Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular analysis of hybridization between native westslope cutthroat trout (oncorhynchus clarki lewisi) and introduced rainbow trout (O.mykiss) in southeastern British Columbia

Westslope cutthroat trout (Oncorhynchus clarki lewisi, WCT) and introduced rainbow trout (0. mykiss, RBT) readily hybridize and introgression has occurred in many drainages across the historic range of WCT. In British Columbia, the upper Kootenay River drainage is the heart of WCT distribution and is thought to be a refuge for genetically pure populations. In this study, I assess the extent and distribution of WCT x RBT hybridization in the upper Kootenay River drainage, examine the genotypic structure of hybridizing populations using population genetic analyses, and examine the potential for differential selection between pure WCT and hybrid individuals using cohort analysis. Caudal fin clips were collected from 981 fish at 23 sample sites in 12 different streams in the upper Kootenay River drainage. I used 4 diagnostic nuclear loci to determine the extent of hybridization at each sample site. Fourteen percent (142/981) of individuals were identified as hybrids, 3.4% (33/981) were identified as pure RBT, and the remaining individuals were identified as pure WCT. Mitochondrial D N A analysis indicated that hybrid matings occur between males and females of both species. Although pure RBT were absent from the majority of sites (20/23), I found evidence of hybridization at 78% (18/23) of samples sites and the percentage of heterospecific alleles {% T) ranged from 0.7-97.1%. Only 22% (5/23) of sample sites showed no evidence of hybridization. The majority of hybrid individuals were genotypically classified as WCT backcrosses (59%) and post-F2 individuals (24%). The skewed ratio of pure WCT to RBT (27:1), and the rarity of F] individuals (4 of 142 hybrids), suggests that the spread of RBT alleles is facilitated by hybrids straying to neighbouring populations. Spatial analysis showed clustering among hybridized sites and decreasing hybridization with increasing distance from Koocanusa Reservoir, suggesting that the reservoir acts as a RBT source. I found little evidence of differential selection between pure WCT and hybrid individuals. My results suggest that hybridization is relatively recent in the upper Kootenay River drainage and that it is increasing in magnitude and distribution. In the absence of timely management intervention, the genetic integrity of WCT populations in the heart of their Canadian range may be lost. TABLE OF CONTENTS Abstract ii Table of
Self-Assessment of Grasp Affordance Transfer

Reasoning about object grasp affordances allows an autonomous agent to estimate the most suitable grasp to execute a task. While current approaches for estimating grasp affordances are effective, their prediction is driven by hypotheses on visual features rather than an indicator of a proposal’s suitability for an affordance task. Consequently, these works cannot guarantee any level of performance when executing a task and, in fact, not even ensure successful task completion. In this work, we present a pipeline for self-assessment of grasp affordance transfer (SAGAT) based on prior experiences. We visually detect a grasp affordance region to extract multiple grasp affordance configuration candidates. Using these candidates, we forward simulate the outcome of executing the affordance task to analyse the relation between task outcome and grasp candidates. The relations are ranked by performance success with a heuristic confidence function and used to build a library of affordance task experiences. The library is later queried to perform one-shot transfer estimation of the best grasp configuration on new objects. Experimental evaluation shows that our method exhibits a significant performance improvement up to 11.7% against current state-of-the-art methods on grasp affordance detection. Experiments on a PR2 robotic platform demonstrate our method’s highly reliable deployability to deal with real-world task affordance problems.
Texture Feature Coding Method for Texture Analysis and It’s Application

This paper proposes a new texture analysis method namely texture feature coding method (TFCM). The texture feature coding method transforms a gray-level image into feature image whose each pixel is represented by a texture feature number (TFN). The TFN histogram and TFN co-occurrence matrix are derived to generate many texture features for texture classification. The gray-level co-occurrence matrix (GLCM) and texture spectrum (TS) have been used for comparison in discriminating some of Brodatz’s natural texture images and ultrasonic liver images in experiments. Experimental results reveal that the results using the texture feature coding methods is superior to other two.
Cell accumulation and antileishmanial effect of exogenous and endogenous protoporphyrin IX after photodynamic treatment

fluency using a colorimetric MTT assay for THP-1 cells and a standard microscopic analysis of parasites. Results were expressed as compound concentration activity against 50% of cells or parasites (CC 50 or IC 50 ). Results: ALA or MAL induced an endogenous PpIX with a red fluorescence localized mainly in the mitochondria inside human cells. ALA and MAL-PDT induced a similar range of toxicities on THP-1 cells (CC 50 0.16±0.01mM and 0.33±0.019 mM, respectively) without any apparent inhibition of intracellular parasites in the infected cells as compared to untreated controls. Exogenous PpIX-PDT was toxic to THP-1 cells (CC 50 0.00032±0.00002 mM), L. (L.) infantum (IC 50 0.003±0.0001 mM) and L. (V.) panamensis (IC 50 0.024±0.0001 mM) promastigotes. Conclusions: Despite the effectiveness of exogenous PpIX on promastigotes and the production of PpIX by human infected cells, treatment with ALA or MAL before irradiation was unable to completely destroy L. (L.) infantum or L. (V.) panamensis intracellular amastigotes.
Molecular Pathology and Molecular Pharmacology of Osteosarcoma

Abnormalities of many tumor suppressor genes and oncogenes have been described in osteosarcoma, but separating early or primary from secondary or late genetic lesions has been difficult. Among early lesions, inactivation of both the P53 and RB pathways appears to be a central and perhaps necessary event in osteosarcomagenesis. We propose a working model for the molecular pathology of osteosarcoma and we review the numerous published studies examining the association of various molecular features with either advanced presentation, poor chemotherapy response or decreased patient survival.
STIMULI EFFECTS ON OPTIMAL BEHAVIOR IN A SUNK-COST SITUATION WITH PIGEONS

The contribution of varying the response requirement frequency on the occurrence of escape-optimal and persistence-optimal behavior versus impulsive behavior was evaluated in food-deprived pigeons. According to an ABACA design, the subjects were exposed to the following arrangements of fixed ration (FR) response requirements and probabilities of presentation of each one: for the A conditions the arrangements were FR 10 p=0.50, FR 40 p=0.25, FR 80 p=0.125 or FR 160 p=0.125. For the B condition the arrangements were FR 10 p=0.125, FR 40 p=0.50, FR 80 p=0.25 or FR 160 p=0.125. For the C condition the set was FR 10 p=0.0625, FR 40 p=0.0625, FR 80 p=0.50 and FR 160 p=0.375. These FR response requirements with their respective probabilities were evaluated under two phases of the experiment, a signaled and an unsignaled one. Globally, it was found that the relative frequency of the FR response requirements controlled the occurrence of escape and persistence optimal behavior or impulsive behavior. These effects of the response frequency were modulated by the presence versus absence of a stimulus signaling the response requirement changes. These findings were interpreted as congruent with those previously reported in similar procedures.
The pollution caused by veterinary antibiotics within freshwater

The use of veterinary antibiotics is a common practice within livestock agriculture. Because of its popularity it potentially pollutes freshwater entities. Globally, high concentrations of veterinary pharmaceuticals have been detected, which can have significant ecotoxicological effects. The goal of this research is to improve the understanding of this pollution, by modelling the pathways of 8 types of antibiotics between the application on the field and inflow into freshwater. With help of the model VANTOM (Bailey, 2015) and the Grey Water Footprint (GWF) concept (Hoekstra et al., 2011), the pollution is quantified so that different scenarios and reduction measures can be compared. This is done for a case study of the Vecht catchment.
Color Spectrographic Analysis of Respiratory Sounds: A Promising Technology for Respiratory Monitoring

* Address correspondence to this author at the Department of General Anesthesiology, Cleveland Clinic Lerner College of Medicine, Cleveland, OH, USA, E-mail: djdoyle@hotmail.com movements as well as observing signs, such as nasal flaring, or the use of the accessory muscles of respiration. Later, with the invention of stethoscope, simple acoustical methods of respiratory assessment became available to the clinical community. With the subsequent invention of electronic amplification, a variety of new technologies became available, including respiratory monitoring belts placed on the chest and abdomen [6 9], nasal pressure methods [10, 11], nasal / oral thermistor methods [12, 13] (the thermistor warms up with expired gases), nasal / oral capnography [14, 15], extraction of respiratory information from the photoplethysmograph signal [16, 17], and electrical impedance methods based on a small injected electrical current [18, 19].
Enabling Fast Failure Recovery in OpenFlow networks using RouteFlow

OpenFlow provides a protocol to control a network from an external server called controller. Moreover, RouteFlow presents a framework to run Internet routing protocols in OpenFlow networks by running them in virtual machines or containers. The problem is that OpenFlow networks running RouteFlow do not recover fast from a port failure (e.g., port down event). The failure recovery time is dependent on user configurable parameters and is in seconds. To overcome this problem, we implement a solution in which a port failure of a physical OpenFlow node is detected immediately in its corresponding virtual machine and an immediate action is taken by the routing protocol. Therefore, once a routing protocol running on the corresponding virtual machine detects this failure, it broadcasts the failure in the network and a new failure free path is immediately configured over the OpenFlow network. We implement the proposed solution in an OpenFlow controller and test it over single autonomous and multiple autonomous system scenarios (including OpenFlow and non-Openflow scenarios) of the Internet emulated on the virtual wall testbed of the Fed4Fire facility in Europe. The results show that an OpenFlow network can recover from a failure in a short time interval using the proposed solution.
Interactive Gesture Based System with Email Access and Voice Command for the People with Visual, Hearing and Speech Impairment Using IoT

- The advancement in communication technology in coordination with IoT made the communication easy. These emerging technologies have been helping the mankind with its wide range of applications. However it is difficult for the visually impaired (blind) to access these technologies because they require visual sensitivity. According to the survey in our country 2.78% people have Hearing and Speech Impairment (dumb). In order to communicate with others Visual, Hearing and Speech Impaired people use the motion of their hands and expressions (gestures) as this method of communication involves a lot of ambiguity. So there is a need for a system to establish communication between the Visual, Hearing and Speech Impaired with the society. A large-scale microcontroller system and a data glove equipped with the accelerometer are proposed to facilitate the communication among the dumb, deaf and visually impaired and their communication with the common people. This system can be dynamically reconfigured to work as a "smart device”. In this system, Gestures are made using data glove equipped with accelerometer sensor. And the microcontroller based system converts specified movements into human recognizable voice and generates an email with predefined images and subject.
Mid-infrared photonic crystal cavities

We demonstrate the design, fabrication, and characterization of silicon photonic crystal cavities realized in a silicon on insulator (SOI) platform, operating at a wavelength of 4.4 μm with a quality factor of 13,600. Cavity modes are imaged using the technique of scanning resonant scattering microscopy. To the best of our knowledge, this is the first demonstration of photonic devices fabricated in SOI and operating in the 4-5 μm wavelength range.
Securing RDMA for High-Performance Datacenter Storage Systems

RDMA is increasingly popular for low-latency communication in datacenters, marking a major change in how we build distributed systems. Unfortunately, as we pursue signiﬁcant system re-designs inspired by new technology, we have not given equal thought to the consequences for system security. This paper investigates security issues introduced to datacenter systems by switching to RDMA and challenges in building secure RDMA systems. These challenges include changes in RPC reliability guarantees and unauditable data-accesses. We show how RDMA’s design makes it challenging to build secure storage systems by analyzing recent research systems; then we outline several directions for solutions and future research, with the goal of securing RDMA datacenter systems while they are still in the research and prototype stages.
RNAi suppression of the anthocyanidin synthase gene in Torenia hybrida yields white flowers with higher frequency and better stability than antisense and sense suppression

Post-transcriptional gene silencing, such as antisense suppression, sense suppression (or cosuppression), and RNAi, is often used to down-regulate a target gene in transgenic plants. Novel flower color is industrially important; furthermore, flower color is a convenient tool to monitor the stability of such silencing. Previously, we obtained white torenia through sense suppression of chalcone synthase or dihydroflavonol 4-reductase (Suzuki et al. 2000). However, their phenotypes were not stable. In this study, we suppressed the anthocyanidin synthase gene using three methods in transgenic torenia. About half of the transgenic torenia plants gave white flowers by RNAi suppression of the gene, while antisense and sense suppression yielded a few and no white flowers, respectively. The white flower color obtained by RNAi has been stable for three years in a greenhouse. This study shows the usefulness of RNAi to suppress a target gene.
USING THE INDICATOR AMINO ACID OXIDATION TECHNIQUE TO STUDY THREONINE REQUIREMENTS IN HORSES FED DIFFERENT FEED COMPOSITIONS

OF THESIS USING THE INDICATOR AMINO ACID OXIDATION TECHNIQUE TO STUDY THREONINE REQUIREMENTS IN HORSES FED DIFFERENT FEED COMPOSITIONS Threonine has been reported to be the second limiting amino acid in typical equine diets, but its actual requirement has not been determined in horses. The indicator amino acid oxidation (IAAO) method has been successfully used for evaluating amino acid metabolism and requirements in animals and humans. The objective of this research was to use the IAAO method to estimate threonine requirements in mature horses fed two different feed compositions. In the first study, 6 Thoroughbred mares (4 – 16 years old) received each of 6 levels of threonine intake in a high concentrate diet, in a randomly determined order. The experimental diets consisted of concentrate at 0.95% of body weight (BW), and chopped timothy hay at 0.95% of BW, and met or exceeded NRC recommendations for all nutrients. Threonine intakes for the 6 treatments were 45, 56, 67, 79, 90 and 102 mg/kg BW/d and were generated by mixing the two experimental concentrates, containing 2.9 and 14.8 g threonine/kg diet, in different ratios. In the second study, horses received each of 6 levels of threonine intake, 41, 51, 61, 70, 80, and 89 mg/kg BW/d, in a high forage diet, in a randomly determined order. The experimental diet was concentrate at 0.4% of BW, and chopped timothy hay at 1.6% of BW. Study periods for each study were 7-d long and on d 6, blood samples were collected before and 90 min after feeding to measure amino acid concentrations using HPLC. On d 7, horses underwent IAAO procedures, which included a two hour primed, constant intravenous infusion of [C]sodium bicarbonate to measure total CO2 production and a four hour primed, constant oral administration of [1-C]phenylalanine to estimate phenylalanine oxidation to CO2. Blood and breath samples were collected to measure blood [C]phenylalanine, using GC-MS analysis, and breath CO2 enrichment, using an infrared isotope analyzer. Experimental data were analyzed using a one-way ANOVA, including orthogonal linear and quadratic contrasts, in the mixed procedures of SAS version 9.3, with treatment as the fixed effect and horse nested in treatment as the random effect. Statistical significance was declared at P 0.05). Increasing threonine intake levels in a high forage diet did not affect plasma phenylalanine oxidation by the ANOVA test (P>0.05) but resulted in a linear decrease in phenylalanine oxidation (P=0.04) without a breakpoint by the orthogonal linear contrast. Threonine requirements are still unknown in mature horses fed either high concentrate or high forage diet. The present studies were the first attempt to evaluate threonine requirements in horses by the indicator amino acid oxidation method.
The Mechanism of Binding of Low-Molecular-Weight Active Site Inhibitors to Human α-Thrombin

AbstractThe thrombin inhibitors argatroban, efegatran, NAPAP, CH 1091, CH 248, inogatran and melagatran have been characterised with respect to their mechanism of binding to human α-thrombin. Stopped-flow spectrophotometry was used to follow thrombin-catalysed hydrolysis of the chromogenic substrate S-2238 in the presence of inhibitors. The rate of onset or decay of inhibition was evaluated using progress curve analysis. It was possible to obtain apparent association and dissociation rate constants from the dependence of the rates on the inhibitor concentrations. Inhibition constants calculated from the association and dissociation rate constants were in good agreement with those calculated from steady-state rates. The binding of 6 inhibitors was also monitored directly using stopped-flow spectrofluorimetry when two kinetic components were found with all inhibitors. The faster component accounted for the largest part of the change in the intrinsic fluorescence of thrombin induced by inhibitor binding and .
Unified statistical inference for a novel nonlinear dynamic functional/longitudinal data model

In light of recent work studying massive functional/longitudinal data, such as the resulting data from the COVID-19 pandemic, we propose a novel functional/longitudinal data model which is a combination of the popular varying coefficient (VC) model and additive model. We call it Semi-VCAM in which the response could be a functional/longitudinal variable, and the explanatory variables could be a mixture of functional/longitudinal and scalar variables. Notably some of the scalar variables could be categorical variables as well. The Semi-VCAM simultaneously allows for both substantial flexibility and the maintaining of one-dimensional rates of convergence. A local linear smoothing with the aid of an initial B spline series approximation is developed to estimate the unknown functional effects in the model. To avoid the subjective choice between the sparse and dense cases of the data, we establish the asymptotic theories of the resultant Pilot Estimation Based Local Linear Estimators (PEBLLE) on a unified framework of sparse, dense and ultra-dense cases of the data. Moreover, we construct unified consistent tests to justify whether a parsimony submodel is sufficient or not. These test methods also avoid the subjective choice between the sparse, dense and ultra dense cases of the data. Extensive Monte Carlo simulation studies investigating the finite sample performance of the proposed methodologies confirm our asymptotic results. We further illustrate our methodologies via analyzing the COVID-19 data from China and the CD4 data.
Forbidding $K_{2, t}$ Traces in Triple Systems

Let $H$ and $F$ be hypergraphs. We say $H$ {\em contains $F$ as a trace} if there exists some set $S \subseteq V(H)$ such that $H|_S:=\{E\cap S: E \in E(H)\}$ contains a subhypergraph isomorphic to $F$. In this paper we give an upper bound on the number of edges in a $3$-uniform hypergraph that does not contain $K_{2,t}$ as a trace when $t$ is large. In particular, we show that $$\lim_{t\to \infty}\lim_{n\to \infty} \frac{\mathrm{ex}(n, \mathrm{Tr}_3(K_{2,t}))}{t^{3/2}n^{3/2}} = \frac{1}{6}. $$ Moreover, we show $\frac{1}{2} n^{3/2} + o(n^{3/2}) \leqslant \mathrm{ex}(n, \mathrm{Tr}_3(C_4)) \leqslant \frac{5}{6} n^{3/2} + o(n^{3/2})$.
Alternative splicing of transcripts encoding the α- and α-subunits of mouse glucosidase II in T lymphocytes

Glucosidase II is a processing enzyme of the endoplasmic reticulum that functions to hydrolyze two glucose residues in immature N -linked oligosaccharides attached to newly synthesized polypeptides. We previously reported the cDNA cloning of the alpha- and beta-subunits of mouse glucosidase II from T cells following copurification of these proteins with the highly glycosylated transmembrane protein-tyrosine phosphatase CD45. Subsequent examination of additional cDNA clones, coupled with partial genomic DNA sequencing, has revealed that both subunits are encoded by gene products that undergo alternative splicing in T lymphocytes. The catalytic alpha-subunit possesses two variably expressed segments, box Alpha1, consisting of 22 amino acids located proximal to the amino-terminus, and box Alpha2, composed of 9 amino acids situated between the amino-terminus and the putative catalytic site in the central region of the molecule. Box Beta1, a variably expressed 7 amino acid segment in the beta-subunit of glucosidase II, is located immediately downstream of an acidic stretch near the carboxyl-terminus. Screening of reverse transcribed RNA by polymerase chain reaction confirms the variable inclusion of each of these segments in transcripts obtained from a panel of T-lymphocyte cell lines. Thus, distinct isoforms of glucosidase II exist that may perform specialized functions.
Sherman-Morrison-Woodbury Identity for Tensors

In linear algebra, the sherman-morrison-woodbury identity says that the inverse of a rank-$k$ correction of some matrix can be computed by doing a rank-k correction to the inverse of the original matrix. This identity is crucial to accelerate the matrix inverse computation when the matrix involves correction. Many scientific and engineering applications have to deal with this matrix inverse problem after updating the matrix, e.g., sensitivity analysis of linear systems, covariance matrix update in kalman filter, etc. However, there is no similar identity in tensors. In this work, we will derive the sherman-morrison-woodbury identity for invertible tensors first. Since not all tensors are invertible, we further generalize the sherman-morrison-woodbury identity for tensors with moore-penrose generalized inverse by utilizing orthogonal projection of the correction tensor part into the original tensor and its Hermitian tensor. According to this new established the sherman-morrison-woodbury identity for tensors, we can perform sensitivity analysis for multi-linear systems by deriving the normalized upper bound for the solution of a multilinear system. Several numerical examples are also presented to demonstrate how the normalized error upper bounds are affected by perturbation degree of tensor coefficients.