Miracle-dz/UniFAR-FTUs huggingface dataset:
Silencing of mitochondrial Lon protease deeply impairs mitochondrial proteome and function in colon cancer cells

Lon is a nuclear‐encoded, mitochondrial protease that assists protein folding, degrades oxidized/damaged proteins, and participates in maintaining mtDNA levels. Here we show that Lon is up‐regulated in several human cancers and that its silencing in RKO colon cancer cells causes profound alterations of mitochondrial proteome and function, and cell death. We silenced Lon in RKO cells by constitutive or inducible expression of Lon shRNA. Lon‐silenced cells displayed altered levels of 39 mitochondrial proteins (26% related to stress response, 14.8% to ribosome assembly, 12.7% to oxidative phosphorylation, 8.5% to Krebs cycle, 6.3% to β‐oxidation, and 14.7% to crista integrity, ketone body catabolism, and mtDNA maintenance), low levels of mtDNA transcripts, and reduced levels of oxidative phosphorylation complexes (with >90% reduction of complex I). Oxygen consumption rate decreased 7.5‐fold in basal conditions, and ATP synthesis dropped from 0.25 ± 0.04 to 0.03 ± 0.001 nmol/mg proteins, in the presence of 2‐deoxy‐D‐glucose. Hydrogen peroxide and mitochondrial superoxide anion levels increased by 3‐ and 1.3‐fold, respectively. Mitochondria appeared fragmented, heterogeneous in size and shape, with dilated cristae, vacuoles, and electrondense inclusions. The triterpenoid 2‐cyano‐3,12‐dioxooleana‐1,9,‐dien‐28‐oic acid, a Lon inhibitor, partially mimics Lon silencing. In summary, Lon is essential for maintaining mitochondrial shape and function, and for survival of RKO cells. —Gibellini, L. , Pinti, M. , Boraldi, F. , Giorgio, V. , Bernardi, P., Bartolomeo, R. , Nasi, M. , De Biasi, S. , Missiroli, S. , Carnevale, G. , Losi, L. , Tesei, A. , Pinton, P., Quaglino, D. , Cossarizza, A. , Silencing of mitochondrial Lon protease deeply impairs mitochondrial proteome and function in colon cancer cells. FASEB J. 28, 5122–5135 (2014). www.fasebj. org
Satellites of LMC-mass dwarfs: close friendships ruined by Milky Way mass haloes

Motivated by the recent discovery of several dwarfs near the Large Magellanic Cloud (LMC), we study the accretion of massive satellites onto Milky Way (MW)/M31-like haloes using the ELVIS suite of N-body simulations. We identify 25 surviving LMC-mass subhaloes, and investigate the lower-mass satellites that were associated with these subhaloes before they fell into the MW/M31 haloes. Typically, 7 per cent of the overall z = 0 satellite population of MW/M31 haloes were in a surviving LMC-group before falling into the MW/M31 halo. This fraction can vary between 1 and 25 per cent, being higher for groups with higher mass and/or more recent infall times. Groups of satellites disperse rapidly in phase space after infall, and their distances and velocities relative to the group centre become statistically similar to the overall satellite population after 4–8 Gyr. We quantify the likelihood that satellites were associated with an LMC-mass group as a function of both distance and velocity relative to the LMC at z = 0. The close proximity in distance of the nine Dark Energy Survey candidate dwarf galaxies to the LMC suggest that ∼2–4 are likely associated with the LMC. Furthermore, if several of these dwarfs are genuine members, then the LMC-group probably fell into the MW very recently, ≲2 Gyr ago. If the connection with the LMC is established with follow-up velocity measurements, these ‘satellites of satellites’ represent prime candidates to study the effects of group pre-processing on lower mass dwarfs.
Alternative asymptotics for cointegration tests in large

Johansen’s (1988, 1991) likelihood ratio test for cointegration rank of a Gaussian VAR depends only on the squared sample canonical correlations between current changes and past levels of a simple transformation of the data. We study the asymptotic behavior of the empirical distribution of those squared canonical correlations when the number of observations and the dimensionality of the VAR diverge to infinity simultaneously and proportionally. We find that the distribution almost surely weakly converges to the so-called Wachter distribution. This finding provides a theoretical explanation for the observed tendency of Johansen’s test to find “spurious cointegration”. It also sheds light on the workings and limitations of the Bartlett correction approach to the overrejection problem. We propose a simple graphical device, similar to the scree plot, for a preliminary assessment of cointegration in high-dimensional VARs.
Detecting Malingered Performance With the Wisconsin Card Sorting Test: A Preliminary Investigation in Traumatic Brain Injury

The present study examined the classification accuracy of four potential Wisconsin Card Sorting Test malingering indicators (Bernard and Suhr formulas and two types of Unique responses). Participants were 89 traumatic brain-injury (TBI) patients assigned to malingering and nonmalingering groups on the basis of the Slick, Sherman, and Iversion (1999) criteria. Individual Sensitivities were greater than . 33 with acceptable Specificity. Combined Sensitivity for two of the indicators was greater than . 60. Overall, this study demonstrated three distinct approaches to the WCST used by probable malingerers. The clinical relevance of these findings and directions for future research are discussed.
Neurocognitive functioning in young high-risk offspring having a parent with bipolar I disorder

High soil bulk density and penetration resistance as an indication of soil compaction affect soil infiltration and runoff. Overgrazed rangelands are under severe erosion risk because of soil compaction. The objective of this study was to determine changes in soil bulk density and penetration resistance in a high altitude rangeland within a 3-month grazing period. A 5-ha rangeland (200 × 250 m) was transected with intervals of 25 × 5 m, and soil penetration resistance was measured at 459 points in the 20-cm surface soil layer on 3 different dates (15 July, 15 August, and 15 September). At each intersection of the 50 × 50 m interval grid system, 30 undisturbed soil samples were taken to determine soil bulk density. Semivariogram and punctual kriging analyses were used to define spatial variability in bulk density and penetration resistance measurements. The results indicated that the mean bulk density did not show a clear trend with grazing intervals and produced values of 0.88, 0.93, and 0.82 g cm-3 for July, August, and September, respectively. Soil penetration resistance was higher than the critical penetration resistance (3 MPa) for root growth at all measurement points. The mean soil penetration resistance increased about 8.5% in August as compared with July, and it was more or less constant in the following month.
Bargaining Power of Suppliers and Buyers, and Accounting Conservatism—Evidence from Chinese Manufacturing Listed Companies

Using the panel data of Chinese manufacturing listed companies from 2003 to 2012, this paper examines the effects of suppliers’ and franchisers’ (buyers’) bargaining power on accounting conservatism. The empirical research proves that there is an inverted U-shape relationship between suppliers’ bargaining power and conditional conservatism, with lower left wing and higher right wing. The relationship between franchisers’ (buyers’) bargaining power and conditional conservatism is not significant. On the contrary, there is a U-shape relationship between suppliers’, franchisers’ (buyers’) bargaining power and unconditional conservatism. The relationship between suppliers’ bargaining power and unconditional conservatism has higher left wing and lower right wing. Our research results explain how strong suppliers and franchisers (buyers) affect companies’ accounting practices in the Chinese context. In the meantime, our results provide support to the contracting explanation for accounting conservatism.
Alveolar Epithelial Type II Cells Induce T Cell Tolerance to Specific Antigen1

The lungs face the immunologic challenge of rapidly eliminating inhaled pathogens while maintaining tolerance to innocuous Ags. A break in this immune homeostasis may result in pulmonary inflammatory diseases, such as allergies or asthma. The observation that alveolar epithelial type II cells (Type II) constitutively express the class II MHC led us to hypothesize that Type II cells play a role in the adaptive immune response. Because Type II cells do not express detectable levels of the costimulatory molecules CD80 and CD86, we propose that Type II cells suppress activation of naive T cells. Purified murine Type II cells were unable to activate T cells to specific Ag or in an alloreactive assay. Although IFN-γ treatment up-regulated class II MHC expression, it did not alter the ability of the Type II cells to activate T cells. Rather, the Type II cells were able to suppress T cells from subsequent activation to specific Ag in an Ag-dependent manner. Priming T cells with Type II cells and Ag resulted in T cells that were suppressed to further activation, even after removal from the Type II cells. Thus, Type II cells of the lung help tolerize T cells to nonpathogenic environmental Ags.
Recovery Kinetics of Knee Flexor and Extensor Strength after a Football Match

We examined the temporal changes of isokinetic strength performance of knee flexor (KF) and extensor (KE) strength after a football match. Players were randomly assigned to a control (N = 14, participated only in measurements and practices) or an experimental group (N = 20, participated also in a football match). Participants trained daily during the two days after the match. Match and training overload was monitored with GPS devices. Venous blood was sampled and muscle damage was assessed pre-match, post-match and at 12h, 36h and 60h post-match. Isometric strength as well as eccentric and concentric peak torque of knee flexors and extensors in both limbs (dominant and non-dominant) were measured on an isokinetic dynamometer at baseline and at 12h, 36h and 60h after the match. Functional (KFecc/KEcon) and conventional (KFcon/KEcon) ratios were then calculated. Only eccentric peak torque of knee flexors declined at 60h after the match in the control group. In the experimental group: a) isometric strength of knee extensors and knee flexors declined (P<0.05) at 12h (both limbs) and 36h (dominant limb only), b) eccentric and concentric peak torque of knee extensors and flexors declined (P<0.05) in both limbs for 36h at 60°/s and for 60h at 180°/s with eccentric peak torque of knee flexors demonstrating a greater (P<0.05) reduction than concentric peak torque, c) strength deterioration was greater (P<0.05) at 180°/s and in dominant limb, d) the functional ratio was more sensitive to match-induced fatigue demonstrating a more prolonged decline. Discriminant and regression analysis revealed that strength deterioration and recovery may be related to the amount of eccentric actions performed during the match and athletes' football-specific conditioning. Our data suggest that recovery kinetics of knee flexor and extensor strength after a football match demonstrate strength, limb and velocity specificity and may depend on match physical overload and players' physical conditioning level.
Programmed Death 1–Mediated T Cell Exhaustion during Visceral Leishmaniasis Impairs Phagocyte Function

Control of Leishmania infantum infection is dependent upon Th1 CD4+ T cells to promote macrophage intracellular clearance of parasites. Deficient CD4+ T cell effector responses during clinical visceral leishmaniasis (VL) are associated with elevated production of IL-10. In the primary domestic reservoir of VL, dogs, we define occurrence of both CD4+ and CD8+ T cell exhaustion as a significant stepwise loss of Ag-specific proliferation and IFN-γ production, corresponding to increasing VL symptoms. Exhaustion was associated with a 4-fold increase in the population of T cells with surface expression of programmed death 1 (PD-1) between control and symptomatic populations. Importantly, exhausted populations of CD8+ T cells and to a lesser extent CD4+ T cells were present prior to onset of clinical VL. VL-exhausted T cells did not undergo significant apoptosis ex vivo after Ag stimulation. Ab block of PD-1 ligand, B7.H1, promoted return of CD4+ and CD8+ T cell function and dramatically increased reactive oxygen species production in cocultured monocyte-derived phagocytes. As a result, these phagocytes had decreased parasite load. To our knowledge, we demonstrate for the first time that pan-T cell, PD-1–mediated, exhaustion during VL influenced macrophage-reactive oxygen intermediate production. Blockade of the PD-1 pathway improved the ability of phagocytes isolated from dogs presenting with clinical VL to clear intracellular parasites. T cell exhaustion during symptomatic canine leishmaniasis has implications for the response to vaccination and therapeutic strategies for control of Leishmania infantum in this important reservoir species.
Measurement of Salivary Cortisol Level for the Diagnosis of Critical Illness–Related Corticosteroid Insufficiency in Children*

Objective: To compare serum total, serum free and salivary cortisol in critically ill children. Design: Prospective observational cohort study. Setting: Tertiary pediatric critical care unit at Ronald McDonald Children’s Hospital at Loyola University Medical Center. Patients: We enrolled 59 patients (4 weeks to 18 years of age) between January 2012 and May 2013. Thirty-four patients were included in the salivary to serum free cortisol correlational analysis. Interventions: Blood and saliva samples were obtained simultaneously within 24 hours of admission between the hours of 6 AM and 12 PM. Salivary cortisol was tested by liquid chromatography/tandem mass spectrometry, serum free cortisol by liquid chromatography/tandem mass spectrometry followed by equilibrium dialysis, and serum total cortisol by liquid chromatography/tandem mass spectrometry. Measurements and Main Results: Salivary and serum free cortisol values from 34 patients had a correlation coefficient (r) of 0.87 (95% CI, 0.75–0.93; p < 0.0001). The total serum and salivary cortisol values had a correlation coefficient (r) of 0.67 (95% CI, 0.42–0.81; p < 0.0001). The total serum and serum free cortisol values had a correlation coefficient (r) of 0.83 (95% CI, 0.69–0.91; p < 0.0001). Conclusions: Serum free and salivary cortisol values correlate in critically ill children. Salivary cortisol can be used as a surrogate for serum free cortisol in critically ill pediatric patients. Salivary cortisol is a cost-effective and less invasive measure of bioavailable cortisol and offers an alternate and accurate method for assessing critical illness–related corticosteroid insufficiency in children.
The comparative virulence for chicks of Salmonella enteritidis phage type 4 isolates and isolates of phage types commonly found in poultry in the United States.

Phage type 4 Salmonella enteritidis has been associated with morbidity and mortality in broiler chickens in the United Kingdom. The recent isolation of this phage type from poultry in the United States has raised concerns about whether the current regulatory approach to S. enteritidis should be modified to consider phage type 4 differently from other phage types. The present study assessed and compared the virulence of phage type 4 S. enteritidis isolates, S. enteritidis isolates of other phage types, and an S. pullorum isolate in both single-comb white leghorn and white Plymouth Rock chicks. The mean incidence of severe illness or death following oral inoculation with phage type 4 S. enteritidis was significantly lower than the incidence associated with S. pullorum inoculation in both lines of chicks. Nevertheless, some individual phage type 4 S. enteritidis isolates caused severe effects at a frequency similar to that of S. pullorum in single-comb white leghorn chicks. In general, severe morbidity or mortality following infection with S. enteritidis isolates of all phage types tested occurred more often in single-comb white leghorn chicks than in white Plymouth Rock chicks. The mean frequency at which chicks were severely affected following inoculation with phage type 4 isolates was significantly higher than the mean for isolates of other phage types. However, in both lines of chicks, some significant differences in virulence were apparent within the set of phage type 4 strains tested. The observed virulence for chicks of recent U.S. poultry isolates of phage type 4 S. enteritidis was similar to that of earlier isolates from various sources, including poultry isolates from the United Kingdom.
Caries experience among 45-54 year olds in Adelaide, South Australia.

BACKGROUND Middle-aged adults are an important focus of dental policy with increasing retention of teeth and use of dental services. The aims of the study were to describe the caries experience of 45-54 year olds by dental visit pattern, dental behaviour, socio-demographics and socio-economic status. METHODS A random sample of 45-54 year olds from Adelaide, South Australia was surveyed by self-complete questionnaire during 2004-2005 with up to four follow-up mailings to non-respondents (n=879, response rate = 43.8 per cent). Oral examinations were performed by calibrated dentists on 709 persons (completion rate = 80.7 per cent). RESULTS The mean number (95% CI) of decayed teeth was 0.39 (0.31-0.47), with 5.25 (4.92-5.58) missing teeth, 11.0 (10.62-11.32) filled teeth, and DMFT was 16.61 (16.21-17.01). Multivariate regressions of caries experience by dental visit pattern, dental behaviour, socio-demographics and socio-economic status found: time since last visit of less than 12 months was related (P < 0.05) to fewer decayed teeth (beta = -0.40), more filled teeth (beta = 1.55) and a higher DMFT (beta = 1.24); a last visit for relief of pain was related to more decayed teeth (beta = 0.56); tooth brushing 8+ times per week was related to fewer decayed (beta = -0.36), and missing teeth (beta = -1.13), and lower DMFT (beta = -1.58); not cleaning between teeth was related to more missing teeth (beta = 0.94); males had fewer missing teeth (beta = -0.76); having a diploma/degree was related to fewer missing teeth (beta = -1.07) and lower DMFT (p = -1.27); card holder status was related to more missing teeth (beta= 1.26); and household income of $80,000+ was related to fewer missing teeth (beta= -0.96) and a lower DMFT (beta= -1.35). CONCLUSIONS Dental visit pattern, dental behaviour, socio-demographics and socio-economic status were all related to caries experience. Overall DMFT was lower for those who brushed more frequently, had higher levels of education and higher household income.
Korean American Storeowners’ Perceived Barriers and Motivators for Implementing a Corner Store-Based Program

Based on substantial formative research, the authors developed and implemented a year-long corner store-based program in East Baltimore focusing on Korean American (KA) stores. To understand acceptability of the intervention by storeowners, the authors examined the motivating factors for program participation, barriers to program implementation, perceived effectiveness of intervention materials, and perceptions about the program. Data collection methods included in-depth interviews with seven corner store owners, field notes by interventionists, and a follow-up survey. Stores varied considerably in terms of owners’ perceptions about the program, supportive atmosphere, and acceptability of intervention strategies. The storeowners who showed strong or moderate support for the program were more likely to sustain the stocking of promoted foods such as cooking spray and baked or low-fat chips after the program was completed as compared to less supportive stores. The level of support and active participation of storeowners can greatly influence the success of corner store-based nutrition interventions.
Model‐based security testing: a taxonomy and systematic classification

Model‐based security testing relies on models to test whether a software system meets its security requirements. It is an active research field of high relevance for industrial applications, with many approaches and notable results published in recent years. This article provides a taxonomy for model‐based security testing approaches. It comprises filter criteria (i.e. model of system security, security model of the environment and explicit test selection criteria) as well as evidence criteria (i.e. maturity of evaluated system, evidence measures and evidence level). The taxonomy is based on a comprehensive analysis of existing classification schemes for model‐based testing and security testing. To demonstrate its adequacy, 119 publications on model‐based security testing are systematically extracted from the five most relevant digital libraries by three researchers and classified according to the defined filter and evidence criteria. On the basis of the classified publications, the article provides an overview of the state of the art in model‐based security testing and discusses promising research directions with regard to security properties, coverage criteria and the feasibility and return on investment of model‐based security testing. Copyright © 2015 John Wiley & Sons, Ltd.
Adherence to treatment and supervision for tuberculosis in a DOTS programme among pastoralists in Uganda.

OBJECTIVE To estimate the levels of adherence to anti-tuberculosis medications and associated risk factors in a pastoral community practising transhumance in North-Eastern Uganda. DESIGN A cross-sectional retrospective study of a cohort of tuberculosis (TB) patients and their community volunteers registered from August 2008 to July 2009. Self-reported data were collected on doses missed, doses not supervised, sociodemographic situation, drug availability, perceived drug side effects and use of the directly observed treatment (DOT) card. Medication adherence was defined as having ingested at least 90% of doses given, and supervision adherence was defined as direct observation of at least 90% of doses ingested. Independent predictors of medication adherence were identified using binary and multivariate logistic regression. RESULTS A total of 126 TB patients and an equal number of community volunteers were enrolled in the study. Medication and supervision adherence were estimated at respectively 72% and 63%. Independent predictors of medication adherence were perceived drug side effects (adjusted odds ratio [aOR] 5.0, 95%CI 1.86-13.6), running out of drugs (aOR 5.97, 95%CI 2.27-15.70) and DOT card not filled in (aOR 6.65, 95%CI 2.08-20.66). CONCLUSION Adherence among pastoralists is less than optimal due to poor institutionalisation of the DOTS strategy in a pastoralist community.