Supplementary data for the article: García-Fernández, P.; Aramburu, J. A.; Moreno, M.; Zlatar, M.; Gruden-Pavlović, M. A Practical Computational Approach to Study Molecular Instability Using the Pseudo-Jahn-Teller Effect. Journal of Chemical Theory and Computation 2014, 10 (4), 1824–1833. https://doi.org/10.1021/ct4011097

Supplementary material for: [https://doi.org/10.1021/ct4011097]Related to published version: [http://cherry.chem.bg.ac.rs/handle/123456789/1765

Evaluating Reflected GPS Signal as a Potential Tool for Cotton Irrigation Scheduling

Accurate soil moisture content measurements are vital to precision irrigation management. Remote sensing using the microwave spectrum (such as GPS signals) has been used for measuring large area soil moisture contents. In our previous work, we estimated surface soil moisture contents for bare soil using a GPS Delay Mapping Receiver (DMR) developed by NASA. However, the effect of vegetation was not considered in these studies. Hence the objectives of this study were to: 1) investigate the feasibility of using DMR to determine soil moisture content in cotton production fields; 2) evaluate the attenuation effect of vegetation (cotton) on reflected GPS signal. Field experiments were conducted during the 2013 and 2014 growing seasons in South Carolina. GPS antennas were mounted at three heights (1.6, 2.7, and 4.2 m) over cotton fields to measure reflected GPS signals (DMR readings). DMR readings, soil core samples, and plant measurements were collected about once a week and attenuation effect of plant canopy was calculated. Results showed that DMR was able to detect soil moisture changes within one week after precipitation events that were larger than 25 mm per day. However, the DMR readings were poorly correlated with soil volumetric water content during dry periods. Attenuation effect of plant canopy was not significant. For irrigation purpose, the results suggested that the sensitivity of reflected GPS signals to soil moisture changes needed to be further studied before this technology could be utilized for irrigation scheduling in cotton production. Refinement of this technology will expand the use of advanced remote sensing technology for site-specific and timely irrigation scheduling. This would eliminate the need to install moisture sensors in production fields, which can interfere with farming operations and increase production costs

The role of multimorbidity in short-term mortality of lung cancer patients in Spain: a population-based cohort study

M.A.L.F. received support from the Instituto de Salud Carlos III, Madrid, Spain (grant/award no. CP17/00206-EU-FEDER). This work was supported by the Instituto de Salud Carlos III, Madrid, Spain [EU-FEDER-FIS PI-18/01593], the Consortium for Biomedical Research in Epidemiology and Public Health (CIBER en Epidemiologia y Salud Publica), the Cancer Epidemiological Surveillance Subprogram (VICA) from the Instituto de Salud Carlos III, Madrid, Spain, and the Andalusian Department of Health [PI-0152/2017]. The funders had no role in the design and conduct of the study, data collection, management, analysis, and interpretation of the data, the preparation, review, or approval of the manuscript or the decision to submit the manuscript for publication.Aim: Chronic diseases often occur simultaneously and tend to be associated with adverse health outcomes, but limited research has been undertaken to understand their role in lung cancer mortality. Therefore, this study aims to describe the prevalence and patterns of having one (comorbidity) or ≥ 2 chronic diseases (multimorbidity) among lung cancer patients in Spain, and to examine the association between comorbidity or multimorbidity and short-term mortality risk at six months after cancer diagnosis. Methods: In this population-based cohort study, data were drawn from two Spanish population-based cancer registries, Girona and Granada, and electronic health records. We identified 1259 adult lung cancer patients, diagnosed from 1st January 2011 to 31st December 2012. We identified the most common patterns of individual comorbidities and their pairwise correlations. We used a flexible parametric modelling approach to assess the overall short-term mortality risk 6 months after cancer diagnosis by levels of comorbidity after adjusting for age, sex, smoking status, province of residence, surgery, cancer stage, histology, and body mass index. Results: We found high prevalence of comorbidity in lung cancer patients, especially among the elderly, men, those diagnosed with advanced-stage tumours, smokers, and obese patients. The most frequent comorbidities were chronic obstructive pulmonary disease (36.6%), diabetes (20.7%) and heart failure (16.8%). The strongest pairwise correlation was the combination of heart failure with renal disease (r = 0.20, p < 0.01), and heart failure with diabetes (r = 0.16, p < 0.01). Patients with either one or two or more comorbidities had 40% higher overall mortality risk than those without comorbidities (aHR for comorbidity: 1.4, 95%CI: 1.1–1.7; aHR for multimorbidity: 1.4, 95%CI: 1.1–1.8), when relevant confounding factors were considered. Conclusions: The presence of comorbid diseases, rather than the number of comorbidities, was associated with increasing the risk of short-term lung cancer mortality in Spain. Comorbidity was a consistent and independent predictor of mortality among lung cancer patients, six months after diagnosis. The most common comorbid conditions were age-, obesity- and tobacco-related diseases. Our findings highlight the need to develop targeted preventive interventions and more personalised clinical guidelines to address the needs of lung cancer patients with one or more comorbidities in Spain.Instituto de Salud Carlos III CP17/00206-EU-FEDER EU-FEDER-FIS PI-18/01593Consortium for Biomedical Research in Epidemiology and Public Health (CIBER en Epidemiologia y Salud Publica)Cancer Epidemiological Surveillance Subprogram (VICA) from the Instituto de Salud Carlos III, Madrid, SpainAndalusian Department of Health PI-0152/201

Analyzing the Effect of TCP and Server Population on Massively Multiplayer Games

Many Massively Multiplayer Online Role-Playing Games (MMORPGs) use TCP flows for communication between the server and the game clients. The utilization of TCP, which was not initially designed for (soft) real-time services, has many implications for the competing traffic flows. In this paper we present a series of studies which explore the competition between MMORPG and other traffic flows. For that aim, we first extend a source-based traffic model, based on player’s activities during the day, to also incorporate the impact of the number of players sharing a server (server population) on network traffic. Based on real traffic traces, we statistically model the influence of the variation of the server’s player population on the network traffic, depending on the action categories (i.e., types of in-game player behaviour). Using the developed traffic model we prove that while server population only modifies specific action categories, this effect is significant enough to be observed on the overall traffic. We find that TCP Vegas is a good option for competing flows in order not to throttle the MMORPG flows and that TCP SACK is more respectful with game flows than other TCP variants, namely, Tahoe, Reno, and New Reno. Other tests show that MMORPG flows do not significantly reduce their sending window size when competing against UDP flows. Additionally, we study the effect of RTT unfairness between MMORPG flows, showing that it is less important than in the case of network-limited TCP flows

Supplementary data for the article: García-Fernández, P.; Aramburu, J. A.; Moreno, M.; Zlatar, M.; Gruden-Pavlović, M. A Practical Computational Approach to Study Molecular Instability Using the Pseudo-Jahn-Teller Effect. Journal of Chemical Theory and Computation 2014, 10 (4), 1824–1833. https://doi.org/10.1021/ct4011097

Supplementary material for: [https://doi.org/10.1021/ct4011097]Related to published version: [http://cherry.chem.bg.ac.rs/handle/123456789/1765

Socioeconomic Inequalities and Ethnicity Are Associated with a Positive COVID-19 Test among Cancer Patients in the UK Biobank Cohort.

We explored the role of socioeconomic inequalities in COVID-19 incidence among cancer patients during the first wave of the pandemic. We conducted a case-control study within the UK Biobank cohort linked to the COVID-19 tests results available from 16 March 2020 until 23 August 2020. The main exposure variable was socioeconomic status, assessed using the Townsend Deprivation Index. Among 18,917 participants with an incident malignancy in the UK Biobank cohort, 89 tested positive for COVID-19. The overall COVID-19 incidence was 4.7 cases per 1000 incident cancer patients (95%CI 3.8-5.8). Compared with the least deprived cancer patients, those living in the most deprived areas had an almost three times higher risk of testing positive (RR 2.6, 95%CI 1.1-5.8). Other independent risk factors were ethnic minority background, obesity, unemployment, smoking, and being diagnosed with a haematological cancer for less than five years. A consistent pattern of socioeconomic inequalities in COVID-19 among incident cancer patients in the UK highlights the need to prioritise the cancer patients living in the most deprived areas in vaccination planning. This socio-demographic profiling of vulnerable cancer patients at increased risk of infection can inform prevention strategies and policy improvements for the coming pandemic waves

Early evolution of the T-box transcription factor family

Deèelopmental transcription factors are key players in animal multicellularity, being members of the T-box family that are among the most important. Until recently, T-box transcription factors were thought to be exclusièely present in metazoans. Here, we report the presence of T-box genes in seèeral nonmetazoan lineages, including ichthyosporeans, filastereans, and fungi. Our data confirm that Brachyury is the most ancient member of the T-box family and establish that the T-box family dièersified at the onset of Metazoa. Moreoèer, we demonstrate functional conserèation of a homolog of Brachyury of the protist Capsaspora owczarzaki in Xenopus laeèis. By comparing the molecular phenotype of C. owczarzaki Brachyury with that of homologs of early branching metazoans, we define a clear difference between unicellular holozoan and metazoan Brachyury homologs, suggesting that the specificity of Brachyury emerged at the origin of Metazoa. Experimental determination of the binding preferences of the C. owczarzaki Brachyury results in a similar motif to that of metazoan Brachyury and other T-box classes. This finding suggests that functional specificity between different T-box classes is likely achieèed by interaction with alternatièe cofactors, as opposed to differences in binding specificity