Miracle-dz/UniFAR-FTUs huggingface dataset:
What to compare and how: Comparative transcriptomics for Evo‐Devo

ABSTRACT Evolutionary developmental biology has grown historically from the capacity to relate patterns of evolution in anatomy to patterns of evolution of expression of specific genes, whether between very distantly related species, or very closely related species or populations. Scaling up such studies by taking advantage of modern transcriptomics brings promising improvements, allowing us to estimate the overall impact and molecular mechanisms of convergence, constraint or innovation in anatomy and development. But it also presents major challenges, including the computational definitions of anatomical homology and of organ function, the criteria for the comparison of developmental stages, the annotation of transcriptomics data to proper anatomical and developmental terms, and the statistical methods to compare transcriptomic data between species to highlight significant conservation or changes. In this article, we review these challenges, and the ongoing efforts to address them, which are emerging from bioinformatics work on ontologies, evolutionary statistics, and data curation, with a focus on their implementation in the context of the development of our database Bgee (http://bgee.org). J. Exp. Zool. (Mol. Dev. Evol.) 324B: 372–382, 2015. © 2015 The Authors. J. Exp. Zool. (Mol. Dev. Evol.) published by Wiley Periodicals, Inc.
Public Debt and the Price Level

This paper considers whether monetary and scal policy may sensibly be formulated independently of one another, and argues that the reasons for the two to be interconnected go well beyond the familiar but unappealing possibility of using seignorage as a source of revenue for the government. Particular attention is given to the eects of scal policy upon the price level through the wealth eect of variations in the value of the public debt; such eects are shown to be consistent with rational expectations and frictionless nancial markets, contrary to the doctrine of \Ricardian equivalence", in the case of \non-Ricardian" scal policy. In this case, the eects of variation in the composition of the public debt (as to maturity and degree of indexation) are considered, as well as the eects of growth in its overall size. A number of objections to the possibility of a non-Ricardian policy are considered, notably the assertions that it is not possible for a government to refuse to adjust its budget when its debts grow too large, and the assertion that equilibria in which the price level is determined by the government budget depend upon an implausible equilibrium selection in a model with multiple rational expectations equilibria. The eects of public debt upon the price level are also considered in the case that consumers have adaptive rather than rational expectations about their lifetime budgets. Finally, the nature of optimal scal and monetary policy is considered, as a problem of dynamic Ramsey taxation. It is shown that an optimal policy regime may well involve a \non-Ricardian" scal policy, in which increases in govermment purchases do not result in corresponding increases in the present value of future tax collections, and so cause fluctuations in the equilibrium value of government bonds. At the same time, an appropriate choice both of monetary policy and of the composition of the public debt can make this sort of scal policy compatible with a substantial degree of price stability.
Human tumor cell lines with pleiotropic drug resistance are efficiently killed by interleukin‐2 activated killer cells and by activated monocytes

Two human cell lines, the colon carcinoma Lovo and the transformed intestinal 1–407, and their variants (Lovo/Dx and l‐407/Dx), with pleiotropic resistance to cancer chemothera‐peutic drugs, were examined for their susceptibility to human lnterleukin‐2‐activated killer cells and to activated mono‐cytes. These non‐specific or broadly specific effector cells expressed cytotoxicity levels on pleiotropically resistant tumor cells comparable to those of the parental cell populations. This finding provides a rationale for immunological approaches designed to eradicate residual tumor cells surviving and resistant to cytotoxic chemotherapy.
Zoonotic helminth infections with particular emphasis on fasciolosis and other trematodiases

Zoonotic infections are among the most common on earth and are responsible for >60 per cent of all human infectious diseases. Some of the most important and well-known human zoonoses are caused by worm or helminth parasites, including species of nematodes (trichinellosis), cestodes (cysticercosis, echinococcosis) and trematodes (schistosomiasis). However, along with social, epidemiological and environmental changes, together with improvements in our ability to diagnose helminth infections, several neglected parasite species are now fast-becoming recognized as important zoonotic diseases of humans, e.g. anasakiasis, several fish-borne trematodiasis and fasciolosis. In the present review, we discuss the current disease status of these primary helminth zoonotic infections with particular emphasis on their diagnosis and control. Advances in molecular biology, proteomics and the release of helminth genome-sequencing project data are revolutionizing parasitology research. The use of these powerful experimental approaches, and their potential benefits to helminth biology are also discussed in relation to the future control of helminth infections of animals and humans.
A Low Power Low Noise Amplifier In CMOS

A low power Low Noise Amplifier (LNA) topology, which is new for CMOS technology is proposed. The proposed topology is simulated and fabricated using standard 0.7um CMOS process. The simulations of the proposed topology are carried out at different power consumptions at 430 MHz and the simulation results concluded that the performance of the topology is very impressive at low power consumptions. The amplifier provides a forward gain of 14 dB with a noise figure of 1.62 dB while drawing 30 mW from 3V supply and 10 dB forward gain with a noise figure of 2dB while drawing 6 mW from 1.5V supply at 430 MHz. The simulation at different frequencies also show that the performance of this topology is advantageous over different well-known topologies at high frequencies. The proposed topology includes on chip spiral inductors that are realized with or without patterned groud shield between the on chip spiral inductor and the silicon substrate. So, two different versions of the LNA are fabricated with on chip spiral inductors with or without patterned ground shield. Key-Words: Low noise amplifier, standard 0.7um CMOS process, common source stage with inductive series feedback, inductive degeneration, common gate stage with inductive parallel feedback, pattered ground shield.
Dynamics of coding in communicating with chaos

Recent work has considered the possibility of utilizing symbolic representations of controlled chaotic orbits for communicating with chaotically behaving signal generators. The success of this type of nonlinear digital communication scheme relies on partitioning the phase space properly so that a good symbolic dynamics can be defined. A central problem is then how to encode an arbitrary message into the wave form generated by the chaotic oscillator, based on the symbolic dynamics. We argue that, in general, a coding scheme for communication leads to, in the phase space, restricted chaotic trajectories that live on nonattracting chaotic saddles embedded in the chaotic attractor. The symbolic dynamics of the chaotic saddle can be robust against noise when the saddle has large noise-resisting gaps covering the phase-space partition. Nevertheless, the topological entropy of such a chaotic saddle, or the channel capacity in utilizing the saddle for communication, is often less than that of the chaotic attractor. We present numerical evidences and theoretical analyses that indicate that the channel capacity associated with the chaotic saddle is generally a nonincreasing, devil’s-staircase-like function of the noise-resisting strength. There is usually a range for the noise strength in which the channel capacity decreases only slightly from that of the chaotic attractor. The main conclusion is that nonlinear digital communication using chaos can yield a substantial channel capacity even in noisy environment. @S1063-651X~98! 04708-4#
A bird's eye view of FPGA-based Evolvable Hardware

The Evolvable Hardware research area has achieved very important progresses in the last two decades. However, it is still quite far from being as revolutionary as depicted in the earlier visionary papers. To have a positive impact on the Embedded Design Automation field, Evolvable Hardware systems should start to deal with more complex problems instances efficiently. This paper describes some interesting results achieved so far in the Evolvable Hardware area and gives some hints on what should be done for increasing the efficiency of Evolvable Hardware systems.
A Logical Approach to the Management of Object Identifiers in Non-conventional Database Management Systems

Non-conventional database management systems are used to achieve a better performance when dealing with complex data. One fundamental concept of these systems is object identity (OID), because each object in the database has a unique identifier that is used to access and reference it in relationships to other objects. Two approaches can be used for the implementation of OIDs: physical or logical OIDs. In order to manage complex data, was proposed the Multimedia Data Manager Kernel (NuGeM) that uses a logical technique, named Indirect Mapping. This paper proposes an improvement to the technique used by NuGeM, whose original contribution is management of OIDs with a fewer number of disc accesses and less processing, thus reducing management time from the pages and eliminating the problem with exhaustion of OIDs. Also, the technique presented here can be applied to others OODBMSs.
Analysis and Implementation of a Minimum-Supply Body-Biased CMOS Differential Amplifier Cell

A CMOS differential amplifier cell for minimum supply requirements is presented. The solution uses transistors in strong inversion and an original biasing scheme that exploits the bulk terminals of the transistor pair to accurately set the quiescent current and provide common-mode control. As a result, we avoid the use of the tail current source adopted in traditional differential stages. An implementation based on an auxiliary switched-capacitor network used in the feedback control loop is proposed and theoretically examined. Measurements on a prototype fabricated in a standard 0.35- mum technology (with threshold voltages around 0.5 V) and powered with 1.2 V show an error in the bias current of about 15% with respect to the expected value. It was found that the obtained overall performance is comparable to that of a traditional long-tailed differential pair that uses a higher supply of 1.5 V.
Human Hand Function

1. Historical Overview and general introduction 2. Evolutionary development and anatomy of the hand 3. Sensory neurophysiology 4. Tactile sensing 5. Active haptic sensing 6. Prehension 7. Non-prehensile skilled movements 8. End-effector constraints 9. Hand function across the lifespan 10. Applications 11. Summary, conclusions and future directions
Pharmacokinetics of Miltefosine in Old World Cutaneous Leishmaniasis Patients

ABSTRACT The pharmacokinetics of miltefosine in leishmaniasis patients are, to a great extent, unknown. We examined and characterized the pharmacokinetics of miltefosine in a group of patients with Old World (Leishmania major) cutaneous leishmaniasis. Miltefosine plasma concentrations were determined in samples taken during and up to 5 months after the end of treatment from 31 Dutch military personnel who contracted cutaneous leishmaniasis in Afghanistan and were treated with 150 mg miltefosine/day for 28 days. Samples were analyzed with a validated liquid chromatography-tandem mass spectrometry assay with a lower limit of quantification (LLOQ) of 4 ng/ml. Population pharmacokinetic modeling was performed with nonlinear mixed-effect modeling, using NONMEM. The pharmacokinetics of miltefosine could best be described by an open two-compartment disposition model, with a first elimination half-life of 7.05 days and a terminal elimination half-life of 30.9 days. The median concentration in the last week of treatment (days 22 to 28) was 30,800 ng/ml. The maximum duration of follow-up was 202 days after the start of treatment. All analyzed samples contained a concentration above the LLOQ. Miltefosine is eliminated from the body much slower than previously thought and is therefore still detectable in human plasma samples taken 5 to 6 months after the end of treatment. The presence of subtherapeutic miltefosine concentrations in the blood beyond 5 months after treatment might contribute to the selection of resistant parasites, and moreover, the measures for preventing the teratogenic risks of miltefosine treatment should be reconsidered.
Cytomegalovirus Recruitment of Cellular Kinases to Dissolve the Nuclear Lamina

The passage of large-sized herpesviral capsids through the nuclear lamina and the inner nuclear membrane to leave the nucleus requires a dissolution of the nuclear lamina. Here, we report on the functions of M50/p35, a β-herpesviral protein of murine cytomegalovirus. M50/p35 inserts into the inner nuclear membrane and is aggregated by a second viral protein, M53/p38, to form the capsid docking site. M50/p35 recruits the cellular protein kinase C for phosphorylation and dissolution of the nuclear lamina, suggesting that herpesviruses target a critical element of nuclear architecture.
Stability of the Glenohumeral Joint with Combined Humeral Head and Glenoid Defects

Objectives: Shoulders with recurrent anterior shoulder instability often have combined defects of the humeral head and glenoid. The aim of this study is to define the relationship of combined humeral head and glenoid defects on anterior shoulder instability. We hypothesize that combined humeral head and glenoid defects will produce greater instability than either defect found alone, and that the size of humeral head and glenoid defects which are “critical” and need to be repaired in order to restore glenohumeral stability will be smaller when the defects are found together than when either defect is found alone. Methods: Eighteen shoulder specimens (mean age 57 years) were tested at 60° of glenohumeral abduction and 80° of glenohumeral external rotation (equivalent to 90° of abduction and 90° of external rotation relative to the trunk). Humeral head defect sizes included 6%, 19%, 31%, and 44% of the humeral head diameter. Glenoid defect sizes included 10%, 20%, and 30% of the glenoid width. Outcome measures included Percent of Intact Stability Ratio (stability ratio for a given trial divided by the stability ratio in the intact state for that specimen) and Percent of Intact Translation (distance to dislocation for a given trial divided by the distance to dislocation in the intact state for that specimen). Results: There was a progressive decrease in stability as humeral head defect size increased and as glenoid defect size increased. The decrease in Percent of Intact Stability Ratio reached statistical significance for humeral head defects of 44%, for glenoid defects of 30%, and additionally for a combined 19% humeral head defect with a 20% glenoid defect. The mean Percent of Intact Stability Ratio was 65% for a combined 19% humeral head defect with a 20% glenoid defect. The decrease in Percent of Intact Translation reached statistical significance for humeral head defects of 31% and 44%, for glenoid defects of 20% and 30%, and additionally for a combined 19% humeral head defect with a 10% glenoid defect. The mean Percent of Intact Translation was 69% for a combined 19% humeral head defect with a 10% glenoid defect. Conclusion: The humeral head and glenoid defect sizes required to produce instability are smaller when the defects are found together than when either defect is found alone. In patients with combined humeral head and glenoid defects bony reconstruction may be indicated for humeral head defects as small as 19% of the humeral head diameter and glenoid defects as small as 10-20% of the glenoid width.
Vigilance, boredom proneness and detection time of a malfunction in partially automated driving

A vehicle automation makes it possible to hand over the control task from the driver to an automation, which is in turn monitored by the driver. In this study, it was investigated how long it takes for drivers to detect an automation malfunction and if the detection time can be predicted by performance in a self-developed vigilance task and by individual boredom proneness. 23 participants drove with partial automation (Level 2; [1, 2]) activated for 24 min on a three-lane highway. Dependent measure was the time until they detected a suddenly occurring malfunction of lateral control. No significant relationship between the predictors and detection time was found, which could be caused by the chosen operationalization of the dependent variable.
A Situational Analysis of Antimicrobial Drug Resistance in Africa: Are we Losing the Battle?

Background : The first arrival of a sizable shipment of penicillin at the North African Theatre of Operations for USA military use in 1943 was a landmark that turned a new chapter of antibiotic use in Africa. Over the past decade the expansion of resources and the technological advances have meant that much larger quantities of drugs are available in developing countries than ever before. As a result, many more individuals are receiving necessary treatment or therapy than just ten years ago. This very welcome event is accompanied by the terrible irony that increases in drug availability and use can promote drug resistance and render the same life-saving drugs ineffective. Methods : The study focused on bacterial pathogens. One hundred and three relevant literatures were identified from the PubMed online database. The coverage included research articles concerning antimicrobial resistance involving subjects of an African country. Results : Resistant bacteria are on a war path and evidently have acquired an edge over us. Our actions are evidently fuelling the resistance. The indiscriminate use of antibiotics in humans and livestock, wrong and substandard prescriptions by unqualified ‘medical personnel’ together with poor diagnosis or lack of it are all adding fuel to the already fired train of resistant microbes. Conclusion : To win the war and turn tables as we did with the discovery of penicillin and other antimicrobials in the 1940s, then we must all act now. Antimicrobial stewardship programs-Education, training of laboratory personnel and investment in laboratory infrastructure development are desirable in these situations Keywords : Antibiotics, Resistance, Bacteria Ethiop J Health Sci . Vol. 22, No. 2 July 2012
Order-Based Inference in Natural Logic

This paper develops a version of Natural Logic – an inference system that works directly on natural language syntactic representations, with no intermediate translation to logical formulae. Following work by Sánchez, we develop a small fragment that computes semantic order relations between derivation trees in Categorial Grammar. The proposed system has the following new characteristics: (i) It uses orderings between derivation trees as purely syntactic units, derivable by a formal calculus. (ii) The system is extended for conjunctive phenomena like coordination and relative clauses. This allows a simple account of non-monotonic expressions that are reducible to conjunctions of monotonic ones. (iii) A decision procedure for provability is developed for a fragment of Natural Logic.
The Order and Place of Neuronal Differentiation Establish the Topography of Sensory Projections and the Entry Points within the Hindbrain

Establishing topographical maps of the external world is an important but still poorly understood feature of the vertebrate sensory system. To study the selective innervation of hindbrain regions by sensory afferents in the zebrafish embryo, we mapped the fine-grained topographical representation of sensory projections at the central level by specific photoconversion of sensory neurons. Sensory ganglia located anteriorly project more medially than do ganglia located posteriorly, and this relates to the order of sensory ganglion differentiation. By single-plane illumination microscopy (SPIM) in vivo imaging, we show that (1) the sequence of arrival of cranial ganglion inputs predicts the topography of central projections, and (2) delaminated neuroblasts differentiate in close contact with the neural tube, and they never loose contact with the neural ectoderm. Afferent entrance points are established by plasma membrane interactions between primary differentiated peripheral sensory neurons and neural tube border cells with the cooperation of neural crest cells. These first contacts remain during ensuing morphological growth to establish pioneer axons. Neural crest cells and repulsive slit1/robo2 signals then guide axons from later-differentiating neurons toward the neural tube. Thus, this study proposes a new model by which the topographical representation of cranial sensory ganglia is established by entrance order, with the entry points determined by cell contact between the sensory ganglion cell bodies and the hindbrain.
Comparing phase transitions and peak cost in PP-complete satisfiability problems

The study of phase transitions in algorithmic problems has revealed that usually the critical value of the constrainedness parameter at which the phase transition occurs coincides with the value at which the average cost of natural solvers for the problem peaks. In particular, this confluence of phase transition and peak cost has been observed for the Boolean satisfiability problem and its variants, where the solver used is a Davis-Putnam-type procedure or a suitable modification of it. Here, we investigate the relationship between phase transitions and peak cost for a family of PP-complete satisfiability problems, where the solver used is a symmetric Threshold Counting Davis-Putnam (TCDP) procedure, i.e., a modification of the Counting Davis-Putnam procedure for computing the number of satisfying assignments of a Boolean formula. Our main experimental finding is that, for each of the PP-complete problems considered, the asymptotic probability of solvability undergoes a phase transition at some critical ratio of clauses to variables, but this critical ratio does <i>not</i> always coincide with the ratio at which the average search cost of the symmetric TCDP procedure peaks. Actually, for some of these problems the peak cost occurs at the boundary or even outside of the interval in which the probability of solvability drops from 0.9 to 0.1, and we analyze why this happens.