Miracle-dz/UniFAR-FTUs huggingface dataset:
Popcorn haploids identified by Navajo phenotype and ploidy level

For popcorn, obtaining and identifying haploids are still challenging steps. We aimed to induce and screen haploids in popcorn using the Navajo phenotype, seedling vigor and ploidy level. We used the Krasnodar Haploid Inducer (KHI) in crosses with 20 popcorn source germplasms and five maize controls. The field trial design was completely randomized, with three replications. We assessed the efficacy of induction and of identification of haploids based on haploidy induction rate (HIR) and false positive and negative rates (FPR and FNR). Additionally, we also measured the penetrance of the Navajo marker gene (R1-nj). All putative haploids classified by R1-nj were germinated together with a diploid sample and evaluated for false positives and negatives based on vigor. Seedlings from 14 females were submitted to flow cytometry to determine the ploidy level. The HIR and penetrance were analyzed by fitting a generalized linear model with a logit link function. The HIR of the KHI, adjusted by cytometry, ranged from 0.0 to 1.2%, with a mean of 0.34%. The average FPR from screening based on the Navajo phenotype were 26.2% and 76.4%, by the vigor and ploidy, respectively. The FNR was zero. The penetrance of R1-nj ranged from 30.8 to 98.6%. The average number of seeds per ear in temperate germplasm (76) was lower than that obtained in tropical germplasm (98). There is induction of haploids in germplasm of tropical and temperate origin. We recommend the selection of haploids associating the Navajo phenotype with a direct method of confirming the ploidy level, such as flow cytometry. We also show that haploid screening based on Navajo phenotype and seedling vigor reduces misclassification. The origin and genetic background of the source germplasm influence the R1-nj penetrance. Because the known inducers are maize, developing doubled-haploid technology for popcorn hybrid breeding requires overcoming the unilateral cross-incompatibility.
Long-read proteogenomics to connect disease-associated sQTLs to the protein isoform effectors of disease

A major fraction of loci identified by genome-wide association studies (GWASs) lead to alterations in alternative splicing, but interpretation of how such alterations impact proteins is hindered by the technical limitations of short-read RNA-seq, which cannot directly link splicing events to full-length transcript or protein isoforms. Long-read RNA-seq represents a powerful tool to define and quantify transcript isoforms, and recently, infer protein isoform existence. Here we present a novel approach that integrates information from GWAS, splicing QTL (sQTL), and PacBio long-read RNA-seq in a disease-relevant model to infer the effects of sQTLs on the ultimate protein isoform products they encode. We demonstrate the utility of our approach using bone mineral density (BMD) GWAS data. We identified 1,863 sQTLs from the Genotype-Tissue Expression (GTEx) project in 732 protein-coding genes which colocalized with BMD associations (H4PP ≥ 0.75). We generated deep coverage PacBio long-read RNA-seq data (N=∼22 million full-length reads) on human osteoblasts, identifying 68,326 protein-coding isoforms, of which 17,375 (25%) were novel. By casting the colocalized sQTLs directly onto protein isoforms, we connected 809 sQTLs to 2,029 protein isoforms from 441 genes expressed in osteoblasts. Using these data, we created one of the first proteome-scale resources defining full-length isoforms impacted by colocalized sQTLs. Overall, we found that 74 sQTLs influenced isoforms likely impacted by nonsense mediated decay (NMD) and 190 that potentially resulted in the expression of new protein isoforms. Finally, we identified colocalizing sQTLs in TPM2 for splice junctions between two mutually exclusive exons, and two different transcript termination sites, making it impossible to interpret without long-read RNA-seq data. siRNA mediated knockdown in osteoblasts showed two TPM2 isoforms with opposing effects on mineralization. We expect our approach to be widely generalizable across diverse clinical traits and accelerate system-scale analyses of protein isoform activities modulated by GWAS loci.
Image de-noise based on the stationary wavelet translation with rotation,shift and scale invariance

Since traditional discrete orthonormal wavelet transform being more sensitive to the original position of signal.In the paper,we propose a stationary wavelet transform which possess the properties of rotation,shift and scale invariance.First transforming the image to polar coordinates,and confirming the principal axis orientation to adopt orientation energy function,then rotating the principal axis of image to the level orientation to gain the unifying image in the orientation.By reforming the image and rotation,shift and invariance to the wavelet bases,thus we can eliminate the influence of shift and scale.In the paper,we use Bayesian adaptive threshold estimation to gain the approximate optimization de-noising threshold.The image possesses the most PSNR.Thus we propose a kind of method which uses the input data to gain the asymptotic optimization de-noising threshold.Finally,experimental result show that the method can better reserve the image edge and de-noise at the same time,and being a kind of valid method of image de-noising.
Potential selection and maintenance of manure-originated multi-drug resistant plasmids at sub-clinical antibiotic concentrations

The goal of this study was to determine minimum selection concentrations of various antibiotics using four manure-originated multi-drug resistant plasmids in a surrogate Escherichia coli host. These plasmids carried genes conferring resistance phenotypes to several antibiotic classes including β-lactams, lincosamides, phenicols, macrolides, sulfonamides and tetracyclines. The minimum selection concentrations of antibiotics tested in nutrient-rich medium were determined: 14.1-28.2 mg/L for penicillin G, 0.1 mg/L for oxytetracycline, 0.45 mg/L for chlortetracycline, 2 mg/L for lincomycin, 1 mg/L for florfenicol, 1.3-4 mg/L for azithromycin, 0.13-0.25 mg/L for tetracycline, 0.004-0.01 mg/L for cefotaxime. Penicillin G, oxytetracycline, chlortetracycline, lincomycin and florfenicol had minimum selection concentrations in nutrient-defined medium slightly changed within 3.5-fold range compared to those in nutrient-rich medium. The minimum selection concentrations of antibiotics interfering folic acid synthesis in bacteria were also determined: 63 mg/L for sulfamethoxazole, 11.2 mg/L for sulfisoxazole and 0.06 mg/L for trimethoprim. Mixing two antibiotics changed minimum selection concentrations within 3.7-fold range compared to those in single antibiotic tests. Relatively high plasmid loss rates (> 90%) were observed when culturing plasmid-bearing strains in antibiotic-free nutrient-rich and nutrient-defined media. Overall results suggested that these plasmids can be maintained at concentrations environmentally relevant in waste water treatment plants, sewage, manure and manured soil although they are not stable in antibiotic-free environments. IMPORTANCE Antibiotic resistance crisis is a grave concern in healthcare systems around the world. To combat this crisis, we sought to find out how likely manure-originated multi-drug resistant plasmids are to be selected and maintained in different environment matrices. Our study showed that these plasmids conferring resistance to β-lactams, lincosamides, phenicols, macrolides, sulfonamides and tetracyclines can be selected at minimum selection concentrations which are lower than minimum inhibition concentrations of the E. coli host strain. Lincomycin, oxytetracycline, chlortetracycline, tetracycline, chloramphenicol, trimethoprim had minimum selection concentrations lower than the antibiotic concentrations in several environment matrices reported previously. Our findings suggest that despite the burden and the high rate of plasmid loss, these plasmids can still be selected, maintained and circulated well in some polluted environments.
Effects of alertness on perceptual detection and discrimination

The level of alertness fluctuates throughout the day, exerting modulatory effects on human cognitive processes at any moment. However, our knowledge of how alertness level interacts with specific cognitive demands and perceptual rules of the task is still limited. Here we use perceptual decision-making paradigms to understand how alertness modulates the detection of a stimulus and the capacity to discriminate one stimulus from another. We analyzed data from four different experiments (113 participants in total): 1 - auditory masking detection; 2 - sensorimotor detection; 3 - auditory spatial discrimination; and 4 - auditory phoneme discrimination, and examined the performance of participants during the natural transition from awake (high alertness) to drowsy (low alertness). First, we fitted psychometric functions to the hit rates across different conditions of difficulty for EEG-defined high and low alertness metastable states, respectively. Second, we performed modelling of slope and threshold for the fitted curves as well as signal detection theory measures of perceptual sensitivity (d’) and response bias (criterion). We found lower detection and discrimination sensitivity to stimuli as alertness level decreases, signalled by a shallower slope of the sigmoidal curve and a lower d’, while the threshold increases slightly and equivalently across experiments during lower alertness. There was no change in the criterion to make the decision during the transition. These results suggest that reduced alertness generally decreases the quality of perceptual decision-making. Zooming in, we observed that the decrease in sensitivity measured by slope was stronger for discrimination than for detection decisions, indicating that lower alertness impairs the precision of decisions in discriminating alternatives more than identifying the presence of a stimulus around the threshold. Taken together, these results suggest that alertness has a common effect on perceptual decision-making and differentially modulates detection and discrimination decisions.
The Minimum Degree Ordering with Constraints

A hybrid scheme for ordering sparse symmetric matrices is considered. It is based on a combined use of the top-down nested dissection and the bottom-up minimum degree ordering schemes. A separator set is first determined by some form of incomplete nested dissection. The minimum degree ordering is then applied subject to the constraint that the separator nodes must be ordered last. It is shown experimentally that the quality of the resulting ordering from this constrained scheme exhibits less sensitivity to the initial matrix ordering than that of the original minimum degree ordering. An important application of this approach to find orderings suitable for parallel elimination is also illustrated.
Structure and Function of the Dot/Icm T4SS

The Legionella pneumophila Dot/Icm type IV secretion system (T4SS) delivers effector proteins into host cells during infection. Despite its significance as a potential drug target, our current understanding of its atomic structure is limited to isolated subcomplexes. In this study, we used subtomogram averaging and integrative modeling to construct a nearly-complete model of the Dot/Icm T4SS accounting for seventeen protein components. We locate and provide insights into the structure and function of six new components including DotI, DotJ, DotU, IcmF, IcmT, and IcmX. We find that the cytosolic N-terminal domain of IcmF, a key protein forming a central hollow cylinder, interacts with DotU, providing insight into previously uncharacterized density. Furthermore, our model, in combination with analyses of compositional heterogeneity, explains how the cytoplasmic ATPase DotO is connected to the periplasmic complex via interactions with membrane-bound DotI/DotJ proteins. Coupled with in situ infection data, our model offers new insights into the T4SS-mediated secretion mechanism.
Sequence independent activity of a predicted long disordered segment of the human papillomavirus L2 capsid protein during virus entry

The papillomavirus L2 capsid protein protrudes through the endosome membrane into the cytoplasm during virus entry to bind cellular factors required for intracellular virus trafficking. Cytoplasmic protrusion of HPV16 L2, virus trafficking, and infectivity are inhibited by large deletions in an ∼110 amino acid segment of L2 that is predicted to be disordered. The activity of these mutants can be restored by inserting protein segments with diverse compositions and chemical properties into this region, including scrambled sequences, a tandem array of a short sequence, and the intrinsically disordered region of a cellular protein. The infectivity of mutants with small in-frame insertions and deletions in this segment directly correlates with the size of the segment. These results indicate that the length of the disordered segment, not its sequence or its composition, determines its activity during virus entry. Sequence independent but length dependent activity has important implications for protein function and evolution.
Exact finite-dimensional filters for certain diffusions with nonlinear drift

Let and be independent Wiener processes, and consider the task of estimating a diffusion solving the stochastic DE dx t =f(x t )dt+dw t on the basis of noisy observations defined bydy t =x t dt+db t . This problem is governed by the filtering equation for the unnormalized conditional density with A * the forwarded operator Theorem: if then the fundamental solution of the filtering equation can be written explicity in terms of a small number of statistics satisfying a matrixvector equation. The Lie algebraic interpretation of this result is studied and described. Extensions to many dimensions and applications to optimal stochastic control readily follow.
Visitor Optimization Revisited - Realizing Traversal Graph Pruning by Runtime Bytecode Generation

Visitors and Rewriters are a well-known and powerful design pattern for processing regular data structures in a declarative way, while still writing imperative code. The authors’ “umod” model generator creates Java data models from a concise and algebraic notation, including code for visitor skeleton classes according to traversal annotations. User visitors are derived from these, overriding selected generated methods with payload code. All branches of the visiting trajectory that are not affected can thus be safely pruned according to control flow analysis. In the first version [7], the pruning was implemented by dynamic case distinction. Here we have developed a new solution employing code generation at runtime.
Erratum to: “Elementary embeddings in torsion-free hyperbolic groups”

The notations adopted are those of [Per11]. Proposition 5.11 of [Per11] states that if a torsion-free hyperbolic group A admits a cyclic JSJ-like decomposition Λ, and a non injective morphism f : A → A which restricts to conjugation on each non surface type vertex group, and sends surface type vertex groups to non abelian images, then there is a retraction r : A→ A′ which gives A a structure of hyperbolic floor over A′. Unfortunately, we realised that Proposition 5.11 fails to hold in a few exceptional low complexity cases. The natural modification to overcome this mistake is to proceed to a slight generalization of the notion of hyperbolic floors and hyperbolic towers, which we present in Section 1. As we will see in Section 2, however, this does not affect Theorem 1.2, the main result of the paper. Moreover, Theorem 1.2 is the only result which directly uses Proposition 5.11 in its proof. For a corrected version of the paper, see [Per09]. We sincerely apologize for any confusion caused by this mistake.
Dancer Disordered Eating

The purpose of this study was to assess nutritional status; to examine the prevalence of disordered eating behavior; and to determine if a relationship existed between nutritional status and disordered eating behavior among female dancers. Twenty-one female dance majors from the undergraduate dance department at a major northeastern university participated in the survey which included: three-day food and activity records from the DINE U.S. nutritional program; EAT-26 eating attitudes assessment; and University Dancer Profile (UDP), an instrument designed by the principal researcher. On the EAT-26, 4 out of 21 subjects (19%) scored in eating disorder symptomatic range. The group means for the DINE U.S. nutritional subscales were below recommended levels: caloric intake, 59% (SD = 17.6); protein, 75% (SD = 20.9); calcium, 48% (SD = 19.8); iron, 63% (SD = 27.8); and phosphorus, 80% (SD = 24.7). A Fisher Exact Test for Significance in a 2 x 2 Contingency Table confirmed no significant relationship between disordered eating behavior and nutritional status. On the UDP, 76% of the sample scored in the Body Dissatisfaction range. We can conclude, therefore, that the sample population has normal eating attitudes, yet is preoccupied with body weight and shape, and that the subjects restrict their caloric intake. The results of this study indicate that the female dance population may be at risk for developing subclinical eating disorders within the dance subculture, or Dancer Disordered Eating.
A family of steady vortex rings

Axisymmetric vortex rings which propagate steadily through an unbounded ideal fluid at rest at infinity are considered. The vorticity in the ring is proportional to the distance from the axis of symmetry. Recent theoretical work suggests the existence of a one-parameter family, [npar ]2 ≥ α ≥ 0 (the parameter α is taken as the non-dimensional mean core radius), of these vortex rings extending from Hill's spherical vortex, which has the parameter value α = [npar ]2, to vortex rings of small cross-section, where α → 0. This paper gives a numerical description of vortex rings in this family. As well as the core boundary, propagation velocity and flux, various other properties of the vortex ring are given, including the circulation, fluid impulse and kinetic energy. This numerical description is then compared with asymptotic descriptions which can be found near both ends of the family, that is, when α → [npar ]2 and α → 0.
Public Key Infrastructure and its applications for resource-constrained IoT

The Internet of Things (IoT) is rapidly expanding and IoT devices are being deployed in security-critical scenarios, such as in critical infrastructure monitoring and within e-health, and privacy-sensitive applications in hospitals and homes. With this, questions of security and safety become paramount. The overall theme of the research presented here is to bridge some of the identified gaps in IoT security, with a particular focus on enabling Public Key Infrastructure (PKI) functionality for constrained IoT devices. The contributions of this dissertation are made through six research papers that address identified shortcomings and challenges. The focus is on protocols, mechanisms, and efficient encodings rather than specific cryptographic solutions. The work to improve the state-of-art regarding PKI for IoT includes enrollment, revocation and trust transfer. We design and implement integrated lightweight certificate enrollment solutions for IoT devices and new compact certificate formats. This brings the total communication costs of session establishment and enrollment operations down to feasible levels for constrained IoT devices. An improved design is made to benefit from application layer security, enabling end-to-end communication capable of proxy traversal. To handle revocation of trust, we propose and design lightweight certificate revocation. We show how significant performance improvements compared with existing solutions can be made without sacrificing functionality or compromising security. To address the long-time maintainability of IoT systems, we design a lightweight schema for trust transfer, which allows control of IoT deployments to shift between service providers in a highly automated manner. In addition to improving PKI functionality, we propose mechanisms for secure storage and updates, which complement and strengthen the overall IoT security landscape. We show that standard-based application-layer security mechanisms can be extended to enable secure storage and communication, reducing the memory required for cryptographic solutions and the latency when sending sensor data onto the network. In our last contribution, we propose a design for secure software updates. Based on the existing ACE framework, we use token-based access control to fulfil the need for both authentication and authorisation security services. We have been working with industry partners to share our work in the shape of new standards for a better potential for industrial impact. In summary, several new building blocks required to create, maintain and support secure PKIs capable of including constrained IoT devices are proposed, forming important steps towards making IoT devices first-class Internet citizens.
Displacement damage extremes in silicon depletion regions

Measurements of proton-induced dark current increases in a Si CID (charge injection device) imager have been made following displacement damage by 12- and 63-MeV protons. Populations of 61504 pixels optimize statistics and make possible the first detailed study of rare events. To this end, extreme value statistics allow a quantitative treatment and lead to characterization of a rare device-dependent mechanism. Data comparing the response of two similar CID structures suggest that electric-field-enhanced emission is responsible for the largest dark current increases in the CID structure with the higher electric fields. Comparisons between observations and estimates based on new calculations of the recoil spectrum parameters demonstrate that the largest dark current increases can be predicted in the absence of high fields. In this case the inelastic recoil component of the recoil spectrum plays a dominant role in determining the large dark current increases. Implications for other materials are discussed. >
Diffuse-interface modelling of droplet impact

The impact of micron-size drops on a smooth, flat, chemically homogeneous solid surface is studied using a diffuse-interface model (DIM). The model is based on the Cahn–Hilliard theory that couples thermodynamics with hydrodynamics, and is extended to include non-90° contact angles. The (axisymmetric) equations are numerically solved using a combination of finite- and spectral-element methods. The influence of various process and material parameters such as impact velocity, droplet diameter, viscosity, surface tension and wettability on the impact behaviour of drops is investigated. Relevant dimensionless parameters are defined and, depending on the values of the Reynolds number, the Weber number and the contact angle, which for the cases considered here range from 1.3 to 130, 0.43 to 150 and 45° to 135°, respectively, the model predicts the spreading of a droplet with or without recoil or even rebound of the droplet, totally or partially, from the solid surface. The wettability significantly affects the impact behaviour and this is particularly demonstrated with an impact at Re = 130 and We = 1.5, where for θ < 60° the droplet oscillates a few times before attaining equilibrium while for θ ≥ 60° partial rebound of the droplet occurs, i.e. the droplet breaks into two unequal sized drops. The size of the part that remains in contact with the solid surface progressively decreases with increasing θ until at a value θ ≈ 120° a transition to total rebound happens. When the droplet rebounds totally, it has a top-heavy shape.