Miracle-dz/UniFAR-FTUs huggingface dataset:
Using Grey Model to Predict Protein Remote Homologous Family

Protein remote homology detection is the most basic and core problems of protein structure and function research. The purpose of protein remote homology detection to detect the remote evolutionary relationship between proteins by computation methods. At present, there are many methods for remote homology detection of proteins, but some methods are not very effective. In bioinformatics, it is urgent to further improve the performance of protein remote homology detection. In this study, we propose a new model called PHom-GRA to detect protein remote homology, which is the integration of various ranking methods via using grey relational analysis. Our experiment constructs benchmark dataset with lower homology, in which any two proteins have not more than 40% identity or homology. We achieve an ROC1 score of 0.7372 and an ROC50 score of 0.7968 in jack-knife test.
ECONOMY OF DESIGN OF FLEXIBLE AND RIGID PAVEMENTS

It is generally believed that rigid pavements consisting of cement concrete have more cost of construction than flexible or bituminous pavements. This paper brings forth the economy of design of flexible and rigid pavements. The designs for flexible and rigid pavement for a given road have been worked out for various values of effective California Bearing Ratio (CBR) of subgrade soil varying from 3% to 8% and initial traffic on the road varying from 500 to 6000 commercial vehicles per day. The designs have been evolved using latest relevant guidelines of Indian Roads Congress (IRC). IRC:37-2012 and 2018 have been used for the design of flexible pavements and IRC:58-2015 has been used for the design of rigid pavements. The design of flexible pavement is based upon fatigue and rutting failure of the pavement. For rigid pavement the design is based upon fatigue analysis of bottom up cracking and top down cracking of the pavement. The rate analysis for various items of work as per designs obtained and the cost estimation for the designed pavements have been done as per IRC guidelines. The paper discusses the designs of both flexible and rigid pavements, the effect of CBR of subgrade and traffic on the designed thickness and the economy of construction of these pavements. It is found from the results that the construction of rigid pavements may not always be more costly. The paper in fact shows that they are more economical to construct for conditions of low subgrade strength and high volume of traffic on the road. Keywords— Design, Flexible pavement, Rigid pavement, Thickness of pavement, Cost of pavement
Phylogenetic Reconstruction and Divergence Time Estimation of Blumea DC. (Asteraceae: Inuleae) in China Based on nrDNA ITS and cpDNA trnL-F Sequences

The genus Blumea DC. is one of the economically most important genera of Inuleae (Asteraceae) in China. It is particularly diverse in south China, where 30 species occur, more than half of which are used as herbal medicine or in the chemical industry. However, little is known about the phylogenetic relationships and molecular evolution of this genus in China. We used nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) and chloroplast DNA (cpDNA) trnL-F sequences to reconstruct the phylogenetic relationship and estimate the divergence time of Blumea DC. in China. Results indicated the genus of Blumea DC. was monophyletic and could be divided into two clades, the two clades were resolved that differ with respect to habitat, morphology, chromosome type and chemical composition, of their members. Furthermore, based on the two root time of Asteraceae, the divergence time of Blumea DC. were compare estimated. Results indicated the most recent common ancestor of Asteraceae maybe originated from 76–66 Ma, and Blumea DC. maybe originated from 72.71-52.42 Ma, and had an explosive expansion during Oligocene and Miocene (30.09-11.44 Ma), two major clades were differentiated during the Palaeocene and Oligocene (66.29-46.72 Ma), also the evidence from paleogeography and paleoclimate also supported Blumea DC. had an differentiation and explosive expansion during Oligocene and Miocene.
Searching and mapping genomic subsequences in nanopore raw signals through novel dynamic time warping algorithms

Abstract Nanopore sequencing is a promising technology to generate ultra-long reads based on the direct measurement of electrical current signals when a DNA molecule passes through a nanopore. These ultra-long reads are critical for detecting large structural variations in the genome. However, it is challenging to use nanopore sequencing to identify single nucleotide polymorphisms (SNPs) or other modiﬁcations such as methylations, especially at a low sequencing coverage, due to the high error rate in the base-called reads. It is possible to correct the base-calling error through the subsequence search by mapping a SNP-containing genomic region to the long nanopore raw signal sequences that contain this region and taking consensus of these signals. Nevertheless, the ultra-long raw signals and an order of magnitude di ﬀ erence in the sampling speed between the two sequences make the traditional algorithms infeasible to solve the problem. Here we propose two novel algorithms, the direct subsequence dynamic time warping for nanopore raw signal search (DSDTWnano) and the continuous wavelet subsequence dynamic time warping for nanopore raw signal search (cwSDTWnano), to enable the direct subsequence searching and exact mapping in nanopore raw signals. The proposed algorithms are based on the idea of subsequence-extended dynamic time warping and directly operate on the raw signals, without any loss of information. DSDTWnano could ensure an output of highly accurate query results and cwSDTWnano is the accelerated version of DSDTWnano, with the help of seeding and multi-scale coarsening of signals that are based on continuous wavelet transform. Furthermore, a novel error function is proposed to specify the mapping accuracy between a genomic sequence and an electrical current signal sequence, which may serve as the standard criterion for further genome-to-signal mapping studies. Comprehensive experiments on three
A Pharmacist-Led Program to Taper Opioid Use at Kaiser Permanente Northwest: Rationale, Design, and Evaluation.

INTRODUCTION Primary care practitioners (PCPs) are concerned about adverse effects and poor outcomes of opioid use but may find opioid tapering difficult because of a lack of pain management training or time constraints limiting patient counseling. In 2010, Kaiser Permanente Northwest implemented a pharmacist-led opioid tapering program-Support Team Onsite Resource for Management of Pain (STORM)-to address high rates of opioid use, alleviate PCPs' workload demands, and improve patient outcomes. OBJECTIVE To describe the rationale, structure, and delivery of this unique pharmacist-led program, which partners with PCPs and provides individualized care to help patients reduce opioid use, and the Facilitating Lower Opioid Amounts through Tapering study, which examines the program's effectiveness, cost-effectiveness, and implementation. RESULTS The STORM program includes a pain medicine physician, a social worker or nurse, and pharmacists who have received specialized clinical and communications training. The program has a 2-fold role: 1) to provide PCP education about pain management and opioid use and 2) to offer clinician and patient support with opioid tapering and pain management. After program training, PCPs are equipped to discuss the need for tapering with a patient and to refer to the program. Program pharmacists provide a range of services, including opioid taper plans, nonopioid pain management recommendations, and taper-support outreach to patients. DISCUSSION The STORM program provides individualized care to assist patients with opioid tapering while reducing the burden on PCPs. CONCLUSION The STORM program may be a valuable addition to health care systems and settings seeking options to address their patients' opioid tapering needs.
Gas phase generation and deposition of size-selected metal clusters

This thesis presents modifications to and optimisations of a cluster beam source, one application being the generation of large area catalysis samples. A major modification to the cluster source also enabled coating of clusters in a new way. The impact of Pd\(_5\)\(_6\)\(_1\), Pd\(_5\)\(_5\)and Pd\(_4\) clusters (1, 1.5 and 1 keV) on a thin material film evaporated onto a solid argon matrix led to deposition of large, 5-40 nm diameter, irregularly shaped particles. Furthermore, Pd\(_9\)\(_2\)\(_3\) and Pd\(_2\)\(_0\)\(_0\)\(_0\) clusters, with both 0.5 and 1.5 keV impact energies, have been coated in-flight by impact on the thin film/solid matrix, as verified from the increase in diameters of the deposited particles and the detection of Pd signal by EELS. MoS\(_2\) nano pillar catalyst samples were etched using size-selected metal etch masks. Catalyst samples of ordered MoS\(_2\) nano pillars were fabricated using NSL and a novel way to apply nano spheres was developed. Different etch recipes were used to obtain nano pillars with different diameters and heights; these recipes were also applied to reference MoS\(_2\) samples without etch masks. Generally, the reference catalyst samples, with their roughened surfaces, showed higher HER activity than their corresponding ordered MoS2 nano pillar catalyst samples.
Characteristic of microencapsulated 1,3-dioleoyl-2-palmitoylglycerol and its application in infant formula powder

ABSTRACT 1,3-Dioleoyl-2-palmitoylglycerol (OPO) is used widely as a food additive. However, the structured lipid is sensitive to oxygen and light in the production process. This results in the loss of its original nutrition and production of harmful substances. In this study, the OPO was microencapsulated using whey protein isolate and maltodextrin as the wall material and monostearin as an emulsifier by spray-drying technology added to the infant formula milk, in order to improve its oxidative stability. The OPO microcapsules were released in vitro through the simulated gastrointestinal tract; sensory evaluation of microencapsulated OPO in infant formula powder and nutrition absorption of microencapsulated OPO in infant formula power by animal experiments were investigated. The results showed that OPO microcapsules have a slow-release effect; after 2 h of simulated gastric fluid digestion, only 16.1 ± 3.2% of the oil was released from microencapsulated OPO, and after another 2 h of simulated intestinal fluid digestion, there was 92.3 ± 2.8% of oil released from the microencapsulated OPO. The infant formula with microencapsulated OPO has a uniform colour and no odour. The quality of infant formula with microencapsulated OPO was obviously better than infant formula with OPO by storage test. Everted mice gut sac experiments confirmed that microencapsulation did not affect absorption of mice to OPO in infant formula and prevented the loss of calcium. The study confirmed that addition of microencapsulated OPO makes infant formula more efficient for product quality and nutrition absorption.
Diversity patterns in parasite populations capable for persistence and reinfection with a view towards the human cytomegalovirus

Many parasites like the cytomegalovirus, HIV and Escherichia coli are capable to persist in and reinfect its host. The evolutionary advantage (if so) of these complicated mechanisms have not been quantitatively analyzed so far. Here we take a first step by investigating a host-parasite model for which these mechanisms are driving the evolution of the parasite population. We consider two variants of the model. In one variant parasite reproduction is directed by balancing selection, in the other variant parasite reproduction is neutral. In the former scenario reinfection and persistence have been shown to sustain the maintenance of diversity in the parasite population in certain parameter regimes (Pokalyuk and Wakolbinger, 2018). Here we analyse the diversity patterns in the latter, neutral scenario. We evaluate the biological relevance of both model variants with respect to the human cytomegalovirus (HCMV), an ancient herpesvirus that is carried by a substantial fraction of mankind and manages to maintain a high diversity in its coding regions.
Neural Synaptic Plasticity-Inspired Computing: A High Computing Efficient Deep Convolutional Neural Network Accelerator

Deep convolutional neural networks (DCNNs) have achieved state-of-the-art performance in classification, natural language processing (NLP), and regression tasks. However, there is still a great gap between DCNNs and the human brain in terms of computation efficiency. Inspired by neural synaptic plasticity and stochastic computing (SC), we propose neural synaptic plasticity-inspired computing (NSPC) to simulate the human brain’s neural network activity for inference tasks with simple logic gates. The multiplication and accumulation (MAC) is transformed by the wire connectivity in NSPC, which only requires bundles of wires and small width adders. To this end, the NSPC imitates the structure of neural synaptic plasticity from a circuit wires connection perspective. Furthermore, from the principle of NSPC, we use a data mapping method to convert the convolution operations to matrix multiplications. Based on the methodology of NSPC, fully-pipelined and low latency architecture is designed. The proposed NSPC accelerator exhibits high hardware efficiency while maintaining a comparable network accuracy level. The NSPC based DCNN accelerator (NSPC-CNN) processes DCNN at <inline-formula> <tex-math notation="LaTeX">$1.5625M$ </tex-math></inline-formula> images/<inline-formula> <tex-math notation="LaTeX">$s$ </tex-math></inline-formula> with a power dissipation of <inline-formula> <tex-math notation="LaTeX">$15.42~W$ </tex-math></inline-formula> and an area of <inline-formula> <tex-math notation="LaTeX">$36.4~mm^{2}$ </tex-math></inline-formula>. The NSPC based deep neural network (DNN) accelerator (NSPC-DNN) that implements three fully connected layers DNN consumes only <inline-formula> <tex-math notation="LaTeX">$6.6~mm^{2}$ </tex-math></inline-formula> area and <inline-formula> <tex-math notation="LaTeX">$2.93~W$ </tex-math></inline-formula> power, and achieves a throughput of <inline-formula> <tex-math notation="LaTeX">$400M$ </tex-math></inline-formula> images/<inline-formula> <tex-math notation="LaTeX">$s$ </tex-math></inline-formula>. Compared with conventional fixed-point implementations, the NSPC-CNN achieves <inline-formula> <tex-math notation="LaTeX">$2.77 \times $ </tex-math></inline-formula> area efficiency, <inline-formula> <tex-math notation="LaTeX">$2.25 \times $ </tex-math></inline-formula> power efficiency; the proposed NSPC-DNN exhibits <inline-formula> <tex-math notation="LaTeX">$2.31 \times $ </tex-math></inline-formula> area efficiency and <inline-formula> <tex-math notation="LaTeX">$2.09 \times $ </tex-math></inline-formula> power efficiency.
Optimal Residential Battery Scheduling with Asset Lifespan Consideration

Recent development of renewable generation and increasing penetration of electric vehicles have led to large volumes of residential battery storage systems connected at distribution networks. In this paper, we propose a control algorithm for residential batteries that determines optimal day-ahead battery scheduling and operation with the aim to minimize household energy bills and in the context of dynamic Time of Use (ToU) electricity tariffs. The proposed formulation of the optimization problem takes into consideration the battery’s depreciation cost, which is determined by the accurate enumeration of battery cycles, including partial cycling i.e. battery cycles that do not start or end at 100% of State of Charge (SoC). A key advantage of the proposed formulation is that the problem can be solvable by use of linear programming. In addition, we study and compare the benefits of the optimisation-based algorithm with lifespan consideration to a simple heuristic-based battery control scheme and an optimisation-based algorithm without battery lifecycle consideration. Results show that battery lifespan consideration in the optimization algorithm does not necessarily yield to lower prosumer energy bills, when compared to other approaches, but it can lead to a lower depreciation cost of the battery.
Plasmon modes characterization in hybrid noble/ ferromagnetic nanodisks using an effective medium approximation

Magneto-plasmonic systems composed by noble/ferromagnetic metals structures can be used to control light polarization. The extraordinary optical properties arising from combining strong local enhancements of electromagnetic fields in surface plasmon excitations with the magneto-optical activity inherent to ferromagnetic materials, can be controlled by external magnetic fields that have demonstrated the possibility to control and amplify the magneto-optical properties via plasmonic excitations. In this work, the anisotropic optical and ellipsometric sensitivity to dielectric environment of multi-layered hybrid gold/cobalt magnetoplasmonic nanodisks are studied in the framework of the effective-medium approximation, where the components of the dielectric tensor of the system are modelled using Lorentz-like oscillators. Furthermore, full electromagnetic simulations were performed using the standard Finite Element Method, which allow us to characterize the modes and explore the role of the dielectric environment of the nanodisks in the optical properties of the nanostructures via the variation of a coating silicon dioxide (SiO2) layer thickness. Our model and numerical results show a very good agreement with spectral ellipsometry measurements, where two orthogonal plasmonic modes one in-plane and one out-of-plane- are well characterized. These results lead us to conclude that the effective-medium approximation is good enough to accurately describe the plasmonic behavior of multi-layered confined nanostructures.
Transsaccadic feature interactions in multiple reference frames: an fMRIa study

Transsaccadic integration of visual features can operate in various frames of reference, but the corresponding neural mechanisms have not been differentiated. A recent fMRIa (adaptation) study identified two cortical regions in supramarginal gyrus (SMG) and extrastriate cortex that were sensitive to transsaccadic changes in stimulus orientation (Dunkley et al., 2016). Here, we modified this paradigm to identify the neural correlates for transsaccadic comparison of object orientations in: 1) Spatially Congruent (SC), 2) Retinally Congruent (RC) or 3) Spatially Incongruent (SI)) coordinates. Functional data were recorded from 12 human participants while they observed a grating (oriented 45° or 135°) before a saccade, and then judged whether a post-saccadic grating (in SC, RC, or SI configuration) had the same or different orientation. Our analysis focused on areas that showed a significant repetition suppression (Different > Same) or repetition enhancement (Same > Different) BOLD responses. Several cortical areas were significantly modulated in all three conditions: premotor/motor cortex (likely related to the manual response), and posterior-middle intraparietal sulcus. In the SC condition, uniquely activated areas included left SMG and left lateral occipitotemporal gyrus (LOtG). In the RC condition, unique areas included inferior frontal gyrus and the left lateral BA 7. In the SI condition, uniquely activated areas included the frontal eye field, medial BA 7, and right LOtG. Overall, the SC results were significantly different from both RC and SI. These data suggest that different cortical networks are used to compare pre- and post-saccadic orientation information, depending on the spatial nature of the task. Significance Statement Every time one makes a saccade, the brain must compare and integrate stored visual information with new information. It has recently been shown that ‘transsaccadic integration’ of visual object orientation involves specific areas within parietal and occipital cortex (Dunkley et al., 2016). Here, we show that this pattern of cortical activation also depends on the spatial nature of the task: when the visual object is fixed relative to space, the eye, or relative to neither space nor the eye, different frontal, parietal, and occipital regions are engaged. More generally, these findings suggest that different aspects of trans-saccadic integration flexibly employ different cortical networks.
Concerted 2-5A-Mediated mRNA Decay and Transcription Reprogram Protein Synthesis in dsRNA Response

RNA degradation by RNase L during 2-5A-mediated decay (2-5AMD) is a conserved mammalian stress response to viral and endogenous double-stranded RNA (dsRNA). 2-5AMD onsets rapidly and facilitates a switch of protein synthesis from homeostasis to production of interferons (IFNs). To understand the mechanism of this protein synthesis reprogramming, we examined 2-5AMD in human cells. 2-5AMD triggers polysome collapse characteristic of a translation initiation defect, but translation initiation complexes and ribosomes purified from the translation-arrested cells remain functional. Using spike-in RNA-seq we found that basal messenger RNAs (mRNAs) rapidly decay, while mRNAs encoding IFNs and IFN-stimulated genes evade 2-5AMD and accumulate. The IFN evasion results from the combined effect of better mRNA stability and positive feedback amplification in the IFN response. Therefore, 2-5AMD and transcription act in concert to revamp the cellular mRNA composition. The resulting preferential accumulation of innate immune mRNAs establishes “prioritized” synthesis of defense proteins.
Modelling the climate response to orbital forcing

Modelling the climatic response to orbital forcing is a challenging problem. There are currently two approaches. One uses simplified climate models that can be run for long periods and helps answer questions regarding the relative amplitudes of the climatic response to precession, obliquity, and eccentricity. The second approach uses more sophisticated climate models to examine the regional variations of climates associated with particular orbital forcing. Neither approach completely bridges the gap between astronomical forcing and the environmental response. In this paper, we review both methods, and their application to Quaternary and pre–Quaternary Milankovitch variations. The simplified models suggest that the temporal characteristic of variability will be different for an ice–free Earth but that there are mechanisms for the amplification of the 100 ka eccentricity variations. We also show that the more sophisticated models are relatively robust in predicting low latitude climate response, but that the higher latitudes are more variable. This can be explained in terms of whether the climate system goes through a threshold for the formation of snow and ice sheets. If a climate model has a warm bias, this threshold will be incorrectly represented.