Miracle-dz/UniFAR-FTUs huggingface dataset:
Clusterdv, a simple density-based clustering method that is robust, general and automatic

How to partition a data set into a set of distinct clusters is a ubiquitous and challenging problem. The fact that data sets vary widely in features such as cluster shape, cluster number, density distribution, background noise, outliers and degree of overlap, makes it difficult to find a single algorithm that can be broadly applied. One recent method, based on search of density peaks, can be applied successfully to cluster many kinds of data, but it is not fully automatic, and fails on some simple data distributions. We propose an alternative approach, which estimates density dips between points, and allows robust determination of cluster number and distribution across a wide array of data, without any manual parameter adjustment. We show that this method is able to solve a range of synthetic and experimental data sets, where the underlying structure is known, and identifies consistent and meaningful clusters in new behavioural data. Significance It is common that natural phenomena produce groupings, or clusters, in data, that can reveal the underlying processes. However, the form of these clusters can vary arbitrarily, making it challenging to find a single algorithm that identifies their structure correctly, without prior knowledge of the number of groupings or their distribution. We describe a simple clustering algorithm that is fully automatic and is able to correctly identify the number and shape of groupings in data of many types. We expect this algorithm to be useful in finding unknown natural phenomena present in data from a wide range of scientific fields.
Deriving C4 photosynthesis parameters by fitting intensive A/Ci curves

Measurements of photosynthetic assimilation rate as a function of intercellular CO2 (A/Ci curves) are widely used to estimate photosynthetic parameters for C3 species, yet few parameters have been reported for C4 plants, because of a lack of estimation methods. Here, we extend the framework of widely-used estimation methods for C3 plants to build estimation tools by exclusively fitting intensive A/Ci curves (6-8 more sampling points) for C4 using three versions of photosynthesis models with different assumptions about carbonic anhydrase processes and ATP distribution. We use simulation-analysis, out-of-sample tests, existing in vitro measurements and chlorophyll-fluorescence-measurements to validate the new estimation methods. Of the five/six photosynthetic parameters obtained, sensitivity analyses show that maximal-Rubisco-carboxylation-rate, electron-transport-rate, maximal-PEP-carboxylation-rate and carbonic-anhydrase were robust to variation in the input parameters, while day-respiration and mesophyll-conductance varied. Our method provides a way to estimate carbonic anhydrase activity, a new parameter, from A/Ci curves, yet also shows that models that do not explicitly consider carbonic anhydrase yield approximate results. The two photosynthesis models, differing in whether ATP could freely transport between RuBP and PEP regeneration processes yielded consistent results under high light, but they may diverge under low light intensities. Modeling results show selection for Rubisco of low specificity and high catalytic rate, low leakage of bundle sheath and high PEPC affinity, which may further increase C4 efficiency.
An adaptive direct conversion transmitter

An adaptive direct conversion transmitter in which adjacent channel power measurements are used to simultaneously compensate for both power amplifier (PA) nonlinearity and quadrature modulator (QM) errors is presented. The measured results are presented to identify the sensitivity of the quadrature modulator's parameters (gain and phase imbalance, DC offsets) to temperature and the local oscillator frequency. An analysis of the system is given which details the relationship between the adjacent channel power and the PA nonlinearity and the QM errors; this result explains how a simple algorithm may be used to adjust the parameters based on a scalar measurement of the adjacent channel power. Simulation and measured results of a system using offset QPSK modulation with adaptive PD and QM correction are given. <<ETX>>
A likelihood ratio-based evaluation of strength of authorship attribution evidence in SMS messages using N-grams

An experiment in forensic text comparison (FTC) within the likelihood ratio (LR) framework is described. The experiment attempts to determine the strength of authorship attribution evidence modelled with N-grams, which is perhaps one of the most basic automatic modelling techniques. The SMS messages of multiple authors selected from the SMS corpus compiled by the National University of Singapore were used for same- and different-author comparisons. I varied the number of words used for the N-gram modelling (200, 1000, 2000 or 3000 words), and then assessed the performance of each set. The performance of the LR-based FTC system was assessed with the log likelihood ratio cost (Cllr). It is shown in this study that N-grams can be employed within an LR framework to discriminate same-author and different-author SMS texts, but a fairly large amount of data are needed to do it well (i.e. to obtain Cllr < 0.75). It is concluded that the LR framework warrants further examination with different features and processing techniques.
Frequent nonallelic gene conversion on the human lineage and its effect on the divergence of gene duplicates

Significance Nonallelic gene conversion (NAGC) is a driver of more than 20 diseases. It is also thought to drive the “concerted evolution” of gene duplicates because it acts to eliminate any differences that accumulate between them. Despite its importance, the parameters that govern NAGC are not well characterized. We developed statistical tools to study NAGC and its consequences for human gene duplicates. We find that the baseline rate of NAGC in humans is 20 times faster than the point mutation rate. Despite this high rate, NAGC has a surprisingly small effect on the average sequence divergence of human duplicates—and concerted evolution is not as pervasive as previously thought. Gene conversion is the copying of a genetic sequence from a “donor” region to an “acceptor. ” In nonallelic gene conversion (NAGC), the donor and the acceptor are at distinct genetic loci. Despite the role NAGC plays in various genetic diseases and the concerted evolution of gene families, the parameters that govern NAGC are not well characterized. Here, we survey duplicate gene families and identify converted tracts in 46% of them. These conversions reflect a large GC bias of NAGC. We develop a sequence evolution model that leverages substantially more information in duplicate sequences than used by previous methods and use it to estimate the parameters that govern NAGC in humans: a mean converted tract length of 250 bp and a probability of 2.5×10−7 per generation for a nucleotide to be converted (an order of magnitude higher than the point mutation rate). Despite this high baseline rate, we show that NAGC slows down as duplicate sequences diverge—until an eventual “escape” of the sequences from its influence. As a result, NAGC has a small average effect on the sequence divergence of duplicates. This work improves our understanding of the NAGC mechanism and the role that it plays in the evolution of gene duplicates.
Don’t throw out the sympatric species with the crater lake water: fine-scale investigation of introgression provides weak support for functional role of secondary gene flow in one of the clearest examples of sympatric speciation

Genomic data has revealed complex histories of colonization and repeated gene flow previously unrecognized in some of the most celebrated examples of sympatric speciation and radiation. However, much of the evidence for secondary gene flow into these radiations comes from genome-wide tests, which tells us little about how gene flow potentially influenced sympatric diversification. Here we investigated whole genomes of Barombi Mbo crater lake cichlids for fine-scale patterns of introgression between species with neighboring riverine cichlid populations. We did find evidence of secondary gene flow into the radiation scattered across < 0.24% of the genome; however, the functional and genetic diversity in these regions paint no clear picture of how that variation could have contributed to the ecological and morphological diversity found in the lake. Our results suggest that either variation in novel genetic pathways introduced during secondary gene flow contributed to the radiation, or that secondary gene flow was predominantly neutral with respect to the diversification processes. We also found evidence for differential assortment of ancestral polymorphism found in riverine populations between sympatric sister species, suggesting the presence of a hybrid swarm in the past. While the history of gene flow and colonization appears to be more complicated than once thought, the lack of compelling evidence for secondary gene flow influencing diversification suggests that we should not yet rule out one of the most celebrated examples of sympatric speciation in nature.
Peroxiredoxin-2: A Novel Regulator of Iron Homeostasis in Ineffective Erythropoiesis.

AIMS Iron overload (IO) is a life-threatening complication of chronic hemolytic disorders such as β-thalassemia. IO results in severe cellular oxidative damage, leading to organ failure. Peroxiredoxin-2 (Prx2), a typical 2-cysteine-(Cys)-peroxiredoxin, is an important component of the cytoprotective system, but its response to IO is still to be fully defined. RESULTS We studied the effects of IO on Prx2-knockout mice (Prx2-/-). The absence of Prx2 enhanced toxicity due to IO on erythropoiesis. We found that IO failed to induce the typical hepcidin (Hamp) upregulation in Prx2-/- mice due to its failure to activate the signal transducer and activator of transcription-3 (STAT3) with intact Jak2 signaling. In Prx2-/- mice, the loss of Hamp response was also observed after administration of a single dose of oral iron. When lipopolysaccharide (LPS) was used to explore IL6-STAT3 activation in Prx2-/- mice, STAT3 activation and Hamp upregulation were once again defective. Treatment with PEP-fusion-recombinant-Prx2 (PEP Prx2) significantly increased STAT3 activation with upregulation of Hamp expression in both IO- and LPS-exposed Prx2-/- mice. We also confirmed the beneficial effects of PEP Prx2 on Hamp expression through STAT3 activation in β-thalassemic mice. INNOVATION We propose that Prx2 plays a key role in responding to cytotoxicity of IO, directly targeting STAT3-transcriptional factor in a Jak2-independent fashion and regulating Hamp in response to canonical stimuli. CONCLUSION Collectively, our data highlight a novel role of Prx2 in iron homeostasis. Prx2 is a key cytoprotector against IO that is induced either by iron supplementation or due to chronic hemolysis as in β-thalassemia. Prx2 is required to support STAT3 transcriptional activity and regulation of Hamp expression. Antioxid. Redox Signal. 28, 1-14.
Metabolic process of raffinose family oligosacharrides during cold stress and recovery in cucumber leaves

Raffinose family oligosacharrides (RFOs) accumulate under stress conditions in many plants and have been suggested to act as stress protectants. To elucidate the metabolic process of RFOs under cold stress, levels of RFOs and relative carbohydrates, the expression and activities of main metabolic enzymes and their subcellular compartments were investigated during low temperature treatment and recovery period in cucumber leaves. Cold stress induced the accumulation of stachyose in vacuoles, galactinol in vacuoles and cytosols, and sucrose and raffinose in vacuoles, cytosols and chloroplasts. After cold stress removal, levels of these sugars decreased gradually in respective compartments. Among 4 galactinol synthase genes (CsGS), CsGS1 was not affected by the cold stress, while other three CsGSs were up-regulated by the low temperature. RNA levels of acid-α-galactosidase (GAL) 3, alkaline-α-galactosidase (AGA) 2 and 3, and the activities of GAL and AGA were up-regulated after cold stress removal. The GAL3 protein and GAL activity were exclusively located in the vacuole, whereas the protein of AGA2 and AGA 3 were found in the cytosol and chloroplast respectively. The results indicate that RFOs accumulated during the cold stress in different subcellular compartments in cucumber leaves could be catabolized in situ by different galactosidases after stress removal.
Properties of the HII region populations of M51 and NGC 4449 from Halpha images with ACS on HST

We have used the images from the ACS on HST in Hα, and in the neighboring continuum, to produce flux calibrated images of the large spiral galaxy M51, and the dwarf irregular NGC 4449. From these images we have derived the absolute luminosities in Hα, the areas, and the positions with respect to the galactic centers as reference points, of over 2600 Hii regions in M51 and over 270 Hii regions in NGC 4449. Using this database we have derived luminosity (L)–volume (V) relations for the regions in the two galaxies, showing that within the error limits these obey the equation L ∼ V , which differs from the linear relation expected for regions of constant uniform electron density. We discuss briefly possible models which would give rise to this behavior, notably models with strong density inhomogeneities within the regions. Plotting the luminosity functions for the two galaxies we find a break in the slope for M51 at log(L) = 38.5 dex (units in erg s) for M51 in good agreement with the previous ground-based study by Rand, and above this luminosity NGC 4449 also shows a sharp decline in its luminosity function, although the number of regions is too small to plot the function well at higher luminosities. The cumulative diameter distribution for the Hii regions of M51 shows dual behaviour, with a break at a radius close to 100 pc, the radius of regions with the break luminosity. Here too we indicate the possible physical implications. Subject headings: ISM: general — Hii regions — galaxies: structure)
Neural Trajectories in the Supplementary Motor Area and Motor Cortex Exhibit Distinct Geometries, Compatible with Different Classes of Computation

The supplementary motor area (SMA) is believed to contribute to higher-order aspects of motor control. To examine this contribution, we employed a novel cycling task and leveraged an emerging strategy: testing whether population trajectories possess properties necessary for a hypothesized class of computations. We found that, at the single-neuron level, SMA exhibited multiple response features absent in M1. We hypothesized that these diverse features might contribute, at the population level, to avoidance of ‘population trajectory divergence’ – ensuring that two trajectories never followed the same path before separating. Trajectory divergence was indeed avoided in SMA but not in M1. Network simulations confirmed that low trajectory divergence is necessary when guidance of future action depends upon internally tracking contextual factors. Furthermore, the empirical trajectory geometry – helical in SMA versus elliptical in M1 – was naturally reproduced by networks that did, versus did not, internally track context.
Dialogic space: intersections between dialogic teaching and systemic functional linguistics

Abstract The aim of this article is to foster dialogue between proponents of Alexander’s notion of dialogic teaching and those working with educational linguistics – in particular those working with systemic functional theory. To this end, the article begins by highlighting important points of alignment between dialogic teaching and systemic theory: their shared emphasis on learning as a social and cultural construct; the priority they accord to language in education and its role in mediating learning; and their shared emphasis on the nature of positive educational interventions. Major sections of the article, however, address two issues identified by Alexander as posing particular challenges in the implementation of dialogic teaching: the difficulty of achieving a ‘perfect marriage’ between pedagogical form and content; and the need for students to have opportunities to talk to learn as well as learn to talk. Discussion of these issues draws on recent research into the needs of English as an Additional Language students, and the nature of pedagogical practices designed to address those needs, to explore the possible contribution of systemic theory. While the article is written from the perspective of someone more familiar with systemic theory than dialogic teaching, it highlights points of similarity and difference between the two perspectives in their approaches to education and suggests an ongoing dialogue which is likely to be mutually beneficial.
Juniper Tree-Ring Data from the Kuramin Range (Northern Tajikistan) Reveals Changing Summer Drought Signals in Western Central Asia

Coniferous forests cover the mountains in many parts of Central Asia and provide large potentials for dendroclimatic studies of past climate variability. However, to date, only a few tree-ring based climate reconstructions exist from this region. Here, we present a regional tree-ring chronology from the moisture-sensitive Zeravshan juniper (Juniperus seravschanica Kom.) from the Kuramin Range (Tajikistan) in western Central Asia, which is used to reveal past summer drought variability from 1650 to 2015 Common Era (CE). The chronology accounts for 40.5% of the variance of the June–July self-calibrating Palmer Drought Severity Index (scPDSI) during the instrumental period (1901 to 2012). Seven dry periods, including 1659–1696, 1705–1722, 1731–1741, 1758–1790, 1800–1842, 1860–1875, and 1931–1987, and five wet periods, including 1742–1752, 1843–1859, 1876–1913, 1921–1930, and 1988–2015, were identified. Good agreements between drought records from western and eastern Central Asia suggest that the PDSI records retain common drought signals and capture the regional dry/wet periods of Central Asia. Moreover, the spectral analysis indicates the existence of centennial (128 years), decadal (24.3 and 11.4 years), and interannual (8.0, 3.6, 2.9, and 2.0 years) cycles, which may be linked with climate forces, such as solar activity and El Niño-Southern Oscillation (ENSO). The analysis between the scPDSI reconstruction and large-scale atmospheric circulations during the reconstructed extreme dry and wet years can provide information about the linkages of extremes in our scPDSI record with the large-scale ocean–atmosphere–land circulation systems.
The stoichiometry of larval anuran development in natural wetlands

Abstract Understanding the influence of growth and development on the stoichiometry of organisms with complex lifecycles is necessary to understand the spatial and temporal extent of consumer-driven nutrient dynamics. This can be particularly challenging in temporally variable habitats, such as geographically isolated wetlands (GIW), which dry down seasonally. Larval anurans (tadpoles) are excellent model organisms for studies within the framework of ecological stoichiometry because they undergo major anatomical changes during metamorphosis that likely require a shift in body stoichiometric demands. To examine stoichiometry of larval anurans in GIWs, we measured larval Lithobates sphenocephalus tissue carbon (C), nitrogen (N), phosphorus (P) and calcium (Ca) content, excretion NH4-N, TDN and TDP, and egestion C, N and P across three developmental stage categories (no limbs, hind limbs only, and four limbs). We found that tissue P content increased significantly during later stages when bone development was occurring, which significantly reduced tissue C:P and N:P. Tissue C also increased across stages. Mass-specific excretion of TDN and N:P decreased across stages. Per capita NH4-N excretion rate had a positive relationship with body size, and per capita excretion N:P had a negative relationship with body size. Mass specific bulk egestion and C egestion varied across stages, as well as C:N and C:P, but we could not distinguish which stages were different from one another. Per capita egestion rates of N and P were positively correlated with body size, and both C:N and C:P were negatively related to body size. We found that development stage of larval anurans was an important indicator of tissue, excretion, and egestion stoichiometry and these differences may influence their functional role in aquatic ecosystems throughout their development.
Gene Expression-Based Identification of Antigen-Responsive CD8+ T Cells on a Single-Cell Level

CD8+ T cells are important effectors of adaptive immunity against pathogens, tumors and self antigens. Here, we asked how human cognate antigen-responsive CD8+ T cells and their receptors could be identified in unselected single-cell gene expression data. Single-cell RNA sequencing and qPCR of dye-labelled antigen-specific cells identified large gene sets that were congruently up- or downregulated in virus-responsive CD8+ T cells under different antigen presentation conditions. Combined expression of TNFRSF9, XCL1, XCL2, and CRTAM was the most distinct marker of virus-responsive cells on a single-cell level. Using transcriptomic data, we developed a machine learning-based classifier that provides sensitive and specific detection of virus-responsive CD8+ T cells from unselected populations. Gene response profiles of CD8+ T cells specific for the autoantigen islet-specific glucose-6-phosphatase catalytic subunit-related protein differed markedly from virus-specific cells. These findings provide single-cell gene expression parameters for comprehensive identification of rare antigen-responsive cells and T cell receptors. One-sentence summary Identification of genes, gene sets, and development of a machine learning-based classifier that distinguishes antigen-responsive CD8+ T cells on a single-cell level.
Home‐range size of an Andean bird: Assessing the role of physical condition

Because space‐use patterns are a key aspect of the ecology and distribution of species, identifying factors associated with variation in size of territories and home ranges has been central to studies on population ecology. Space use might vary in response to extrinsic factors like habitat quality and to intrinsic factors like physical condition and individual aggressiveness. However, the role of these factors has been poorly documented in the tropics, particularly in high‐elevation bird species. We report the home‐range size of a Neotropical Andean bird, the gray‐browed brush finch (Arremon assimilis), and evaluate the role of physical condition in explaining variation in home‐range size among individuals. We performed spot mapping to estimate the home ranges of 14 territorial males in Bogotá, Colombia, using minimum convex polygons (MCP) and 95% kernel density estimators (KDE). The mean home‐range size estimated for the 100% MCP was 0.522 ± 0.305 ha (range = 0.15–1.18 ha), whereas the 95% KDE estimation was 0.504 ± 0.471 ha (range = 0.13–1.88). We calculated the real mass index of each bird as a proxy of physical condition to assess whether individuals in better physical condition had larger home ranges. Because we found no relation between our estimations of physical condition and home‐range size, we conclude that space use in this species might depend more on ecological factors such as habitat quality or neighbor density than on individual traits.
Self-aligned contact submicron E/D MODFET IC process: device characteristics and simple circuit applications

A high-speed, low-power GaAs enhancement/depletion (E/D) IC process for MSI applications (10/sup 3/ devices) is described. The process relies on high-quality molecular-beam-epitaxy (MBE)-grown modulation-doped wafers, and an etch-stop reactive ion etch (RIE) process that preserves the inherent uniformity and control achievable with this growth technique. <<ETX>>