conduct indirect comparisons of treatment effects. Methods: A narrative review was conducted. Results: Well-conducted methodological studies provide good evidence that adjusted indirect comparisons can lead to results similar to those from direct comparisons. The internal validity of several statistical methods to conduct indirect comparisons, therefore, has been established. Meta-regression, logistic regression, or adjusted indirect comparisons should be the methods of first choice. Unadjusted indirect comparisons are always unacceptable. Deciding whether to combine direct and indirect evidence will be a matter of informed judgment based on the similarities and dissimilarities of populations and interventions. Unverifiable assumptions with respect to the similarity of compared studies and low power are serious limitations of indirect comparisons. Conclusions: In the absence of sufficient head-to-head evidence, adjusted indirect comparisons can be viewed as additional analytical tools to determine the comparative efficacy and effectiveness of competing interventions. Researchers who use indirect comparisons need to keep the limitations in mind.
Sucrose Monoester Micelles Size Determined by Fluorescence Correlation Spectroscopy (FCS)

One of the several uses of sucrose detergents, as well as other micelle forming detergents, is the solubilization of different membrane proteins. Accurate knowledge of the micelle properties, including size and shape, are needed to optimize the surfactant conditions for protein purification and membrane characterization. We synthesized sucrose esters having different numbers of methylene subunits on the substituent to correlate the number of methylene groups with the size of the corresponding micelles. We used Fluorescence Correlation Spectroscopy (FCS) and two photon excitation to determine the translational D of the micelles and calculate their corresponding hydrodynamic radius, Rh. As a fluorescent probe we used LAURDAN (6-dodecanoyl-2-dimethylaminonaphthalene), a dye highly fluorescent when integrated in the micelle and non-fluorescent in aqueous media. We found a linear correlation between the size of the tail and the hydrodynamic radius of the micelle for the series of detergents measured.
Using dynamic programming to segment star shape based on human perception and optimization formulation

Objects existed in the world are usually composed of a finite number of primitive components. Itpsilas always beneficial to decompose these objects into basic components when facing the indexing, recognition, or retrieval issues. In this work we intended to devise an algorithm to effectively and efficiently decompose 2D projections of objects into primitive components. This decomposition process is important in different application domains, such as 3D object recognition, human behavior analysis, and content-based image retrieval.
Experimental Evaluation of Congestion Avoidance

The Internet is currently undergoing a significant change. The majority of Internet transfers have historically occurred between wired network devices. The popularity of WiFi, combined with the uptake of smartphones and tablets, has changed this assumption and the majority of Internet connections will soon utilise a wireless link. Congestion avoidance controls the rate at which packets leave a TCP sender. This research re-evaluates different congestion avoidance mechanisms over real world wired and wireless links. This paper does not assert that present mechanisms are poor, nor that wireless has never been a consideration, but that the switch to a mobile and wireless majority necessitates a review, with wireless characteristics at the forefront of design considerations. The results of this study show that TCP Cubic and TCP Hybla perform similarly and generally outperform Veno and Westwood in both wired and wireless scenarios. All tested algorithms featured large delays in 3G links. The results suggest that queuing on the 3G links added between 370ms and 570ms of delay. It is suggested that additional research into congestion avoidance and buffering mechanisms over wireless links is needed.
End-effector robust trajectory tracking control for flexible robot manipulators

This work proposes a robust control strategy for end-effector trajectory tracking of flexible robot manipulators in the presence of parametric uncertainties and dynamic modeling errors. Using an ideal manifold, the desired performance of the system is described in terms of vibration damping and end-effector flexural error compensating. The control law is derived based on the estimated dynamics such that the motion of the system would converge and remain to the ideal manifold for the idea case that the parametric uncertainties and modeling errors can be ignored. To achieve the robustness of the system, the robust control scheme is developed and added into the control system. Stability of the whole control system is investigated using the Lyapunov stability theory. Simulations are carried out to illustrate the effectiveness of the proposed control method.
Metalloproteinases MMP-9, MMP-2 and their tissue inhibitors TIMP-1, TIMP-2 in peripheral transbronchial lung biopsies of patients with sarcoidosis.

INTRODUCTION The imbalance between metalloproteinases (MMPs) and their tissue inhibitors TIMPs) may be involved in the pathogenesis of lung sarcoidosis, a granulomatous inflammatory disease which may lead to lung fibrosis. OBJECTIVES The aim of the study was to verify whether the expression of MMP-9, MMP-2, TIMP-1, and TIMP-2 in peripheral lung biopsies of patients with sarcoidosis correlate with lung function tests, radiological pattern, and bronchoalveolar lavage (BAL) cells. We compared the expression of MMPs and TIMPs between patients with sarcoid-positive vs. - negative biopsy and fibrosing vs. non-fibrosing high-resolution computed tomography (HRCT)pattern. PATIENTS AND METHODS We examined patients with histologically proven stage II and III sarcoidosis (n = 17). Immunohistochemistry with antibodies against the studied molecules was performed in the lung and bronchial tissue specimens obtained from transbronchial lung biopsies. The radiological pattern was evaluated based on HRCT. The total cell number and percentage of cells were calculated in the BAL samples. RESULTS MMPs and TIMPs were present in the cells of sarcoid granuloma, and were more prevalent in the parenchyma than in the bronchi. We found no correlation between MMP-9, MMP-2, TIMP-1, TIMP-2 and HRCT pattern or BAL cells. There were inverse associations between MMP-9 and FEV1 (% predicted), and also between MMP-2 and maximal expiratory flow 25-75% (L and % predicted) in patients with sarcoidosis diagnosed by transbronchial lung biopsy. There were no differences in the measured parameters between patients with and without fibrotic changes and between those with negative vs. positive lung biopsy results. CONCLUSIONS Our study provides an indirect evidence for a potential involvement of MMPs/TIMPs in the sarcoid inflammation of the distal airways.
Peritoneal phosphate clearance is influenced by peritoneal dialysis modality, independent of peritoneal transport characteristics.

BACKGROUND AND OBJECTIVES Hyperphosphatemia is an independent risk factor for mortality in ESRD, but factors regulating phosphate clearance on peritoneal dialysis (PD) are incompletely understood. The objective of this study was to test the hypothesis that peritoneal phosphate clearance is better with continuous ambulatory PD (CAPD) as compared with continuous cyclic PD (CCPD) after adjusting for membrane transport status. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS In this cross-sectional and retrospective study, measurements of peritoneal phosphate clearance of 129 prevalent PD patients were reviewed. Patients were divided according to membrane transport status (high, high average, low average-low categories) and PD modality (CAPD or CCPD). RESULTS Among high transporters, peritoneal phosphate clearances were comparable in both modalities. However, treatment with CAPD was associated with increased peritoneal phosphate clearance compared with CCPD among high-average transporters (42.4 +/- 11.4 versus 36.4 +/- 8.3 L/wk/1.73 m(2), P = 0.01), and low-average-low transporters (35.6 +/- 5.9 versus 28.9 +/- 11 L/wk/1.73 m(2), P = 0.034). On multivariate linear regression, PD modality, membrane transport category, and peritoneal creatinine clearance, but not Kt/V urea, were independently associated with peritoneal phosphate clearance. CONCLUSIONS Peritoneal phosphate clearance is determined by PD modality and membrane transport category, suggesting that PD regimes with longer dwell times may help control hyperphosphatemia in lower transporters.
Altered Pressure‐Natriuresis Relationship in Young Spontaneously Hypertensive Rats

In the present study, the pressure-natriuretic responses of 3- to 5- and 6- to 9-week-old spontaneously hypertensive rats (SHR) and Wistar-Kyoto rats (WKY) were characterized to determine whether the relationship between sodium excretion and renal perfusion pressure is altered during the development of hypertension. Differences in the neural tone and renal hormone levels in SHR and WKY were minimized by denervating the kidney and fixing plasma concentrations of aldosterone, vasopressin, norepinephrine, and cortisol by intravenous infusion. Renal perfusion pressure was varied using adjustable occluders on the lower aorta. The slopes of the relationships between sodium excretion and renal perfusion pressure were not significantly different in 3- to 5-weekold SHR and WKY (0.31 ± 0.05 vs 0.42 ± 0.06 μ.Eq/min/g kidney weight); however, the v-intercept of this relationship was significantly shifted to the right by 15 mm Hg in SHR compared to WKY. Blood pressure was moderately elevated even in the 3- to 5-week-old SHR in comparison to WKY (98 ± 5 vs 81 ± 6 mm Hg). As the degree of hypertension became more severe, the slope of the pressurenatriuresis relationship became significantly lower in 6- to 9-week-old SHR compared to the corresponding slope observed in age-matched WKY (0.16 ± 0.02 vs 0.31 ± 0.04 ju, Eq/min/g kidney weight). These results indicate that the relationship between sodium excretion and renal perfusion pressure is altered even in very young SHR. Thus, the resetting of kidney function occurs very early and may be necessary for the development of hypertension in SHR.
Helicobacter pylori–host cell interactions mediated by type IV secretion

Helicobacter pylori is a human‐specific gastric pathogen that colonizes over half the world's population. Infection with this bacterium is associated with a spectrum of gastric pathologies ranging from mild gastritis to peptic ulcers and gastric cancer. A strong predictor of severe disease outcome is infection with a bacterial strain harbouring the cag (cytotoxin associated gene) pathogenicity island (PAI), a 40 kb stretch of DNA that encodes homologues of several components of a type IV secretion system (TFSS). One gene within the cag PAI, cagA, has been shown to encode a substrate for the TFSS which is translocated into host cells and causes multiple changes in host cell signalling. Here we review recent advances in the characterization of type IV secretion, the activities of CagA and CagA‐independent effects of the TFSS, which are contributing to our understanding of H. pylori pathogenesis.
The Evolution and Structure Prediction of Coiled Coils across All Genomes

Coiled coils are α-helical interactions found in many natural proteins. Various sequence-based coiled-coil predictors are available, but key issues remain: oligomeric state and protein–protein interface prediction and extension to all genomes. We present SpiriCoil (http://supfam.org/ SUPERFAMILY/spiricoil), which is based on a novel approach to the coiled-coil prediction problem for coiled coils that fall into known superfamilies: hundreds of hidden Markov models representing coiled-coil-containing domain families. Using whole domains gives the advantage that sequences flanking the coiled coils help. SpiriCoil performs at least as well as existing methods at detecting coiled coils and significantly advances the state of the art for oligomer state prediction. SpiriCoil has been run on over 16 million sequences, including all completely sequenced genomes (more than 1200), and a resulting Web interface supplies data downloads, alignments, scores, oligomeric state classifications, three-dimensional homology models and visualisation. This has allowed, for the first time, a genomewide analysis of coiled-coil evolution. We found that coiled coils have arisen independently de novo well over a hundred times, and these are observed in 16 different oligomeric states. Coiled coils in almost all oligomeric states were present in the last universal common ancestor of life. The vast majority of occasions that individual coiled coils have arisen de novo were before the last universal common ancestor of life; we do, however, observe scattered instances throughout subsequent evolutionary history, mostly in the formation of the eukaryote superkingdom. Coiled coils do not change their oligomeric state over evolution and did not evolve from the rearrangement of existing helices in proteins; coiled coils were forged in unison with the fold of the whole protein. Introduction The ability to rapidly sequence DNA has led to an explosion in the amount of sequence data available for partial and whole genomes. As a result, the field of genomics, with its various subfields, has
Effects of Alarms on Control of Robot Teams

Annunciator driven supervisory control (ADSC) is a widely used technique for directing human attention to control systems otherwise beyond their capabilities. ADSC requires associating abnormal parameter values with alarms in such a way that operator attention can be directed toward the involved subsystems or conditions. This is hard to achieve in multirobot control because it is difficult to distinguish abnormal conditions for states of a robot team. For largely independent tasks such as foraging, however, self-reflection can serve as a basis for alerting the operator to abnormalities of individual robots. While the search for targets remains unalarmed the resulting system approximates ADSC. The described experiment compares a control condition in which operators perform a multirobot urban search and rescue (USAR) task without alarms with ADSC (freely annunciated) and with a decision aid that limits operator workload by showing only the top alarm. No differences were found in area searched or victims found, however, operators in the freely annunciated condition were faster in detecting both the annunciated failures and victims entering their cameras’ fields of view.
Novel Carotenoid Oxidase Involved in Biosynthesis of 4,4′-Diapolycopene Dialdehyde

ABSTRACT Biosynthesis of C30 carotenoids is relatively restricted in nature but has been described in Staphylococcus and in methylotrophic bacteria. We report here identification of a novel gene (crtNb) involved in conversion of 4,4′-diapolycopene to 4,4′-diapolycopene aldehyde. An aldehyde dehydrogenase gene (ald) responsible for the subsequent oxidation of 4,4′-diapolycopene aldehyde to 4,4′-diapolycopene acid was also identified in Methylomonas. CrtNb has significant sequence homology with diapophytoene desaturases (CrtN). However, data from knockout of crtNb and expression of crtNb in Escherichia coli indicated that CrtNb is not a desaturase but rather a novel carotenoid oxidase catalyzing oxidation of the terminal methyl group(s) of 4,4′-diaponeurosporene and 4,4′-diapolycopene to the corresponding terminal aldehyde. It has moderate to low activity on neurosporene and lycopene and no activity on β-carotene or ζ-carotene. Using a combination of C30 carotenoid synthesis genes from Staphylococcus and Methylomonas, 4,4′-diapolycopene dialdehyde was produced in E. coli as the predominant carotenoid. This C30 dialdehyde is a dark-reddish purple pigment that may have potential uses in foods and cosmetics.