Miracle-dz/UniFAR-FTUs huggingface dataset:
The physical basis for increases in precipitation extremes in simulations of 21st-century climate change

Global warming is expected to lead to a large increase in atmospheric water vapor content and to changes in the hydrological cycle, which include an intensification of precipitation extremes. The intensity of precipitation extremes is widely held to increase proportionately to the increase in atmospheric water vapor content. Here, we show that this is not the case in 21st-century climate change scenarios simulated with climate models. In the tropics, precipitation extremes are not simulated reliably and do not change consistently among climate models; in the extratropics, they consistently increase more slowly than atmospheric water vapor content. We give a physical basis for how precipitation extremes change with climate and show that their changes depend on changes in the moist-adiabatic temperature lapse rate, in the upward velocity, and in the temperature when precipitation extremes occur. For the tropics, the theory suggests that improving the simulation of upward velocities in climate models is essential for improving predictions of precipitation extremes; for the extratropics, agreement with theory and the consistency among climate models increase confidence in the robustness of predictions of precipitation extremes under climate change.
Antimicrobial resistance profile of Aeromonas species isolated from Libya

Aeromonas species are Gram-negative, oxidasepositive rods in the family Aeromonadaceae . These organisms have been isolated from untreated drinking water and different types of foods particularly seafood and frozen chicken. Aeromonas species are recognized as agents of serious infections in immunocompromised individuals including septicemia in patients with hepatic cirrhosis with a rapidly fatal outcome. Significant association of Aeromonas species with diarrhoea, particularly in children, and soft tissue infections following water-related injuries were reported from several developing countries. (Published: 24 May 2013) Citation: Libyan J Med 2013, 8: 21320 - http://dx.doi. org/10.3402/ljm.v8i0. 21320
CUI Networks: A Graphical Representation for Conditional Utility Independence

We introduce CUI networks, a compact graphical representation of utility functions over multiple attributes. CUI networks model multiattribute utility functions using the well studied and widely applicable utility independence concept. We show how conditional utility independence leads to an effective functional decomposition that can be exhibited graphically, and how local, compact data at the graph nodes can be used to calculate joint utility. We discuss aspects of elicitation and network construction, and contrast our new representation with previous graphical preference modeling.
Rapamycin regulates macrophage activation by inhibiting NLRP3 inflammasome-p38 MAPK-NFκB pathways in autophagy- and p62-dependent manners

Excessive and prolonged activation of macrophages underlies many inflammatory and autoimmune diseases. To regulate activation and maintain homeostasis, macrophages have multiple intrinsic mechanisms, one of which is modulation through autophagy. Here we demonstrate that autophagy induction by rapamycin suppressed the production of IL-1β and IL-18 in lipopolysaccharide- and adenosine triphosphate-activated macrophages at the post-transcriptional level by eliminating mitochondrial ROS (mtROS) and pro-IL1β in a p62/SQSTM1-dependent manner. In addition, rapamycin activated Nrf2 through up-regulation of p62/SQSTM1, which further contributed to the reduction of mtROS. Reduced IL-1β subsequently diminished the activation of p38 MAPK-NFκB pathways, leading to transcriptional down-regulation of IL-6, IL-8, MCP-1, and IκBα in rapamycin-treated macrophages. Therefore, our results suggest that rapamycin negatively regulates macrophage activation by restricting a feedback loop of NLRP3 inflammasome-p38 MAPK-NFκB pathways in autophagy- and p62/SQSTM1-dependent manners.
Effect of the Concentration of Depleted Uranium in Soil on Its Uptake by Tomato Plant

Depleted Uranium (dU) is usually used in the weapon to increase its destruction power inflected to the target. Therefore, this study was conducted to detrmine the effect of of a range of dU concentration in the soil an incident of the desrruction of military tank in southern part of Iraq on radioisotope content in soil and in tomato plant grown in the area. The dU concentration in the incident spots located in Safwan destrict close to Jabel Sanam, north of Rumala oil field was 4000 mg Kg-1 in the soil. The soil also was found to contain a considerable level of 234Th, 226Ra and 40K. Tomato growth was reduced with the increase of dU concentration compared to those grown in same soil of no dU content. It even has failed to grow in the soil with high level of dU. Tomato plant uptake of 238U as determined by radioactivity of its direct daughter 234Th was found to increase with the increase of dU concentration in soil. The dU concentration higher than 500 mg kg-1 soil was lethal to tomato plant.
Review and Comparison of Computational Approaches for Joint Longitudinal and Time‐to‐Event Models

Joint models for longitudinal and time‐to‐event data are useful in situations where an association exists between a longitudinal marker and an event time. These models are typically complicated due to the presence of shared random effects and multiple submodels. As a consequence, software implementation is warranted that is not prohibitively time consuming. While methodological research in this area continues, several statistical software procedures exist to assist in the fitting of some joint models. We review the available implementation for frequentist and Bayesian models in the statistical programming languages R, SAS and Stata. A description of each procedure is given including estimation techniques, input and data requirements, available options for customisation and some available extensions, such as competing risks models. The software implementations are compared and contrasted through extensive simulation, highlighting their strengths and weaknesses. Data from an ongoing trial on adrenal cancer patients are used to study different nuances of software fitting on a practical example.
Investigation of spatiotemporal patterns in mean temperature and mean trophic level of MEDITS survey catches in the Mediterranean Sea

Mean temperature (MTC) and mean trophic level (MTL) spatiotemporal patterns of MEDITS survey catches were examined in 13 geographic statistical areas (GSAs) of the Mediterranean between 1994 and 2016. The study aimed to detect changes in the demersal community structure related to anthropogenic impacts. A generalized additive modelling approach was used to examine the effects of year and GSA on the MTC and MTL indexes and on bottom temperature by haul. For the MTC index, the year was significant only in 4 GSAs, while for MTL it was significant in 5. Higher MTC values were observed in central and eastern areas. Bottom temperature increased after 2010, and also from west to east and from north to south. Our results indicate that the recently observed increase in bottom sea temperature has not resulted in an immediate response by demersal marine communities, but areas with higher warming rates or shallow depths were found to be more susceptible to sea warming. For MTL, decreasing trends were observed in only 2 GSAs, while the temporal trends observed in 5 GSAs may have reflected changes in fishing activity patterns. However, higher MTL values were observed in GSAs with generally higher exploitation rates, indicating that factors other than fishing play an important structuring role in marine communities. The present results indicate differences among Mediterranean subareas in regard to changes in the community structure attributed to environmental conditions and exploitation patterns and have implications for the ecology and dynamics of the stocks.
Debunking in a world of tribes

Social media aggregate people around common interests eliciting collective framing of narratives and worldviews. However, in such a disintermediated environment misinformation is pervasive and attempts to debunk are often undertaken to contrast this trend. In this work, we examine the effectiveness of debunking on Facebook through a quantitative analysis of 54 million users over a time span of five years (Jan 2010, Dec 2014). In particular, we compare how users usually consuming proven (scientific) and unsubstantiated (conspiracy-like) information on Facebook US interact with specific debunking posts. Our findings confirm the existence of echo chambers where users interact primarily with either conspiracy-like or scientific pages. However, both groups interact similarly with the information within their echo chamber. Then, we measure how users from both echo chambers interacted with 50,220 debunking posts accounting for both users consumption patterns and the sentiment expressed in their comments. Sentiment analysis reveals a dominant negativity in the comments to debunking posts. Furthermore, such posts remain mainly confined to the scientific echo chamber. Only few conspiracy users engage with corrections and their liking and commenting rates on conspiracy posts increases after the interaction.
PHYTOREMEDIATION AS A TOOL FOR THE REMEDIATION OF WASTEWATER RESULTING FROM DYEING ACTIVITIES

The production of dye is usually associated with several intermediate products and waste which are usually toxic and bio-hazardous and often disturb the environmental equilibrium. The present study is aimed at selecting macrophytes with the highest efficiency in the remediation of wastewater generated from dyeing activities. The test macrophytes were introduce into three different troughs for each plant containing 100% wastewater, 50% wastewater and control (100% borehole water). After 21 days the macrophytes were removed for further analysis. The reduction efficiency, Heavy metal bioconcentration and bio translocation factor of the macrophytes was determined. The result obtained shows that the test macrophytes improved the pH but were not able to improve the color of the wastewater. Lemna minor have the highest reduction efficiency for BOD, COD, Oil, and Grease while Pistia stratiotes have the highest reduction efficiency for TDS and TSS, Eicchornia crassipes have the highest reduction efficiency for Cl and Salvinia molesta have the highest reduction efficiency for phenol and ammonical Nitrogen. All macrophytes recorded high reduction efficiency for heavy metal removal but Pistia stratiotes and Eicchornia crassipes had the highest bioconcentration and translocation. These macrophytes should be introduced to the local dye users as a costless and environmentally friendly way of treating wastewater resulting from dyeing activity.
Job satisfaction and health experience of people with a lower-limb amputation in comparison with healthy colleagues.

OBJECTIVES To describe indicators of job dissatisfaction among amputee employees and to compare job satisfaction and health experience of working amputee employees with that of control subjects. DESIGN A cross-sectional study, mailed questionnaire. SETTING Patients were recruited by the orthopedic workshops of the Netherlands. PARTICIPANTS One hundred forty-four patients who had an acquired unilateral major amputation of the lower limb at least 2 years before, were aged 18 to 60 years (mean age, 43y), and were living and working in the Netherlands. One hundred forty-four control subjects matched for age, gender, and type of job. INTERVENTIONS Not applicable. MAIN OUTCOME MEASURES Statistical analysis of responses to a questionnaire regarding patient characteristics and amputation-related factors, amputee patients' opinions about their work and the social atmosphere at work, and their general health (RAND 36-Item Health Survey [RAND-36]). RESULTS People with an amputation had greater job satisfaction (70%) than did the able-bodied control group (54%). The wish for (better) modifications in the workplace and the presence of comorbidity were significantly related to job dissatisfaction in people with limb loss. Amputee employees were less often hindered by the failures of others and by fluctuations in temperature. People with limb loss showed a worse physical health experience than controls on the RAND-36. CONCLUSIONS The vocational satisfaction of people with limb loss may be improved by better workplace modifications, depending on the functional capabilities of the person and the functional demands of the job; improvement may also be achieved by vocational rehabilitation programs, especially for those with an amputation in combination with other morbidity. Despite experiencing more health problems, the amputee group expressed greater job satisfaction than the able-bodied group, reflecting a great appreciation of job reintegration by people with a lower-limb amputation.
Pax6 Interactions with Chromatin and Identification of Its Novel Direct Target Genes in Lens and Forebrain

Pax6 encodes a specific DNA-binding transcription factor that regulates the development of multiple organs, including the eye, brain and pancreas. Previous studies have shown that Pax6 regulates the entire process of ocular lens development. In the developing forebrain, Pax6 is expressed in ventricular zone precursor cells and in specific populations of neurons; absence of Pax6 results in disrupted cell proliferation and cell fate specification in telencephalon. In the pancreas, Pax6 is essential for the differentiation of α-, β- and δ-islet cells. To elucidate molecular roles of Pax6, chromatin immunoprecipitation experiments combined with high-density oligonucleotide array hybridizations (ChIP-chip) were performed using three distinct sources of chromatin (lens, forebrain and β-cells). ChIP-chip studies, performed as biological triplicates, identified a total of 5,260 promoters occupied by Pax6. 1,001 (133) of these promoter regions were shared between at least two (three) distinct chromatin sources, respectively. In lens chromatin, 2,335 promoters were bound by Pax6. RNA expression profiling from Pax6+/− lenses combined with in vivo Pax6-binding data yielded 76 putative Pax6-direct targets, including the Gaa, Isl1, Kif1b, Mtmr2, Pcsk1n, and Snca genes. RNA and ChIP data were validated for all these genes. In lens cells, reporter assays established Kib1b and Snca as Pax6 activated and repressed genes, respectively. In situ hybridization revealed reduced expression of these genes in E14 cerebral cortex. Moreover, we examined differentially expressed transcripts between E9.5 wild type and Pax6−/− lens placodes that suggested Efnb2, Fat4, Has2, Nav1, and Trpm3 as novel Pax6-direct targets. Collectively, the present studies, through the identification of Pax6-direct target genes, provide novel insights into the molecular mechanisms of Pax6 gene control during mouse embryonic development. In addition, the present data demonstrate that Pax6 interacts preferentially with promoter regions in a tissue-specific fashion. Nevertheless, nearly 20% of the regions identified are accessible to Pax6 in multiple tissues.
N E

With increasing in heterogeneity of the mobile and wireless networks, including the use of licensed and unlicensed spectrum, and diversity in types of User Equipment (UEs), managing how traffic flows through network while maintaining high level of users’ quality of experience is crucial. In this paper, we present a novel traffic management mechanism that maintains the users’ quality of experience as well as guaranteeing fairness among users. This traffic management has two separate elements, one that is located at the UE and one that is located at the cloud-based network controller. While each UE maximizes their utility function, which is modelled based on the QoS parameters, selfishly, at the network side, the attempt is to maximize fairness among all users’ flows.
Barakol Extracted from Cassia siamea Stimulates Chloride Secretion in Rat Colon

Barakol is a purified extract of Cassia siamea, a plant that has been used as a laxative in traditional medicine. In this study, the effect of barakol on anion transport across the rat colon epithelium was investigated. Colonic epithelium was mounted in Ussing chambers and bathed with Ringer's solution. Addition of 1 mM barakol to the basolateral solution produced a slow increase in short-circuit current (Isc) in proximal colon and distal colon by 24.5 ± 2.2 and 24.2 ± 1.4 μA/cm2, respectively. Barakol increased Isc in a concentration-dependent manner with an EC50 value of 0.4 mM. The barakol-stimulated increase in Isc was inhibited by subsequent treatment with 500 μM diphenylamine-2-carboxylic acid or 400 μM glibenclamide added to the apical solution and 200 μM bumetanide added to the basolateral solution. Pretreatment of the tissues with 200 μM bumetanide, but not 10 μM amiloride, completely abolished the barakol-increased Isc. Ion substitution experiments showed an inhibition of barakol-stimulated Isc in chloride-free solution but not in bicarbonate-free solution. In addition, pretreatment of tissues with 10 μM tetrodotoxin or 10 μM indomethacin, but not 1 μM atropine or 10 μM hexamethonium, partially inhibited the Isc response by barakol. The present results demonstrated the stimulatory effect of barakol on the bumetanide-sensitive chloride secretion in rat colon. The effect of barakol was partly mediated by the stimulation of submucosal nerves and through the release of cyclooxygenase metabolites. These findings thus provide an explanation for the underlying mechanism of barakol as a secretagogue in mammalian colon.
A comprehensive, high-resolution genomic transcript map of human skeletal muscle.

We present the Human Muscle Gene Map (HMGM), the first comprehensive and updated high-resolution expression map of human skeletal muscle. The 1078 entries of the map were obtained by merging data retrieved from UniGene with the RH mapping information on 46 novel muscle transcripts, which showed no similarity to any known sequence. In the map, distances are expressed in megabase pairs. About one-quarter of the map entries represents putative novel genes. Genes known to be specifically expressed in muscle account for <4% of the total. The genomic distribution of the map entries confirmed the previous finding that muscle genes are selectively concentrated in chromosomes 17, 19, and X. Five chromosomal regions are suspected to have a significant excess of muscle genes. Present data support the hypothesis that the biochemical and functional properties of differentiated muscle cells may result from the transcription of a very limited number of muscle-specific genes along with the activity of a large number of genes, shared with other tissues, but showing different levels of expression in muscle. [The sequence data described in this paper have been submitted to the EMBL data library under accession nos. F23198-F23242. ]
ChimeraScan: a tool for identifying chimeric transcription in sequencing data

SUMMARY Next generation sequencing (NGS) technologies have enabled de novo gene fusion discovery that could reveal candidates with therapeutic significance in cancer. Here we present an open-source software package, ChimeraScan, for the discovery of chimeric transcription between two independent transcripts in high-throughput transcriptome sequencing data. AVAILABILITY http://chimerascan.googlecode. com CONTACT cmaher@dom.wustl. edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Anti‐carious Effects of Galla chinensis: A Systematic Review

As a natural traditional Chinese medicine, Galla chinensis has been widely used since ancient times for its astringency, stypticity, detoxification, and antibacterial activity. Our group has concentrated on the research about its potential of being an applicable anti‐caries agent. The crude extract and some other components purified from it show remarkable efficacy on anticaries, and the most likely mechanism is proposed through specific research. For the fact that crude drugs consist of numerous compounds, and their bioactivity is a result of synergistic effects and/or antagonistic effects of several compounds, it is difficult to clarify the exact mechanism and evaluate the safety and effectiveness of G. chinensis. This review article systematically summarizes previous findings from the following aspects: (1) inhibitory effect on oral bacteria; (2) the demineralization inhibition property; (3) the remineralization‐enhancing property; and (4) stability and toxicity evaluation, and thus indicates the further research direction. Copyright © 2015 John Wiley & Sons, Ltd.
Modular SDN Programming with Pyretic

Managing today’s computer networks is a complex and error-prone task. These networks consist of a wide variety of devices, from routers and switches, to firewalls, network-address translators, load balancers, and intrusion-detection systems. Network administrators must express policies through tedious box-by-box configuration, while grappling with a multitude of protocols and baroque, vendor-specific interfaces. In contrast, Software-Defined Networking (SDN) is redefining the way we manage networks. In SDN, a controller application uses a standard, open messaging interface like OpenFlow [1], to specify how network elements or switches should handle incoming packets. Programmers develop their own new controller applications on top of a controller platform which provides a programming API built on top of OpenFlow. Separating the controller platform and applications from the network elements allows anyone—not just the equipment vendors—to program new network control software. In just a few years, SDN has enabled a wealth of innovation, including prominent commercial successes like Nicira’s network virtualization platform and Google’s wide-area traffic-engineering system. Most of the major switch vendors support the OpenFlow API, and many large information-technology companies are involved in SDN consortia like the Open Networking Foundation and the Open Daylight initiative. SDN is creating exciting new opportunities for networksavvy software developers and software-savvy network practitioners alike. But how should programmers write these controller applications? The first generation of SDN controller platforms offer programmers a low-level API closely resembling the interface to the switches. This forces programmers to program in “assembly language,” by manipulating bit patterns in packets and carefully managing the shared rule-table space. In the Frenetic project [2], we are designing simple, reusable, high-level abstractions for programming SDNs, and efficient runtime systems that automatically generate the low-level rules on switches [3, 4, 5, 6, 7]. Our abstractions cover the main facets of managing Figure 1: Software Defined Network (SDN)
Accounting Quality and Debt Contracting

We study the role of borrower accounting quality in debt contracting. Specifically, we examine how accounting quality affects the borrower's choice of private versus public debt market and how the design of debt contracts vary with accounting quality in the two markets. We find that accounting quality affects the choice of the market, with poorer accounting quality borrowers preferring private debt, i.e., bank loans. This is consistent with banks possessing superior information access and processing abilities that reduce adverse selection costs for borrowers. We also find that accounting quality has an economically significant but differential impact on contract design in the two markets consistent with differences in recontracting flexibility across the two markets. In the case of private debt, since there is greater recontracting flexibility, both the price (i.e., interest) and non‐price (i.e., maturity and collateral) terms are significantly more stringent for poorer accounting quality borrowers, unlik.