Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of Increasing the Affinity of CarD for RNA Polymerase on Mycobacterium tuberculosis Growth, rRNA Transcription, and Virulence

ABSTRACT CarD is an essential RNA polymerase (RNAP) interacting protein in Mycobacterium tuberculosis that stimulates formation of RNAP-promoter open complexes. CarD plays a complex role in M. tuberculosis growth and virulence that is not fully understood. Therefore, to gain further insight into the role of CarD in M. tuberculosis growth and virulence, we determined the effect of increasing the affinity of CarD for RNAP. Using site-directed mutagenesis guided by crystal structures of CarD bound to RNAP, we identified amino acid substitutions that increase the affinity of CarD for RNAP. Using these substitutions, we show that increasing the affinity of CarD for RNAP increases the stability of the CarD protein in M. tuberculosis. In addition, we show that increasing the affinity of CarD for RNAP increases the growth rate in M. tuberculosis without affecting 16S rRNA levels. We further show that increasing the affinity of CarD for RNAP reduces M. tuberculosis virulence in a mouse model of infection despite the improved growth rate in vitro. Our findings suggest that the CarD-RNAP interaction protects CarD from proteolytic degradation in M. tuberculosis, establish that growth rate and rRNA levels can be uncoupled in M. tuberculosis and demonstrate that the strength of the CarD-RNAP interaction has been finely tuned to optimize virulence. IMPORTANCE Mycobacterium tuberculosis, the causative agent of tuberculosis, remains a major global health problem. In order to develop new strategies to battle this pathogen, we must gain a better understanding of the molecular processes involved in its survival and pathogenesis. We have previously identified CarD as an essential transcriptional regulator in mycobacteria. In this study, we detail the effects of increasing the affinity of CarD for RNAP on transcriptional regulation, CarD protein stability, and virulence. These studies expand our understanding of the global transcription regulator CarD, provide insight into how CarD activity is regulated, and broaden our understanding of prokaryotic transcription.
The bacteriocin piscicolin 126 retains antilisterial activity in vivo.

OBJECTIVE We have conducted a series of experiments to show that the bacteriocin piscicolin 126 (P126) retains antilisterial activity after injection into a mouse. METHODS Groups of mice were challenged intravenously with Listeria monocytogenes and treated with purified P126 at varying times before and after challenge to determine whether administration of this peptide reduced numbers of colonizing L. monocytogenes and the symptoms of listeriosis. RESULTS The bacteriocin P126 retained antilisterial activity after injection into the mouse. During the early time-points of listerial infection, the purified P126 was found to significantly reduce the listerial load in the liver and spleen and, further, that this reduction translated to reduced clinical signs of disease. CONCLUSIONS This is the first report of a Class IIA bacteriocin displaying in vivo antimicrobial activity. Such a result provides preliminary evidence that this class of molecules may be useful in controlling systemic bacterial infections.
Visual PLC-programming using signal interpreted Petri nets

In this contribution, we present a graphical programming approach for Programmable Logic Controllers (PLCs) based on a special type of Petri net, the Signal Interpreted Petri Net (SIPN). We give an introduction to PLCs and an overview of the languages used to program them. From this overview, we conclude that for PLCs a language is missing that is capable of a simple graphical description of sequential and concurrent behavior. SIPN is such a language. We present the SIPN approach and some corresponding analysis methods. Furthermore, we report on some experiments done in a university course, that show that the method is indeed useful in solving control problems. Since programming a controller without tool-support is nearly impossible, we present a tool for graphical editing and compilation of SIPN. In the development of the tool, not only the implementation of the SIPN as it is defined in theory played a role, but the projected application area and user interest were also considered.
An Architecture for Modular Data Centers

Several factors are driving high-scale deployments of large data centers built upon commodity components. These commodity clusters are far cheaper than mainframe systems of the past but they bring serious heat and power density issues. Also the high failure rate of the individual components drives significant administrative costs. This proposal outlines an architecture for data center design based upon 20'x8'x8' modules that substantially changes how these systems are acquired, administered, and then later recycled.
The Contribution of Ant‐Plant Protection Studies to Our Understanding of Mutualism 1

One common class of ant‐plant mutualism involves ants that defend plants from natural enemies in return for food and sometimes shelter. Studies of these interactions have played a major role in shaping our broad understanding of mutualism. Their central contribution has come via their development of approaches to measuring the benefits, costs, and net outcomes of mutualism, and their explicit consideration of variability in all of these phenomena. Current research on these interactions is suggesting ecological and evolutionary hypotheses that may be applicable to many other forms of mutualism. It is also generating comparative data for testing the few general theories about mutualism that currently exist.
An Image Rendering Pipeline for Focused Plenoptic Cameras

In this paper, we present a complete processing pipeline for focused plenoptic cameras. In particular, we propose 1) a new algorithm for microlens center calibration fully in the Fourier domain, 2) a novel algorithm for depth map computation using a stereo focal stack, and 3) a depth-based rendering algorithm that is able to refocus at a particular depth or to create all-in-focus images. The proposed algorithms are fast, accurate, and do not need to generate subaperture images or epipolar plane images which is capital for focused plenoptic cameras. Also, the resolution of the resulting depth map is the same as the rendered image. We show results of our pipeline on Georgiev's dataset and real images captured with different Raytrix cameras.
A Systematic Review of the Epidemiology of Echinococcosis in Domestic and Wild Animals

Background Human echinococcosis is a neglected zoonosis caused by parasites of the genus Echinococcus. The most frequent clinical forms of echinococcosis, cystic echinococcosis (CE) and alveolar echinococcosis (AE), are responsible for a substantial health and economic burden, particularly to low-income societies. Quantitative epidemiology can provide important information to improve the understanding of parasite transmission and hence is an important part of efforts to control this disease. The purpose of this review is to give an insight on factors associated with echinococcosis in animal hosts by summarising significant results reported from epidemiological studies identified through a systematic search. Methodology and Principal Findings The systematic search was conducted mainly in electronic databases but a few additional records were obtained from other sources. Retrieved entries were examined in order to identify available peer-reviewed epidemiological studies that found significant risk factors for infection using associative statistical methods. One hundred studies met the eligibility criteria and were suitable for data extraction. Epidemiological factors associated with increased risk of E. granulosus infection in dogs included feeding with raw viscera, possibility of scavenging dead animals, lack of anthelmintic treatment and owners' poor health education and indicators of poverty. Key factors associated with E. granulosus infection in intermediate hosts were related to the hosts' age and the intensity of environmental contamination with parasite eggs. E. multilocularis transmission dynamics in animal hosts depended on the interaction of several ecological factors, such as hosts' population densities, host-prey interactions, landscape characteristics, climate conditions and human-related activities. Conclusions/Significance Results derived from epidemiological studies provide a better understanding of the behavioural, biological and ecological factors involved in the transmission of this parasite and hence can aid in the design of more effective control strategies.
Teaching Medication Adherence in US Colleges and Schools of Pharmacy

Objective. To determine and describe the nature and extent of medication adherence education in US colleges and schools of pharmacy. Methods. A mixed-methods research study was conducted that included a national survey of pharmacy faculty members, a national survey of pharmacy students, and phone interviews of 3 faculty members and 6 preceptors. Results. The majority of faculty members and students agreed that background concepts in medication adherence are well covered in pharmacy curricula. Approximately 40% to 65% of the students sampled were not familiar with several adherence interventions. The 6 preceptors who were interviewed felt they were not well-informed on adherence interventions, unclear on what students knew about adherence, and challenged to provide adherence-related activities for students during practice experiences because of practice time constraints. Conclusions. Intermediate and advanced concepts in medication adherence, such as conducting interventions, are not adequately covered in pharmacy curriculums; therefore stakeholders in pharmacy education must develop national standards and tools to ensure consistent and adequate medication adherence education.
Identification of inactivity behavior in Smart Home

To help elderly people live independently at home, the TIMC-IMAG laboratory developed Health Smart Homes called “HIS”. These smart Homes are composed of several sensors to monitor the activities of daily living of the patients. Volunteers have accepted to be monitored during 2 years in their own flats. During one year, we carried out our survey on one elderly patient. Thanks to this experimentation, we will access to relevant information like physiological, environmental and activity. This paper focuses on daily living activity. We will introduce an original data splitting method based on the relationship between the frame of time and the location in the flat. Moreover we will present two different methods to determine a threshold of critical inactivity and eventually we will discuss their possible utilities.
Sound speed measurements in zirconium using the front surface impact technique

We have performed a series of experiments impacting zirconium samples of varying purity level directly onto lithium fluoride (LiF) windows to determine both the Hugoniot and sound speed as a function of stress up to 70 GPa. This front surface impact (FSI) geometry is useful for determining sound speed in shock-compression experiments because wave interactions are mostly eliminated and multiple sample thicknesses are not needed in each experiment. The experimental results show two kinks in the sound speed which correlate well with the location of the α → ω and ω → β transitions, respectively. A rarefaction shock also forms in the release wave in experiments conducted at 31 GPa giving further evidence that this phase transition is being observed.
Could the Recent Zika Epidemic Have Been Predicted?

Given knowledge at the time, the recent 2015-2016 zika virus (ZIKV) epidemic probably could not have been predicted. Without the prior knowledge of ZIKV being already present in South America, and given the lack of understanding of key epidemiologic processes and long-term records of ZIKV cases in the continent, the best related prediction was for potential risk of an Aedes-borne disease epidemic. Here we use a recently published two-vector capacity model to assess the predictability of the conditions conducive to epidemics of diseases like zika, chikungunya or dengue, transmitted by the independent or concurrent presence of Aedes aegypti and Aedes albopictus. We compare the potential risk of transmission forcing the model with the observed climate and with state-of-the-art operational forecasts from the North American Multi Model Ensemble (NMME), finding that the predictive skill of this new seasonal forecast system is highest for multiple countries in Latin America and the Caribbean during the December-February and March-May seasons, and slightly lower –but still of potential use to decision-makers– for the rest of the year. In particular, we find that above-normal suitable conditions for the occurrence of the zika epidemic at the beginning of 2015 could have been successfully predicted for several zika hotspots, and in particular for Northeast Brazil: the heart of the epidemic. Nonetheless, the initiation and spread of an epidemic depends on the effect of multiple factors beyond climate conditions, and thus this type of approach must be considered as a guide and not as a formal predictive tool of vector-borne epidemics.
Control of Inward Rectifier K Channel Activity by Lipid Tethering of Cytoplasmic Domains

Interactions between nontransmembrane domains and the lipid membrane are proposed to modulate activity of many ion channels. In Kir channels, the so-called “slide-helix” is proposed to interact with the lipid headgroups and control channel gating. We examined this possibility directly in a cell-free system consisting of KirBac1.1 reconstituted into pure lipid vesicles. Cysteine substitution of positively charged slide-helix residues (R49C and K57C) leads to loss of channel activity that is rescued by in situ restoration of charge following modification by MTSET+ or MTSEA+, but not MTSES− or neutral MMTS. Strikingly, activity is also rescued by modification with long-chain alkyl-MTS reagents. Such reagents are expected to partition into, and hence tether the side chain to, the membrane. Systematic scanning reveals additional slide-helix residues that are activated or inhibited following alkyl-MTS modification. A pattern emerges whereby lipid tethering of the N terminus, or C terminus, of the slide-helix, respectively inhibits, or activates, channel activity. This study establishes a critical role of the slide-helix in Kir channel gating, and directly demonstrates that physical interaction of soluble domains with the membrane can control ion channel activity.
Virtual Machine Image Content Aware I/O Optimization for Mobile Virtualization

Mobile virtualization introduces extra layers in software stacks, which leads to performance degradation. Especially, each I/O operation has to pass through several software layers to reach the NAND-flash-based storage systems. This paper targets at optimizing I/O for mobile virtualization, since I/O becomes one of major performance bottlenecks that seriously affects the performance of mobile devices. Among all the I/O operations, a large percentage is updating metadata. Frequent updating metadata not only degrades overall I/O performance but also severely reduces flash memory lifetime. In this paper, we propose a novel I/O optimization techniqueto identify the metadata of a guest file system which is storedin a VM (Virtual Machine) image file and frequently updated. Then, these metadata are stored in a small additional NVM(Non-Volatile Memory) which is faster and more endurableto greatly improve flash memory's performance and lifetime. To the best of our knowledge, this is the first work to identifythe file system metadata from regular data in a guest OS VMimage file under mobile virtualization. The proposed schemeis evaluated on a real hardware embedded platform. Theexperimental results show that the proposed techniques canimprove write performance to 45.21% in mobile devices withvirtualization.
Law R, Dieckmann U & Metz JAJ (2000). Introduction. In: The Geometry of Ecological Interactions:

Species form different kinds of patches; these patches form a mosaic and together constitute the community. Recognition of the patch is fundamental to an understanding of structure. Patches are dynamically related to each other. But there are also departures from this inherent tendency to orderliness. At any given time, therefore, structure is the resultant of causes which make for order, and those that tend to upset it. Both sets of causes must be appreciated. Abbreviated from Watt (1947, p. 2) Pattern and process in the plant community
Elucidating the significance of spatial memory on movement decisions by African savannah elephants using state–space models

Spatial memory facilitates resource acquisition where resources are patchy, but how it influences movement behaviour of wide-ranging species remains to be resolved. We examined African elephant spatial memory reflected in movement decisions regarding access to perennial waterholes. State–space models of movement data revealed a rapid, highly directional movement behaviour almost exclusively associated with visiting perennial water. Behavioural change point (BCP) analyses demonstrated that these goal-oriented movements were initiated on average 4.59 km, and up to 49.97 km, from the visited waterhole, with the closest waterhole accessed 90% of the time. Distances of decision points increased when switching to different waterholes, during the dry season, or for female groups relative to males, while selection of the closest waterhole decreased when switching. Overall, our analyses indicated detailed spatial knowledge over large scales, enabling elephants to minimize travel distance through highly directional movement when accessing water. We discuss the likely cognitive and socioecological mechanisms driving these spatially precise movements that are most consistent with our findings. By applying modern analytic techniques to high-resolution movement data, this study illustrates emerging approaches for studying how cognition structures animal movement behaviour in different ecological and social contexts.
Diabetic papillopathy with macular edema treated with intravitreal bevacizumab

A 46-year-old diabetic male presented with acute painless visual loss in his left eye (OS). Visual acuity was 6/36 OS with an unremarkable anterior segment examination (OU). Posterior segment showed a swollen left optic disc with large diffuse macular edema and moderate nonproliferative diabetic retinopathy (NPDR). The right eye fundus showed only mild NPDR. Optical coherence tomography and fundus fluorescein angiography were performed which revealed left macular edema and a hyperfluorescent left optic disc. Computerized tomography scan orbit and brain was normal. The patient received an intravitreal bevacizumab injection OS followed by focal laser photocoagulation 1 month later. His optic disc swelling and the macular edema subsided rapidly after the injection and his visual acuity improved to 6/6 with disc pallor.
Primary and Secondary Transport of Cations in Bacteria a

Bacterial physiology makes sense in the chemiosmotic framework, but it does not encourage fundamentalism. It is now well established that bacteria transport many sugars, amino acids, and other nutrients with the aid of secondary porters; and that the electrochemical potential of protons across the plasma membrane provides the driving force, just as Mitchell envisaged (Reviews: Mitchellis2 and Harold3). But the activities of these porters are supplemented by a variety of primary transport systems energized by ATP and by other phosphoryl donors, and organisms differ from one another in their complement of transport systems. The movements of K+ and Na+ ions illustrate the interplay between the primary and secondary modes of energy-linked transport. This essay is concerned with the fermentative bacterium Streptococcus faecalis. Streptococci lack respiratory chains and anaerobic redox pathways, relying on glycolysis or arginine fermentation for the production of ATP. Like other bacteria (indeed, living cells in general), streptococci accumulate K+ ions and extrude both N a + and protons. The cytoplasmic K+ level is typically 500 m M or more though the external one may be as low as 50 p M , giving a concentration gradient of lo4. The usual growth media contain 100-200 m M Na+, but the cytoplasmic N a + level is 1 m M or less. The cytoplasmic pH, 7.5 to 8, is normally at least one unit more alkaline than that of the medium, and the membrane potential is of the order of -120 mV (interior negative). A little reflection will show that a t least two of the cations involved must be transported actively, and we seek to discover both how and why. We still do not fully understand how the free energy represented by the ATP/ADP couple is used for ion transport and have much to learn about the functional purposes of this energy expenditure. However, we think that we have now identified the main catalytic systems and characterized them in terms of their ion fluxes and energy inputs. With the players recognizable, the plot seems a little less obscure.
THE VELOCITY OF SOUND.

Abstract A new method for measuring the velocity of sound over short distances has been devised in which sixty pulses per second cause a sinusoidal curve to appear upon an oscilloscopic screen.As the receiving microphone is moved away from the sound oscillator, the crest of the sine curve moves across the oscilloscope, completing the circle in one-sixtieth of a second. The actual velocity of the sound is easily calculated after the distance moved bv the microphone has been measured. Application of the probability laws and the error curve shows that the method is very accurate, providing the alternating current maintains itself invariably at sixty cycles per second. The average of twelve hundred measurements gives 331.364 ± 0.043 meters per second at zero degrees centrigrade.
A Fast Transaction-Oriented Logging Scheme for Undo Ro overy

A special UNDO log algorithm combining the advantages of update in place strategies with the shadow page concept is introduced. It is to support applications demanding high rates of possibly long update transactions as well as fast UNDO recovery. By doubling the disk space for the database, UNDO loggng can be performed with a minimum of additional I/O operations. Thus, we gain a performance comparable to systems without any UNDO loggg. Since in this algorithm one logical slot consists of two physical blocks, the name TWIST (twin slot) algorithm is proposed.