Miracle-dz/UniFAR-FTUs huggingface dataset:
Distributional Analysis

In distributional or average-case analysis, the goal is to design an algorithm with good-on-average performance with respect to a specific probability distribution. Distributional analysis can be useful for the study of general-purpose algorithms on "non-pathological" inputs, and for the design of specialized algorithms in applications in which there is detailed understanding of the relevant input distribution. For some problems, however, pure distributional analysis encourages "overfitting" an algorithmic solution to a particular distributional assumption and a more robust analysis framework is called for. This chapter presents numerous examples of the pros and cons of distributional analysis, highlighting some of its greatest hits while also setting the stage for the hybrids of worst- and average-case analysis studied in later chapters.
Trends in pKa Values for polyprotic carboxylic acids

In this work we have reported the pKa values for straight chain (without branches) oligomers of Acrylic acid using CBS-QB3 gas phase energies with solvation free energies from CPCM/HF 6-31G(d) and SMD/B3LYP (2df,p). We have found that the negative log of the first acid dissociation constant decreases with the chain length. Within a chain, the microscopic pKa for the COOH groups present at the end of the chain is maximum and minimum for centrally located COOH groups.
Distribution, production, and ecophysiology of Picocystis strain ML in Mono Lake, California

A recently described unicellular chlorophytic alga isolated from meromictic Mono Lake, California, occupies a niche that spans two environments: the upper oxic mixolimnion and the deeper anoxic and highly reducing monimolimnion. This organism, Picocystis sp. strain ML, accounts for nearly 25% of the primary production during the winter bloom and more than 50% at other times of the year. In incubations, it is heavily grazed by the brine shrimp, Artemia monica. We assessed growth and photosynthetic parameters over broad ranges of irradiance, salinity, and pH and under oxic and anoxic conditions. Picocystis appears to be particularly adapted to low irradiance; we observed an order of magnitude increase in the cellular pigment concentrations, as well as marked increases in cellspecific photosynthetic parameters for cells acclimated to low‐growth irradiance. Growth rates of 0.3–1.5 d−1 were observed over a salinity range of 0–260‰ and a pH range of 4–12, with maximal growth at ~50 mmol photons m−2 s−1, 40‰, and pH 6–10. Growth and oxygenic photosynthesis were observed under anoxic conditions at rates comparable to those measured under oxic conditions. The ability of the organism to acclimate and grow under such a broad range of environmental conditions makes it an important component of the Mono Lake ecosystem and likely contributes to its dominance of the monimolimnion/mixolimnion interface.
Lattice Kerker Effect Goes Plasmonic

The Kerker effect, generally requiring co-existence of electric and magnetic responses, is difficult to observe in conventional non-magnetic plasmonic nanostructures. We found that delicate interplay between localized surface plasmon resonances and collective lattice oscillations in arrays of plasmonic Al nanostructures leads to the emergence of lattice Kerker effect. Variation of Al arrays geometry allows to tailor suppressed reflection throughout UV and visible wavelength ranges, which is hard to achieve on using other plasmonics or all-dielectric materials.
Performance Evaluation of Scheduling in 5G-mmWave Networks under Human Blockage

The millimetre-wave spectrum provisions enormous enhancement to the achievable data rate of 5G networks. However, human blockages affecting the millimetre-wave signal can severely degrade the performance if proper resource allocation is not considered. In this paper, we assess how conventional schedulers, such as the Proportional Fair scheduler, react to the presence of blockage. Our results show that the resource allocation may disfavour users suffering from blockage, leading to low data rate for those users. To circumvent this problem, we show that the data rate of those users can be improved by using a scheduler adapted to react to upcoming blockage events. The adapted scheduler aims at proactively allocating the resources before a blockage happens, mitigating losses. Such adaptation is motivated by recent progress in blockage prediction for millimetre-wave signals in a dynamic human blockage scenario. Our extensive simulations indicate gains in the 1st percentile rate and fairness with respect to Proportional Fair scheduler when blockage conditions are severe.
Non-backtracking Spectrum: Unitary Eigenvalues and Diagonalizability.

Much effort has been spent on characterizing the spectrum of the non-backtracking matrix of certain classes of graphs, with special emphasis on the leading eigenvalue or the second eigenvector. Much less attention has been paid to the eigenvalues of small magnitude; here, we fully characterize the eigenvalues with magnitude equal to one. We relate the multiplicities of such eigenvalues to the existence of specific subgraphs. We formulate a conjecture on necessary and sufficient conditions for the diagonalizability of the non backtracking matrix. As an application, we establish an interlacing-type result for the Perron eigenvalue.
Persistent homology in cosmic shear: Constraining parameters with topological data analysis

In recent years, cosmic shear has emerged as a powerful tool for studying the statistical distribution of matter in our Universe. Apart from the standard two-point correlation functions, several alternative methods such as peak count statistics offer competitive results. Here we show that persistent homology, a tool from topological data analysis, can extract more cosmological information than previous methods from the same data set. For this, we use persistent Betti numbers to efficiently summarise the full topological structure of weak lensing aperture mass maps. This method can be seen as an extension of the peak count statistics, in which we additionally capture information about the environment surrounding the maxima. We first demonstrate the performance in a mock analysis of the KiDS+VIKING-450 data: We extract the Betti functions from a suite of N-body simulations and use these to train a Gaussian process emulator that provides rapid model predictions; we next run a Markov chain Monte Carlo analysis on independent mock data to infer the cosmological parameters and their uncertainties. When comparing our results, we recover the input cosmology and achieve a constraining power on S8 ≡ σ8Ωm/0.3 that is 3% tighter than that on peak count statistics. Performing the same analysis on 100 deg2 of Euclid-like simulations, we are able to improve the constraints on S8 and Ωm by 19% and 12%, respectively, while breaking some of the degeneracy between S8 and the dark energy equation of state. To our knowledge, the methods presented here are the most powerful topological tools for constraining cosmological parameters with lensing data.
Isolation of proteolytic, lipolytic, and bioemulsifying bacteria for improvement of the aerobic treatment of poultry processing wastewater

Proteolysis, lipolysis, as well as, emulsification play important roles for the biological treatment of poultry processing wastewater. Three isolates identified by 16S rRNA gene sequence analysis as belonging to Bacillus subtilis, Bacillus thuringiensis, andLysinibacillus fusiformis, were then selected. The three combined strains provided a 71.2± 0.20% reduction of the chemical oxygen demand (COD) and produced a high biosurfactant 1250 ± 10 mg/L. Moreover, all three bacteria were able to form good biofilm. The combined bacteria strains performed well in terms of COD reduction, protease, and lipase and biosurfactant production at an initial pH of 7.0 and over a wide range (1000 to 5000 mg/L) of organic loads. Key words: Proteolytic, lipolytic, poultry, wastewater, treatment, biosurfactant.
Validity and reliability of the Turkish version of the Michigan Neuropathy Screening Instrument

Background/aim The aim of this study was to demonstrate the validity and reliability of the Turkish version of the Michigan Neuropathy Screening Instrument (MNSI-TR). Materials and methods The study included 127 patients aged 45–76 years who were previously diagnosed with type 1 or 2 diabetes. Stability of the instrument was assessed by intraclass correlation coefficient. Reliability of the MNSI-TR was assessed using the Kuder–Richardson formula 20 test, item-total correlations, and floor/ceiling effect. Validity was evaluated with receiver operating characteristic curve analysis. A logistic regression model was used to determine to what degree the MNSI-TR explain nerve conduction study (NCS) results in the prediction of neuropathy. Results With a cut-off value of 3.5 for the questionnaire, sensitivity and specificity of the MNSI-TR were 75.5% and 68.1%, respectively. A cut-off of 2.75 for the physical assessment part of the scale resulted in 87.5% sensitivity and 93.6% specificity. The scale was able to diagnose neuropathy in the rate of 71.5% of the patients diagnosed with neuropathy by NCS. Conclusion The MNSI-TR is a valid and reliable method for evaluating diabetic peripheral neuropathy in Turkish speaking societies. It must be obtained a minimum of 4 points from the questionnaire part and a minimum of 2.5 points from the physical assessment part for the diagnosis of neuropathy
Convergent morphological responses to loss of flight in rails (Aves: Rallidae)

Abstract The physiological demands of flight exert strong selection pressure on avian morphology and so it is to be expected that the evolutionary loss of flight capacity would involve profound changes in traits. Here, we investigate morphological consequences of flightlessness in a bird family where the condition has evolved repeatedly. The Rallidae include more than 130 recognized species of which over 30 are flightless. Morphological and molecular phylogenetic data were used here to compare species with and without the ability to fly in order to determine major phenotypic effects of the transition from flighted to flightless. We find statistical support for similar morphological response among unrelated flightless lineages, characterized by a shift in energy allocation from the forelimbs to the hindlimbs. Indeed, flightless birds exhibit smaller sterna and wings than flighted taxa in the same family along with wider pelves and more robust femora. Phylogenetic signal tests demonstrate that those differences are independent of phylogeny and instead demonstrate convergent morphological adaptation associated with a walking ecology. We found too that morphological variation was greater among flightless rails than flighted ones, suggesting that relaxation of physiological demands during the transition to flightlessness frees morphological traits to evolve in response to more varied ecological opportunities.
HLX affects cell cycle and proliferation in AML cells via the JAK/STAT signaling pathway

Acute myelogenous leukemia (AML) is a class of malignant tumors derived from hematopoietic stem or progenitor cells. The H2.0-like homeobox gene (HLX) encodes transcription factors that function in promoting normal hematopoietic cell proliferation and tumor immunity. The present study analyzed the effect of downregulating the HLX on cell cycle distribution and cell proliferation in AML. Moreover, the current study detected changes in the expression of genes and proteins in the Janus kinase (JAK)/STAT signaling pathway to investigate the mechanism of the action of HLX in tumor immunity in AML. HLX expression in AML cell lines was silenced using small interfering siRNA, and MTS/PMS-assay colorimetric assays were used to assess the effect of knockdown of HLX on AML cell proliferation. Flow cytometry was used to analyze changes in cell cycle distribution, while reverse transcription-quantitative PCR and western blotting were used to detect changes in the expression levels of key components of the JAK/STAT signaling pathway, such as p21-activated kinase 1 (PAK1), neuropilin 1 (NRP1), B-cell translocation gene 1 (BTG1) and STAT5. It was found that HLX was differentially expressed in AML cell lines of various subtypes, and HLX expression was higher in the AML/M3 subtype NB4 cell line compared with the control group. Knockdown of HLX in NB4 cells significantly inhibited cell proliferation and arrested cells in the G0/G1 phase. Moreover, STAT5 protein expression, as well as NRP1 and PAK1 expression levels were downregulated, while BTG1 expression was upregulated when HLX was knocked out by siRNA. Collectively, the results suggested that downregulation of HLX may cause G0/G1 phase arrest and inhibit the proliferation of AML cells by activating the JAK/STAT signaling pathway.
An efficient protocol for DNA isolation from the genus Pyrus.

This paper communicates an economical, handy, quicker and reliable protocol of DNA isolation from different parts e.g. herbarium specimens, bark, wood, leaves etc. of pears. The protocol is recommended under the normal lab conditions without using any sophisticated equipment and costly kits/chemicals. Best quality of DNA was extracted from any part of the plant. The PCR product was amplified for 18S rRNA genes of various Pyrus genotypes. The genes were cleaned with gel elution Kit (K0513, Fermentas) and sequenced accordingly. The sequence data obtained was BLAST against the entire available nucleotide database using online tool at NCBI access and the land races were successfully discriminated. The protocol presented here is recommended for reliable extraction of best quality and high yield of DNA from woody plants.
Has a river dam affected the life‐history traits of a freshwater prawn?

Abstract In recent years, species richness and diversity in aquatic ecosystems has declined as environments are increasingly impacted by anthropic actions. Freshwater prawns are well adapted to survive in a disturbed and heterogeneous environment. For instance, Amazon river prawn (Macrobrachium amazonicum) populations vary in migratory behavior between rivers and estuaries, depending on factors such as dams. However, there is limited information on the influence of environmental conditions on life‐history traits of this species, which we investigate here using two distinct and unconnected aquatic systems, a dammed river and an estuary, in the eastern Brazilian Amazon. The biological characteristics of M. amazonicum populations in the two environments were compared and related to environmental parameters, which differed significant differences between the two environments and between seasons. Dissolved oxygen, precipitation, and temperature varied most significantly with the seasons in both the estuary and river. M. amazonicum prawns in the estuary were larger and heavier than those in the river during rainy periods. The mass–length ratios and condition factor varied significantly between the M. amazonicum populations in the estuary and river, with negative allometric growth (grows faster in length than in weight) predominating in both populations, and condition factor was better in the estuary for males and in the river for females. The relative frequencies of occurrence of the different female maturation stages and the male morphotypes were related to precipitation and turbidity in both environments and also to salinity in the estuary. In these two distinct aquatic systems, the abiotic parameters determined by the seasonal precipitation cycle profoundly influenced the development of this crustacean, despite its ecological plasticity. Overall, the study showed that river damming triggered environmental changes in the freshwater river ecosystem and played a key role in determining the life‐history characteristics of M. amazonicum in these contrasting aquatic systems.
Global Measurements of Brown Carbon and Estimated Direct Radiative Effects

Brown carbon (BrC) is an organic aerosol material that preferentially absorbs light of shorter wavelengths. Global‐scale radiative impacts of BrC have been difficult to assess due to the lack of BrC observational data. To address this, aerosol filters were continuously collected with near pole‐to‐pole latitudinal coverage over the Pacific and Atlantic basins in three seasons as part of the Atmospheric Tomography Mission. BrC chromophores in filter extracts were measured. We find that globally, BrC was highly spatially heterogeneous, mostly detected in air masses that had been transported from regions of extensive biomass burning. We calculate the average direct radiative effect due to BrC absorption accounted for approximately 7% to 48% of the top of the atmosphere clear‐sky instantaneous forcing by all absorbing carbonaceous aerosols in the remote atmosphere, indicating that BrC from biomass burning is an important component of the global radiative balance.
The status and phylogeography of the liverwort genus Apometzgeria Kuwah. (Metzgeriaceae)

Abstract Three species have been formerly segregated from Metzgeria in the genus Apometzgeria. One of the species, A. frontipilis, is endemic to South America but the second, A. pubescens, is currently understood as having a bipolar range with populations across the Holarctic and in southern South America. The third species, A. longifrondis, was described from China (and is not included in this study). Species of bryophytes that range across continents and have little or no morphological variation among populations may nevertheless harbor morphologically cryptic genetic lineages. We used nuclear and plastid sequence data to examine the phylogenetic relationship between Apometzgeria and Metzgeria, and phylogeographic patterns in taxa assigned to Apometzgeria. Two species often assigned to Apometzgeria are phylogenetically embedded within Metzgeria in two separate clades, one comprising all Holarctic A. pubescens and a second with A. pubescens from South America and all accessions of A. frontipilis. Phylogenetic and haplotype analyses reveal a lack of phylogeographic structure among A. pubescens plants from throughout its Holarctic distribution. However, A. pubescens in South America is more closely related to A. frontipilis and species of Metzgeria from South America than to any A. pubescens from the Northern Hemisphere. Thus, A. pubescens is Holarctic in distribution and morphologically similar plants form a divergent lineage in South America. Our results do not support Apometzgeria as a separate genus in the Metzgeriaceae.
Fast multipoint evaluation and interpolation of polynomials in the LCH-basis over FPr

Lin, Chung and Han introduced in 2014 the LCH-basis in order to derive FFT-based multipoint evaluation and interpolation algorithms with respect to this polynomial basis. Considering an affine space of n = 2j points, their algorithms require O(n · log2 n) operations in F2r. The LCH-basis has then been extended over finite fields of characteristic p by Lin et al. in 2016 and an n-point evaluation algorithm has been derived for n = pj with complexity O(n · logp n · p). However, the problem of interpolating polynomials represented in such a basis over FPr has not been addressed. In this paper, we fill this gap and also derive a faster algorithm for evaluating polynomials in the LCH-basis at multiple points over FPr. We follow a different approach where we represent the multipoint evaluation and interpolation maps by well-defined matrices. We present factorizations of such matrices into the product of sparse matrices which can be evaluated efficiently. These factorizations lead to fast algorithms for both the multipoint evaluation and the interpolation of polynomials represented in the LCH-basis at n = pj points with optimized complexity O(n · log2 n · log2 p · log2 log2 p). A particular attention is paid to provide in-place algorithms with high memory-locality. Our implementations written in C confirm that our approach improves the original transforms.
NCPower: Power Modelling for NVM-based Neuromorphic Chip

Spiking neural networks (SNN) on non-volatile memory (NVM) based neuromorphic computing (NC) chips have been regarded as a promising solution in power constrained scenarios, such as Internet of Things (IoT), due to its low energy consumption. The high power efficiency of NC is due to various aspects including the non-von Neumann architecture of NC chip, low power NVM, and the event driven computation of SNN etc., and introduces a large space for low power design exploration. Therefore, a comprehensive quantitative study of the power modelling for such neuromorphic computing system is important for low power design. In this work, we propose NCPower, an energy consumption estimator for NVM-based neuromorphic chip. We systemically developed analytical models based on physical laws, and verify them by comparing the analytical results with measurement results from different neuromorphic chips. We integrated NCPower in a simulator, and analyzed the accuracy and energy consumption of both the traditional multi-spike based SNN and the new single-spike based SNN. It shows that the single-spike model has 7X energy efficiency over the multi-spike model, with similar accuracy under the CIFAR-10 dataset.
MiR-92a - a key player in cardiovascular remodeling

Small non-coding, highly conserved microRNAs (miRs) play a crucial role in gene regulation, especially in post-transcriptional gene silencing, and are important for vascular homeostasis as well as during pathophysiological vascular remodeling processes. MiR-92a is known to attenuate endothelial cell proliferation, and angiogenesis. Conversely, down regulation of miR-92a improves these endothelial cell-dependent processes. We recently showed that inhibition of miR-92a also accelerates the re-endothelialization process and thus prevents neointima formation following wire-induced injury of murine femoral arteries. Thus, inhibition of miR-92a may represent a promising therapeutic strategy for the treatment of vascular diseases.
Design of a Conventional-Transistor-Based Analog Integrated Circuit for On-Chip Learning in a Spiking Neural Network

Spiking Neural Network (SNN) is of special interest among the various NN algorithms. While the SNN has been trained before using the biologically plausible Spike Time Dependent Plasticity (STDP) rule on conventional computers and specialized digital neuromorphic chips, analog hardware is more suitable for such temporal-domain-based training. Further, complete memory-computing intertwining can be achieved with analog hardware only, thereby removing the von Neumann bottleneck altogether. Hence, in this paper, we have designed an analog hardware SNN with neuron and synapse blocks, which are based on conventional silicon transistors and capacitors. Our synapse-block exhibits STDP rule for weight-update. Our neuron-block follows the biologically plausible Leaky Integrate Fire (LIF) model with mechanism for spike generation and homoeostasis property. Then we have shown on-chip learning on a popular Machine Learning (ML) data-set (Fisher’s Iris) through SPICE simulations of the complete hardware. Previous reports on analog hardware SNN mostly involve the use of emerging devices, which are much harder to fabricate compared to conventional silicon transistors that are used here. Those reports also do not show iterative learning through full circuit-level design and simulation of the SNN, unlike this paper. Moreover, other existing reports of analog SNN, which use conventional transistors, do not show training on popularly used ML data-sets, unlike this paper.