Miracle-dz/UniFAR-FTUs huggingface dataset:
Aberrant Upregulation of Astroglial Ceramide Potentiates Oligodendrocyte Injury

Oligodendroglial injury is a pathological hallmark of many human white matter diseases, including multiple sclerosis (MS) and periventricular leukomalacia (PVL). Critical regulatory mechanisms of oligodendroglia destruction, however, remain incompletely understood. Ceramide, a bioactive sphingolipid pivotal to sphingolipid metabolism pathways, regulates cell death in response to diverse stimuli and has been implicated in neurodegenerative disorders. We report here that ceramide accumulates in reactive astrocytes in active lesions of MS and PVL, as well as in animal models of demyelination. Serine palmitoyltransferase, the rate‐limiting enzyme for ceramide de novo biosynthesis, was consistently upregulated in reactive astrocytes in the cuprizone mouse model of demyelination. Mass spectrometry confirmed the upregulation of specific ceramides during demyelination, and revealed a concomitant increase of sphingosine and a suppression of sphingosine‐1‐phosphate, a potent signaling molecule with key roles in cell survival and mitogenesis. Importantly, this altered sphingolipid metabolism during demyelination was restored upon active remyelination. In culture, ceramide acted synergistically with tumor necrosis factor, leading to apoptotic death of oligodendroglia in an astrocyte‐dependent manner. Taken together, our findings implicate that disturbed sphingolipid pathways in reactive astrocytes may indirectly contribute to oligodendroglial injury in cerebral white matter disorders.
Isotopic segregation between sympatric seabird species increases with nutritional stress

Dietary segregation is essential for the coexistence of closely related species of animals. However, little is known about how changes in availability of food resources might affect trophic interactions of wild animals breeding in sympatry. Here, we examined how interannual variations in relative food availability (as reflected in blood levels of stress hormone corticosterone, CORT) affect food partitioning (assessed via a comparison of stable isotope δ15N and δ13C ratios of blood) between the common murre (Uria aalge) and thick-billed murre (Uria lomvia), breeding on a single colony in the Bering Sea. During a 6-year study, CORT varied among years but not between species, whereas stable isotope ratios varied among years and between species. Isotopic distance between species increased with increasing CORT. These results indicate that, when food was not limiting, both species relied on similar food resources. As foraging conditions deteriorated, murres diverged in their diets. We conclude that the degree of dietary segregation between Uria spp. varies with changes in the availability of food and is greatest during food shortages.
Nitrogen and energy balance in growing mink (Mustela vison) fed different levels of bacterial protein meal produced with natural gas

Abstract The objective of this study was to estimate the effect of increasing the dietary content of bacterial protein meal (BPM) on energy and protein metabolism in growing mink kits. Sixteen male mink kits of the standard brown genotype were randomly fed one of four diets: A control (Diet I) based on high-quality fish meal, and three experimental diets in which 20% (Diet II), 40% (Diet III) and 60% (Diet IV) of the digested nitrogen (DN) was replaced with BPM. Nitrogen balance and respiration experiments (indirect calorimetry) were carried out when the animals were approximately 9.5, 14.5, 17.5, 23.5 and 28.5 weeks of age. The apparent digestibility of crude protein and energy decreased significantly with increasing dietary BPM. The retained nitrogen was 0.45, 0.54, 0.52 and 0.40 g/kg0.75 on Diets I, II, III and IV, respectively, the observed differences between diets being non-significant (p = 0.06). Heat production (HE) was between 645 and 665 kJ/kg0.75 on all diets (p = 0.78). Retained energy (RE) was approximately 150 – 160 kJ/kg0.75 on Diets I to III, whereas it was −11 kJ/kg0.75 on Diet IV, the differences being significant (p < 0.001). A lower feed intake and apparent digestibility of energy caused the negative RE on Diet IV. The amount of HE from oxidation of protein decreased from 32.7% on Diet I to 26.6% on Diet IV, and oxidation of fat increased from 53.8% on Diet I to 63.5% Diet IV. In conclusion, protein and energy metabolism remained unaffected when up to 40% of DN was derived from BPM.
Learning from 6,000 projects: lightweight cross-project anomaly detection

Real production code contains lots of knowledge - on the domain, on the architecture, and on the environment. How can we leverage this knowledge in new projects? Using a novel lightweight source code parser, we have mined more than 6,000 open source Linux projects (totaling 200,000,000 lines of code) to obtain 16,000,000 temporal properties reflecting normal interface usage. New projects can be checked against these rules to detect anomalies - that is, code that deviates from the wisdom of the crowds. In a sample of 20 projects, ~25% of the top-ranked anomalies uncovered actual code smells or defects.
A new role for Rab GTPases during early mitotic stages

A recent study revealed new roles for the Rab11 GTPase during mitosis. Rab11 is involved in recycling endosome localization to mitotic spindle poles via dynein-mediated transport. This process is in contrast to Golgi membranes, which disperse in mitosis and do not appear to directly contribute to mitotic functions. Rab11-depletion prevents recycling endosome organization at spindle poles, delays mitotic progression, and disrupts spindle pole protein recruitment, astral microtubule organization, and mitotic spindle orientation. However, Rab11 is not the only endocytic and/or trafficking protein that regulates mitotic progression. Clathrin and two small GTPases (Rab6A’, Rab5) play key roles in spindle organization and function. In this commentary, we discuss the roles of all these canonical endocytic and membrane trafficking proteins during mitosis and speculate on possible cross-communication between them and their molecular pathways that ensure faithful progression through mitosis.
Categorization in Macaca fascicularis.

KANTHI ARUM WIDAYATI. Categorization in Macaca fascicularis. Supervised by BAMBANG SURYOBROTO, AKICHIKA MIKAMI, ACHMAD FARAJALLAH. Categorization is an ability to group individuals or events into different classes mediated by conceptualized mental images. There are several levels of categorization and within a taxonomy the levels are nested. At the most concrete level of categorization, all or most members of the category shared common physical attributes that differ from other categories. The higher the level of category, the fewer common attributes between members of the group. In addition to humans, the ability to categorize has also been proposed in animals. One example of categorization in animal is species discrimination. Using matching-tosample task, present experiment tested ability of the long-tailed macaque (Macaca fascicularis) in discriminating dichotomous-stimuli of different animals. The species has been shown to be able to see photos as representations of real object so I used facial photos of humans and animals for the stimuli. First, I tested their ability to classify humans and macaques into separate group. Second, I tested their ability to discriminate their conspecific from other macaques. And the last, I tested whether the subjects were able to discriminate non-human animals from humans. In all of these experiments I found that the subjects showed high performance in categorizing objects, even when I discarded details of visual informations, such as color and local shapes. The ability to identify objects with reduced representation of physical properties means the subjects were able to generalize attributes of members of the group. This would indicate that the subjects created a higher level abstraction. On the other hand, in discriminating intrageneric macaque species I found that they were able to extract uniqueness of each species. More over, I also found that the subjects were able to put photos of non-human animals that shared very few similarities in physical percepts into one group. I suggested that the subjects could create a more abstract concept based on non-percepts relations as a basis to put the objects into one category. Thus, I concluded that M. fascicularis were able to perform multiple levels of categorizations.
Identification of Differentially Methylated Genes in Normal Prostate Tissues from African American and Caucasian Men

Purpose: Aberrant DNA methylation changes are common somatic alterations in prostate carcinogenesis. We examined the methylation status of six genes in prostate tissue specimens from African American (AA) and Caucasian (Cau) males. Experimental Design: We used pyrosequencing to quantitatively measure the methylation status of GSTP1, AR, RARβ2, SPARC, TIMP3, and NKX2-5. Real-time PCR was used to determine gene expression, and gene reactivation was analyzed by 5-aza-2′-deoxycytidine and/or trichostatin A treatment. Results: Statistical analysis showed significantly higher methylation in the prostate cancer tissue samples in comparison with matched normal samples for GSTP1 (P = 0.0001 for AA; P = 0.0008 for Cau), RARβ2 (P < 0.001 for AA and Cau), SPARC (P < 0.0001 for AA and Cau), TIMP3 (P < 0.0001 for AA and Cau), and NKX2-5 (P < 0.0001 for AA; P = 0.003 for Cau). Overall, we observed significant differences (P < 0.05) in the methylation level for all genes, except GSTP1, in the AA samples in comparison with the Cau samples. Furthermore, regression analysis revealed significantly higher methylation for NKX2-5 (P = 0.008) and TIMP3 (P = 0.039) in normal prostate tissue samples from AA in comparison with Cau, and a statistically significant association of methylation with age for NKX2-5 (P = 0.03) after adjusting for race. Conclusion: Our findings show higher methylation of several genes in prostate tissue samples from AA in comparison with Cau and may potentially contribute to the racial differences that are observed in prostate cancer pathogenesis. Clin Cancer Res; 16(14); 3539–47. ©2010 AACR.
Ecological momentary assessment of Purging Disorder

Purging Disorder (PD) is characterized by purging after normal or small amounts of food among individuals who are not underweight. Several studies indicate that PD is associated with distress and impairment, underscoring the need for intervention. However, little is known about factors that trigger and maintain purging in PD. This study examined antecedents and consequences of purging using Ecological Momentary Assessment (EMA), a design that involved repeated assessments of current psychological states in participants’ natural environments. Women with PD (N = 24) were recruited from the community to make multiple daily ratings of affect, shape/weight concerns, violation of dietary rules, and stomach discomfort using random-, interval-, and eventcontingent recordings over a two-week period. Multilevel model analyses were used to examine between-day differences (purge versus non-purge day) and within-day changes in psychological variables relative to purging behavior. Results supported study hypotheses that negative affect and shape/weight concerns would be higher and positive affect would be lower on days when participants purged compared to days they did not purge. In addition, antecedent analyses supported within-day increases in negative affect, shape/weight concerns, and stomach discomfort prior to purging; however, only changes in positive affect and shape/weight concerns on purge days differed from naturallyoccurring changes observed on non-purge days. For consequence analyses, negative affect, shape/weight concerns, and stomach discomfort decreased following purging on purge days, and trajectories of change were significantly different from non-purge days. Finally, exploratory analyses suggested that lower levels of impulsivity enhanced associations between antecedent affect and purging. These data are crucial to understand why women with PD purge after consuming normal or small amounts of food and may point to specific targets for the development of effective interventions.
How should COPD patients exercise during respiratory rehabilitation? Comparison of exercise modalities and intensities to treat skeletal muscle dysfunction

Background: Physical exercise is an important component of respiratory rehabilitation because it reverses skeletal muscle dysfunction, a clinically important manifestation of COPD associated with reduced health-related quality of life (HRQL) and survival. However, there is controversy regarding the components of the optimal exercise protocol. A study was undertaken to systematically evaluate and summarise randomised controlled trials (RCTs) comparing different exercise protocols for COPD patients. Methods: Six electronic databases, congress proceedings and bibliographies of included studies were searched without imposing language restrictions. Two reviewers independently screened all records and extracted data on study samples, interventions and methodological characteristics of included studies. Results: The methodological quality of the 15 included RCTs was low to moderate. Strength exercise led to larger improvements of HRQL than endurance exercise (weighted mean difference for Chronic Respiratory Questionnaire 0.27, 95% CI 0.02 to 0.52). Interval exercise seems to be of similar effectiveness as continuous exercise, but there are few data on clinically relevant outcomes. One small RCT which included patients with mild COPD compared the effect of high and low intensity exercise (at 80% and 40% of the maximum exercise capacity, respectively) and found larger physiological training effects from high intensity exercise. Conclusions: Strength exercise should be routinely incorporated in respiratory rehabilitation. There is insufficient evidence to recommend high intensity exercise for COPD patients and investigators should conduct larger high quality trials to evaluate exercise intensities in patients with moderate to severe COPD.
pH-Dependent Antimicrobial Properties of Copper Oxide Nanoparticles in Staphylococcus aureus

The antimicrobial properties of CuO nanoparticles have been investigated, but the underlying mechanisms of toxicity remain the subject of debate. Here, we show that CuO nanoparticles exhibit significant toxicity at pH 5 against four different Staphylococcus aureus (S. aureus) strains, including Newman, SA113, USA300, and ATCC6538. At this pH, but not at pH 6 and 7, 5 mM CuO nanoparticles effectively caused reduction of SA113 and Newman cells and caused at least 2 log reduction, whereas 20 mM killed most strains but not USA300. At 5 mM, the nanoparticles were also found to dramatically decrease reductase activity in SA113, Newman, and ATCC6538 cells, but not USA300 cells. In addition, analysis of X-ray absorption near-edge structure and extended X-ray absorption fine structure confirmed that S. aureus cells exposed to CuO nanoparticles contain CuO, indicating that Cu2+ ions released from nanoparticles penetrate bacterial cells and are subsequently oxidized intracellularly to CuO at mildly acidic pH. The CuO nanoparticles were more soluble at pH 5 than at pH 6 and 7. Taken together, the data conclusively show that the toxicity of CuO nanoparticles in mildly acidic pH is caused by Cu2+ release, and that USA300 is more resistant to CuO nanoparticles (NPs) than the other three strains.
Relationship between exports, imports, and economic growth in France: evidence from cointegration analysis and Granger causality with using geostatistical models

This paper introduces a new way of investigating linear and nonlinear Granger causality between exports, imports and economic growth in France over the period 1961-2006 with using geostatistical models (kiriging and inverse distance weighting). Geostatistical methods are the ordinary methods for forecasting the locations and making map in water engineerig, environment, environmental pollution, mining, ecology, geology and geography. Although, this is the first time which geostatistics knowledge is used for economic analyzes. In classical econometrics there do not exist any estimator which have the capability to find the best functional form in the estimation. Geostatistical models investigate simultaneous linear and various nonlinear types of causality test, which cause to decrease the effects of choosing functional form in autoregressive model. This approach imitates the Granger definition and structure but improve it to have better ability to investigate nonlinear causality. Results of both VEC and Improved-VEC (with geostatistical methods) are similar and show existance of long run unidirectional causality from exports and imports to economic growth. However the F-statistic of improved-VEC is larger than VEC indicating that there are some exponential and spherical functions in the VEC structure instead of the linear form.
MicroRNAs and metastasis-related gene expression in Egyptian breast cancer patients.

AIM AND BACKGROUND MicroRNAs (miRNAs) are a class of naturally occurring small noncoding RNAs that regulate gene expression, cell growth, differentiation and apoptosis by targeting mRNAs for translational repression or cleavage. The present study was conducted to study miRNAs in Egyptian breast cancer (BC) and their relation to metastasis, tumor invasion and apoptosis in addition to their association with the ER and PR statuses. METHODS Real Time RT-PCR was performed to identify the miRNA expression level of eight miRNAs and eight metastatic-related genes in 40 breast cancer samples and their adjacent non-neoplastic tissues. The expression levels of each miRNA relative to U6 RNA were determined. Also, miRNA expression profiles of the BC and their corresponding ANT were evaluated. RESULTS The BC patients showed an up-regulation in miRNAs (mir-155, mir-10, mir-21 and mir-373) with an upregulation in MMP2, MMp9 and VEGF genes. We found down regulation in mir-17p, mir-126, mir-335, mir-30b and also TIMP3, TMP1 and PDCD4 genes in the cancer tissue compared to the adjacent non-neoplastic tissues. Mir -10b, mir -21, mir-155 and mir373 and the metastatic genes MMP2, MMP9 and VEGF were significantly associated with an increase in tumor size (P<0.05). No significant difference was observed between any of the studied miRNAs regarding lymph node metastasis. Mir-21 was significantly over-expressed in ER-/PR- cases. CONCLUSION Specific miRNAs (mir-10, mir-21, mir-155, mir-373, mir-30b, mir-126, mir-17p, mir-335) are associated with tumor metastasis and other clinical characteristics for BC, facilitating identification of individuals who are at risk.
Contribution of quorum sensing to the virulence of Pseudomonas aeruginosa in pressure ulcer infection in rats

The impact of quorum sensing (QS) in in vivo models of infection has been widely investigated, but there are no descriptions for ischemic wound infection. To explore the role of QS in Pseudomonas aeruginosa in the establishment of ischemic wound infection, we challenged a pressure ulcer model in rats with the PAO‐1, PAO‐1 derivatives ΔlasIΔrhlI and ΔlasRΔrhlR strains, which cannot induce the virulence factor under QS control, thus the reduced tissue destruction was expended in these mutant strains. However unexpectedly, on postwounding day 3, the inflammatory responses in the three groups were similarly severe and the numbers of bacteria in tissue samples did not differ among the three strains. Biofilm formation was immature in QS‐deficient strains, defined by the absence of dense bacterial aggregates and extracellular polymeric substance, which was confirmed by scanning electron microscopy. The Pseudomonas aeruginosa QS signal, acylated homoserine lactone, was only quantified from wound samples in the PAO‐1 group. The swimming and twitching motilities were significantly enhanced in the ΔlasRΔrhlR group compared with the PAO‐1 group in vitro. A significantly larger wound area was correlated with the bacterial motility. The inflammation in the early phase of bacterial challenge to wounds with immature biofilm formation in the QS‐deficient strains indicated that the role of QS was more crucial for the chronic phase than for the acute phase of infection. The present findings indicate a difference in the importance of QS in ischemic wound infections compared with other infection models.
Soilless Root Substrate pH Measurement Technique for Titration

Measurement of substrate pH entails procurement of the substrate solution and measurement of the solution pH. Acid-base reactions are completed at the time of testing. Determination of substrate pH during development of a titration curve is more complex because it involves initially the reaction of a base with the substrate. Five factors that can influence the resulting pH values were investigated in this study and include amount of water added to substrate, method to procure substrate solution for pH determination, chemical form of base used, time allowed for acid-base reaction and the addition of CaSO 4 . Substrate in this study consisted of 3 sphagnum peatmoss : 1 perlite (by volume) amended with wetting agent. Dolomitic limestone (6 g·L -1 substrate) was added to substrate for the water amount and solution procurement method experiments. Except for the water amount experiment, deionized water was added by weight to achieve 95% container capacity. Dishes were incubated at 20 °C for specified times. To identify the minimal level of water necessary to ensure complete contact between base and substrate for neutralization, addi- tions equivalent to 95%, 100%, 120%, and 150% container capacity were tested. The 95% level proved adequate. The saturated media extraction and pour-through bulk solution displacement methods for pH determination resulted in higher pH measurements in the incubated substrate than the squeeze bulk solution displacement method. This indicated that the former two methods diluted the soil solution. The squeeze method was deemed most effective. NaOH resulted in higher pH endpoints than Ca(OH) 2 . This was apparently due to a higher affinity of Ca 2+ for peatmoss exchange sites. Since Ca 2+ is the predominant cation associated with liming materials for soilless substrates, Ca(OH) 2 is more appropri- ate for titration. From the tested incubation times of 0, 2, 4, 8, 24, 48, and 96 hours, the duration of 24 hours was found to be adequate to allow complete reaction of base with substrate acidity. The best procedure for determining pH in a substrate titration situation included a water level of 95% container capacity, Ca(OH) 2 base, an incubation time of 24 hours and the squeeze solution displacement method. The additional CaSO 4 was not necessary. Chemical names used: calcium sulfate (CaSO 4 ), sodium hydroxide (NaOH), calcium hydroxide (Ca(OH) 2 ), calcium ion (Ca 2+ ).
Overcoming delay in the diagnosis of lung cancer: a qualitative study.

AIM To explore factors influencing the delay in reporting symptoms of lung cancer and to develop an early reporting tool that would prompt people to report symptoms early and request a chest X-ray. METHOD An expert panel of 16 healthcare professionals, lung cancer survivors and lay representatives was established to discuss the content and format of a possible early reporting tool. Six focus groups were held with 39 healthcare professionals and members of the public to explore factors influencing the delay in reporting symptoms and to develop the tool. FINDINGS The study revealed poor knowledge of lung cancer symptoms. Issues that influenced delay in reporting symptoms included a tendency to attribute other meanings to the symptoms, self-management of cough and fear of healthcare professionals' attitudes, for example blame and stigma associated with smoking. CONCLUSION Early presentation and assessment for treating lung cancer can improve survival. However, there seems to be a delay between patients noticing symptoms and reporting them to a doctor. Nurses play a key role in helping people overcome barriers to reporting possible lung cancer symptoms. Information interventions such as the one developed in this study could support nurses in this work.