Miracle-dz/UniFAR-FTUs huggingface dataset:
The origin and early evolution of vascular plant shoots and leaves

The morphology of plant fossils from the Rhynie chert has generated longstanding questions about vascular plant shoot and leaf evolution, for instance, which morphologies were ancestral within land plants, when did vascular plants first arise and did leaves have multiple evolutionary origins? Recent advances combining insights from molecular phylogeny, palaeobotany and evo–devo research address these questions and suggest the sequence of morphological innovation during vascular plant shoot and leaf evolution. The evidence pinpoints testable developmental and genetic hypotheses relating to the origin of branching and indeterminate shoot architectures prior to the evolution of leaves, and demonstrates underestimation of polyphyly in the evolution of leaves from branching forms in ‘telome theory’ hypotheses of leaf evolution. This review discusses fossil, developmental and genetic evidence relating to the evolution of vascular plant shoots and leaves in a phylogenetic framework. This article is part of a discussion meeting issue ‘The Rhynie cherts: our earliest terrestrial ecosystem revisited’.
Optical Properties of ZnO Thin Film

Abstract In this work, we studied with a Matlab program, some of optical properties of zinc oxide (ZnO) deposited on glass (SiO2). The parameters studied include the refraction index, extinction coefficient, optical band gap, and complex dielectric constant versus incident photon energy, and transmittance, absorbance and reflectance spectrum of ZnO thin film deposited on glass (SiO2) for different thickness. The films were found to exhibit high transmittance (75- 95%), low absorbance and low reflectance in the visible / near infrared region up to 1000 nm. However, the absorbance of the films was found to be high in the ultra violet region with peak around 380 nm.
Cortical changes in starfish (Asterina pectinifera) oocytes during 1-methyladenine-induced maturation and fertilisation/activation

Summary Maturation of the starfish oocyte cortex to produce an effective cortical granule reaction and fertilisation envelope is believed to develop in three phases: (1) pre-methyladenine (1-MA) stimulation; (2) post-1-MA stimulation, pregerminal vesicle breakdown; and (3) post-germinal vesicle breakdown. The present study was initiated to identify what each of these phases may encompass, specifically with respect to structures associated with the oocyte cortex, including cortical granules, microvilli and vitelline layer. 1-MA treatment brought about an orientation of cortical granules such that they became positioned perpendicular to the oocyte surface, and an ∼ 4-fold decrease in microvillar length. A-23187 activation of immature oocytes treated with (10 min; pregerminal vesicle breakdown) or without 1-MA resulted in a reduction in cortical granule number of 21% and 41%, respectively (mature oocytes underwent a 96% reduction in cortical granules). Elevation of the fertilisation envelope in both cases was significantly retarded compared with activated mature oocytes. In activated mature oocytes, the vitelline layer elevated 20.0 ± 5.4 μm from the egg's surface, whereas in immature oocytes treated with just A-23187 or with 1-MA (10 min) and A-23187, it lifted 0.35 ± 0.1 and 0.17 ± 0.04 μm, respectively. The fertilisation envelopes of activated (or fertilised) immature oocytes also differed morphologically from those of mature oocytes. In activated, immature oocytes, the fertilisation envelope was not uniform in its thickness and possessed thick and thin regions as well as fenestrations. Additionally, it lacked a complete electron-dense stratum that characterised the fertilisation envelopes of mature oocytes. The nascent perivitelline space of immature oocytes was also distinguished by the presence of numerous vesicles which appeared to be derived from microvilli. Differences in the morphology of cortices from activated (fertilised) and non-activated, immature and mature oocytes substantiate previous investigations demonstrating three phases of cortical maturation, and are consistent with physiological changes that occur during oocyte maturation, involving ionic conductance of the plasma membrane, establishment of slow and fast blocks to polyspermy and elevation of a fertilisation envelope.
New algorithms and lower bounds for the parallel evaluation of certain rational expressions

This paper presents new algorithms for the parallel evaluation of certain polynomial expression. In particular, for the parallel evaluation of x<supscrpt>n</supscrpt>,we introduce an algorithm which takes two steps of <underline>parallel division</underline> and [log<subscrpt>2</subscrpt>n] steps of parallel addition, while the usual algorithm takes [log<subscrpt>2</subscrpt>n] steps of parallel multiplication. Hence our algorithm is faster than the usual algorithms when multiplication takes more time than addition. Similar algorithm for the evaluation of other polynomial expressions are also introduced. Lower bounds on the time needed for the parallel evaluation of rational expressions are given. All the algorithms presented in the paper are shown to be asymptotically optimal. Moreover, we prove that by using parallelism the evaluation of any first order rational recurrence, e.g., [equation], and any <underline>non-linear</underline> polynomial recurrence can be sped up at most by a constant factor, no matter how many processors are used.
Design Automation and Test Solutions for Digital Microfluidic Biochips

Microfluidics-based biochips are revolutionizing high-throughput sequencing, parallel immunoassays, blood chemistry for clinical diagnostics, and drug discovery. These devices enable the precise control of nanoliter volumes of biochemical samples and reagents. They combine electronics with biology, and they integrate various bioassay operations, such as sample preparation, analysis, separation, and detection. Compared to conventional laboratory procedures, which are cumbersome and expensive, miniaturized biochips offer the advantages of higher sensitivity, lower cost due to smaller sample and reagent volumes, system integration, and less likelihood of human error. This tutorial paper provides an overview of droplet-based ¿digital¿ microfluidic biochips. It describes emerging computer-aided design (CAD) tools for the automated synthesis and optimization of biochips from bioassay protocols. Recent advances in fluidic-operation scheduling, module placement, droplet routing, pin-constrained chip design, and testing are presented. These CAD techniques allow biochip users to concentrate on the development of nanoscale bioassays, leaving chip optimization and implementation details to design-automation tools.
Risk Factors of a Suicide Reattempt by Seasonality and the Method of a Previous Suicide Attempt: A Cohort Study in a Japanese Primary Care Hospital.

Suicide has a great impact on the individual whose life is lost and the bereaved family members. The risk of a suicide reattempt is particularly high during the first 12 months after a suicide attempt. In this cohort study, risk factors for a suicide reattempt were explored among 291 patients at suicide risk. Clinical and demographic data were collected from a Japanese primary care hospital. Past psychiatric history and multiple diagnoses were associated with suicide reattempts in both genders. Drug overdose, past psychiatric history, and the summer season were linked to suicide reattempts among males. Past psychiatric history and multiple diagnoses were linked to suicide reattempts among females. Appropriate assessment of past psychiatric history, season and method of suicide attempt, gender, and diagnosis may play a role in preventing suicide.
Genetic Algorithms based method for time optimization in robotized site

Industrial implementation of robots is to perform the assigned tasks in the minimum possible time in the cycle comes up to increase productivity and reduce the cost. The cycle time is strongly linked to the robot trajectory cycle to the task. However, the optimization of the robot trajectory cycle the robot visited a set of points which represent the robotics task. Similar to persons in traveling the robot execute the task into shorter time if has a shorter path. However the trajectory cycle of the robot is strongly related to the displacement in coordinate space rather than operational space. In fact, the shorter distance between two task points is the shorter distance between two configurations. Since robot has different configurations in each task point the minimum trajectory should be chosen between each successive configuration. However the order of visiting the task point also affects the trajectory distance. Moreover the relative robot position to the task also has a trivial effect on the task time. In this work we develop a method to optimize the order of visiting the task point taking into consideration the robot configuration and the placement of the robot in the robotized site. Mainly, this method is based on Genetic Algorithms and it takes into consideration the multiplicity solutions of the robot Inverse Kinematics Model (IKM), the task point visit order and the placement of robot at the same time.
Drought and Salt Stress Tolerance of an Arabidopsis Glutathione S-Transferase U17 Knockout Mutant Are Attributed to the Combined Effect of Glutathione and Abscisic Acid1[C][W][OA]

Although glutathione S-transferases (GSTs) are thought to play major roles in oxidative stress metabolism, little is known about the regulatory functions of GSTs. We have reported that Arabidopsis (Arabidopsis thaliana) GLUTATHIONE S-TRANSFERASE U17 (AtGSTU17; At1g10370) participates in light signaling and might modulate various aspects of development by affecting glutathione (GSH) pools via a coordinated regulation with phytochrome A. Here, we provide further evidence to support a negative role of AtGSTU17 in drought and salt stress tolerance. When AtGSTU17 was mutated, plants were more tolerant to drought and salt stresses compared with wild-type plants. In addition, atgstu17 accumulated higher levels of GSH and abscisic acid (ABA) and exhibited hyposensitivity to ABA during seed germination, smaller stomatal apertures, a lower transpiration rate, better development of primary and lateral root systems, and longer vegetative growth. To explore how atgstu17 accumulated higher ABA content, we grew wild-type plants in the solution containing GSH and found that they accumulated ABA to a higher extent than plants grown in the absence of GSH, and they also exhibited the atgstu17 phenotypes. Wild-type plants treated with GSH also demonstrated more tolerance to drought and salt stresses. Furthermore, the effect of GSH on root patterning and drought tolerance was confirmed by growing the atgstu17 in solution containing l-buthionine-(S,R)-sulfoximine, a specific inhibitor of GSH biosynthesis. In conclusion, the atgstu17 phenotype can be explained by the combined effect of GSH and ABA. We propose a role of AtGSTU17 in adaptive responses to drought and salt stresses by functioning as a negative component of stress-mediated signal transduction pathways.
Occurrence of aflatoxins in oilseeds providing cocoa-butter substitutes

Four oilseeds providing cocoa-butter substitutes--shea, pentadecima, illipe, and salseed--when tested as substrates for aflatoxin production by two strains of Aspergillus parasiticus, gave varying levels of aflatoxin. Aflatoxins were found at low levels occurring naturally in moldy shea-nuts, but none of 21 commercial shea-nut samples contained greater than 20 micrograms of aflatoxin B1 per kg.
GenDecoder: genetic code prediction for metazoan mitochondria

Although the majority of the organisms use the same genetic code to translate DNA, several variants have been described in a wide range of organisms, both in nuclear and organellar systems, many of them corresponding to metazoan mitochondria. These variants are usually found by comparative sequence analyses, either conducted manually or with the computer. Basically, when a particular codon in a query-species is linked to positions for which a specific amino acid is consistently found in other species, then that particular codon is expected to translate as that specific amino acid. Importantly, and despite the simplicity of this approach, there are no available tools to help predicting the genetic code of an organism. We present here GenDecoder, a web server for the characterization and prediction of mitochondrial genetic codes in animals. The analysis of automatic predictions for 681 metazoans aimed us to study some properties of the comparative method, in particular, the relationship among sequence conservation, taxonomic sampling and reliability of assignments. Overall, the method is highly precise (99%), although highly divergent organisms such as platyhelminths are more problematic. The GenDecoder web server is freely available from .
Integration of shape from X modules: combining stereo and shading

Stereo algorithms suffer from the lack of local surface texture due to smoothness of depth constraint or local mismatches in disparity estimates. The stereo methods only provide a coarse depth map which can be associated with a low pass image of the depth map. Shape from shading algorithms produce better estimates of local surface areas, but some have problems with variable albedo and spherical surfaces. Thus, shape from shading methods produce better detailed depth information, and can be associated with the high pass image of the depth map image. In order to compute a better depth map, a method is presented for integrating the high-frequency information from the shape from shading and the low frequency information from stereo. <<ETX>>
Evidence for a multiclonal origin of multicentric advanced lesions of Kaposi sarcoma.

BACKGROUND Kaposi sarcoma (KS) is a complex tumor of uncertain clonality. Studying the viral clonality of the human herpesvirus 8 (HHV-8) in KS to determine clonality of the tumors, a strategy that has been used previously with Epstein-Barr virus and its associated tumors, may elucidate whether multicentric (disseminated) KS lesions correspond to metastatic lesions or to expansions of independent clones. METHODS A series of 139 KS biopsies (from skin, lymph node, or tonsil) was obtained from 98 patients, with 59 biopsies from 18 patients with disseminated multicentric KS skin lesions. The degree of spindle cell infiltration in biopsies was established by direct observation of hematoxylin-eosin-stained sections, and HHV-8 viral load was quantified by real-time polymerase chain reaction. To determine cellular clonality, the size heterogeneity of the HHV-8-fused terminal repeat (TR) region was determined by probing of electrophoresed restricted genomic DNA from KS biopsies for the HHV-8 TR sequence. RESULTS HHV-8 clonality analysis was performed on the 62 samples for which sufficient DNA was obtained. Most samples corresponded to histologically nodular lesions with high spindle cell infiltration and high viral load. A clonal HHV-8 pattern was determined for 59 samples; 11 were found to be monoclonal and 48 to be oligoclonal. The informative samples that were from disseminated KS skin lesions (n = 26, from six patients) were either monoclonal or oligoclonal, and the size of HHV-8 episomes varied between these samples. CONCLUSION Although some tumor KS lesions were monoclonal expansions of HHV-8-infected spindle cells, most advanced lesions were oligoclonal proliferations. Furthermore, individual KS disseminated tumor skin lesions were found to represent distinct expansions of HHV-8-infected spindle cells. Thus, our results suggest that KS lesions, especially in patients with advanced skin tumors, are reactive proliferations rather than true malignancies with metastatic dissemination.
Behavioral equivalence in the polymorphic pi-calculus

We investigate parametric polymorphism in message-based concurrent programming, focusing on behavioral equivalences in a typed process calculus analogous to the polymorphic lambda-calculus of Girard and Reynolds. Polymorphism constrains the power of observers by preventing them from directly manipulating data values whose types are abstract, leading to notions of equivalence much coarser than the standard untyped ones. We study the nature of these constraints through simple examples of concurrent abstract data types and develop basic theoretical machinery for establishing bisimilarity of polymorphic processes. We also observe some surprising interactions between polymorphism and aliasing, drawing examples from both the polymorphic pi-calculus and ML.
Risk factors for Kaposi's sarcoma in men seropositive for both human herpesvirus 8 and human immunodeficiency virus

Objective: To identify risk factors for Kaposi's sarcoma (KS) among men seropositive for both human herpesvirus 8 (HHV-8) and HIV. Design: Cross-sectional study of 91 HHV-8 seropositive, HIV seropositive men who have sex with men (57 with KS), and 70 controls at lower risk for KS. Methods: Patients received clinical evaluations. Blood, oral fluids, semen, rectal brush, rectal swab, and urine were collected, and tests for HHV-8 were performed. Results: Men with KS were more likely to have HHV-8 DNA in peripheral blood mononuclear cells (PBMC) than men without KS [35.1 versus 5.9%, odds ratio (OR), 8.6, 95% confidence interval (CI), 1.9–39.9]. The prevalence of HHV-8 DNA in oral fluids was similar for the two groups (37.0 versus 32.4%; OR, 1.2; 95% CI, 0.5–3.0). HHV-8 DNA was rarely detected in specimens of other types from these men, or in any specimens from the 70 controls. Among men with KS, HHV-8 DNA in PBMC was associated with new KS lesions (OR, 4.5; 95% CI, 1.4–14.5), and HHV-8 DNA in oral fluids was associated with oropharyngeal KS lesions (OR, 3.1; 95% CI, 1.0–10.1). Men with high HHV-8 antibody titers were more likely to have KS (OR, 9.6; 95% CI, 1.2–78.2), but were less likely to have new KS lesions (OR, 0.2; 95% CI, 0.0–1.1) or HHV-8 DNA in PBMC (OR, 0.2; 95% CI, 0.0–1.6) or oral fluids (OR, undefined; P = 0.001). Conclusions: In HHV-8- and HIV-seropositive men, HHV-8 DNA is associated with KS. Among men without KS, HHV-8 DNA is most commonly found in oral fluids. High HHV-8 antibody titers may protect against circulating HHV-8 and new KS lesions.
Verification of cardiac mechanics software: benchmark problems and solutions for testing active and passive material behaviour

Models of cardiac mechanics are increasingly used to investigate cardiac physiology. These models are characterized by a high level of complexity, including the particular anisotropic material properties of biological tissue and the actively contracting material. A large number of independent simulation codes have been developed, but a consistent way of verifying the accuracy and replicability of simulations is lacking. To aid in the verification of current and future cardiac mechanics solvers, this study provides three benchmark problems for cardiac mechanics. These benchmark problems test the ability to accurately simulate pressure-type forces that depend on the deformed objects geometry, anisotropic and spatially varying material properties similar to those seen in the left ventricle and active contractile forces. The benchmark was solved by 11 different groups to generate consensus solutions, with typical differences in higher-resolution solutions at approximately 0.5%, and consistent results between linear, quadratic and cubic finite elements as well as different approaches to simulating incompressible materials. Online tools and solutions are made available to allow these tests to be effectively used in verification of future cardiac mechanics software.
Environmental relevance of heavy metal-substituted chlorophylls using the example of water plants

Following experiments which studied the substitution of the central ion of isolated chlorophylls by heavy metal ions in vitro, in vivo experiments with submersed water plants were carried out. It was discovered that the substitution of the central atom of chlorophyll, magnesium, by heavy metals (mercury, copper, cadmium, nickel, zinc, lead) in vivo is an important damage mechanism in stressed plants. This substitution prevents photosynthetic light-harvesting in the affected chlorophyll molecules, resulting in a breakdown of photosynthesis. The reaction varies with light intensity. In low light irradiance all the central atoms of the chlorophylls are accessible to heavy metals, with heavy metal chlorophylls being formed, some of which are much more stable towards irradiance than Mg-chlorophyll. Consequently, plants remain green even when they are dead. In high light, however, almost all chlorophyll decays, showing that under such conditions most of the chlorophylls are inaccessible to heavy metal ions.
Realistic Indoor Wi-Fi and Femto Deployment Study as the Offloading Solution to LTE Macro Networks

This paper investigates the downlink performance of indoor deployed Wi-Fi and Femto as the offloading solution to the LTE macro cellular networks in a realistic large-scale dense-urban scenario. With an assumed broadband traffic volume growth of 50x compared to today's levels, it is evaluated that a dual-carrier LTE macro network will not be able to provide sufficient service coverage with a 1 Mbps minimum data rate and, indoor coverage is identified as the major bottleneck. We evaluate the performance of indoor Wi-Fi and Femto cell deployment to offload the congested LTE macro network. We show that, in a dual-carrier LTE macro case with a total of 30 MHz spectrum, Wi-Fi access point density of 230/km2 is required to meet the set target of 90% coverage with a minimum user data rate of 1 Mbps. For the same scenario it was found that an out-band Femto access point density of 1200/km2 is required. Furthermore, we show that in-band Femto cell cannot meet the set network requirement even at a very high access point density. We also show that Wi-Fi and Femto cell can offload the same amount of traffic when they are deployed at the same access point density.
Beautiful mirrors and precision electroweak data

The standard model (SM) with a light Higgs boson provides a very good description of the precision electroweak observable data coming from the CERN LEP, SLD and Fermilab Tevatron experiments. Most of the observables, with the notable exception of the forward-backward asymmetry of the bottom quark, point towards a Higgs boson mass far below its current experimental bound. The disagreement, within the SM, between the values for the weak mixing angle as obtained from the measurement of the leptonic and hadronic asymmetries at lepton colliders, may be taken to indicate new physics contributions to the precision electroweak observables. In this article we investigate the possibility that the inclusion of additional bottomlike quarks could help resolve this discrepancy. Two inequivalent assignments for these new quarks are analyzed. The resultant fits to the electroweak data show a significant improvement when compared to that obtained in the SM. While in one of the examples analyzed the exotic quarks are predicted to be light, with masses below 300 GeV, and the Higgs boson tends to be heavy, in the second one the Higgs boson is predicted to be light, with a mass below 250 GeV, while the quarks tend to be heavy, with masses of about 800 GeV. The collider signatures associated with the new exotic quarks, as well as the question of unification of couplings within these models and a possible cosmological implication of the new physical degrees of freedom at the weak scale are also discussed.