Machine learning extracts marks of thiamine’s role in cold acclimation in the transcriptome of Vitis vinifera

IntroductionThe escalating challenge of climate change has underscored the critical need to understand cold defense mechanisms in cultivated grapevine Vitis vinifera. Temperature variations can affect the growth and overall health of vine.MethodsWe used Self Organizing Maps machine learning method to analyze gene expression data from leaves of five Vitis vinifera cultivars each treated by four different temperature conditions. The algorithm generated sample-specific “portraits” of the normalized gene expression data, revealing distinct patterns related to the temperature conditions applied.ResultsOur analysis unveiled a connection with vitamin B1 (thiamine) biosynthesis, suggesting a link between temperature regulation and thiamine metabolism, in agreement with thiamine related stress response established in Arabidopsis before. Furthermore, we found that epigenetic mechanisms play a crucial role in regulating the expression of stress-responsive genes at low temperatures in grapevines.DiscussionApplication of Self Organizing Maps portrayal to vine transcriptomics identified modules of coregulated genes triggered under cold stress. Our machine learning approach provides a promising option for transcriptomics studies in plants

Přechod mezi střední a vysokou školou a role různých modelů přijímacích řízení

The study evaluates the potential impact of alternative models of university entrance exams – a model based on field-specific knowledge and a model relying on general aptitude tests – in the context of the Czech education system since 1998, a system that can be described as highly stratified and suffering from a notable excess of demand for higher education over supply. Using the dataset Sonda Maturant 1998, the authors show that entrance exams based on general aptitude tests may outperform the field-specific knowledge model in terms of providing access to talented students from a lower socioeconomic background. The simulations show that under the general aptitude regime the relative chances of an applicant with a university-educated father are only one-quarter higher than the relative chances of a student with a less educated father, compared to more than a one-third difference in the case of the regime emphasising field-specific knowledge. For mother’s education, the respective odds ratios differ by the even larger margin of 28 percentage points

Dynamic changes of left ventricular performance and left atrial volume induced by the mueller maneuver in healthy young adults and implications for obstructive sleep apnea, atrial fibrillation, and heart failure.

Using the Mueller maneuver (MM) to simulate obstructive sleep apnea (OSA), our aim was to investigate acute changes in left-sided cardiac morphologic characteristics and function which might develop with apneas occurring during sleep. Strong evidence supports a relation between OSA and both atrial fibrillation and heart failure. However, acute effects of airway obstruction on cardiac structure and function have not been well defined. In addition, it is unclear how OSA might contribute to the development of atrial fibrillation and heart failure. Echocardiography was used in healthy young adults to measure various parameters of cardiac structure and function. Subjects were studied at baseline, during, and immediately after performance of the MM and after a 10-minute recovery. Continuous heart rate, blood pressure, and pulse oximetry measurements were made. During the MM, left atrial (LA) volume index markedly decreased. Left ventricular (LV) end-systolic dimension increased in association with a decrease in LV ejection fraction. On release of the maneuver, there was a compensatory increase in blood flow to the left side of the heart, with stroke volume, ejection fraction, and cardiac output exceeding baseline. After 10 minutes of recovery, all parameters returned to baseline. In conclusion, sudden imposition of severe negative intrathoracic pressure led to an abrupt decrease in LA volume and a decrease in LV systolic performance. These changes reflected an increase in LV afterload. Repeated swings in afterload burden and chamber volumes may have implications for the future development of atrial fibrillation and heart failure

Machine learned-based visualization of the diversity of grapevine genomes worldwide and in Armenia using SOMmelier

In the proposed study three major issues have been addressed: Firstly, the diversity of grapevine accessions worldwide and particularly in Armenia, a small country located in the largely volcanic Armenian Highlands, is incredibly rich in cultivated and especially wild grapes; secondly, the information hidden in their (whole) genomes, e.g., about the domestication history of grapevine over the last 11,000 years and phenotypic traits such as cultivar utilization and a putative resistance against powdery mildew, and, thirdly machine learning methods to extract and to visualize this information in an easy to percept way. We shortly describe the Self Origanizing Maps (SOM) portrayal method called “SOMmelier” (as the vine-genome “waiter”) and illustrate its power by applying it to whole genome data of hundreds of grapevine accessions. We also give a short outlook on possible future directions of machine learning in grapevine transcriptomics and ampelogaphy

High Prevalence of Abnormal Nocturnal Oximetry in Patients With Hypertrophic Cardiomyopathy

ObjectivesWe sought to determine the prevalence of nocturnal oxygen desaturation and obstructive sleep apnea (OSA) in a population of patients with hypertrophic cardiomyopathy (HCM).BackgroundThe coexistence of sleep apnea and HCM, 2 common cardiovascular conditions, has been largely unrecognized in the treatment of patients with HCM. The nocturnal hypoxia-induced hyperadrenergic state in OSA is expected to worsen hemodynamics and outcomes in HCM.MethodsOne hundred subjects with HCM between June 1, 2006, and July 14, 2008, were screened with nocturnal oximetry. Clinical variables were collected for statistical analysis. Oximetry was classified abnormal (suspicion of sleep-disordered breathing) in the presence of repetitive desaturation (≥5 events/h) followed by a rapid return to baseline oxygen saturation (SaO2) level with a decrease of ≥4% and threshold of 90%.ResultsSeventy-one (71%) patients with HCM had abnormal nocturnal oximetry (71 ± 9%, 95% confidence interval: 62% to 80%). Subjects with abnormal oximetry were older (age 59.5 ± 15.3 years) and more were hypertensive (n = 39 [55%]) than those with normal oximetry (age 45.8 ± 18.5 years, n = 9 [31%], p < 0.001, p = 0.03). Patients with HCM were more symptomatic in the presence of abnormal oximetry (New York Heart Association functional class II to III) (62% vs. 83%, p = 0.023). HCM patients had a higher prevalence of abnormal nocturnal oximetry (n = 71, 71%) compared with a control group of similar age and sex distribution (n = 49, 49%) (p = 0.001).ConclusionsAbnormal nocturnal oximetry is common in patients with HCM, suggesting that OSA is prevalent. OSA may impact hemodynamics and symptoms in HCM. Further studies are needed to determine the long-term benefit of OSA treatment on hemodynamics and disease progression in HCM

Can Immigrants Hurt Trade?

This paper estimates the impact of immigrant network spillovers on international trade. Contrary to previous studies focusing mostly on the trade enhancing role of immigrant networks, the present framework allows for potential trade diverting effects. A simple matching model that incorporates both trade creation and diversion channels furthermore points at the importance of relative as opposed to absolute measures of immigrant networks. Using a new dataset of 19 OECD countries, I find that while immigrant networks indeed facilitate exports from host to source country, they simultaneously hurt trade with the host country’s other trading partners. In addition, I find that the impact of information-related trade barriers might be negatively related to the economic size of the trading partner. In particular, the larger the trading partner, the smaller the trade benefits of lower information costs due to a shared common language.International trade, immigration, informal trade barriers.

Expatriates and Trade

The study quantifies the contribution to bilateral trade flows of expatriates from the OECD economies living in less developed countries. Similarly to the results of the existing research that focused on immigrants moving in the opposite direction, the expatriates promote trade between the country of origin and country of residence. The expatriates’ facilitation of trade is nonetheless relatively weaker and works likely through different channels. Using a unique dataset on bilateral migration stocks, a 10 percent increase in the size of an expatriate community leads to a 0.6 percent average increase in its OECD trade partner’s imports against a 2.5 percent impact of immigrants in OECD countries. The import facilitating role of expatriate networks is centered in host countries with low institutional quality. In economies lying within the lowest third of the institutional quality distribution, a 10 percent increase in expatriate stock would lead to a 1.7 percent increase in imports into their country of origin. The figures on expatriates’ role in exports are not statistically different from zero.International trade, migration, informal trade barriers.

Fair Trade - Is It Really Fair?

One of the arguments against the Fair Trade scheme is that the guaranteed minimum price tends to depress world prices and thus the incomes of non-participating farmers (e.g. The Economist, 2006). We develop a model that distinguishes between the impact of the introduction of a Fair Trade market per se and the effect of minimum price policies given that a Fair Trade market actually exists. The model suggests that the claims against Fair Trade might not be correct. The introduction of a Fair Trade market may increase the incomes of both participating and non-participating farmers. The minimum contracting price as part of Fair Trade standards, however, precludes the full realization of the program’s potential benefits. The minimum price also paradoxically increases the profits of the middlemen whose local monopsony power the Fair Trade scheme originally aimed to retrench. Furthermore, the total surplus generated by Fair Trade cooperatives declines as the guaranteed price increases.Certification, regulation, price setting, coffee, Fair Trade, monopsony