Miracle-dz/UniFAR-FTUs huggingface dataset:
The role of cell type-specific responses in IFN-β therapy of multiple sclerosis

The mechanism of IFN-β therapy in relapsing-remitting multiple sclerosis (RRMS) is not well understood, but induction of apoptosis in specific leukocyte subsets is likely to be important. Enhanced expression of TNFSF10 or TNF-related apoptosis-inducing ligand (TRAIL) mRNA in unseparated leukocytes has been put forward as a therapeutic response marker, but it is unclear which leukocyte subsets express TRAIL. We investigated the basis of TRAIL expression in response to IFN-β by studying activation of STATs 1, 3, and 5, p38 MAPK, and NF-κB in different leukocyte subsets of patients with RRMS. Monocytes, B cells, and T cells showed substantial differences in the activation of p38 and the STATs in response to i.m. injection of IFN-β1a or stimulation in vitro. Induction of cell-surface TRAIL, analyzed in nine leukocyte subsets, was observed only on monocytes and granulocytes and correlated with the activation of p38 and/or NF-κB in these subsets only, in agreement with previous work in fibroblasts showing that the induction of TRAIL in response to IFN-β depends on the activation of p38 and NF-κB as well as STATs 1 and 2. We propose that, in myeloid cells, the differential activation of p38 and NF-κB and induction of TRAIL, which sensitizes cells to apoptosis, can help to explain differences in responsiveness to IFN-β therapy among patients with RRMS and, furthermore, that such differential patterns of activation and expression may also be important in understanding the therapeutic responses to IFN-α/β in hepatitis and cancer.
Stabilization and Destabilization of Nonlinear Differential Equations by Noise

This paper considers the stabilization and destabilization by a Brownian noise perturbation that preserves the equilibrium of the ordinary differential equation x'(t) = f(x(t)). In an extension of earlier work, we lift the restriction that f obeys a global linear bound, and show that when f is locally Lipschitz, a function g can always be found so that the noise perturbation g(X(t)) dB(t) either stabilizes an unstable equilibrium, or destabilizes a stable equilibrium. When the equilibrium of the deterministic equation is nonhyperbolic, we show that a nonhyperbolic perturbation suffices to change the stability properties of the solution.
Deformation-induced ATP release from red blood cells requires CFTR activity.

Recently, it was reported that rabbit and human red blood cells (RBCs) release ATP in response to mechanical deformation. Here we investigate the hypothesis that the activity of the cystic fibrosis transmembrane conductance regulator (CFTR), a member of the ATP binding cassette, is required for deformation-induced ATP release from RBCs. Incubation of rabbit RBCs with either of two inhibitors of CFTR activity, glibenclamide (10 μM) or niflumic acid (20 μM), resulted in inhibition of deformation-induced ATP release. To demonstrate the contribution of CFTR to deformation-induced ATP release from human RBCs, cells from healthy humans, patients with cystic fibrosis (CF), or patients with chronic obstructive lung disease (COPD) unrelated to CF were studied. RBCs of healthy humans and COPD patients released ATP in response to mechanical deformation. In contrast, deformation of RBCs from patients with CF did not result in ATP release. We conclude that deformation-induced ATP release from rabbit and human RBCs requires CFTR activity, suggesting a previously unrecognized role for CFTR in the regulation of vascular resistance.
The ecological distribution and comparative photobiology of symbiotic dinoflagellates from reef corals in Belize: Potential implications for coral bleaching

The photobiology and distribution of dinoflagellates in the genus Symbiodinium was investigated for eight common reef coral species over a depth range of 1‐25 m on a coral reef in Belize. The genetic identification of symbionts using polymerase chain reaction‐denaturing gradient electrophoresis of the internal transcribed spacer 2 region revealed marked differences in host specificity and depth zonation for certain symbiont types. Each host taxon was found to associate with a limited subset of symbionts that exist in the region. Intraspecific variation was greatest at the shallower sites (1‐8 m), where as many as five distinctive symbionts were distributed among a single host population (e.g., Montastraea faveolata). At depth (15‐25 m), variation from colony to colony was minimal, where one algal type associated with most or all the colonies of a species. The maximal photochemical efficiency and light‐acclimated efficiency of photosystem II (PSII) were determined by active chlorophyll fluorescence and used to assess potential differences in photosynthetic potential. Under normal ambient conditions, little or no physiological differences were noted among different symbionts occurring in the same species of coral at a particular depth, yet interspecific differences in PSII efficiency were noted between coral species at the same depth. Short‐term bleaching experiments showed that symbionts B1 and C7 within M. faveolata experienced a higher degree of thermally induced photoinhibition relative to A4a symbionts in Porites astreoides. The differential patterns of PSII inactivation observed within M. faveolata could be explained by the presence of different symbiont populations within this coral. Differences in in situ maximum excitation pressure on PSII between symbionts within some corals may provide a predictive measure of how different species of coral or individual colonies with different symbionts would respond to natural thermal stress events.
Lessons from the DREAM2 Challenges

Regardless of how creative, innovative, and elegant our computational methods, the ultimate proof of an algorithm's worth is the experimentally validated quality of its predictions. Unfortunately, this truism is hard to reduce to practice. Usually, modelers produce hundreds to hundreds of thousands of predictions, most (if not all) of which go untested. In a best‐case scenario, a small subsample of predictions (three to ten usually) is experimentally validated, as a quality control step to attest to the global soundness of the full set of predictions. However, whether this small set is even representative of the global algorithm's performance is a question usually left unaddressed. Thus, a clear understanding of the strengths and weaknesses of an algorithm most often remains elusive, especially to the experimental biologists who must decide which tool to use to address a specific problem. In this chapter, we describe the first systematic set of challenges posed to the systems biology community in the framework of the DREAM (Dialogue for Reverse Engineering Assessments and Methods) project. These tests, which came to be known as the DREAM2 challenges, consist of data generously donated by participants to the DREAM project and curated in such a way as to become problems of network reconstruction and whose solutions, the actual networks behind the data, were withheld from the participants. The explanation of the resulting five challenges, a global comparison of the submissions, and a discussion of the best performing strategies are the main topics discussed.
The International Journal on Advances in Security is published by IARIA

ing is permitted with credit to the source. Libraries are permitted to photocopy or print, providing the reference is mentioned and that the resulting material is made available at no cost. Reference should mention: International Journal On Advances in Security, issn 1942-2636 vol. 1, no. 1, year 2008, http://www.iariajournals. org/security/" The copyright for each included paper belongs to the authors. Republishing of same material, by authors or persons or organizations, is not allowed. Reprint rights can be granted by IARIA or by the authors, and must include proper reference. Reference to an article in the journal is as follows: <Author list>, “<Article title>” International Journal On Advances in Security, issn 1942-2636 vol. 1, no. 1, year 2008,<start page>:<end page> , http://www.iariajournals. org/security/" IARIA journals are made available for free, proving the appropriate references are made when their
Journal of Experimental Psychology: Human Learning and Memory Evidence against a Semantic-episodic Distinction £-john R. Necessarily a Functional One, It Has Often

The possible empirical bases for the semantic-episodic distinction are examined. Two kinds of results are particularly relevant. The first concerns whether the same functional laws can be demonstrated for semantic as for episodic memory. Failure to demonstrate such generalities argues for the distinction, whereas success at demonstrating generalities argues against the need for such a distinction. The second kind of diagnostic result concerns whether one can demonstrate transfer between semantic and episodic memory. Failure to find transfer argues for a separation, whereas evidence for transfer argues against any real separation between the memories. A review of the literature relevant to these two criteria yields considerable evidence against the semantic-episodic distinction. Three experiments are reported that provide new evidence against the distinction. The experiments test whether learning episodic material interferes with the retrieval of semantic information. The dependent measure was the time to respond true or false to a categoriza-tion statement (e.g., "A spaniel is a dog."). Before participating in that task, subjects learned sentences that provided information about the item and category. The results indicated that the time to make the semantic judgment was affected by the item-category relation in the prior study sentences. Generally, the study effects, as well as some other findings, were correctly predicted by the ACT theory, which makes no semantic-episodic distinction. However, contrary to the ACT theory, it was found that learning additional information about a concept does not interfere with making positive semantic memory judgments and possibly facilitates. Tulving (1972) proposed a distinction be-memory for specific events and is temporally tween semantic and episodic memory, dated. Semantic memory is essential for Episodic memory is an autobiographical language use and contains organized knowledge about symbols and concepts detached from autobiographical reference. TulvingBoth authors contributed equally to this article; d seyeral other possible d iff ere nces be-the order of authors was determined by a com toss. r , • i j-i_ j f c We thank Bill Jones and Ed Smith for their comments tween them, including the mode of reference on this manuscript. We also thank Barbara Adams for (autobiographical VS. cognitive) and re-taking responsibility for the programming, execution, trieval characteristics. Though in his 1972 and analysis of Experiment 3. article he stated that this distinction is not
Non-invasive distress evaluation in preterm newborn infants

With the increased survival of very preterm infants, there is a growing concern for their developmental outcomes. Infant cry characteristics reflect the development and possibly the integrity of the central nervous system. In this paper, relationships between fundamental frequency (F0) and vocal tract resonance frequencies (F1–F3) are investigated for a set of preterm newborns, by means of a multi-purpose voice analysis tool (BioVoice), characterised by high-resolution and tracking capabilities. Also, first results about possible distress occurring during cry in preterm newborn infants, as related to the decrease of central blood oxygenation, are presented. To this aim, a recording system (Newborn Recorder) has been developed, that allows synchronised, non-invasive monitoring of blood oxygenation and audio recordings of newborn infant's cry. The method has been applied to preterm newborns at the Intensive Care Unit, A.Meyer Children Hospital, Firenze, Italy.
Functional genomics of tomato in a post-genome-sequencing phase

Completion of tomato genome sequencing project has broad impacts on genetic and genomic studies of tomato and Solanaceae plants. The reference genome sequence derived from Solanum lycopersicum cv ‘Heinz 1706’ serves as the firm basis for sequencing-based approaches to tomato genomics. In this article, we first present a brief summary of the genome sequencing project and a summary of the reference genome sequence. We then focus on recent progress in transcriptome sequencing and small RNA sequencing and show how the reference genome sequence makes these analyses more comprehensive than before. We discuss the potential of in-depth analysis that is based on DNA methylome sequencing and transcription start-site detection. Finally, we describe the current status of efforts to resequence S. lycopersicum cultivars to demonstrate how resequencing can allow the use of intraspecific genomic diversity for detailed phenotyping and breeding.
Maternal Cardiac Output Changes After Crystalloid or Colloid Coload Following Spinal Anesthesia for Elective Cesarean Delivery: A Randomized Controlled Trial

BACKGROUND:Minimizing hypotension associated with spinal anesthesia for cesarean delivery by administration of IV fluids and vasopressors reduces fetal and maternal morbidity. Most studies have concentrated on noninvasive systolic blood pressure (SBP) measurements to evaluate the effect of such regimens. We used a suprasternal Doppler flow technique to measure maternal cardiac output (CO) variables in parturients receiving a phenylephrine infusion combined with the rapid administration of crystalloid or colloid solution at the time of initiation of anesthesia (coload). We hypothesized that a colloid coload compared with a crystalloid coload would produce a larger sustained increase in CO and therefore reduce vasopressor requirements. METHODS:We recruited 60 healthy term women scheduled for elective cesarean delivery under spinal anesthesia for this randomized double-blind study. Baseline heart rate, baseline SBP, and CO variables including stroke volume, corrected flow time, and contractility were recorded in the left lateral tilt position. At the time of spinal injection, subjects were allocated to receive a rapid 1-L coload of either 6% w/v hydroxyethyl starch solution (HES) or Hartmann (crystalloid) solution (HS). A phenylephrine infusion was titrated to maintain maternal baseline SBP. CO was measured at 5-minute intervals for 20 minutes after initiation of spinal anesthesia. The primary outcome, CO, was compared between groups, as were secondary outcomes: phenylephrine dose and maternal hemodynamic and fetal outcome data. RESULTS:Maternal demographics, surgical times, and fetal outcome data were similar between groups. There were no significant differences between groups in any measured CO variable at any time point. CO was transiently higher than baseline at 5 minutes in the HS group and at 5 and 10 minutes in the HES group (range, 0.13–1.74 L/min); the overall mean difference in CO between crystalloid and colloid over the study period was 0.06 L/min (95% confidence interval: −0.46 to 0.58). Stroke volume was higher than baseline in both groups throughout; peak velocity was consistently higher than baseline only in the HES group; and corrected flow time increased in both groups; the effect was transient in the HS but sustained in the HES group. Heart rate was not different at any time point within or between groups but did decrease over time. The total phenylephrine dose from time of spinal anesthesia to delivery was similar between groups. CONCLUSION:We found no difference in CO in women randomized to colloid or crystalloid coload. In addition, there were no differences in vasopressor requirements or hemodynamic stability. We conclude that there is no advantage in using colloid over crystalloid when used in combination with a phenylephrine infusion during spinal anesthesia for elective cesarean delivery.
What you see is what you (don't) get: a comment on Funke's (2014) opinion paper

In an opinion paper published in this journal, Funke (2014) argues that two different types of assessment instruments for complex problem solving (CPS), computer-simulated microworlds (CSMs), and minimal complex systems (MCSs), might require different types of causal cognition. CPS denotes the ability to successfully deal with new, intransparent, and dynamically changing problem situations (Funke, 2001) and is considered one of the most important skills of the 21st century. Given the recent attention CPS has received from both academic and educational stances, for instance, through the Programme for International Student Assessment, which tested CPS in 15-year-old students across more than 40 countries (OECD, 2014), the topic addressed by Funke (2014) is both timely and of high relevance.
Application of Measurements of Transepithelial Electrical Resistance of Intestinal Epithelial Cell Monolayers To Evaluate Probiotic Activity

ABSTRACT Among five potentially probiotic lactobacilli investigated, Lactobacillus plantarum MF1298 and Lactobacillus salivarius DC5 showed the highest increase in the transepithelial electrical resistance (TER) of polarized monolayers of Caco-2 cells, and this increase was shown to be dose dependent. Furthermore, preincubation with MF1298 attenuated a decrease in TER induced by Listeria monocytogenes.
Pseudogenization of the tooth gene enamelysin (MMP20) in the common ancestor of extant baleen whales

Whales in the suborder Mysticeti are filter feeders that use baleen to sift zooplankton and small fish from ocean waters. Adult mysticetes lack teeth, although tooth buds are present in foetal stages. Cladistic analyses suggest that functional teeth were lost in the common ancestor of crown-group Mysticeti. DNA sequences for the tooth-specific genes, ameloblastin (AMBN), enamelin (ENAM) and amelogenin (AMEL), have frameshift mutations and/or stop codons in this taxon, but none of these molecular cavities are shared by all extant mysticetes. Here, we provide the first evidence for pseudogenization of a tooth gene, enamelysin (MMP20), in the common ancestor of living baleen whales. Specifically, pseudogenization resulted from the insertion of a CHR-2 SINE retroposon in exon 2 of MMP20. Genomic and palaeontological data now provide congruent support for the loss of enamel-capped teeth on the common ancestral branch of crown-group mysticetes. The new data for MMP20 also document a polymorphic stop codon in exon 2 of the pygmy sperm whale (Kogia breviceps), which has enamel-less teeth. These results, in conjunction with the evidence for pseudogenization of MMP20 in Hoffmann's two-toed sloth (Choloepus hoffmanni), another enamel-less species, support the hypothesis that the only unique, non-overlapping function of the MMP20 gene is in enamel formation.
Evaluating Online Review Helpfulness Based on Elaboration Likelihood Model: the Moderating Role of Readability

It is important to understand factors affecting the perceived online review helpfulness as it helps solve the problem of information overload in online shopping. Moreover, it is also crucial to explore the factors’ relative importance in predicting review helpfulness in order to effectively detect potential helpful reviews before they exert influences. Applying Elaboration Likelihood Model (ELM), this study first investigates the effects of central cues (review subjectivity and elaborateness) and peripheral cues (reviewer rank) on review helpfulness with readability as a moderator. Second, it also explores their relative predicting power using the machine learning technique. ELM is tested in online context and the results are compared between experience and search goods. Our results provide evidence that for both types of products review subjectivity can play a more significant role when the content readability is high. Furthermore, this study reveals that the dominant predictor is varied for different product types.
Intonation and interpretation: phonetics and phonology

Intonational meaning is located in two components of language, the phonetic implementation and the intonational grammar. The phonetic implementation is widely used for the expression of universal meanings that derive from ‘biological codes’, meaning dimensions based on aspects of the production process of pitch variation. Three codes are identified, Ohala’s Frequency Code, the Effort Code and the Production Code. In each case, ‘informational’ meanings (which relate to the message) are identified, while for the first two codes also ‘affective’ meanings (relating to the state of the speaker) are discussed. Speech communities will vary in the extent to which they employ those meanings, and in the choices they make when they conflict. What they will never do, however, is change the natural form-function relations that they embody. By contrast, grammaticalised meanings often mimic the natural meanings, but linguistic change may create quite arbitrary form-meaning relations when forms are phonologised, and the semantics is systematised. English grammaticalised intonational meaning concerns information status.
Surface Mesh Smoothing, Regularization, and Feature Detection

We describe a hybrid algorithm that is designed to reconstruct a piecewise smooth surface mesh from noisy input. While denoising, our method simultaneously regularizes triangle meshes on flat regions for further mesh processing and preserves crease sharpness for faithful reconstruction. A clustering technique, which combines K-means and geometric a priori information, is first developed and refined. It is then used to implement vertex classification so that we can not only apply different smoothing operators on different vertex groups for different purposes, but also succeed in crease detection, where the tangent plane of the surface is discontinuous, without any significant cost increase. Consequently we are capable of efficiently obtaining different mesh segmentations, depending on user input and thus suitable for various applications.
Multi-agent coordination using nearest neighbor rules: revisiting the Vicsek model

Recently, Jadbabaie, Lin, and Morse (IEEE TAC, 48(6)2003:988-1001) offered a mathematical analysis of the discrete time model of groups of mobile autonomous agents raised by Vicsek et al. in 1995. In their paper, Jadbabaie et al. showed that all agents shall move in the same heading, provided that these agents are periodically linked together. This paper sharpens this result by showing that coordination will be reached under a very weak condition that requires all agents are finally linked together. This condition is also strictly weaker than the one Jadbabaie et al. desired.
Use of Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy To Identify Microbial Metabolic Products on Carbonate Mineral Surfaces

ABSTRACT This paper demonstrates the use of attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy to detect microbial metabolic products on carbonate mineral surfaces. By creating an ATR-FTIR spectral database for specific organic acids using ATR-FTIR spectroscopy we were able to distinguish metabolic acids on calcite surfaces following Escherichia coli growth. The production of these acids by E. coli was verified using high-performance liquid chromatography with refractive index detection. The development of this technique has allowed us to identify microbial metabolic products on carbonate surfaces in nutrient-limited cave environments.