Miracle-dz/UniFAR-FTUs huggingface dataset:
Prohibitin 1 suppresses liver cancer tumorigenesis in mice and human hepatocellular and cholangiocarcinoma cells

Prohibitin 1 (PHB1) is best known as a mitochondrial chaperone, and its role in cancer is conflicting. Mice lacking methionine adenosyltransferase α1 (MATα1) have lower PHB1 expression, and we reported that c‐MYC interacts directly with both proteins. Furthermore, c‐MYC and MATα1 exert opposing effects on liver cancer growth, prompting us to examine the interplay between PHB1, MATα1, and c‐MYC and PHB1's role in liver tumorigenesis. We found that PHB1 is highly expressed in normal hepatocytes and bile duct epithelial cells and down‐regulated in most human hepatocellular carcinoma (HCC) and cholangiocarcinoma (CCA). In HCC and CCA cells, PHB1 expression correlates inversely with growth. PHB1 and MAT1A positively regulate each other's expression, whereas PHB1 negatively regulates the expression of c‐MYC, MAFG, and c‐MAF. Both PHB1 and MATα1 heterodimerize with MAX, bind to the E‐box element, and repress E‐box promoter activity. PHB1 promoter contains a repressive E‐box element and is occupied mainly by MAX, MNT, and MATα1 in nonmalignant cholangiocytes and noncancerous tissues that switched to c‐MYC, c‐MAF, and MAFG in cancer cells and human HCC/CCA. All 8‐month‐old liver‐specific Phb1 knockout mice developed HCC, and one developed CCA. Five‐month‐old Phb1 heterozygotes, but not Phb1 flox mice, developed aberrant bile duct proliferation; and one developed CCA 3.5 months after left and median bile duct ligation. Phb1 heterozygotes had a more profound fall in the expression of glutathione synthetic enzymes and higher hepatic oxidative stress following left and median bile duct ligation. Conclusion: We have identified that PHB1, down‐regulated in most human HCC and CCA, heterodimerizes with MAX to repress the E‐box and positively regulates MAT1A while suppressing c‐MYC, MAFG, and c‐MAF expression; in mice, reduced PHB1 expression predisposes to the development of cholestasis‐induced CCA. (Hepatology 2017;65:1249‐1266).
Mean velocity and temperature profiles in a sheared diabatic turbulent boundary layer

In the atmospheric surface layer, modifications to the logarithmic mean velocity and air temperature profiles induced by thermal stratification or convection are accounted for via stability correction functions ϕm and ϕh, respectively, that vary with the stability parameter ς. These two stability correction functions are presumed to be universal in shape and independent of the surface characteristics. To date, there is no phenomenological theory that explains all the scaling laws in ϕh with ς, how ϕh relates to ϕm, and why ϕh ⩽ ϕm is consistently reported. To develop such a theory, the recently proposed links between the mean velocity profile and the Kolmogorov spectrum of turbulence, which were previously modified to account for the effects of buoyancy, are generalized here to include the mean air temperature profile. The resulting theory explains the observed scaling laws in ϕm and ϕh reported in many field and numerical experiments, predicts their behaviors across a wide range of atmospheric stability .
Analyzing students' software redesign strategies

The design of software is known to be difficult for novice computer scientists. In this paper, we focus on software redesign and on the refactoring necessary to implement a redesign. Redesigning an application aims to improve non-functional aspects such as extensibility, without changing the functionality. Redesign is a complex task, involving knowledge and skills from software design in general and the use of design patterns in particular. This study is part of an educational design research project aiming at developing scaffolding for students' software redesign activities in the form of procedural guidance. We investigated students' strategies and usage of concepts during a software redesign assignment using students' reports and team colllaboration recordings as data sources, thus focusing on the process instead of on the design results, in contrast with existing studies. We identified several difficulties that can serve as starting points for procedural guidance. For instance, students seem to avoid using a structured analysis method. Our findings indicate that students' activities were mainly directed towards the code rather than the design problem.
Oxygen modulates cell death in the proliferating retina

Many factors probably regulate the process of natural cell death during development. It is present in both the early undifferentiated retina and later following differentiation. Melanin production plays a role in regulating retinal development and when it is absent, cell proliferation and death are enhanced. Here we examine the effects of hyperoxia on this process, as oxygen has been shown to reduce cell death among differentiated photoreceptors late in development. However, in this study we examine its effects much earlier in pigmented and albino pigmentation phenotypes, when most cells are still actively dividing and are not committed to a specific fate. Newborn mice were exposed to high oxygen levels for 24 h and then returned to normal air for varying periods and their retinae examined. Hyperoxia had a dramatic effect on the number of dying cells, reducing them by almost 60% in pigmented animals and by over 80% in albinos. Following the return to normal air there was a gradual increase in their number over 360 min back to normal levels in pigmented mice; however, in albinos there was a complete rebound in levels of cell death within 40 min, reflecting the increased metabolic stress present in albino retinae due to their abnormal levels of proliferation. These results highlight the important role played by oxygen during early natural cell death in the retina and reveal the different developmental conditions present in the retinae of the two pigmentation phenotypes examined.
Changes in the Age and Education Profile of Displaced Workers

This analysis of data from the Displaced Workers Surveys suggests that between the periods 1983–87 and 1993–97, although the likelihood of involuntary job loss declined among most age groups, including older workers, it rose for middle-aged and older workers relative to younger workers. Three potential explanations for this shift the authors investigate are changes in educational attainment, changes in the relationship between education and displacement, and industry shifts that had adverse effects on older workers relative to younger workers. The results of the analysis indicate that the relative displacement rate among college graduates increased over time, but there were few significant changes in the relationship between displacement and education within or across age groups. The probability of displacement increased significantly for workers in service-related industries across all age groups. The results do not conclusively indicate why older workers' relative risk of displacement increased but do rule out several possibilities.
Food Security Status and Barriers to Fruit and Vegetable Consumption in Two Economically Deprived Communities of Oakland, California, 2013–2014

Introduction Food security status may moderate how people perceive barriers to fruit and vegetable consumption. This study aimed to 1) describe the association between fruit and vegetable consumption and microbarriers and mezzobarriers to consumption, and 2) test whether these associations differ by food security status. Methods We surveyed adults (n = 531) living in 2 economically deprived communities in Oakland, California, in 2013 and 2014. Multivariate linear regression assessed associations between microbarriers (taste, cost, busyness) and mezzobarriers (produce selection, quality, and purchase ease) and fruit and vegetable consumption, derived from a 26-item dietary screener. Interactions were tested by food security status. Results Respondents consumed a mean 2.4 (standard deviation, 1.5) servings of fruits and vegetables daily; 39% of the sample was food insecure. Being too busy to prepare healthy foods was associated with reduced fruit and vegetable consumption (βbusyness = −0.40; 95% confidence interval [CI], −0.52 to −0.28) among all respondents. Food security moderated the relationship between fruit and vegetable consumption and taste, cost, and perceived ease of purchase of healthy foods. Among the food secure, disliking healthy food taste (βtaste = −0.38; 95% CI, −0.60 to −0.15) and cost (βcost = −0.29; 95% CI, −0.44 to −0.15) concerns were associated with lower consumptions of fruits and vegetables. Mezzobarriers were not significantly associated with consumption in either group. Conclusion Perceived time constraints influenced fruit and vegetable consumption. Taste and cost influenced fruit and vegetable consumption among the food secure and may need to be considered when interpreting analyses that describe dietary intake and designing diet-related interventions.
Epstein-Barr Virus mRNA Export Factor EB 2 Is Essential for Intranuclear Capsid Assembly and Production of gp 350

Most human herpesviruses, including Epstein-Barr virus (EBV), express a protein which functions primarily as an mRNA export factor. Previously, we deleted the gene for the Epstein-Barr virus mRNA export factor EB2 from the EBV genome and then introduced the mutated genome into 293 cells. Using a transcomplementation assay in which ectopic expression of the transcription factor EB1/ZEBRA was sufficient to induce the EBV productive cycle, we showed that Ori-Lyt-dependent replication of the EBV DNA occurs in the absence of EB2, indicating that EB2 is not essential for the expression and export of early mRNAs. However, in the absence of EB2, no infectious viral particles are produced (H. Gruffat, J. Batisse, D. Pich, B. Neuhierl, E. Manet, W. Hammerschmidt, and A. Sergeant, J. Virol. 76:9635–9644, 2002). In this report, we now show that EB2 is essential for the nuclear export of most, but not all, late mRNAs produced from intronless genes that translate into proteins involved in intranuclear capsid assembly and maturation. As a consequence, we show that EB2 is essential for the proper assembly of intranuclear capsids. Interestingly, the late BLLF1 gene contains an intron, and both unspliced and spliced mRNAs must be exported to the cytoplasm to be translated into gp350 and gp220, respectively (M. Hummel, D. A. Thorley-Lawson, and E. Kieff, J. Virol. 49:413–417, 1984). Our results also demonstrate that although BLLF1 spliced mRNAs are exported to the cytoplasm independently of EB2, EB2 is essential for the nuclear export of unspliced BLLF1 mRNA. In the same assay, herpes simplex virus 1 ICP27 completely inhibited the nuclear export of BLLF1 spliced mRNAs whereas unspliced BLLF1 mRNAs were exported, confirming that in a physiological assay, ICP27 inhibits splicing.
Fractional Skin Harvesting: Autologous Skin Grafting without Donor-site Morbidity

Background: Conventional autologous skin grafts are associated with significant donor-site morbidity. This study was conducted to determine feasibility, safety, and efficacy of a new strategy for skin grafting based on harvesting small columns of full-thickness skin with minimal donor-site morbidity. Methods: The swine model was used for this study. Hundreds of full-thickness columns of skin tissue (~700 µm diameter) were harvested using a custom-made harvesting device, and then applied directly to excisional skin wounds. Healing in donor and graft sites was evaluated over 3 months by digital photographic measurement of wound size and blinded, computer-aided evaluation of histological features and compared with control wounds that healed by secondary intention or with conventional split-thickness skin grafts (STSG). Results: After harvesting hundreds of skin columns, the donor sites healed rapidly without scarring. These sites reepithelialized within days and were grossly and histologically indistinguishable from normal skin within 7 weeks. By contrast, STSG donor sites required 2 weeks for reepithelialization and retained scar-like characteristics in epidermal and dermal architecture throughout the experiment. Wounds grafted with skin columns resulted in accelerated reepithelialization compared with ungrafted wounds while avoiding the “fish-net” patterning caused by STSG. Conclusion: Full-thickness columns of skin can be harvested in large quantities with negligible long-term donor-site morbidity, and these columns can be applied directly to skin wounds to enhance wound healing.
Towards Open-Ended 3D Rotation and Shift Invariant Object Detection for Robot Companions

Robot companions need to be able to constantly acquire knowledge about new objects for instance in order to detect them in the environment. This ability is necessary since it is hard to predict what objects the robot may face in the operation phase during development. This paper presents ideas and results on two topics. The first topic is on the design of an open-ended object detection system that uses scale invariant feature key-point descriptors that are trained with a one-class radial basis function support vector machine. Unlike using other classifier-based approaches our method does not assume the number classes to be known a priori. The method is shown to be stable against full 3D rotation of the object relative to the sensor. The second issue in this paper deals with a solution on how to provide new object information to the robot. A modern range imaging sensor in conjunction with a conventional color imaging sensor is used for a first figure-background separation. The experiments presented support the basic statements in this paper. Conclusions are drawn and future work is addressed
Comparative performance analysis of spectral estimation algorithms and computational optimization of a multispectral imaging system for print inspection

We have analyzed the performance of simulated multispectral systems for the spectral recovery of reflectance of printer inks from camera responses, including noise. To estimate reflectance we compared the performance of four algorithms which were not comparatively tested using the same data sets before. The criteria for selection of the algorithms were robustness against noise, amount of data needed as inputs (training set, spectral responsivities) and lacking of use of dimensionality reduction techniques. Three different sensor sets and training sets were used. We analyzed the differences in the spanning of the subspaces found for the three training sets, concluding that the ink reflectances have characteristic features. The best performance was obtained using the kernel and the radial basis function neural-net-based algorithms for the training set composed of printer inks reflectances, whereas for the other two training sets (composed of samples from the ColorChecker DC and Vhrel's reflectances' set) the quality of the recovered samples was more uniform among the algorithms. We also have performed an optimization to choose the best sensor set for the multispectral system with a reduced number of sensors. © 2012 Wiley Periodicals, Inc. Col Res Appl, 39, 16–27, 2014
Post-stimulus endogenous and exogenous oscillations are differentially modulated by task difficulty

We investigate the modulation of post-stimulus endogenous and exogenous oscillations when a visual discrimination is made more difficult. We use exogenous frequency tagging to induce steady-state visually evoked potentials (SSVEP) while subjects perform a face-car discrimination task, the difficulty of which varies on a trial-to-trial basis by varying the noise (phase coherence) in the image. We simultaneously analyze amplitude modulations of the SSVEP and endogenous alpha activity as a function of task difficulty. SSVEP modulation can be viewed as a neural marker of attention toward/away from the primary task, while modulation of post-stimulus alpha is closely related to cortical information processing. We find that as the task becomes more difficult, the amplitude of SSVEP decreases significantly, approximately 250–450 ms post-stimulus. Significant changes in endogenous alpha amplitude follow SSVEP modulation, occurring at approximately 400–700 ms post-stimulus and, unlike the SSVEP, the alpha amplitude is increasingly suppressed as the task becomes less difficult. Our results demonstrate simultaneous measurement of endogenous and exogenous oscillations that are modulated by task difficulty, and that the specific timing of these modulations likely reflects underlying information processing flow during perceptual decision-making.
Genome Signatures of Escherichia coli O157:H7 Isolates from the Bovine Host Reservoir

ABSTRACT Cattle comprise a main reservoir of Shiga toxin-producing Escherichia coli O157:H7 (STEC). The significant differences in host prevalence, transmissibility, and virulence phenotypes among strains from bovine and human sources are of major interest to the public health community and livestock industry. Genomic analysis revealed divergence into three lineages: lineage I and lineage I/II strains are commonly associated with human disease, while lineage II strains are overrepresented in the asymptomatic bovine host reservoir. Growing evidence suggests that genotypic differences between these lineages, such as polymorphisms in Shiga toxin subtypes and synergistically acting virulence factors, are correlated with phenotypic differences in virulence, host ecology, and epidemiology. To assess the genomic plasticity on a genome-wide scale, we have sequenced the whole genome of strain EC869, a bovine-associated E. coli O157:H7 isolate. Comparative phylogenomic analysis of this key isolate enabled us to place accurately bovine lineage II strains within the genetically homogenous E. coli O157:H7 clade. Identification of polymorphic loci that are anchored both in the chromosomal backbone and horizontally acquired regions allowed us to associate bovine genotypes with altered virulence phenotypes and host prevalence. This study catalogued numerous novel lineage II-specific genome signatures, some of which appear to be associated intimately with the altered pathogenic potential and niche adaptation within the bovine rumen. The presented extended list of polymorphic markers is valuable in the development of a robust typing system critical for forensic, diagnostic, and epidemiological studies of this emerging human pathogen.
Smad7 in T cells drives T helper 1 responses in multiple sclerosis and experimental autoimmune encephalomyelitis

Autoreactive CD4+ T lymphocytes play a vital role in the pathogenesis of multiple sclerosis and its animal model, experimental autoimmune encephalomyelitis. Since the discovery of T helper 17 cells, there is an ongoing debate whether T helper 1, T helper 17 or both subtypes of T lymphocytes are important for the initiation of autoimmune neuroinflammation. We examined peripheral blood CD4+ cells from patients with active and stable relapsing–remitting multiple sclerosis, and used mice with conditional deletion or over-expression of the transforming growth factor-β inhibitor Smad7, to delineate the role of Smad7 in T cell differentiation and autoimmune neuroinflammation. We found that Smad7 is up-regulated in peripheral CD4+ cells from patients with multiple sclerosis during relapse but not remission, and that expression of Smad7 strongly correlates with T-bet, a transcription factor defining T helper 1 responses. Concordantly, mice with transgenic over-expression of Smad7 in T cells developed an enhanced disease course during experimental autoimmune encephalomyelitis, accompanied by elevated infiltration of inflammatory cells and T helper 1 responses in the central nervous system. On the contrary, mice with a T cell-specific deletion of Smad7 had reduced disease and central nervous system inflammation. Lack of Smad7 in T cells blunted T cell proliferation and T helper 1 responses in the periphery but left T helper 17 responses unaltered. Furthermore, frequencies of regulatory T cells were increased in the central nervous system of mice with a T cell-specific deletion and reduced in mice with a T cell-specific over-expression of Smad7. Downstream effects of transforming growth factor-β on in vitro differentiation of naïve T cells to T helper 1, T helper 17 and regulatory T cell phenotypes were enhanced in T cells lacking Smad7. Finally, Smad7 was induced during T helper 1 differentiation and inhibited during T helper 17 differentiation. Taken together, the level of Smad7 in T cells determines T helper 1 polarization and regulates inflammatory cellular responses. Since a Smad7 deletion in T cells leads to immunosuppression, Smad7 may be a potential new therapeutic target in multiple sclerosis.
Correlation of quinolone MIC and inhibition of DNA, RNA, and protein synthesis and induction of the SOS response in Escherichia coli

The effects of nalidixic acid and four fluoroquinolones on DNA, RNA, and protein synthesis in the presence and absence of 20 mg of chloramphenicol per liter were examined by comparing the killing kinetics, MIC, morphological response, and maximum concentration to induce recA in Escherichia coli. All agents demonstrated paradoxical killing kinetics, in that above an optimum concentration the rate of bactericidal action was slower. Filamentation of E. coli AB1157 was observed with all quinolones up to the optimum bactericidal concentration. Addition of chloramphenicol reduced the bactericidal activity, inhibited filamentation, and abolished recA induction, but it had no effect on DNA synthesis inhibition by any of the agents. Excellent correlation was obtained between the concentration required to inhibit DNA synthesis by 50%, the MIC, the maximum concentration to induce recA, and the optimum bactericidal concentration. Evidence from this study and previously published data suggest that the primary mechanism of action of quinolones is independent of the SOS response and does not require active protein synthesis; however, induction of recA and SOS responses is consequential and enhances cell death.
The Ages of Elliptical Galaxies from Mid-Infrared Emission

The mid-infrared (10-20 μm) luminosity of elliptical galaxies is dominated by the integrated emission from circumstellar dust in red giant stars. As a single stellar population evolves, the rate of dusty mass loss from red giant stars decreases with time, so the mid-infrared luminosity should also decline with stellar age. To seek such a correlation, we have used archival Infrared Space Observatory (ISO) observations to determine surface brightness profiles and central fluxes at 15 μm in 17 early-type galaxies for which stellar ages have been determined from optical spectral indices. The radial surface brightness distributions at 15 μm generally follow the stellar de Vaucouleurs profile, as expected. We find that the surface brightness ratio μ15 μm/μI band is systematically higher in elliptical galaxies with ages ≲5 Gyr and in galaxies that exhibit evidence of recent mergers. Within the accuracy of our observations, μ15 μm/μI band shows no age dependence for ages ≳5 Gyr. The corresponding flux ratios F15 μm/FI band within apertures scaled to the effective radius (Re/8) are proportional to the μ15 μm/μI band ratios at larger galactic radii, indicating that no 15 μm emission is detected from central dust clouds visible in optical images in some of our sample galaxies. Emission at 15 μm is observed in noncentral massive clouds of dust and cold gas in NGC 1316, an elliptical galaxy that is thought to have had a recent merger. Recent Spitzer Space Telescope data also indicate the presence of polycyclic aromatic hydrocarbon (PAH) emission at 8 μm. Several ellipticals have extended regions of 15 μm emission that have no obvious counterparts at other frequencies.