Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome sequences reveal divergence times of malaria parasite lineages

SUMMARY Objective The evolutionary history of human malaria parasites (genus Plasmodium) has long been a subject of speculation and controversy. The complete genome sequences of the two most widespread human malaria parasites, P. falciparum and P. vivax, and of the monkey parasite P. knowlesi are now available, together with the draft genomes of the chimpanzee parasite P. reichenowi, three rodent parasites, P. yoelii yoelli, P. berghei and P. chabaudi chabaudi, and one avian parasite, P. gallinaceum. Methods We present here an analysis of 45 orthologous gene sequences across the eight species that resolves the relationships of major Plasmodium lineages, and provides the first comprehensive dating of the age of those groups. Results Our analyses support the hypothesis that the last common ancestor of P. falciparum and the chimpanzee parasite P. reichenowi occurred around the time of the human-chimpanzee divergence. P. falciparum infections of African apes are most likely derived from humans and not the other way around. On the other hand, P. vivax, split from the monkey parasite P. knowlesi in the much more distant past, during the time that encompasses the separation of the Great Apes and Old World Monkeys. Conclusion The results support an ancient association between malaria parasites and their primate hosts, including humans.
Phytoestrogens in postmenopausal indications: A theoretical perspective

This review discusses plant-derived compounds with estrogenic activity. The authors rightly emphasize the need for the intake of foods containing phytoestrogens in view of their positive effects on postmenopausal indications. This is particularly significant in the light of the current wave of enthusiasm for vegetarian food, in general, and phytoestrogens, in particular. Phytoestrogens are plant-derived hormone-like diphenolic compounds of dietary origin. These compounds are weakly estrogenic and could play a role in the prevention of other estrogen-related conditions, namely, cardiovascular diseases, menopausal symptoms, postmenopausal osteoporosis, neuroprotective effects, and hormone-dependent cancers (breast and endometrium cancer).
The effect of Big Data Analytics Capability on Firm Performance

Big data analytics (BDA) has emerged as an important area of study for both academics and practitioners. Despite of rising potential value of BDA, a few studies have been conducted to investigate the effect of BDA on firm performance. In this research in progress, according to the challenges of BDA dimensions (volume, variety, velocity, veracity and value) we propose the BDA capability dimensions in line with IT capability concept. BDA infrastructure capability, BDA management capability, BDA personnel capability and relational BDA capability provide the overall BDA Capability concept. The study, by employing dynamic capability, proposes that BDA capability impacts on firm financial and market performance by mediated effect of operational performance. The finding of this research by providing essential BDA capability and its effect on firm performance can apply as a roadmap and fill the gap between managers' expectation of BDA and what is emerged of BDA implementation.
Collision-free scheduling of multi-bridge machining systems: a colored traveling salesman problem-based approach

Multi-bridge machining systems U+0028 MBMS U+0029 have gained wide applications in industry due to their high production capacity and efficiency. They contain multiple bridge machines working in parallel within their partially overlapping workspaces. Their scheduling problems can be abstracted into a serial-colored travelling salesman problem in which each salesman has some exclusive cities and some cities shared with its neighbor U+0028 s U+0029. To solve it, we develop a greedy algorithm that selects a neighboring city satisfying proximity. The algorithm allows a salesman to select randomly its shared cities and runs accordingly many times. It can thus be used to solve job scheduling problems for MBMS. Subsequently, a collision-free scheduling method is proposed to address both job scheduling and collision resolution issues of MBMS. It is an extension of the greedy algorithm by introducing time window constraints and a collision resolution mechanism. Thus, the augmented greedy algorithm can try its best to select stepwise a job for an individual machine such that no time overlaps exist between it and the job sequence of the neighboring machine dealt in the corresponding overlapping workspace; and remove such a time overlap only when it is inevitable. Finally, we conduct a case study of a large triplebridge waterjet cutting system by applying the proposed method.
Multi-sensor module for a mobile robot operating in harsh environments

Mobile robots are routinely deployed to support fire brigades in search and rescue missions. To help the robot evaluate situations involving fires, a novel multi-sensor module has been designed and implemented. Ambient air is drawn into inner chambers by a micro air pump and then parameters including temperature, humidity, airflow rate, particle (smoke) density, critical toxic, hazardous and explosive gases/VOC levels are recorded. Three different kinds of gas sensor have been incorporated into the module, which are metal oxide (MOX) gas sensor, Solidly Mounted Resonator (SMR) sensor, and Non-Dispersive Infrared (NDIR) gas sensor; targeting CO, NO2, CO2, toluene and ammonia. The gas sensing unit is deployed on a commercial robot and performs well under simulated smoke conditions.
Optimal Real-Time Traffic Control in Metro Stations

Train movements across railway stations are still operated by human dispatchers. Motivated by an application provided by Azienda Trasporti Milanesi (ATM), the major Italian municipal transport company, we developed a real-time automated traffic control system to operate trains in metro stations. The system optimally controls the trains in a metro station by identifying a suitable routing and by establishing an optimum schedule of the performed operations. For each candidate routing an instance of the blocking, no-wait job-shop scheduling problem with convex costs is solved to optimality by branch and bound. A new, effective lower bound is developed to speed up the enumeration process. Computational testing in a real environment proved that the algorithm is able to solve relevant practical instances within the very tight time limit imposed by the application. The system has been in operation in the Milan metro since July 2007. To our knowledge, this is the first example of successful application of optimization methods to real-time traffic control in metro stations.
Application of economic principles in healthcare priority setting

In healthcare, resources are often insufficient to meet all claims on them. In this respect, resources are considered scarce and have to be managed by prioritizing between competing claims. Economics as a discipline explicitly addresses this reality by acknowledging resource scarcity. However, the extent to which economics actually influences such prioritizing decisions in healthcare is unclear. The purpose of this paper is to review the use of economics in priority setting decision making. We outline the key principles of economics as they apply to priority setting and review the methods reported in the literature with respect to these. We find that these methods, even economic methods (e.g., those typically used in conducting economic evaluations such as cost–effectiveness analyses) do not tend to explicitly incorporate economic principles. We argue therefore that these methods, when applied to the context of priority setting, are not sufficient and that what is required is a broader framework that can incorporate the output from economic methods yet also be pragmatically applicable. We then go on to present an alternative approach – namely program budgeting and marginal analysis. Finally, we put forward our case for using program budgeting and marginal analysis in priority setting practice and set out some future research challenges.
Nonaccidental head injury in infants--the "shaken-baby syndrome".

Trauma is the most common cause of death in childhood, and inflicted head injury is the most common cause of traumatic death in infancy.1–3 Beginning with the classic descriptions of Kempe et al.4 and Caffey5 and with subsequent clinical, biomechanical, and radiologic studies, the diagnostic features of nonaccidental head injury in infants and toddlers have become widely recognized. This review outlines the mechanisms, typical features, differential diagnosis, and acute management of the most frequently encountered form of infantile inflicted head injury, the so-called shaken-baby syndrome. Biomechanics and Terminology The names applied to the syndromes of inflicted head injury in .
Fast Macromodel-based Signal Integrity Assessment for RF and Mixed-Signal Modules

This paper presents a macromodel-based approach for fast signal integrity assessment for highly integrated radio frequency (RF) and mixed-signal system on chip (SoC) applications. In particular, we introduce a complexity reduction process that enables the signal integrity verification via analog circuit simulations, and we apply the methodology to complex radio transceiver chips in order to characterize the influence of parasitic elements on the signal processing performance of the system. Some preliminary tests show that the proposed methodology leads to significant simulation speedup factors with respect to standard approaches for the specific application herewith considered.
Micro-displacement measurement using a long period fiber grating in a self-referenced fiber optic intensity sensor

This work describes a sensor, in which the sensing head comprises a long period fiber grating (LPG) whose attenuation peak varies as function of its bending. The level of LPG bending is induced by the displacement of a micrometer translation stage (MTS) being possible therefore to measure microdisplacements. The sensing head is integrated in a fiber optic intensity sensor, referenced in frequency, which is immune to intensity fluctuations other than the ones caused by the LPG.
The Magic of RFID

Many modern technologies give the impression they work by magic, particularly when they operate automatically and their mechanisms are invisible. A technology called RFID (radio frequency identification), which is relatively new to the mass market, has exactly this characteristic and for many people seems a lot like magic. RFID is an electronic tagging technology that allows an object, place, or person to be automatically identified at a distance without a direct line-of-sight, using an electromagnetic challenge/response exchange. Typical applications include labeling products for rapid checkout at a point-of-sale terminal, inventory tracking, animal tagging, timing marathon runners, secure automobile keys, and access control for secure facilities.
Characterization of a mouse strain expressing Cre recombinase from the 3′ untranslated region of the dopamine transporter locus

Dopamine (DA) neurotransmission has been implicated in several neurological and psychiatric disorders. The dopamine transporter (DAT) is highly expressed in dopaminergic neurons of the ventral mesencephalon and regulates neurotransmission by transporting DA back into the presynaptic terminals. To mediate restricted DNA recombination events into DA neurons using the Cre/loxP technology, we have generated a knockin mouse expressing Cre recombinase under the transcriptional control of the endogenous DAT promoter. To minimize interference with DAT function by preservation of both DAT alleles, Cre recombinase expression was driven from the 3′ untranslated region (3′UTR) of the endogenous DAT gene by means of an internal ribosomal entry sequence. Crossing this murine line with a LacZ reporter showed colocalization of DAT immunocytochemistry and β‐galactosidase staining in all regions analyzed. This knockin mouse can be used for generating tissue specific knockouts in mice carrying genes flanked by loxP sites, and will facilitate the analysis of gene function in dopaminergic neurons. genesis 44:383–390, 2006. Published 2006 Wiley‐Liss, Inc.
Synthetic Lethal Interaction of the Mitochondrial Phosphatidylethanolamine and Cardiolipin Biosynthetic Pathways in Saccharomyces cerevisiae*

Saccharomyces cerevisiae mitochondria contain enzymes required for synthesis of the phospholipids cardiolipin (CL) and phosphatidylethanolamine (PE), which are enriched in mitochondrial membranes. Previous studies indicated that PE may compensate for the lack of CL, and vice versa. These data suggest that PE and CL have overlapping functions and that the absence of both lipids may be lethal. To address this hypothesis, we determined whether the crd1Δ mutant, which lacks CL, was viable in genetic backgrounds in which PE synthesis was genetically blocked. Deletion of the mitochondrial PE pathway gene PSD1 was synthetically lethal with the crd1Δ mutant, whereas deletion of the Golgi and endoplasmic reticulum pathway genes PSD2 and DPL1 did not result in synthetic lethality. A 20-fold reduction in phosphatidylcholine did not affect the growth of crd1Δ cells. Supplementation with ethanolamine, which led to increased PE synthesis, or with propanolamine, which led to synthesis of the novel phospholipid phosphatidylpropanolamine, failed to rescue the synthetic lethality of the crd1Δpsd1Δ cells. These results suggest that mitochondrial biosynthesis of PE is essential for the viability of yeast mutants lacking CL.
Switching on Chromatin: Mechanistic Role of Histone H4-K16 Acetylation

DNA in eukaryotic organisms does not exist free in cells, but instead is present as chromatin, a complex assembly of DNA, histone proteins, and chromatin-associated proteins. Chromatin exhibits a complex hierarchy of structures, but in its simplest form it is composed of long linear arrays of nucleosomes. Nucleosomes contain 147 base pairs of DNA wrapped around a histone octamer, consisting of two copies each of histones H2A, H2B, H3 and H4, where 15-38 amino terminal residues of each histone protein extends past the DNA gyres to form histone “tails” 1. Chromatin provides a versatile regulatory platform for nearly all cellular processes that involve DNA, and improper chromatin regulation results in a wide range of diseases, including various cancers and congenital defects. One major way that chromatin regulates DNA utilization is through a wide range of post-translational modification of histones, including serine and threonine phosphorylation, lysine acetylation, methylation, ubiquitination, and sumoylation, and arginine methylation 2. Histone H4 K16 acetylation is a modification that occurs on the H4 histone tail and is one of the most frequent of the known histone modifications. We have demonstrated that this mark both disrupts formation of higher-order chromatin structure and changes the functional interaction of chromatin-associated proteins 3. Our results suggest a dual mechanism by which H4 K16 acetylation can ultimately facilitate genomic functions.
Improved UTE-based attenuation correction for cranial PET-MR using dynamic magnetic field monitoring.

PURPOSE Ultrashort echo time (UTE) MRI has been proposed as a way to produce segmented attenuation maps for PET, as it provides contrast between bone, air, and soft tissue. However, UTE sequences require samples to be acquired during rapidly changing gradient fields, which makes the resulting images prone to eddy current artifacts. In this work it is demonstrated that this can lead to misclassification of tissues in segmented attenuation maps (AC maps) and that these effects can be corrected for by measuring the true k-space trajectories using a magnetic field camera. METHODS The k-space trajectories during a dual echo UTE sequence were measured using a dynamic magnetic field camera. UTE images were reconstructed using nominal trajectories and again using the measured trajectories. A numerical phantom was used to demonstrate the effect of reconstructing with incorrect trajectories. Images of an ovine leg phantom were reconstructed and segmented and the resulting attenuation maps were compared to a segmented map derived from a CT scan of the same phantom, using the Dice similarity measure. The feasibility of the proposed method was demonstrated in in vivo cranial imaging in five healthy volunteers. Simulated PET data were generated for one volunteer to show the impact of misclassifications on the PET reconstruction. RESULTS Images of the numerical phantom exhibited blurring and edge artifacts on the bone-tissue and air-tissue interfaces when nominal k-space trajectories were used, leading to misclassification of soft tissue as bone and misclassification of bone as air. Images of the tissue phantom and the in vivo cranial images exhibited the same artifacts. The artifacts were greatly reduced when the measured trajectories were used. For the tissue phantom, the Dice coefficient for bone in MR relative to CT was 0.616 using the nominal trajectories and 0.814 using the measured trajectories. The Dice coefficients for soft tissue were 0.933 and 0.934 for the nominal and measured cases, respectively. For air the corresponding figures were 0.991 and 0.993. Compared to an unattenuated reference image, the mean error in simulated PET uptake in the brain was 9.16% when AC maps derived from nominal trajectories was used, with errors in the SUV max for simulated lesions in the range of 7.17%-12.19%. Corresponding figures when AC maps derived from measured trajectories were used were 0.34% (mean error) and -0.21% to +1.81% (lesions). CONCLUSIONS Eddy current artifacts in UTE imaging can be corrected for by measuring the true k-space trajectories during a calibration scan and using them in subsequent image reconstructions. This improves the accuracy of segmented PET attenuation maps derived from UTE sequences and subsequent PET reconstruction.
The Optical-Geometrical Illusion “Corner Poggendorff” Re-Examined

In 1988 Greene noted, if a straight pair of obliques are drawn outside of two orthogonal lines, the segments appear to be angled slightly one relative to the other. This illusion, designated as “corner Poggendorff,” is different from the Poggendorff effect (the two obliques seem to lie on a parallel path). The results of the present experiments (N = 76 students) suggest that the general conditions for the corner Poggendorff are similar to those for the Judd illusion.
Empirical Correlates of the MMPI–2 Restructured Clinical (RC) Scales in Psychiatric Inpatients

We identified empirical correlates of the MMPI–2 Restructured Clinical (RC) scales in 1,872 male and 498 female psychiatric inpatients drawn from 2 large tertiary care medical centers. We generated clinical criteria from a systematic review of the patients' intake and discharge medical records. We report zero order correlations between RC scales and clinical criteria and relative risk ratios for dichotomous variables. We found the RC scales to be correlated with conceptually relevant criteria such that for each scale, we identified significant increases in the risk for a variety of emotional, cognitive, and behavioral problems among individuals whose T score exceed 64.
The Proem of Parmenides

T nHE fragments of Parmenides are an important monument of Greek poetry at the beginning of the fifth century B.C. In time they cannot be far removed from Pindar's Pythian x, written in 498, or from Aeschylus' Supplices, which was surely written before 490. With these flights of lyrical genius the poem has little in common, but it belongs to the same age, and it has suffered from being too often considered either in isolation as a contribution to truth or as an episode in purely philosophical poetry. But it presents questions to the literary critic which have little direct relation to its metaphysics, and particularly in the Proem Parmenides attempts a manner of writing so unusual that it is easy to dismiss it as an eccentricity of a philosopher attempting a task for which nature had not equipped him. But Parmenides was a careful and singularly exact writer, and the composition of his Proem no doubt cost him as much pains as the exposition of reality which it precedes. In it he had something to say of great importance, and he adopted a remarkable method to which Greek poetry presents hardly any parallel. The origins of his method have been studied, but a knowledge of them does not explain either what he meant to say or what his contemporaries would see in his words. If we can understand what the Proem meant in the thought of his time, we may perhaps understand better how Parmenides viewed his calling as a philosopher. '
A Comparison of Plyometric Training Techniques for Improving Vertical Jump Ability and Energy Production

This study was done to determine which plyometric training technique is best for improving vertical jumping ability, positive energy production, and elastic energy utilization. Data were collected before and after 12 weeks of jump training and were analyzed by ANOVA. Subjects (N = 28) performed jumps under 3 testing conditions—squat jump, countermovement jump, and depth jump—and were randomly assigned to 1 of 3 groups: control, depth jump training, or countermovement jump training. The 12-week program resulted in significant increases in vertical jump height for both training groups. The depth jump group significantly improved their vertical jump height in all 3 jumps. None of the training methods improved utilization of elastic energy. In activities involving dynamic stretch-shorten cycles, drop jump training was superior to countermovement jump training due to neuromuscular specificity. This study provides support for the strength and conditioning professional to include plyometric depth jump training as part of the athlete's overall program for improving vertical jumping ability and concentric contractile performance.