Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Evaluation of Natural Populations of the Endangered Conifer Thuja koraiensis Using Microsatellite Markers by Restriction-Associated DNA Sequencing

Thuja koraiensis Nakai is an endangered conifer of high economic and ecological value in Jilin Province, China. However, studies on its population structure and conservation genetics have been limited by the lack of genomic data. Here, 37,761 microsatellites (simple sequence repeat, SSR) were detected based on 875,792 de novo-assembled contigs using a restriction-associated DNA (RAD) approach. Among these SSRs, 300 were randomly selected to test for polymorphisms and 96 obtained loci were able to amplify a fragment of expected size. Twelve polymorphic SSR markers were developed to analyze the genetic diversity and population structure of three natural populations. High genetic diversity (mean NA = 5.481, HE = 0.548) and moderate population differentiation (pairwise Fst = 0.048–0.078, Nm = 2.940–4.958) were found in this species. Molecular variance analysis suggested that most of the variation (83%) existed within populations. Combining the results of STRUCTURE, principal coordinate, and neighbor-joining analysis, the 232 individuals were divided into three genetic clusters that generally correlated with their geographical distributions. Finally, appropriate conservation strategies were proposed to protect this species. This study provides genetic information for the natural resource conservation and utilization of T. koraiensis and will facilitate further studies of the evolution and phylogeography of the species.
A discrete Nash Theorem with low complexity and dynamic equilibria

Nash's Theorem guarantees the existence of Nash equilibria for strategic-form games. The typical proof of the result uses Brouwer's Fixed Point Theorem on probabilistic strategies. We show that Tarski's Fixed Point Theorem can be used to establish a similar result for discrete equilibria in a much larger class of games that we call conversion/preference games. Our result rests on a graph characterisation of Nash equilibria that i) reifies the decision procedure for pure Nash equilibria, ii) allows us to compute the equilibria in quadratic time in the number of game situations, and iii) makes the equilibria explicitly dynamic in nature. We also briefly discuss the extended range of technical applications of non-cooperative game theory that results from the new theorem, including for gene regulation and cell-level signal transduction.
On Improving Evolutionary Algorithms by Using Data Mining for the Oil Collector Vehicle Routing Problem

This paper presents some proposals to improve the performance of an evolutive algorithm applied to a problem known as the “Oil Collector Vehicle Routing Problem” (OCVRP) used in a Brazilian oil company to collect oil in artificial lift wells. This paper focus on the analysis of evolutive algorithms added with procedures of local search and data mining. Three algorithms were developed: a basic model of genetic algorithm (BGA), another using additional procedures of local search (GA1) and a third that employed procedures of local search and data mining (GA2). Computational results show that the algorithm GA2 outperforms the other versions concerning the quality of solutions, indicating that the inclusion of a data mining procedure can significantly improve the performance of this kind of metaheuristic.
Mutation of the Glucosinolate Biosynthesis Enzyme Cytochrome P450 83A1 Monooxygenase Increases Camalexin Accumulation and Powdery Mildew Resistance

Small secondary metabolites, including glucosinolates and the major phytoalexin camalexin, play important roles in immunity in Arabidopsis thaliana. We isolated an Arabidopsis mutant with increased resistance to the powdery mildew fungus Golovinomyces cichoracearum and identified a mutation in the gene encoding cytochrome P450 83A1 monooxygenase (CYP83A1), which functions in glucosinolate biosynthesis. The cyp83a1-3 mutant exhibited enhanced defense responses to G. cichoracearum and double mutant analysis showed that this enhanced resistance requires NPR1, EDS1, and PAD4, but not SID2 or EDS5. In cyp83a1-3 mutants, the expression of genes related to camalexin synthesis increased upon G. cichoracearum infection. Significantly, the cyp83a1-3 mutant also accumulated higher levels of camalexin. Decreasing camalexin levels by mutation of the camalexin synthetase gene PAD3 or the camalexin synthesis regulator AtWRKY33 compromised the powdery mildew resistance in these mutants. Consistent with these observations, overexpression of PAD3 increased camalexin levels and enhanced resistance to G. cichoracearum. Taken together, our data indicate that accumulation of higher levels of camalexin contributes to increased resistance to powdery mildew.
beta-Lactamases in laboratory and clinical resistance

beta-Lactamases are the commonest single cause of bacterial resistance to beta-lactam antibiotics. Numerous chromosomal and plasmid-mediated types are known and may be classified by their sequences or phenotypic properties. The ability of a beta-lactamase to cause resistance varies with its activity, quantity, and cellular location and, for gram-negative organisms, the permeability of the producer strain. beta-Lactamases sometimes cause obvious resistance to substrate drugs in routine tests; often, however, these enzymes reduce susceptibility without causing resistance at current, pharmacologically chosen breakpoints. This review considers the ability of the prevalent beta-lactamases to cause resistance to widely used beta-lactams, whether resistance is accurately reflected in routine tests, and the extent to which the antibiogram for an organism can be used to predict the type of beta-lactamase that it produces.
Vitamin D3 regulates steroidogenesis in granulosa cells through AMP‐activated protein kinase (AMPK) activation in a mouse model of polycystic ovary syndrome

Polycystic ovary syndrome (PCOS) is an endocrine and metabolic disorder in reproductive‐aged women. Hormonal abnormality caused by steroidogenesis disturbances appears to be the main culprit of the clinical picture in PCOS. Vitamin D3 could regulate steroidogenesis in granulosa cells, but the mechanism of action of vitamin D3 on steroidogenesis remains unknown. AMP‐activated protein kinase (AMPK) has a modulating role in steroid hormone production. We investigated the effect of vitamin D3 on steroidogenesis in cultured granulosa cells of dehydroepiandrosterone‐induced PCOS mice and studied the involvement of AMPK signalling pathway in the current process. Immunoblotting assay showed that vitamin D3 could increase phosphorylation of AMPK alpha and acetyl‐CoA carboxylase, main substrate of AMPK. Vitamin D3 and 5‐aminoimidazole‐4‐carboxamide‐1‐β‐D‐riboside or Aicar (AMPK activator) not only reduced gene expression of steroidogenic enzymes (P450scc or Cyp11a1, StAR, Cyp19a1 and 3B‐HSD), but also reduced production of progesterone and 17B‐estradiol assessed by radioimmunoassay. Pretreatment with compound C (AMPK inhibitor) decreased APMK phosphorylation and eliminated the effects of vitamin D3 and Aicar on steroidogenic enzymes expression and estradiol and progesterone production. This study showed that vitamin D3 has the main role in regulating of steroidogenesis in granulosa cells of mouse polycystic ovary through activation of the AMPK signalling pathway.
MTHFR C677T, A1298C and MS A2756G Gene Polymorphisms and Male Infertility Risk in a Chinese Population: A Meta-Analysis

Background Methylenetetrahydrofolate reductase gene (MTHFR C677T and A1298C) and methionine synthase gene (MS A2756G) polymorphisms have shown an association with male infertility risk in several ethnic populations. Although several studies have evaluated these associations in Chinese populations, their small sample sizes and inconsistent outcomes have prevented strong conclusions. Therefore, the present meta-analysis was performed with published studies to evaluate the associations of the three single nucleotide polymorphisms (SNPs) and male infertility in a Chinese population. Methods We conducted a search of PubMed, Embase, Web of Science, Chinese National Knowledge Infrastructure (CNKI), China biology medical literature (CBM), VIP, and Chinese literature (Wan Fang) databases up to May 31, 2016. Odds ratios (ORs) and 95% confidence intervals (95%CIs) were used to assess the strength of associations with a random-effect model or a fixed-effect model based on the heterogeneity analysis results. Sensitivity analysis was used to confirm the reliability and stability of the meta-analysis. Results A total of nine studies, including 1,713 cases and 1,104 controls, were included in the meta-analysis. The pooled results indicated that the MTHFR C667T polymorphism was significantly associated with increased risk of male infertility in the Chinese population in the allele model (T vs. C: OR = 1.47, 95%CI = 1.32–1.63), the dominant model (TT + CT vs. CC: OR = 1.51, 95%CI = 1.30–1.77), the additive model (TT vs. CC: OR = 2.08, 95%CI = 1.68–2.58) and the recessive model (TT vs. CT+CC: OR = 1.58, 95%CI = 1.31–1.90), whereas the MTHFR A1298C and MS A2756G polymorphisms were not risk factors. There was no significant heterogeneity in any genotype contrasts among the studies. The sensitivity analysis indicated that the results of this meta-analysis were relatively stable. Conclusion This study suggests that the MTHFR C667T polymorphism may contribute to the genetic susceptibility to male infertility in the Chinese population, whereas MTHFR A1298C and MS A2756G polymorphisms may be unrelated to male infertility. Studies with larger sample sizes and representative population-based cases and well-matched controls are needed to validate our results.
Tenofovir: A new option for the treatment of chronic hepatitis B

Treatment of chronic hepatitis B (CHB) continues to evolve. Over the last decade, progressively lower levels of serum HBV DNA have been used as a threshold for treatment. A high degree of antiviral potency and a low rate of resistance are the two most important factors in the choice of an agent for therapy of CHB. Achieving rapid viral suppression is also a key factor in choosing the first line of therapy. Swift and potent viral suppression decreases the risk of hepatic decompensation, development of hepatocellular carcinoma and subsequent need for liver transplantation. Currently, entecavir and tenofovir are the most potent nucleoside and nucleotide analogs with the lowest rate of resistance in treatment-naive patients. This review will evaluate the safety and efficacy of the use of tenofovir disoproxil fumarate, the newest agent, for the treatment of patients with CHB.
Practical schemes for smooth MAC layer handoff in 802.11 wireless networks

The limited service range of the access points demands mobile wireless stations to handoff frequently between different cells in the IEEE 802.11 infrastructure networks. However, the handoff scheme used in the current 802.11 infrastructure networks is far from graceful. In this paper, we propose a smooth MAC layer handoff scheme and a greedy smooth MAC layer handoff scheme. Our schemes scan channels in a smooth manner so that the handoff can have less impact on upper layer applications. In order to limit the frequency of channel scanning, an adaptive mechanism is used to dynamically adjust the threshold triggering the channel scanning operations. We have implemented our handoff schemes using commodity 802.11 devices and extensive experiments have been conducted to evaluate the performance. The experimental results demonstrate that our schemes reduce packet delay and loss during handoff. Our handoff schemes are implemented in the client side only and do not require changes to access points. Therefore, our schemes can be deployed in the existing 802.11 networks
Complexity of Self-Assembled Shapes

The connection between self-assembly and computation suggests that a shape can be considered the output of a self-assembly “program,” a set of tiles that fit together to create a shape. It seems plausible that the size of the smallest self-assembly program that builds a shape and the shape's descriptional (Kolmogorov) complexity should be related. We show that under the notion of a shape that is independent of scale this is indeed so: in the Tile Assembly Model, the minimal number of distinct tile types necessary to self-assemble an arbitrarily scaled shape can be bounded both above and below in terms of the shape's Kolmogorov complexity. As part of the proof of the main result, we sketch a general method for converting a program outputting a shape as a list of locations into a set of tile types that self-assembles into a scaled up version of that shape. Our result implies, somewhat counter-intuitively, that self-assembly of a scaled up version of a shape often requires fewer tile types, and suggests that the independence of scale in self-assembly theory plays the same crucial role as the independence of running time in the theory of computability.
The Complexity of Drawing Graphs on Few Lines and Few Planes

It is well known that any graph admits a crossing-free straight-line drawing in $\mathbb{R}^3$ and that any planar graph admits the same even in $\mathbb{R}^2$. For a graph $G$ and $d \in \{2,3\}$, let $\rho^1_d(G)$ denote the minimum number of lines in $\mathbb{R}^d$ that together can cover all edges of a drawing of $G$. For $d=2$, $G$ must be planar. We investigate the complexity of computing these parameters and obtain the following hardness and algorithmic results. - For $d\in\{2,3\}$, we prove that deciding whether $\rho^1_d(G)\le k$ for a given graph $G$ and integer $k$ is ${\exists\mathbb{R}}$-complete. - Since $\mathrm{NP}\subseteq{\exists\mathbb{R}}$, deciding $\rho^1_d(G)\le k$ is NP-hard for $d\in\{2,3\}$. On the positive side, we show that the problem is fixed-parameter tractable with respect to $k$. - Since ${\exists\mathbb{R}}\subseteq\mathrm{PSPACE}$, both $\rho^1_2(G)$ and $\rho^1_3(G)$ are computable in polynomial space. On the negative side, we show that drawings that are optimal with respect to $\rho^1_2$ or $\rho^1_3$ sometimes require irrational coordinates. - Let $\rho^2_3(G)$ be the minimum number of planes in $\mathbb{R}^3$ needed to cover a straight-line drawing of a graph $G$. We prove that deciding whether $\rho^2_3(G)\le k$ is NP-hard for any fixed $k \ge 2$. Hence, the problem is not fixed-parameter tractable with respect to $k$ unless $\mathrm{P}=\mathrm{NP}$.
Peptide Inhibitors Targeting the Neisseria gonorrhoeae Pivotal Anaerobic Respiration Factor AniA

ABSTRACT Neisseria gonorrhoeae causes the sexually transmitted infection gonorrhea, which is highly prevalent worldwide and has a major impact on reproductive and neonatal health. The superbug status of N. gonorrhoeae necessitates the development of drugs with different mechanisms of action. Here, we focused on targeting the nitrite reductase AniA, which is a pivotal component of N. gonorrhoeae anaerobic respiration and biofilm formation. Our studies showed that gonococci expressing AniA containing the altered catalytic residues D137A and H280A failed to grow under anaerobic conditions, demonstrating that the nitrite reductase function is essential. To facilitate the pharmacological targeting of AniA, new crystal structures of AniA were refined to 1.90-Å and 2.35-Å resolutions, and a phage display approach with libraries expressing randomized linear dodecameric peptides or heptameric peptides flanked by a pair of cysteine residues was utilized. Biopanning experiments led to the identification of 29 unique peptides, with 1 of them, C7-3, being identified multiple times. Evaluation of their ability to interact with AniA using enzyme-linked immunosorbent assay and computational docking studies revealed that C7-3 was the most promising inhibitor, binding near the type 2 copper site of the enzyme, which is responsible for interaction with nitrite. Subsequent enzymatic assays and biolayer interferometry with a synthetic C7-3 and its derivatives, C7-3m1 and C7-3m2, demonstrated potent inhibition of AniA. Finally, the MIC50 value of C7-3 and C7-3m2 against anaerobically grown N. gonorrhoeae was 0.6 mM. We present the first peptide inhibitors of AniA, an enzyme that should be further exploited for antigonococcal drug development.
A simple 2D straight-leg passive dynamic walking model without foot-scuffing problem

This paper presents a simple 2D passive dynamic walking model with straight legs based on a novel hip joint, called T-joint. The model directly solves the common foot-scuffing problem in straight-legged walkers without introducing any new degree of freedom or additional motion phase, which is unavoidable in kneed robots. The mathematic model of the new walker is a 4D hybrid dynamical system, which can be reduced to a 3D Poincaré map. A stable period-1 walking gait is found by searching the map with a proposed algorithm. Numerical studies show that the model performs well for disturbances on initial conditions and also on a large slope. The stable walking gait is verified by a virtual prototype in ADAMS. This study has been successfully used to make an efficient walking robot called Xingzhe, which has set a new world record for the longest distance after 134km non-stoping walking.
Domain specific syntax based approach for text classification in machine learning context

Due to the vast amount of data, searching and obtaining relevant information on the web is a challenging task. Despite that a broad range of classification techniques have been proposed to improve the information retrieval methods, many difficulties are still present because of the continuous increase in the amount of web contents, as well as its diversity. In this paper, we propose a method that automatically identifies and classifies user queries by using a domain specific syntax approach — this approach is based on the syntactical pattern of each type of search query. A framework is developed to test the performance of the proposed method. Experimental results show that our approach leads to accurate identification of different query types.
Independent Living Capacity Evaluation in Home-Based Primary Care: Considerations and Outcomes of a Quality Improvement Project

ABSTRACT Objectives: This article describes results of a quality improvement project review of 5 years of capacity evaluations for independent living conducted in one Home-Based Primary Care (HBPC) Program. Methods: A retrospective chart review was conducted for all patients evaluated for independent living capacity through the Boston VA HBPC Program (N = 25) to identify differences in outcomes for those with and without capacity. Descriptive information included referral sources, capacity decisions, time remaining in the home, and trajectory of patients following evaluation. Results: All patients evaluated had been diagnosed with a cognitive disorder, and on average, a relatively lower prevalence of mental illness compared with the national HBPC population. Referrals were made primarily by the HBPC team. Patients with capacity were found to have remained in their home longer than those who lacked capacity. Conclusions: Referral for a higher level of care was typically only recommended when no further intervention could be implemented and active risk in the home could not be managed. Clinical Implications: In home capacity evaluations are complex and challenging, yet results help family and HBPC team support patients’ preferences for staying in their own home as long as possible.
Sperm mitochondrial DNA deletion in Iranian infertiles with asthenozoospermia

Asthenozoospermia is an important cause of male infertility. The mutations in sperm mitochondrial DNA (mtDNA) result in either functionless or malfunctioning some proteins, subsequently affecting sperm motility leading to asthenozoospermia. The purpose of this study was to investigate sperm mtDNA 4,977‐bp deletion in infertile men with low sperm motility/immotile spermatozoa compared to healthy subjects with high sperm motility. Semen samples of 256 asthenozoospermic infertiles and 200 controls from northern Iran were collected. After extraction of spermatozoa total DNA, Gap‐polymerase chain reaction (Gap‐PCR) was performed. The deletion was observed in 85.93% of patients with asthenozoospermia compared with 14% in controls [OR = 37.5397, 95% confidence interval = 12.937–108.9276, p < . 0001]. It is concluded that there is a strong association between sperm mtDNA 4,977‐bp deletion and asthenozoospermia‐induced infertility in the population examined. Large‐scale mtDNA deletions in spermatozoa may induce bioenergetic disorders. Nevertheless, to validate our results broader research may be needed.
Input Power Factor Compensation for High-Power CSC Fed PMSM Drive Using d -Axis Stator Current Control

In this paper, an input power factor compensation method is proposed for a high-power pulse-width-modulated current-source-converter (CSC)-fed permanent magnet synchronous motor (PMSM) drive system. The proposed method is based on controlling the d-axis stator current component in the field-oriented control (FOC) scheme of the drive system. The CSC-fed PMSM drive system and its FOC scheme are first introduced. Then, the relationships between the machine side, dc-link, and the line side are investigated. Based on the analysis, a new d-axis stator current control scheme that can ensure unity input power factor for the operating speed range is proposed. The main feature of the proposed scheme is to compensate the line-side power factor without the need for modulation index control in either the rectifier or the inverter. Therefore, offline Selective Harmonic Elimination (SHE) modulation schemes can be implemented on both line- and machine-side converters to minimize the total harmonic distortion. This results in reduced switching frequency and reduced switching losses. Simulation results for a 2.44 MW medium-voltage system and experimental results from a low-voltage 6.5 kW IPM motor drive are provided to verify the effectiveness of the proposed compensation method.
Tractability through Exchangeability: A New Perspective on Efficient Probabilistic Inference

Exchangeability is a central notion in statistics and probability theory. The assumption that an infinite sequence of data points is exchangeable is at the core of Bayesian statistics. However, finite exchangeability as a statistical property that renders probabilistic inference tractable is less well-understood. We develop a theory of finite exchangeability and its relation to tractable probabilistic inference. The theory is complementary to that of independence and conditional independence. We show that tractable inference in probabilistic models with high treewidth and millions of variables can be explained with the notion of finite (partial) exchangeability. We also show that existing lifted inference algorithms implicitly utilize a combination of conditional independence and partial exchangeability.
Road traffic prediction by incorporating online information

Road traffic conditions are typically affected by events such as extreme weather or sport games. With the advance of Web, events and weather conditions can be readily retrieved in real-time. In this paper, we propose a traffic condition prediction system incorporating both online and offline information. RFID-based system has been deployed for monitoring road traffic. By incorporating data from both road traffic monitoring system and online information, we propose a hierarchical Bayesian network to predict road traffic condition. Using historical data, we establish a hierarchical Bayesian network to characterize the relationships among events and road traffic conditions. To evaluate the model, we use the traffic data collected in Western Massachusetts as well as online information about events and weather. Our proposed prediction achieves an accuracy of 93% overall.