Miracle-dz/UniFAR-FTUs huggingface dataset:
Ancient roles of non-coding RNAs in eukaryotic evolution

RNAs not coding for proteins, non-coding RNAs (ncRNAs) have many important roles in all kingdoms of life. Especially in eukaryotes, the regulatory functions of ncRNAs have been suggested as a major force in the evolution of complex traits. Cellular processes that are regulated by ncRNAs include for example cell differentiation, organ development and defense against viruses and transposable elements. This is achieved through a number of mechanisms like RNA destabilization and modification, transcriptional and translational control and chromatin modifications. Dictyostelium discoideum is a social amoeba and the best studied organism representing Amoebozoa, one of the eukaryotic supergroups. It has for long served as an excellent model for many basic cellular events like chemotaxis, differentiation and development and recently also for infection. The ncRNA population in D. discoideum is in many ways typical of eukaryotes but also harbors particularities. In this thesis I have studied spliceosomal RNAs as well as the RNA interference and microRNA pathways, which probably were present in the last eukaryotic common ancestor. I have also characterized Class I RNAs which seems to be specific to social amoebae. In addition, we have described the signal recognition particle RNA in several protists and also the involvement of a ncRNA during host interaction and stress in Giardia lamblia. Combining the well established molecular tools and knowledge about various pathways in D. discoideum, with the growing understanding of ncRNA, could in the future give important information about the function of ncRNAs as well as their ancient roles and evolution.
Bandit-Based Planning and Learning in Continuous-Action Markov Decision Processes

Recent research leverages results from the continuous-armed bandit literature to create a reinforcement-learning algorithm for continuous state and action spaces. Initially proposed in a theoretical setting, we provide the first examination of the empirical properties of the algorithm. Through experimentation, we demonstrate the effectiveness of this planning method when coupled with exploration and model learning and show that, in addition to its formal guarantees, the approach is very competitive with other continuous-action reinforcement learners.
Pharmacokinetic Considerations and Efficacy of Levofloxacin in an Inhalational Anthrax (Postexposure) Rhesus Monkey Model

ABSTRACT Because the treatment of inhalational anthrax cannot be studied in human clinical trials, it is necessary to conduct efficacy studies using a rhesus monkey model. However, the half-life of levofloxacin was approximately three times shorter in rhesus monkeys than in humans. Computer simulations to match plasma concentration profile, area under the concentration-time curve (AUC), and time above MIC for a human oral dose of 500 mg levofloxacin once a day identified a dosing regimen in rhesus monkeys that would most closely match human exposure: 15 mg/kg followed by 4 mg/kg administered 12 h later. Approximately 24 h following inhalational exposure to approximately 49 times the 50% lethal doses of Bacillus anthracis (Ames strain), monkeys were treated daily with vehicle, levofloxacin, or ciprofloxacin for 30 days. Ciprofloxacin was administered at 16 mg/kg twice a day. Following the 30-day treatment, monkeys were observed for 70 days. Nine of 10 control monkeys died within 9 days of exposure. No clinical signs were observed in fluoroquinolone-treated monkeys during the 30 treatment days. One monkey died 8 days after levofloxacin treatment, and two monkeys from the ciprofloxacin group died 27 and 36 days posttreatment, respectively. These deaths were probably related to the germination of residual spores. B. anthracis was positively cultured from several tissues from the three fluoroquinolone-treated monkeys that died. MICs of levofloxacin and ciprofloxacin from these cultures were comparable to those from the inoculating strain. These data demonstrate that a humanized dosing regimen of levofloxacin was effective in preventing morbidity and mortality from inhalational anthrax in rhesus monkeys and did not select for resistance.
PROJECT A VALIDITY RESULTS: THE RELATIONSHIP BETWEEN PREDICTOR AND CRITERION DOMAINS

A predictor battery of cognitive ability, perceptual-psychomotor ability, temperament/personality, interest, and job outcome preference measures was administered to enlisted soldiers in nine Army jobs. These measures were summarized in terms of 24 composite scores. The relationships between the predictor composite scores and five components of job performance were analyzed. Scores from the cognitive and perceptual-psychomotor ability tests provided the best prediction of job-specific and general task proficiency, while the temperament/personality composites were the best predictors of giving extra effort, supporting peers, and exhibiting personal discipline. Composite scores derived from the interest inventory were correlated more highly with task proficiency than with demonstrating effort and peer support. In particular, vocational interests were among the best predictors of task proficiency in combat jobs. The results suggest that the Army can improve the prediction of job performance by adding non-cognitive predictors to its present battery of predictor tests.
Characterization of the Golgi Retention Motif of Rift Valley Fever Virus GN Glycoprotein

ABSTRACT As Rift Valley fever (RVF) virus, and probably all members of the family Bunyaviridae, matures in the Golgi apparatus, the targeting of the virus glycoproteins to the Golgi apparatus plays a pivotal role in the virus replication cycle. No consensus Golgi localization motif appears to be shared among the glycoproteins of these viruses. The viruses of the family Bunyaviridae synthesize their glycoproteins, GN and GC, as a polyprotein. The Golgi localization signal of RVF virus has been shown to reside within the GN protein by use of a plasmid-based transient expression system to synthesize individual GN and GC proteins. While the distribution of individually expressed GN significantly overlaps with cellular Golgi proteins such as β-COP and GS-28, GC expressed in the absence of GN localizes to the endoplasmic reticulum. Further analysis of expressed GN truncated proteins and green fluorescent protein/GN chimeric proteins demonstrated that the RVF virus Golgi localization signal mapped to a 48-amino-acid region of GN encompassing the 20-amino-acid transmembrane domain and the adjacent 28 amino acids of the cytosolic tail.
Are People Really Social in Porn 2.0?

Social Web 2.0 features have become a vital component in a variety of multimedia systems, e.g., YouTube, Last.fm. Interestingly, adult video websites are also starting to adopt these Web 2.0 principles, giving rise to the term "Porn 2.0". This paper examines a large Porn 2.0 social network, through data covering 563k users. We explore a number of unusual behavioural aspects that set this apart from more traditional multimedia social networks. We particularly focus on the role of gender and sexuality, to understand how these different groups behave. A number of key differences are discovered relating to social demographics, modalities of interaction and content consumption habits, shedding light on this understudied area of online activity.
CD40 expression and its association with low-grade inflammation in a Greek population of type 1 diabetic juveniles: evidence for differences in CD40 mRNA isoforms expressed by peripheral blood mononuclear cells.

BACKGROUND CD40 signalling has been associated with the pathogenesis of autoimmune diseases and diseases with low-grade chronic inflammation. OBJECTIVE To investigate, early in the course of type 1 diabetes (T1DM) patients, the expression of CD40 system components, as well as to explore the association of plasma and urine concentrations of CD40 with known inflammatory markers in T1DM. METHODS Plasma, urine and peripheral blood mononuclear cells (PBMCs) from 70 T1DM patients without clinically detected chronic complications and 40 healthy controls (HCs) were examined using ELISA, western-blot, semi-quantitative RT-PCR and DNA-sequencing. RESULTS Patients had significantly higher plasma soluble CD40 (sCD40) levels associated with higher Interleukin-6 (IL-6), matrix metalloproteinase-9 (MMP-9) and CRP levels compared with healthy controls. This difference was also evident between poorly and well-controlled diabetic patients. The elevated plasma sCD40 levels do not appear to be due to diminished renal excretion since sCD40 concentrations in the urine were also elevated, suggesting an increased CD40 production. An upregulation of PBMCs' CD40 was evident in T1DM patients associated with higher sCD40, IL-6 and CRP levels. Furthermore, the main CD40 isoform (isoform-I) was solely expressed in poorly controlled diabetics' PBMCs, who also demonstrated cellular CD40 upregulation, higher plasma CD40, CRP, IL-6 and MMP-9 levels compared with the well-controlled diabetics and the control group, who co-expressed type I and II isoforms. CONCLUSIONS Homeostatic dysregulation of CD40 and its association with inflammatory markers in T1DM patients, especially in those with poor glycaemic control, implies a pathophysiological role of CD40 in the low-grade inflammatory process in T1DM.
Improving cross-domain n-gram language modelling with skipgrams

In this paper we improve over the hierarchical Pitman-Yor processes language model in a cross-domain setting by adding skipgrams as features. We find that adding skipgram features reduces the perplexity. This reduction is substantial when models are trained on a generic corpus and tested on domain-specific corpora. We also find that within-domain testing and cross-domain testing require different backoff strategies. We observe a 30-40% reduction in perplexity in a cross-domain language modelling task, and up to 6% reduction in a within-domain experiment, for both English and Flemish-Dutch.
HORNET: A Cycle-Level Multicore Simulator

We present hornet, a parallel, highly configurable, cycle-level multicore simulator based on an ingress-queued wormhole router network-on-chip (NoC) architecture. The parallel simulation engine offers cycle-accurate as well as periodic synchronization; while preserving functional accuracy, this permits tradeoffs between perfect timing accuracy and high speed with very good accuracy. When run on six separate physical cores on a single die, speedups can exceed a factor of over 5, and when run on a two-die 12-core system with 2-way hyperthreading, speedups exceed 12×. Most hardware parameters are configurable, including memory hierarchy, interconnect geometry, bandwidth, crossbar dimensions, parameters driving power, and thermal effects. A highly parametrized table-based NoC design allows a variety of routing and virtual channel allocation algorithms out of the box, ranging from simple dimension-ordered routing to complex Valiant, ROMM, O1Turn or PROM schemes, BSOR, and adaptive routing. Hornet can run in network-only mode using synthetic traffic or traces, or directly emulate a MIPS-based multicore. Hornet is freely available under the open-source MIT license at http://csg.csail. mit.edu/hornet/.
Zonation of bacterioplankton communities along aging upwelled water in the northern Benguela upwelling

Upwelling areas are shaped by enhanced primary production in surface waters, accompanied by a well-investigated planktonic succession. Although bacteria play an important role in biogeochemical cycles of upwelling systems, little is known about bacterial community composition and its development during upwelling events. The aim of this study was to investigate the succession of bacterial assemblages in aging upwelled water of the Benguela upwelling from coastal to offshore sites. Water from the upper mixed layer at 12 stations was sampled along two transects from the origin of the upwelling to a distance of 220 km. 16S rRNA gene amplicon sequencing was then used in a bacterial diversity analysis and major bacterial taxa were quantified by catalyzed reporter deposition-fluorescence in situ hybridization. Additionally, bacterial cell numbers and bacterial production were assessed. Community statistical analysis revealed a reproducible zonation along the two transects, with four clusters of significantly different microbial assemblages. Clustering was mainly driven by phytoplankton composition and abundance. Similar to the temporal succession that occurs during phytoplankton blooms in temperate coastal waters, operational taxonomic units (OTUs) affiliated with Bacteroidetes and Gammaproteobacteria were dominant during algal blooming whereas “Pelagibacterales” were highly abundant in regions with low algal abundance. The most dominant heterotrophic OTU (9% of all reads) was affiliated with “Pelagibacterales” and showed a strong negative correlation with phytoplankton. By contrast, the second most abundant heterotrophic OTU (6% of all reads) was affiliated with the phylum Verrucomicrobia and correlated positively with phytoplankton. Together with the close relation of bacterial production and phytoplankton abundance, our results showed that bacterial community dynamics is strongly driven by the development and composition of the phytoplankton community.
VISION IN THE CTENID SPIDER CUPIENNIUS SALEI: SPECTRAL RANGE AND ABSOLUTE SENSITIVITY

Electroretinograms were recorded from all eyes of the wandering spider Cupiennius salei (Ctenidae) and were found to be simple cornea-negative potential differences with amplitudes of up to 10 mV. In both the principal eyes and all of the secondary eyes, the spectral response curves show a prominent green peak at 520 or 540 nm and a shoulder in the ultraviolet between 340 and 380 nm. The largest response in the ultraviolet measures between 65 % and 80 % of the green peak. Selective chromatic adaptation to either green or ultraviolet monochromatic light does not change these relative response levels and fails to indicate the presence of more than one spectral type of receptor. In the range 450–500 nm, however, the Dartnall curve clearly deviates from the spectral sensitivity (SS) curve. Since the SS curves of all eyes have a small shoulder in the blue at 480 nm, the existence of two or even three visual pigments is a possibility. Intensity curves were determined with white and monochromatic light. For white light, absolute corneal illuminance thresholds were clearly below 0.01 lx. For monochromatic light stimuli, a corneal illuminance of approximately 3×1012 photons cm-2 s-1 is needed to elicit a half-maximal response. At threshold, the equivalent value is 3×109 photons cm-2 s-1, which corresponds to a retinal illuminance of 5.9×109 photons cm-2 s-1. Consequently, Cupiennius salei should be able to use its visual sense not only shortly after sundown but also under much poorer light conditions, such as those provided by moonlight. The log-linear response range of all eyes covers a stimulus intensity range of 4 log units. The sensitivity of the principal eyes increases by up to 0.81 log units at night as compared with daytime. The chromophore of the visual pigment of all eyes is 11- cis retinal.
Monocilia in the embryonic mouse heart suggest a direct role for cilia in cardiac morphogenesis

Primary cilia are required for signaling, chemosensing and mechanosensing in many fluid‐filled organs, thus cilia could also have a direct role in heart development. They are essential to the development of cardiac left–right (LR) asymmetry by means of their function at the embryonic organizer (node). We show that cilia are found in the mouse embryo heart at embryonic day (e) 9.5–e12.5. We demonstrate abnormal development of the endocardial cushions (ECCs) and compact myocardium (CM) in e9.5 mouse embryos with absent cilia. In contrast, hearts from embryos with abnormal LR development due to paralyzed, but structurally normal, node cilia show less severe ECC defects and normal CM. These observations suggest that a subset of cilia called cardiac cilia are required in cardiac development independently from their function in LR development. One possible function of cardiac cilia is as mechanosensors, integrating flow, cardiac function, and morphogenesis. Developmental Dynamics 237:2304–2314, 2008. © 2008 Wiley‐Liss, Inc.
Discriminatory proofreading regimes in non-equilibrium systems

We use ideas from kinetic proofreading, an error-correcting mechanism in biology, to identify new kinetic regimes in non-equilibrium systems. These regimes are defined by the sensitivity of the occupancy of a state of the system to a change in its energy. In biological contexts, higher sensitivity corresponds to stronger discrimination between molecular substrates with different energetics competing in the same reaction. We study this discriminatory ability in systems with discrete states that are connected by a general network of transitions. We find multiple regimes of different discriminatory ability when the energy of a given state of the network is varied. Interestingly, the occupancy of the state can even increase with its energy, corresponding to an "anti-proofreading" regime. The number and properties of such discriminatory regimes are limited by the topology of the network. Finally, we find that discriminatory regimes can be changed without modifying any "hard-wired" structural aspects of the system but rather by simply changing external chemical potentials.
A First-Person Account of the Quandaries of a Professional

Stine M. Levy GUEST EDITOR’S NOTE: Stine M. Levy is well known for her work with the Indiana Resource Center for Autism. She was also one of the first professionctls to publish on higb-functioning autism. Stine has been a mentor ctndguiding light to mctny of us parents and professionals in the field. Trust Stine to bring up the thorny issues involved with diagnosis: What are the consequences of labeling individuals with bigb-functioning autism and Asperger syndrome?
The Learning Curve of IT Knowledge Workers in a Computing Call Center

We analyze learning and knowledge transfer in a computing call center. The information technology (IT) technical services provided by call centers are characterized by constant changes in relevant knowledge and a wide variety of support requests. Under this IT problem-solving context, we analyze the learning curve relationship between problem-solving experience and performance enhancement. Based on data collected from a university computing call center consisting of different types of consultants, our empirical findings indicate that (a) the learning effect---as measured by the reduction of average resolution time---occurs with experience, (b) knowledge transfer within a group occurs among lower-level consultants utilizing application-level knowledge (as opposed to technical-level knowledge), and (c) knowledge transfers across IT problem types. These estimates of learning and knowledge transfer contribute to the development of an empirically grounded understanding of IT knowledge workers' learning behavior. The results also have implications for operational decisions about the staffing and problem-solving strategy of call centers.
A Comparison of Female Professionals' Role Profiles with Occupational Adjustment and Life Satisfaction.

This exploratory study on 50 female health professionals examined the impact that multiple roles (work/family) had on occupational adjustment and life satisfaction. Results indicate some evidence that as the number of occupational roles increased, life satisfaction scores tended to decrease; however, as the number of family roles increased, scores on occupational adjustment and life satisfaction scales tended to increase.
Modeling and Predicting Mental Workload in En Route Air Traffic Control: Critical Review and Broader Implications

Objective: We perform a critical review of research on mental workload in en route air traffic control (ATC). We present a model of operator strategic behavior and workload management through which workload can be predicted within ATC and other complex work systems. Background: Air traffic volume is increasing worldwide. If air traffic management organizations are to meet future demand safely, better models of controller workload are needed. Method: We present the theoretical model and then review investigations of how effectively traffic factors, airspace factors, and operational constraints predict controller workload. Results: Although task demand has a strong relationship with workload, evidence suggests that the relationship depends on the capacity of the controllers to select priorities, manage their cognitive resources, and regulate their own performance. We review research on strategies employed by controllers to minimize the control activity and information-processing requirements of control tasks. Conclusion: Controller workload will not be effectively modeled until controllers' strategies for regulating the cognitive impact of task demand have been modeled. Application: Actual and potential applications of our conclusions include a reorientation of workload modeling in complex work systems to capture the dynamic and adaptive nature of the operator's work. Models based around workload regulation may be more useful in helping management organizations adapt to future control regimens in complex work systems.
Facial expression of emotion: A comparison of posed expressions versus spontaneous expressions in an interpersonal communication setting

Many assumptions about the operation of nonverbal behaviors in interpersonal communication have been based upon studies which have not focused on interpersonal communication settings. Especially, most studies of facial expression have examined posed rather than spontaneous expressions, and the relatively few studies of spontaneous expressions have employed stimuli and/or settings of dubious relevance to everyday communication. The present study compares the identifiability of posed vs. spontaneous facial expressions of emotion elicited during ostensibly natural conversation. While posed expressions, as in earlier studies, were quite unambiguous, spontaneous expressions of emotion were found to be remarkably difficult to identify. Implications are discussed for the generalizability of certain nonverbal research results to interpersonal communication settings, for related methodological considerations, for revised conceptualizations of the function of facial expression, and for the more general issue of com.
What We Don't Learn from Clinical Trials in Epilepsy

Summary: The randomized, double‐blind trial design offers the most accurate data regarding the efficacy of antiepileptic treatments. However, translating the results of a trial into clinical care can be complex due to the intrinsic tension between the requirements for scientific methods that minimize systematic and random error, and the need for clinically relevant and generalizable data. The interpretation of the trial results is complicated further by the probable inaccuracy of self‐reported seizure rates and spontaneously reported adverse effects in most trials. Patient preference may be a feasible outcome measure that allows patient‐oriented validation of the results, and also inherently weighs the positive and negative effects of a treatment in a single endpoint.