Miracle-dz/UniFAR-FTUs huggingface dataset:
A comprehensive comparison of tools for differential ChIP-seq analysis

ChIP-seq has become a widely adopted genomic assay in recent years to determine binding sites for transcription factors or enrichments for specific histone modifications. Beside detection of enriched or bound regions, an important question is to determine differences between conditions. While this is a common analysis for gene expression, for which a large number of computational approaches have been validated, the same question for ChIP-seq is particularly challenging owing to the complexity of ChIP-seq data in terms of noisiness and variability. Many different tools have been developed and published in recent years. However, a comprehensive comparison and review of these tools is still missing. Here, we have reviewed 14 tools, which have been developed to determine differential enrichment between two conditions. They differ in their algorithmic setups, and also in the range of applicability. Hence, we have benchmarked these tools on real data sets for transcription factors and histone modifications, as well as on simulated data sets to quantitatively evaluate their performance. Overall, there is a great variety in the type of signal detected by these tools with a surprisingly low level of agreement. Depending on the type of analysis performed, the choice of method will crucially impact the outcome.
Why you should care about don't cares: Exploiting internal don't care conditions for hardware Trojans

Hardware Trojans are a significant security threat due to the globalization of hardware design and supply chain. We demonstrate a new type of hardware Trojan hidden behind internal don't care conditions. The proposed Trojans can pass through formal equivalence checking; they may reside after logic synthesis optimizations; and they are resilient to switching probability and side channel analysis. The new Trojans can create a surface for fault attack to retrieve secret information or downgrade performance by increasing power consumption. Experimental results show that these Trojans may stay after logic synthesis and that secret information can be retrieved using fault attack. We present detectability analysis and suggest synthesis optimizations as well as countermeasures that can help mitigate this new Trojan.
Human physiological and metabolic responses to an attempted winter crossing of Antarctica: the effects of prolonged hypobaric hypoxia.

An insufficient supply of oxygen to the tissues (hypoxia), as is experienced upon high‐altitude exposure, elicits physiological acclimatization mechanisms alongside metabolic remodeling. Details of the integrative adaptive processes in response to chronic hypobaric hypoxic exposure remain to be sufficiently investigated. In this small applied field study, subjects (n = 5, male, age 28–54 years) undertook a 40 week Antarctica expedition in the winter months, which included 24 weeks residing above 2500 m. Measurements taken pre‐ and postexpedition revealed alterations to glucose and fatty acid resonances within the serum metabolic profile, a 7.8 (±3.6)% increase in respiratory exchange ratio measured during incremental exercise (area under curve, P > 0.01, mean ± SD) and a 2.1(±0.8) % decrease in fat tissue (P < 0.05) postexpedition. This was accompanied by an 11.6 (±1.9) % increase (P > 0.001) in VO2 max corrected to % lean mass postexpedition. In addition, spine bone mineral density and lung function measures were identified as novel parameters of interest. This study provides, an in‐depth characterization of the responses to chronic hypobaric hypoxic exposure in one of the most hostile environments on Earth.
Promising approach to reducing Malaria transmission by ivermectin: Sporontocidal effect against Plasmodium vivax in the South American vectors Anopheles aquasalis and Anopheles darlingi

Background The mosquito resistance to the insecticides threatens malaria control efforts, potentially becoming a major public health issue. Alternative methods like ivermectin (IVM) administration to humans has been suggested as a possible vector control to reduce Plasmodium transmission. Anopheles aquasalis and Anopheles darlingi are competent vectors for Plasmodium vivax, and they have been responsible for various malaria outbreaks in the coast of Brazil and the Amazon Region of South America. Methods To determine the IVM susceptibility against P. vivax in An. aquasalis and An. darlingi, ivermectin were mixed in P. vivax infected blood: (1) Powdered IVM at four concentrations (0, 5, 10, 20 or 40 ng/mL). (2) Plasma (0 hours, 4 hours, 1 day, 5, 10 and 14 days) was collected from healthy volunteers after to administer a single oral dose of IVM (200 μg/kg) (3) Mosquitoes infected with P. vivax and after 4 days was provided with IVM plasma collected 4 hours post-treatment (4) P. vivax-infected patients were treated with various combinations of IVM, chloroquine, and primaquine and plasma or whole blood was collected at 4 hours. Seven days after the infective blood meal, mosquitoes were dissected to evaluate oocyst presence. Additionally, the ex vivo effects of IVM against asexual blood-stage P. vivax was evaluated. Results IVM significantly reduced the prevalence of An. aquasalis that developed oocysts in 10 to 40 ng/mL pIVM concentrations and plasma 4 hours, 1 day and 5 days. In An. darlingi to 4 hours and 1 day. The An. aquasalis mortality was expressively increased in pIVM (40ng/mL) and plasma 4 hours, 1, 5 10 and 14 days post-intake drug and in An. darlingi only to 4 hours and 1 day. The double fed meal with mIVM by the mosquitoes has a considerable impact on the proportion of infected mosquitoes for 7 days post-feeding. The oocyst infection prevalence and intensity were notably reduced when mosquitoes ingested blood from P. vivax patients that ingested IVM+CQ, PQ+CQ and IVM+PQ+CQ. P. vivax asexual development was considerably inhibited by mIVM at four-fold dilutions. Conclusion In conclusion, whole blood spiked with IVM reduced the infection rate of P. vivax in An. aquasalis and An. darlingi, and increased the mortality of mosquitoes. Plasma from healthy volunteers after IVM administration affect asexual P. vivax development. These findings support that ivermectin may be used to decrease P. vivax transmission.
Emotion Regulation and Complex Brain Networks: Association Between Expressive Suppression and Efficiency in the Fronto-Parietal Network and Default-Mode Network

Emotion regulation (ER) refers to the “implementation of a conscious or non-conscious goal to start, stop or otherwise modulate the trajectory of an emotion” (Etkin et al., 2015). Whereas multiple brain areas have been found to be involved in ER, relatively little is known about whether and how ER is associated with the global functioning of brain networks. Recent advances in brain connectivity research using graph-theory based analysis have shown that the brain can be organized into complex networks composed of functionally or structurally connected brain areas. Global efficiency is one graphic metric indicating the efficiency of information exchange among brain areas and is utilized to measure global functioning of brain networks. The present study examined the relationship between trait measures of ER (expressive suppression (ES) and cognitive reappraisal (CR)) and global efficiency in resting-state functional brain networks (the whole brain network and ten predefined networks) using structural equation modeling (SEM). The results showed that ES was reliably associated with efficiency in the fronto-parietal network and default-mode network. The finding advances the understanding of neural substrates of ER, revealing the relationship between ES and efficient organization of brain networks.
Transition from weak to strong energetic ion transport in burning plasmas

The change in nonlinear energetic particle mode (EPM) dynamics that accompanies the transition from weak to strong energetic ion transport is discussed in this work. It is demonstrated that the nonlinear threshold in fast ion energy density for the onset of strong convective transport occurring in avalanches is close to the linear EPM excitation threshold. This phenomenology is strictly related to the resonant character of the modes, which tend to be radially localized where the drive is strongest. After the convective loss phase, during which nonlinear EPM mode structure is displaced outwards, fast ion transport continues owing to diffusive processes. Theoretical analyses, presented here, are the basis for consistency analyses of operation scenarios in proposed burning plasma experiments. Comparisons between theoretical predictions and both simulation and experimental results are also briefly discussed.
The calibration of the DSCOVR EPIC multiple visible channel instrument using MODIS and VIIRS as a reference

The Deep Space Climate Observatory (DSCOVR), launched on 11 February 2015, is a satellite positioned near the Lagrange-1 (L1) point, carrying several instruments that monitor space weather, and Earth-view sensors designed for climate studies. The Earth Polychromatic Imaging Camera (EPIC) onboard DSCOVR continuously views the sun illuminated portion of the Earth with spectral coverage in the UV, VIS, and NIR bands. Although the EPIC instrument does not have any onboard calibration abilities, its constant view of the sunlit Earth disk provides a unique opportunity for simultaneous viewing with several other satellite instruments. This arrangement allows the EPIC sensor to be intercalibrated using other well-characterized satellite instrument reference standards. Two such instruments with onboard calibration are MODIS, flown on Aqua and Terra, and VIIRS, onboard Suomi-NPP. The MODIS and VIIRS reference calibrations will be transferred to the EPIC instrument using both all-sky ocean and deep convective clouds (DCC) ray-matched EPIC and MODIS/VIIRS radiance pairs. An automated navigation correction routine was developed to more accurately align the EPIC and MODIS/VIIRS granules. The automated navigation correction routine dramatically reduced the uncertainty of the resulting calibration gain based on the EPIC and MODIS/VIIRS radiance pairs. The SCIAMACHY-based spectral band adjustment factors (SBAF) applied to the MODIS/ VIIRS radiances were found to successfully adjust the reference radiances to the spectral response of the specific EPIC channel for over-lapping spectral channels. The SBAF was also found to be effective for the non overlapping EPIC channel 10. Lastly, both ray-matching techniques found no discernable trends for EPIC channel 7 over the year of publically released EPIC data.
Fate of Salmonella enterica and Enterohemorrhagic Escherichia coli Cells Artificially Internalized into Vegetable Seeds during Germination

ABSTRACT Vegetable seeds contaminated with bacterial pathogens have been linked to fresh-produce-associated outbreaks of gastrointestinal infections. This study was undertaken to observe the physiological behavior of Salmonella enterica and enterohemorrhagic Escherichia coli (EHEC) cells artificially internalized into vegetable seeds during the germination process. Surface-decontaminated seeds of alfalfa, fenugreek, lettuce, and tomato were vacuum-infiltrated with four individual strains of Salmonella or EHEC. Contaminated seeds were germinated at 25°C for 9 days, and different sprout/seedling tissues were microbiologically analyzed every other day. The internalization of Salmonella and EHEC cells into vegetable seeds was confirmed by the absence of pathogens in seed-rinsing water and the presence of pathogens in seed homogenates after postinternalization seed surface decontamination. Results show that 317 (62%) and 343 (67%) of the 512 collected sprout/seedling tissue samples were positive for Salmonella and EHEC, respectively. The average Salmonella populations were significantly larger (P < 0.05) than the EHEC populations. Significantly larger Salmonella populations were recovered from the cotyledon and seed coat tissues, followed by the root tissues, but the mean EHEC populations from all sampled tissue sections were statistically similar, except in pregerminated seeds. Three Salmonella and two EHEC strains had significantly larger cell populations on sprout/seedling tissues than other strains used in the study. Salmonella and EHEC populations from fenugreek and alfalfa tissues were significantly larger than those from tomato and lettuce tissues. The study showed the fate of internalized human pathogens on germinating vegetable seeds and sprout/seedling tissues and emphasized the importance of using pathogen-free seeds for sprout production. IMPORTANCE The internalization of microorganisms into vegetable seeds could occur naturally and represents a possible pathway of vegetable seed contamination by human pathogens. The present study investigated the ability of two important bacterial pathogens, Salmonella and enterohemorrhagic Escherichia coli (EHEC), when artificially internalized into vegetable seeds, to grow and disseminate along vegetable sprouts/seedlings during germination. The data from the study revealed that the pathogen cells artificially internalized into vegetable seeds caused the contamination of different tissues of sprouts/seedlings and that pathogen growth on germinating seeds is bacterial species and vegetable seed-type dependent. These results further stress the necessity of using pathogen-free vegetable seeds for edible sprout production.
A Comparison of Passive–Aggressive and Negativistic Personality Disorders

Passive–aggressive personality disorder (PAPD) has historically played an important role in clinical theorizing and was diagnosable prior to the Diagnostic and Statistical Manual of Mental Disorders (4th ed. [DSM–IV]; American Psychiatric Association, 1994), in which the construct was relabeled negativistic (NEGPD), expanded to include negative affective symptoms, and appendicized. In this study we tested the hypothesis that the expansion of PAPD to include content related to negative moods and nonspecific personality pathology compromised its discriminant validity. In an undergraduate sample (N = 1,215), a self-report measure of PAPD was only moderately related to NEGPD and showed less diagnostic overlap with other personality disorders than NEGPD. Furthermore, a conjoint factor analysis yielded a strong first factor (moodiness) that appeared less specific to passive–aggressive behavior than 3 other factors (irresponsibility, inadequacy, and contempt). We conclude that future research on this potentially important clinical construct should focus on core passive–aggressive features and abandon the negativistic content that has been added to it in successive editions of the DSM.
Coupling DSSAT and HYDRUS-1D for simulations of soil water dynamics in the soil-plant-atmosphere system

Abstract Accurate estimation of the soil water balance of the soil-plant-atmosphere system is key to determining the availability of water resources and their optimal management. Evapotranspiration and leaching are the main sinks of water from the system affecting soil water status and hence crop yield. The accuracy of soil water content and evapotranspiration simulations affects crop yield simulations as well. DSSAT is a suite of field-scale, process-based crop models to simulate crop growth and development. A “tipping bucket” water balance approach is currently used in DSSAT for soil hydrologic and water redistribution processes. By comparison, HYDRUS-1D is a hydrological model to simulate water flow in soils using numerical solutions of the Richards equation, but its approach to crop-related process modeling is rather limited. Both DSSAT and HYDRUS-1D have been widely used and tested in their separate areas of use. The objectives of our study were: (1) to couple HYDRUS-1D with DSSAT to simulate soil water dynamics, crop growth and yield, (2) to evaluate the coupled model using field experimental datasets distributed with DSSAT for different environments, and (3) to compare HYDRUS-1D simulations with those of the tipping bucket approach using the same datasets. Modularity in the software design of both DSSAT and HYDRUS-1D made it easy to couple the two models. The pairing provided the DSSAT interface an ability to use both the tipping bucket and HYDRUS-1D simulation approaches. The two approaches were evaluated in terms of their ability to estimate the soil water balance, especially soil water contents and evapotranspiration rates. Values of the d index for volumetric water contents were 0.9 and 0.8 for the original and coupled models, respectively. Comparisons of simulations for the pod mass for four soybean and four peanut treatments showed relatively high d index values for both models (0.94–0.99).
Time course of depression and outcome of myocardial infarction.

BACKGROUND Depression predicts worse outcomes after myocardial infarction (MI), but whether its time course in the month following MI has prognostic importance is unknown. Our objective was to evaluate the prognostic importance of transient, new, or persistent depression on outcomes at 6 months after MI. METHODS In a prospective registry of acute MI (Prospective Registry Evaluating outcomes after Myocardial Infarction: Events and Recovery [PREMIER]), depressive symptoms were measured in 1873 patients with the Patient Health Questionnaire (PHQ) during hospitalization and 1 month after discharge and were classified as transient (only at baseline), new (only at 1 month), or persistent (at both times). Outcomes at 6 months included (1) all-cause rehospitalization or mortality and (2) health status (angina, physical limitation, and quality of life using the Seattle Angina Questionnaire). RESULTS Compared with nondepressed patients, all categories of depression were associated with higher rehospitalization or mortality rates, more frequent angina, more physical limitations, and worse quality of life. The adjusted hazard ratios for rehospitalization or mortality were 1.34, 1.71, and 1.42 for transient, new, and persistent depression, respectively (all P<.05). Corresponding odds ratios were 1.62, 2.73, and 2.64 (all P<.01) for angina and 1.69, 2.25, and 3.27 (all P<.05) for physical limitation. Depressive symptoms showed a stronger association with health status compared with traditional measures of disease severity. CONCLUSION Depressive symptoms after MI, irrespective of whether they persist, subside, or newly develop in the first month after hospitalization, are associated with worse outcomes after MI.
NITRATE TRANSPORTER GENES FROM THE DIATOM CYLINDROTHECA FUSIFORMIS (BACILLARIOPHYCEAE): mRNA LEVELS CONTROLLED BY NITROGEN SOURCE AND BY THE CELL CYCLE

The molecular characterization of components involved in nitrate uptake and assimilation in phytoplankton is likely to provide new insights into these processes, their regulation, and their effect on primary production. We report the cloning and initial characterization of the first nitrate transporter genes in a marine organism, from the diatom Cylindrotheca fusiformis Reimann et Lewin. A clone isolated from a silicon‐responsive cDNA library was shown by sequence comparison to encode a homolog of high‐affinity nitrate transporters. The C. fusiformis nitrate transporter cDNA was named NAT (NitrAte Transporter). The NAT cDNA was used to isolate a genomic clone that contained two additional nitrate transporter genes, NAT1 and NAT2, arranged in tandem. The cDNA and two genomic sequences were highly conserved, and only 18 of 1446 nucleotides in the coding region differed. At least four copies of NAT genes were present in C. fusiformis and as shown by hybridization, multiple copies were present in other diatom species. The transcript abundance of NAT genes in cultures with different nitrogen sources was monitored by RNase protection assays. NAT mRNA levels were high in the presence of nitrate, at nearly the same level during nitrogen starvation, and also high in urea‐containing cultures. Lower mRNA levels occurred in nitrite‐grown cultures. NAT transcript levels were highly repressed with NH4Cl or NH4NO3 as the nitrogen source, although very low amounts were detected. These results suggested that monitoring NAT mRNA levels could serve as a marker for (1) nitrate uptake in nitrate medium, (2) nitrogen starvation, and (3) ammonium use by virtue of absence of expression. NAT mRNA levels were not directly regulated by light or dark, but were apparently related to cellular growth and protein synthesis. Using light/dark synchronized cultures to monitor cell cycle responses, NAT mRNA levels were high in early G1 phase, decreased through the remainder of G1, then increased during DNA synthesis in S phase and into G2, and finally decreased after M phase. In silicon‐starvation synchronized cultures, levels were high at the G1/S phase boundary, high throughout S and G2, and finally decreased after M phase. It was clear that NAT expression, and by inference nitrate uptake, did not occur at continuous levels throughout the cell cycle. The results of the RNase protection experiments suggested that transcriptional regulation is a major contributing factor in the control of diatom nitrate uptake. The cloning of the C. fusiformis nitrate transporter genes provides a new tool for investigating diatom nitrogen uptake and metabolism. In addition, the regulation of NAT expression by nitrogen source is likely to be useful in developing techniques to specifically control the expression of genes fused to NAT regulatory sequences in transgenic diatoms.
Therapeutic Potential of Targeting Wnt/β‐Catenin Pathway in Treatment of Colorectal Cancer: Rational and Progress

Wnt/β‐catenin pathway is one of the main/frequent dysregulated pathways in several tumor types, including colon cancer. Aberrant activation of this pathway is associated with cell proliferation, invasive behaviors, and cell resistance, suggesting its potential value as a therapeutic target in treatment of CRC. Several agents have been developed for targeting of this pathway (e.g, natural agents: curcumin, 3,3‐diindolylmethane, phytoestrogen; Synthetic/small Wnt inhibitors: Rofecoxib; PRI‐724, CWP232291; and monoclonal antibody against frizzled receptors, Vanituctumab). This review summarizes the current knowledge about the therapeutic potential of targeting Wnt pathway with particular emphasis on preclinical/clinical studies in treatment of colorectal cancer. J. Cell. Biochem. 118: 1979–1983, 2017. © 2017 Wiley Periodicals, Inc.
Resource Scarcity, Effort, and Performance in Physically Demanding Jobs: An Evolutionary Explanation

Based on evolutionary theory, we predicted that cues of resource scarcity in the environment (e.g., news of droughts or food shortages) lead people to reduce their effort and performance in physically demanding work. We tested this prediction in a 2-wave field survey among employees and replicated it experimentally in the lab. In Study 1, employees who perceived resources in the environment to be scarce reported exerting less effort when their jobs involved much (but not little) physical work. In Study 2, participants who read that resources in the environment were scarce performed worse on a task demanding more (carrying books) but not less (transcribing book titles) physical work. This result was found even though better performance increased participants’ chances of additional remuneration, and even though scarcity cues did not affect individuals’ actual ability to meet their energy needs. We discuss implications for managing effort and performance, and the potential of evolutionary psychology to explain core organizational phenomena.