Miracle-dz/UniFAR-FTUs huggingface dataset:
Systematic studies on Thysanotus R.Br. (Asparagales: Laxmanniaceae).

Thysanotus R.Br. (Asparagales; Laxmanniaceae) is a genus native to Australia with c. 50 species distributed chiefly in Australia. To date, Thysanotus lacks proper and detailed systematic studies based on molecular and/or non-molecular data. Therefore, carrying out a detailed systematic study using molecular and/or non-molecular data seemed important. Furthermore, generic placement of Murchisonia Brittan has always been controversial and this placement required testing under a phylogenetic framework. The generic relationships within Laxmanniaceae/Lomandraceae are considered uncertain; therefore, a phylogenetic analysis using molecular and morphological data is necessary to properly understand the generic relationships of Laxmanniaceae. Detailed studies on stem anatomy and morphology were carried out in order to understand the systematic significance and phylogenetic signal of these characters. The cp DNA (trnL intron and trnL–F intergenic spacer) and nuclear ITS2 gene regions were amplified and the results compared and combined with a morphological analysis. Phylogenetic analyses were carried out using Arthropodium R.Br and Eustrephus R.Br as outgroup taxa. There was sufficient variation in general morphology, seed micromorphology and stem anatomy and were potentially useful in understanding phylogenetic relationships of Thysanotus. A number of synapomorphies based on general morphology and stem anatomy such as absence of pendent flowers and absence of irregular shaped epidermal cells were recognised. The molecular data and the combined data yielded highly resolved consensus trees and enabled us to recognise three main lineages within the genus, each representing life history adaptations. Murchisonia was consistently nested within Thysanotus in all analyses showing a need for the return of both species to Thysanotus. Insights to intraspecific variation were also discernable from morphological, molecular and the combined analyses in species such as T. patersonii and T. juncifolius. Two new Thysanotus species, T. unicupensis and T. racemoides are also described. Our data strongly support the current circumscription of Laxmanniaceae, but suggest that there are three main lineages within the family, rather than the two previously recognised subfamilies.
The Nitrogen Content of Different Varieties of Peas as a Factor Affecting Infestations by Macrosiphum pisi (Kltb.) (Homoptera: Aphididae). A Preliminary Report

The influence of varietal differences in plants on infestation by aphids has received considerable attention in control studies. Painter (14), in 1941, concluded that the composition of the available food in the host plant plays possibly the most important role in determining the relative resistance to aphid attacks. In biological studies on Aphis rumicis L. , Davidson (8) found that factors that influence the physiological activity of the plant affect also the progress of aphid infestation. The same author (6) also pointed out that aphids exhibit a wide range of fecundity on different hosts. “The sap of certain varieties of beans”, writes Davidson, “appears to have a direct inhibiting effect upon the reproductive capacity of the aphids, whereas that of other varieties seems to have the opposite effect. ”
Neuroprotective Mitochondrial Glutamate Receptors

Mitochondria isolated from rat brain have NMDA-type glutamate receptors that appear to enhance mitochondrial calcium buffering capacity. Glutamate receptors of the N-methyl-D-aspartate (NMDA) type participate in both physiological and pathological synaptic events, with excessive activation of these receptors resulting in calcium overload and excitotoxicity. Korde and Maragos prepared isolated mitochondria from rat brains and found that these preparations responded to glutamate or NMDA agonists with increased calcium uptake, compared with the calcium uptake by mitochondria in the absence of these ligands. The NR2a subunit of the NMDA receptor was detected to be associated with mitochondria by electron microscopy of purified mitochondrial preparations or hippocampal slices, and Western blotting of submitochondrial preparations indicated that the NR1 and NR2a subunits were associated with the inner mitochondrial membrane. Mitochondria prepared from GT1-7, a neuronal cell line, in which the NR1 subunit was knocked down exhibited only basal calcium uptake that was not enhanced by the addition of NMDA. In contrast, expression of NR1 and NR2a targeted specifically to the mitochondria resulted in cells that had enhanced ATP production and exhibited less death in response to cytotoxic concentrations of glutamate. Mitochondria from these NMDA receptor–targeted cells had increased calcium uptake, suggesting that increased capacity for calcium buffering may contribute to the protective effects. Although compared with their abundance in the synaptic plasma membrane, the abundance of NMDA receptors in mitochondria is low, these data suggest that mitochondrial NMDA receptors may play a role in the calcium buffering capacity of mitochondria. A. S. Korde, W. F. Maragos, Identification of an N-methyl-D-aspartate receptor in isolated nervous system mitochondria. J. Biol. Chem. 287, 35192–35200 (2012). [Abstract] [Full Text]
Dynamic Interference-Sensitive Run-time Adaptation of Time-Triggered Schedules

Over-approximated Worst-Case Execution Time (WCET) estimations for multi-cores lead to safe, but over-provisioned, systems and underutilized cores. To reduce WCET pessimism, interference-sensitive WCET (isWCET) estimations are used. Although they provide tighter WCET bounds, they are valid only for a specific schedule solution. Existing approaches have to maintain this isWCET schedule solution at run-time, via time-triggered execution, in order to be safe. Hence, any earlier execution of tasks, enabled by adapting the isWCET schedule solution, is not possible. In this paper, we present a dynamic approach that safely adapts isWCET schedules during execution, by relaxing or completely removing isWCET schedule dependencies, depending on the progress of each core. In this way, an earlier task execution is enabled, creating time slack that can be used by safety-critical and mixed-criticality systems to provide higher Quality-of-Services or execute other best-effort applications. The Response-Time Analysis (RTA) of the proposed approach is presented, showing that although the approach is dynamic, it is fully predictable with bounded WCET. To support our contribution, we evaluate the behavior and the scalability of the proposed approach for different application types and execution configurations on the 8-core Texas Instruments TMS320C6678 platform, obtaining significant performance improvements compared to static approaches.
Paleontological Context for the Developmental Mechanisms of Evolution

The emerging field of evolutionary developmental biology (evo‐devo) seeks to identify the specific genetic basis for plant evolution. Whereas molecular biological studies are rapidly exposing the developmental mechanisms of evolution, paleontological studies reveal the sequence in which evolutionary changes have occurred. Aspects of both fields are reviewed in this article. Plant structure develops along genetically patterned pathways, some of which produce distinctive morphological features. Such features serve as “fingerprints” for regulatory mechanisms, thus providing a record of growth regulation for both living species and plant fossils. Transformational series of structure through geological time form the contextual framework for inferring evolution from the fossil record, but the most widely practiced application of transformational series for plants, Telome Theory, has no developmental basis. By contrast, the fossil record of leaf evolution in seed plants documents morphological changes to which a growing understanding of genetic pathways can be correlated. Leaves are defined by a number of features, including determinacy and adaxial/abaxial identity. Fossils of early seed plants show stepwise acquisition of these characters, from which we can infer developmental modifications leading to the evolution of the characters. Previous work has revealed that an interregulated network of genes is involved in the specification of these features. The genes identified as being involved in various aspects of leaf development provide clues to the evolution of each character. In particular, expression of the AS1 and AS2 genes appears to facilitate both determinacy and bilateral patterning. The novel expression pattern of these genes may have been the key innovation that resulted in the evolution of leaves in seed plants. Combining molecular biological studies with knowledge of evolutionary patterns gleaned from the fossil record brings a new depth of understanding to the evolution of fundamental plant form.
The zoobenthos of the freshwater tidal Hudson River and its response to the zebra mussel (Dreissena polymorpha) invasion

We describe the composition of the zoobenthos of the freshwater, tidal Hudson River, its relationships to environmental variables, and its response to the zebra mussel (Dreissena polymorpha) invasion. We collected samples using a petite PONAR grab and a 0.5-mm mesh sieve at 28 sites throughout the freshwater, tidal Hudson in 1990-97. The fauna contained more than 200 species, and was dominated by tubificid oligochaetes, unionid mussels, amphipods, and chironomid midges. Average density and biomass of the zoobenthos were 10,000/m 2 and 7.4 g DM/m 2 (before the zebra mussel invasion). The composition of the fauna was determined chiefly by the presence or absence of rooted vegetation and by salinity. Within the range of sediments sampled (clay to medium sand), sediment grain size and organic content had only a weak influence on the fauna. We discuss the biology, distribution, and response to the zebra mussel invasion for all common zoobenthic species in the Hudson. The zebra mussel invasion caused populations of benthic planktivores (bivalves, tanytarsine midges, and Chaoborus) to decline by 35-100%. Populations of other benthic animals typically rose in shallow-water, vegetated sites, and fell in unvegetated, deepwater sites. On a riverwide basis, the zebra mussel invasion caused density and biomass of all other benthic animals to fall by 38% and 57 %, respectively. Benthic animals played important roles in the Hudson ecosystem as suspension-feeders, fish food, and sediment mixers. The zebra mussel invasion changed the importance of these roles.
Phylogeography of the commensal Rattus exulans with implications for its use as bioproxy for human migrations

The Pacific rat, Rattus exulans, or Kiore as it is called by Maori, is a small human commensal associated with the human settlement of the Pacific. Archaeological evidence from Island Melanesia connects the distribution of the species with the presumed ancestors of all Polynesians, the so-called Lapita. Excavations have uncovered artefacts unprecedented in the region, comprising a style of distinctively dentate-stamped pottery, fish hooks and animal remains among others. The earliest animal remains are from pigs and R. exulans, which was clearly introduced into this region by the people as part of their cultural complex. On these grounds R. exulans has previously been used as proxy to infer human migration pathways throughout the Pacific. Accessibility of human archaeological material is scarce and by way of proxy a much higher sampling resolution for the commensal allows more specific inferences. While the origin of the Lapita is still widely disputed among disciplines from archaeology over linguistics and genetics, attention is focused on the Bismarck Archipelago, as an essential stepping stone for the distribution of these human migrants into the Pacific. The genetics of R. exulans might contribute to an assessment of the established theories of the Lapita origin. However, to make inferences regarding human migration based on the species, more knowledge is needed about its population structure and distribution history. In this thesis I establish the current population structure of R. exulans by extensive sampling of mitochondrial D-loop sequences across its distributional range with a strong focus on the Bismarck Archipelago. The population is deeply divided into three major geographic regions with more recent regional substructures. With the help of a chronology-based reconstruction of ancestral regional distribution I infer the geographic origin of these observed haplogroups and evaluate the chronology in the light of palaeoclimatic events to distinguish natural dispersal events from those that are human mediated. The marked differentiation of the Philippines and of Remote Oceania is almost certainly connected to a
Uromonitor® as a novel sensitive and specific urine-based test for recurrence surveillance of patients with non-muscle invasive bladder cancer

Bladder cancer is the most frequent malignancy of the urinary system and is ranked the seventh most diagnosed cancer in men worldwide. About 70-75% of all newly diagnosed patients with bladder cancer will present disease confined to the mucosa or submucosa, the non-muscle invasive bladder cancer (NMIBC) subtype. Of those, approximately 70% will recur after transurethral resection (TUR). Due to this high rate of recurrence, patients are submitted to an intensive follow-up program that should be maintained throughout many years, or even throughout life, resulting in an expensive follow-up, with cystoscopy being the most cost-effective procedure for NMIBC screening. Currently, the gold standard procedure for detection and follow-up of NMIBC is based on the association of cystoscopy and urine cytology. As cystoscopy is a very invasive approach, over the years, many different non-invasive (both in serum and urine samples) assays have been developed in order to search genetic and protein alterations related to the development, progression and recurrence of bladder cancer. TERT promoter mutations and FGFR3 hotspot mutations are the most frequent somatic alterations in bladder cancer and constitute the most reliable biomarkers for bladder cancer. Based on these findings, an ultra-sensitive assay called Uromonitor® was developed that corresponds to a urine-based assay capable of detecting trace amounts of the two most common alterations in NMIBC, TERT promoter and FGFR3 mutation, in urine samples. The Uromonitor® test was performed in a cohort of 72 patients, firstly diagnosed with bladder cancer and under surveillance for NMIBC, to access its sensitivity and specificity in the detection of NMIBC recurrence. Uromonitor® was shown to be highly sensitive and specific in detecting recurrence of bladder cancer in patients under surveillance of non-muscle invasive bladder cancer.
Modulatory Role of microRNAs in Triple Negative Breast Cancer with Basal-Like Phenotype

Simple Summary Triple Negative breast cancer (TNBC) is an aggressive tumor showing high histological grade, high recurrence, and frequent metastasis, accounting for about 25% of breast cancer-related deaths. Emerging roles and molecular mechanisms by which miRNAs impact pathogenesis and prognosis of basal-phenotype TNBC and their potential clinical utility are analyzed in the present review. Progress achieved in TNBC molecular taxonomy had minimal clinical impact, while miRNAs could act as prognostic/predictive biomarkers for TNBC subtypes. As there are currently no other therapeutic options to treat TNBC apart from chemotherapy, various studies were reviewed to draw the conclusion that ncRNAs might be candidates for drug development and drug resistance. Targeted approaches to epigenetic mechanisms and clarification of the molecular mechanisms of specific miRNAs in TNBC subtypes are fully justified. This review might provide a collection of biomarkers potentially useful in clinical settings and shows that the combination of miRNA-based therapeutic strategies with conventional therapies might synergize anticancer effects improving patient outcome. Abstract Development of new research, classification, and therapeutic options are urgently required due to the fact that TNBC is a heterogeneous malignancy. The expression of high molecular weight cytokeratins identifies a biologically and clinically distinct subgroup of TNBCs with a basal-like phenotype, representing about 75% of TNBCs, while the remaining 25% includes all other intrinsic subtypes. The triple negative phenotype in basal-like breast cancer (BLBC) makes it unresponsive to endocrine therapy, i.e., tamoxifen, aromatase inhibitors, and/or anti-HER2-targeted therapies; for this reason, only chemotherapy can be considered an approach available for systemic treatment even if it shows poor prognosis. Therefore, treatment for these subgroups of patients is a strong challenge for oncologists due to disease heterogeneity and the absence of unambiguous molecular targets. Dysregulation of the cellular miRNAome has been related to huge cellular process deregulations underlying human malignancy. Consequently, epigenetics is a field of great promise in cancer research. Increasing evidence suggests that specific miRNA clusters/signatures might be of clinical utility in TNBCs with basal-like phenotype. The epigenetic mechanisms behind tumorigenesis enable progress in the treatment, diagnosis, and prevention of cancer. This review intends to summarize the epigenetic findings related to miRNAome in TNBCs with basal-like phenotype.
Digital Multiplier-Less Spiking Neural Network Architecture of Reinforcement Learning in a Context-Dependent Task

Neuromorphic engineers develop event-based spiking neural networks (SNNs) in hardware. These SNNs closer resemble the dynamics of biological neurons than conventional artificial neural networks and achieve higher efficiency thanks to the event-based, asynchronous nature of the processing. Learning in the hardware SNNs is a more challenging task, however. The conventional supervised learning methods cannot be directly applied to SNNs due to the non-differentiable event-based nature of their activation. For this reason, learning in SNNs is currently an active research topic. Reinforcement learning (RL) is a particularly promising learning method for neuromorphic implementation, especially in the field of autonomous agents’ control. An SNN realization of a bio-inspired RL model is in the focus of this work. In particular, in this article, we propose a new digital multiplier-less hardware implementation of an SNN with RL capability. We show how the proposed network can learn stimulus-response associations in a context-dependent task. The task is inspired by biological experiments that study RL in animals. The architecture is described using the standard digital design flow and uses power- and space-efficient cores. The proposed hardware SNN model is compared both to data from animal experiments and to a computational model. We perform a comparison to the behavioral experiments using a robot, to show the learning capability in hardware in a closed sensory-motor loop.
Design of a Bit-Interleaved Low Power 10T SRAM Cell with Enhanced Stability

The technology is shrinking in recent days which leads to growing concerns related to various design metrics. Leakage power tends to grow with the array size as most of the Static Random Access Memory (SRAM) cells operate in standby mode. The data to be written into the SRAM become difficult as the supply voltage decreases. So, stability in write mode requires enhancement. As SRAM is used for the on-chip computations, the faster write operation is required. The half-select issue in SRAM design needs to be eliminated so that bit interleaving architecture can be employed for the SRAM array enabling the protection from soft errors. A new Proposed 10 Transistor Bit-Interleaved SRAM cell has been designed addressing the above concerns. Employment of high-threshold voltage devices in read path and absence of NMOS device in one of the inverters reduces leakage power. Cut-off switch enables faster write operation and enhanced write stability. Cross point selection in write mode eliminates the half-select issue observed by carrying 1000 Monte-Carlo simulations. It has lower leakage power while holding 0 compared to 8 Transistor, Fully Differential 8 Transistor and Write Assist Low Power 11 Transistor SRAM cells at the worst fast-fast process corner for 0.9 V supply voltage. Write 1 Power Delay Product is lower than 8 Transistor, Fully Differential 8 Transistor and Write Assist Low Power 11 Transistor SRAM cells at slow-slow corner at 0.9V supply voltage. All the design metrics have been evaluated by performing post-layout simulation in Cadence Virtuoso in 45-nm technology.
Antigenic waves of virus–immune coevolution

Significance Viruses, such as influenza, evolve under the selection of host immune systems. Previously infected individuals become immune, forcing the virus to find susceptible hosts or mutate, chasing it away in antigenic space. We formulate this viral escape process in terms of a low-dimensional wave moving in antigenic space. The dimensionality of the antigenic space impacts the persistence, as well as stability, of viral evolution. We uncover a characteristic timescale for the persistence of the viral strain, which is an order of magnitude longer than individual host immunity and emerges collectively from the pressure of the chasing immune systems. These results offer intuition about the antigenic turnover of viruses and highlight the importance of the effective dimensionality of coevolution. The evolution of many microbes and pathogens, including circulating viruses such as seasonal influenza, is driven by immune pressure from the host population. In turn, the immune systems of infected populations get updated, chasing viruses even farther away. Quantitatively understanding how these dynamics result in observed patterns of rapid pathogen and immune adaptation is instrumental to epidemiological and evolutionary forecasting. Here we present a mathematical theory of coevolution between immune systems and viruses in a finite-dimensional antigenic space, which describes the cross-reactivity of viral strains and immune systems primed by previous infections. We show the emergence of an antigenic wave that is pushed forward and canalized by cross-reactivity. We obtain analytical results for shape, speed, and angular diffusion of the wave. In particular, we show that viral–immune coevolution generates an emergent timescale, the persistence time of the wave’s direction in antigenic space, which can be much longer than the coalescence time of the viral population. We compare these dynamics to the observed antigenic turnover of influenza strains, and we discuss how the dimensionality of antigenic space impacts the predictability of the evolutionary dynamics. Our results provide a concrete and tractable framework to describe pathogen–host coevolution.