Miracle-dz/UniFAR-FTUs huggingface dataset:
Initial Events during the Evolution of C4 Photosynthesis in C3 Species of Flaveria1[W][OPEN]

The initial stages of C4 photosynthetic evolution in Flaveria species is apparent in the C3 species Flaveria pringlei and Flaveria robusta, which show increases in organelle number and size in bundle sheath cells and a redistribution of mitochondria to the inner region of the bundle sheath. The evolution of C4 photosynthesis in many taxa involves the establishment of a two-celled photorespiratory CO2 pump, termed C2 photosynthesis. How C3 species evolved C2 metabolism is critical to understanding the initial phases of C4 plant evolution. To evaluate early events in C4 evolution, we compared leaf anatomy, ultrastructure, and gas-exchange responses of closely related C3 and C2 species of Flaveria, a model genus for C4 evolution. We hypothesized that Flaveria pringlei and Flaveria robusta, two C3 species that are most closely related to the C2 Flaveria species, would show rudimentary characteristics of C2 physiology. Compared with less-related C3 species, bundle sheath (BS) cells of F. pringlei and F. robusta had more mitochondria and chloroplasts, larger mitochondria, and proportionally more of these organelles located along the inner cell periphery. These patterns were similar, although generally less in magnitude, than those observed in the C2 species Flaveria angustifolia and Flaveria sonorensis. In F. pringlei and F. robusta, the CO2 compensation point of photosynthesis was slightly lower than in the less-related C3 species, indicating an increase in photosynthetic efficiency. This could occur because of enhanced refixation of photorespired CO2 by the centripetally positioned organelles in the BS cells. If the phylogenetic positions of F. pringlei and F. robusta reflect ancestral states, these results support a hypothesis that increased numbers of centripetally located organelles initiated a metabolic scavenging of photorespired CO2 within the BS. This could have facilitated the formation of a glycine shuttle between mesophyll and BS cells that characterizes C2 photosynthesis.
Extracting active pathways from gene expression data

MOTIVATION A promising way to make sense out of gene expression profiles is to relate them to the activity of metabolic and signalling pathways. Each pathway usually involves many genes, such as enzymes, which can themselves participate in many pathways. The set of all known pathways can therefore be represented by a complex network of genes. Searching for regularities in the set of gene expression profiles with respect to the topology of this gene network is a way to automatically extract active pathways and their associated patterns of activity. METHOD We present a method to perform this task, which consists in encoding both the gene network and the set of profiles into two kernel functions, and performing a regularized form of canonical correlation analysis between the two kernels. RESULTS When applied to publicly available expression data the method is able to extract biologically relevant expression patterns, as well as pathways with related activity.
3D Euler spirals for 3D curve completion

Shape completion is an intriguing problem in geometry processing with applications in CAD and graphics. This paper defines a new type of 3D curves, which can be utilized for curve completion. It can be considered as the extension to three dimensions of the 2D Euler spiral. We prove several properties of these curves - properties that have been shown to be important for the appeal of curves. We illustrate their utility in two applications. The first is "fixing" curves detected by algorithms for edge detection on surfaces. The second is shape illustration in archaeology, where the user would like to draw curves that are missing due to the incompleteness of the input model.
Speed advantage of optimized metal S/D in 25 nm dual-gate fully-depleted CMOS

With shrinking dimensions, control of extrinsic impedance is becoming increasingly performance limiting. Improvements to source/drain (S/D) technology thus become critical to technology scaling. Metal S/D is a promising approach. A doped S/D device was modeled with a two-component S/D profile: an ultra-steep extension profile offset from the gate edge, and a stronger primary S/D profile aligned to the metal contact. The metal S/D was offset from the gate edge to improve the short channel margin. By reducing series resistance and allowing for lower fringe capacitance, a metal S/D device allows for substantial improvement in speed and/or power. An offset from the metal S/D to the gate should be used to reduce short channel effects. If doped S/D is used, then ultra-low resistance contacts are mandatory.
Elimination of bus voltage impact on temperature sensitive electrical parameter during turn-on transition for junction temperature estimation of high-power IGBT modules

Junction temperature is of great importance to safe operating area of IGBT modules. Various information of the IGBT operating state is reflected on electrical characteristics during turn-on transient. A unified extraction method for internal junction temperature via dynamic thermo-sensitive electrical parameters (DTSEP) during turn-on transient is proposed. Two DTSEP, turn-on delay time (tdon) and the maximum increasing rate of collector current dic/dt(max), are combined to eliminate the bus voltage impact. Using the inherent emitter-auxiliary inductor LeE in high-power modules, the temperature-dependent DTSEPs can be converted into a low-voltage and measurable signal. Finally, experiment results are exhibited to verify the effectiveness of proposed method.
GFRalpha3 is expressed predominantly in nociceptive sensory neurons

Activation of the RET receptor tyrosine kinase by glial‐derived neurotrophic factor family members is dependent on a family of coreceptors, GFRα1–4. GFRα3 preferentially binds the newest member of the glial‐derived neurotrophic factor family of ligands, artemin. The major site of GFRα3 expression is in the dorsal root ganglion; however, the class of sensory neurons that expresses GFRα3 has not been reported previously. Using immunohistochemical methods, we show that the majority of dorsal root ganglion cells that express GFRα3 also express vanilloid receptor type 1, peripherin, RET, trkA and calcitonin gene‐related peptide. In addition, a significant subpopulation of GFRα3‐expressing cells also binds the lectin IB4. We demonstrate that GFRα3 artemin neurons are immunopositive for markers expected of nociceptors and include a subset of neurons distinct from the GDNF‐responsive population. Our results indicate artemin may exert selective effects on pain sensation.
Provenance and metamorphism of the Swakane Gneiss: Implications for incorporation of sediment into the deep levels of the North Cascades continental magmatic arc, Washington

The Swakane Gneiss, interpreted to represent sedimentary strata metamorphosed at 8–12 kbar, is the deepest exposed crustal levels within the exhumed North Cascades continental magmatic arc, yet the nature and age of its protolith and the mechanism by which it was transported to deep-crustal levels remains unclear. Zircons from 11 paragneiss and schist samples were analyzed for U-Pb age and Hf-isotope composition in order to investigate the tectonic history of the Swakane Gneiss from protolith deposition to metamorphism within the North Cascades arc. Zircons interpreted to have crystallized in situ during metamorphism and/or melt-crystallization within the Swakane Gneiss at depth have ca. 74–66 Ma ages. Detrital-zircon age and Hf-isotope characteristics demonstrate provenance shifts that correlate with maximum depositional ages of ca. 93–81 Ma. Samples deposited between ca. 93 and 88 Ma have dominantly Mesozoic age peaks with initial εHf values between depleted mantle and chondritic uniform reservoir (CHUR), whereas ca. 86–81 Ma sample show the addition of distinct Proterozoic populations (ca. 1380 and 1800–1600 Ma) and Late Cretaceous zircons with unradiogenic Hf-isotope compositions. Similar detrital-zircon age and Hf-isotope patterns are observed in several Upper Cretaceous forearc and accretionary wedge units between southern California and Alaska along the North American continental margin. The connection between the Swakane Gneiss and these potential protoliths located outboard of Cordilleran arc systems indicate burial by either underplating of accretionarywedge sediments or underthrusting of forearc sediments. Therefore, the protolith and incorporation history for the Swakane Gneiss is likely similar to those of deep crustal metasedimentary units elsewhere in the North Cascades (i.e., the Skagit Gneiss Complex) and to the south along the continental margin (i.e., the Pelona-Orocopia-Rand schists and Schist of Sierra de Salinas). These observations suggest that burial of sediment outboard of continental magmatic arc systems may be a major mechanism for the transfer of sediment to the deep levels of continental arcs. LITHOSPHERE; v. 10; no. 3; p. 460–477; GSA Data Repository Item 2018144 | Published online 3 April 2018 https://doi.org/10.1130/L712.1
Exploring Genetic Mutations on Mitochondrial DNA Cancer Data with Interactive Tabletop and Active Tangibles

Biological data is becoming so complex, it is difficult for scientists and other professionals to interpret and understand it. New tools are needed to better support the manipulation and understanding of data in order to improve analyses and the formation of new hypotheses. Tangible mtDNA is an active tangible and tabletop system that allows multiple users with diverse expertise to collaborate in exploring and understanding mitochondrial DNA sequencing data in breast cancer patients. In an evaluation of the system, 5 expert biologists found it to be effective for data exploration and useful in supporting understanding, collaboration and discussion of DNA datasets.
Pyramid Sketch: a Sketch Framework for Frequency Estimation of Data Streams

Sketch is a probabilistic data structure, and is used to store and query the frequency of any item in a given multiset. Due to its high memory efficiency, it has been applied to various fields in computer science, such as stream database, network traffic measurement, etc. The key metrics of sketches for data streams are accuracy, speed, and memory usage. Various sketches have been proposed, but they cannot achieve both high accuracy and high speed using limited memory, especially for skewed datasets. To address this issue, we propose a sketch framework, the Pyramid sketch, which can significantly improve accuracy as well as update and query speed. To verify the effectiveness and efficiency of our framework, we applied our framework to four typical sketches. Extensive experimental results show that the accuracy is improved up to 3.50 times, while the speed is improved up to 2.10 times. We have released our source codes at Github [1].
Seroprevalence and Risk Factors for Taenia solium Cysticercosis in Rural Pigs of Northern Peru

Taenia solium is a cestode parasite that causes cysticercosis in both humans and pigs. A serological survey was undertaken to assess the seroprevalence and risk factors associated with porcine cysticercosis in the rural district of Morropon, Peru. Pigs aged between 2 and 60 months were assessed by the Enzyme-linked Immunoelectrotransfer blot (EITB) assay to determine their serological status against porcine cysticercosis in a cross-sectional study. A total of 1,153 pigs were sampled. Porcine seroprevalence was 45.19% (42.31–48.06). The information about the animals and households was analyzed and risk factors associated with seroprevalence were determined by a multivariate logistic regression analysis. In the porcine population, the risk of being seropositive increased by 7% with every month of age (OR 1.07, 95% CI 1.05–1.09), and by 148% for pigs living in East Morropon (OR 2.48, 95% CI 1.82–3.37). Whereas, the presence of latrines in a household decreased the risk of being seropositive by 49% (OR 0.51; 95% CI 0.39–0.67). Sex and rearing system did not represent either risk or protective factors associated with the seroprevalence of porcine cysticercosis. The findings of this study could be used for further development of control programs that might focus on similar population groups within rural communities of developing countries where cysticercosis is endemic.
MODELING MOBILE AGENTS

Agent oriented software implies the realization of software components which are mobile autonomous and solve problems by creating new software compo nents during run time moving between locations ini tiating or joining groups of other software components Modeling and simulating those multiagent systems re quires speci c mechanisms for variable structure mod eling JAMES a Java Based Agent Modeling Environ ment for Simulation realizes variable structure models including mobility from the perspective of single au tonomous agents JAMES itself is based on parallel DEVS and adopts its abstract simulator model Sim ulation takes place as a sending of messages between concurrently active and distributed entities which re ect the model s current structure Thus modeling and simulation are coined equally by an agent based perspective
Modulation of Ca2+ influx in the ovine somatotroph by growth hormone-releasing factor.

Voltage-gated Ca2+ currents were recorded using the nystatin-perforated whole cell recording configuration on the ovine somatotrophs. With the use of Ca(2+)-tetraethylammonium chloride bath solution and Cs+ electrode solution, two types of Ca2+ currents were obtained with a predominant long-lasting (L) current blocked by nifedipine. A transient (T) current was isolated in the presence of nifedipine (3 microM) and was not blocked by omega-conotoxin (5 microM), but diminished to 47 +/- 5% of control by Ni2+ (0.3 mM) or to 52 +/- 10% of control by amiloride (0.5 mM). The nifedipine-blockable L-type current was not affected by omega-conotoxin (5 microM); it was, however, attenuated to 80 +/- 4% of control by Ni2+ (0.3 mM) and to 48 +/- 6% of control by amiloride (0.5 nM). Cd2+ (1 mM) totally prevented both T and L currents. Application of growth hormone-releasing factor (GRF, 10 nM) reversibly increased the amplitude of both Ca2+ currents without modifying their kinetic properties. The effect of GRF was observed approximately 30 s after application, peaked (142 +/- 11% of control, n = 5) rapidly, and lasted > 10 min if GRF treatment was continuous. Intracellular Ca2+ concentration ([Ca2+]i) was increased by GRF (10 nM) within seconds, reaching a peak within 30 s and lasting > 250 s. Blockade of Ca2+ channels (Cd2+, 1 mM) or the use of Ca(2+)-free solution reduced basal [Ca2+]i and significantly (P < 0.05) diminished the effect of GRF on [Ca2+]i. (ABSTRACT TRUNCATED AT 250 WORDS)
Ultrafast initiation of a neural race by impending errors

The brain makes decisions by means of races between neural units representing alternative choices. In the present study, we record the eyemovements made in the Wheeless task, when a visual stimulus is followed after a short delay by another stimulus demanding a different response. The behaviour can be very precisely described as a race between three independent decision processes: one Go process for each of the responses, and a Stop process that tries to cancel the first, now erroneous, response. To explain the high success rate for cancellation that we observe, the onset time for the Stop process must be some 10–20 ms shorter than for Go. As well as extending our understanding of the dynamics of complex decision‐making, this task provides a rapid, non‐invasive method for quantifying disorders of higher neural function.
Pernio of the hips in young girls wearing tight-fitting jeans with a low waistband.

Sir, In 1980 Beacham et al. (1) described equestrian cold panniculitis in overweight young women wearing tightfitting uninsulated riding trousers. They developed reddish tender plaques on the thighs due to prolonged cold exposure during equestrian activities in the winter. Cold panniculitis and pernio (chilblains), which is a relatively mild form of cold injury, has also been described in children wearing cold wet shoes or boots (2) and in mountaineers after wading across rivers (3). It is especially the fat-rich hip and lateral thigh regions of young women that are affected. The recent fashion among young women for tight jeans with a low waistband, exposing the upper part of the hip region to cold may result in hip pernio, as described in the following cases.
Low-Resonant-Frequency Micro Electret Generator for Energy Harvesting Application

A vibration-driven electret generator has been developed for energy harvesting applications. By using parylene as the spring material, a low-resonant-frequency MEMS generator is realized. Electrostatic levitation is adopted for the gap control. Large in-plane amplitude of 0.5 mm at the resonant frequency as low as 21 Hz has been achieved. We also demonstrate electret-powered operation of LED using a low-power-consumption impedance conversion circuit.
Brain architecture: a design for natural computation

Fifty years ago, John von Neumann compared the architecture of the brain with that of the computers he invented and which are still in use today. In those days, the organization of computers was based on concepts of brain organization. Here, we give an update on current results on the global organization of neural systems. For neural systems, we outline how the spatial and topological architecture of neuronal and cortical networks facilitates robustness against failures, fast processing and balanced network activation. Finally, we discuss mechanisms of self-organization for such architectures. After all, the organization of the brain might again inspire computer architecture.
Ontological analyses of roles

This paper discusses roles from ontological point of views. We first propose a most general type including roles and role-like entities in a new way. Then, we discuss ongoing property of roles to in-depth understand temporal aspects of roles. We identify two kinds of roles: original roles and derived roles. Our new findings in this research include all original roles are ongoing and all the derived occurrent-dependent roles are either retrospective or prospective. Finally, we propose a temporal model of derived roles.
Effects of Unsaturated Fatty Acid Esters of Testosterone on Neuronal, Behavioral and Hormonal Parameters in Male Rats Subjected to the Formalin Test

Chronic diseases are often accompanied by inflammatory and degenerative processes. Estrogens have repeatedly been found to be involved in these processes. Testosterone (T) is the main precursor of estrogen in the brain and T replacement in chronic diseases has become important in recent years, prompting research on new T-conjugated molecules. We recently synthesized three new molecules including unsaturated fatty acid esters: T-linoleate (TL), T-oleate (TO) and T-eicosapentanoate (TEPA). These substances were s.c. administered for 7 days to intact male rats subjected to the formalin test (FT). Three other groups were included as comparisons: NAIVE, receiving no substance, OIL, treated with almond oil (vehicle), and TN, treated with T-undecanoate, a saturated fatty acid. Spontaneous behaviors and pain-induced responses were determined during the FT, hormones (T and dihydrotestosterone, DHT) were determined in blood, while estrogen receptors (ERα and β) were detected at the genomic and proteomic levels in the hippocampus, hypothalamus and spinal cord. In the hippocampus, ERα and ERβ mRNA levels were increased respectively by TN and TL treatments with respect to OIL, whereas the hypothalamus TO and TL caused a decrease of ERα mRNA levels. At the proteomic level, TO, TL and TEPA decreased the levels of ERα in the hypothalamus, whereas TEPA decreased ERβ in the spinal cord, hippocampus and hypothalamus. There was no effect of treatment on the spontaneous behaviors, while the TO and TL groups showed lower pain-induced behaviors (paw jerk frequency and licking duration) than the OIL group. TN increased paw jerk frequency and decreased licking duration with respect to OIL. The treatments had no effect on T and DHT plasma levels. These results clearly indicate the possibility of pain and ER modulation by T-esters.
Palaeoenvironmental and climatic inferences from the late early Pleistocene lacustrine deposits in the eastern Tiberino Basin (central Italy)

Abstract Within the Neogene-Quaternary evolution of the Mediterranean intermountain basins, the eastern Tiberino Basin provides new multifaceted chronological, biostratigraphic, palaeoecological, and palaeoenvironmental information, appreciably improving the knowledge of palaeoenvironmental and climate conditions during the middle-late Matuyama Chron (late early Pleistocene). Shallow to relatively deep lacustrine deposits and alluvial plain deposits, magnetostratigraphically calibrated, hold malacofaunas, ostracofaunas, and carpological remains, as well as a pollen record. Palaeocarpological remains widely originated from the local (azonal) vegetation of waterlogged environments. Nonetheless, some taxa show transitional morphology between possibly extinct Pliocene-Pleistocene forms and living taxa. The pollen record highlights a conifer-dominated forest phase, indicating a temperate-wet interglacial period, well aligned inside the schemes for the same latitudinal band. The abundance of tree taxa currently absent from the Italian peninsula points to pre-Jaramillo late early Pleistocene biostratigraphical characters, here compared to other sections from central Italy, and contributes to a better definition of modes and timing of their disappearance in southern Europe. Malacofaunas and ostracods, still with late early Pleistocene features, together with Charophyte, mark repeated fluctuations in energy, temperature, and chemical composition of water. The overall record identifies an incipient diachronous cooling trend, for the first time recognized in southern Europe.
Development of bioassessment methode for water quality assessment of Cihampelas Stream in the Citarum River Basin

Cihampelas Stream is a tributary of the Citarum that flows across the Regency and Bandung area along 8,5 km. Cihampelas Stream are utilized by the community for domestic activities, tourism, agriculture, and fisheries. This study aims to determine the water quality based on Macrozoobenthos Index of Biotic Integrity and Periphytic Diatom Index of Biotic Integrity and its correlation with the Pollution Index (water classes). This research was conducted at four Cihampelas Stream stations representing the minimal areas of disturbance to the predicted areas of disturbance such as Cilengkrang, Cisurupan, Pasanggrahan, and Mekarmulya. Water sampling, macrozoobenthos, and periphytic diatom was conducted from July to September 2016 four times at two-week intervals. Assessment of water quality using Macrozoobenthos Index of Biotic Integrity shows that Cihampelas Stream is categorized from very good to bad category with index value ranging from 4─18. The water quality of the Cihampelas Stream shows very good to bad category based on the value of the Periphytic Diatom Index of Biotic Integrity which ranges from 3─15. Based on Pollution Index, along Cihampelas Stream is fulfilled class I to exceed class IV of water quality standard. Spearman correlation analysis results shows that Pollution Index (water classes) has negative correlation and stronger to Macrozoobenthos Index of Biotic Integrity compared to Periphytic Diatom Index of Biotic Integrity.