Miracle-dz/UniFAR-FTUs huggingface dataset:
A confinable female-lethal population suppression system in the malaria vector, Anopheles gambiae

Malaria is among the world’s deadliest diseases, predominantly affecting sub-Saharan Africa, and killing over half a million people annually. Controlling the principal vector, the mosquito Anopheles gambiae, as well as other anophelines, is among the most effective methods to control disease spread. Here we develop an innovative genetic population suppression system termed Ifegenia (Inherited Female Elimination by Genetically Encoded Nucleases to Interrupt Alleles) in this deadly vector. In this bicomponent CRISPR-based approach, we disrupt a female-essential gene, femaleless (fle), demonstrating complete genetic sexing via heritable daughter gynecide. Moreover, we show that Ifegenia males remain reproductively viable, and can load both fle mutations and CRISPR machinery to induce fle mutations in subsequent generations, resulting in sustained population suppression. Through modeling, we demonstrate that iterative releases of non-biting Ifegenia males can act as an effective, confinable, controllable, and safe population suppression and elimination system.
Asymmetric horseshoe-like assembly of peroxisomal yeast oxalyl-CoA synthetase

Abstract Oxalyl-CoA synthetase from Saccharomyces cerevisiae is one of the most abundant peroxisomal proteins in yeast and hence has become a model to study peroxisomal translocation. It contains a C-terminal Peroxisome Targeting Signal 1, which however is partly dispensable, suggesting additional receptor bindings sites. To unravel any additional features that may contribute to its capacity to be recognized as peroxisomal target, we determined its assembly and overall architecture by an integrated structural biology approach, including X-ray crystallography, single particle cryo-electron microscopy and small angle X-ray scattering. Surprisingly, it assembles into mixture of concentration-dependent dimers, tetramers and hexamers by dimer self-association. Hexameric particles form an unprecedented asymmetric horseshoe-like arrangement, which considerably differs from symmetric hexameric assembly found in many other protein structures. A single mutation within the self-association interface is sufficient to abolish any higher-level oligomerization, resulting in a homogenous dimeric assembly. The small C-terminal domain of yeast Oxalyl-CoA synthetase is connected by a partly flexible hinge with the large N-terminal domain, which provides the sole basis for oligomeric assembly. Our data provide a basis to mechanistically study peroxisomal translocation of this target.
Structural basis of how the BIRC6/SMAC complex regulates apoptosis and autophagy

Inhibitor of apoptosis proteins (IAPs) bind to pro-apoptotic proteases, keeping them inactive and preventing cell death. BIRC6 is an exceptionally large, multidomain IAP that inhibits its targets by means of its atypical ubiquitin ligase activity and in addition, functions as an inhibitor of autophagy by depleting LC3B. Little is known of the mechanisms by which BIRC6 interacts with its targets and fulfills these two roles. Here, we determined the cryo-EM structure of BIRC6 alone and in complex with two mitochondrial pro-apoptotic proteins, HTRA2 and SMAC. We show BIRC6 is an antiparallel homodimer that forms a crescent shape that arcs around a spacious cavity. The cavity is surrounded by binding sites for client proteins, where they interact with the flexible UBC domain that mediates ubiquitin ligation. Functional data reveal that multivalent binding of SMAC in the central cavity obstructs substrate binding, impeding ubiquitination of both autophagy and apoptotic target proteins. Together our data reveal the molecular mechanisms of how SMAC specifically binds and inhibits BIRC6 to promote apoptosis, and how this regulatory mechanism also extends to autophagy substrates. The interaction sites are hot spots of cancer and atrophy mutations, highlighting the importance of carefully balancing the interplay between BIRC6 and SMAC.
β-catenin interacts with the TAZ1 and TAZ2 domains of CBP/p300 to activate gene transcription

The transcriptional co-regulator β-catenin is a critical effector of the canonical Wnt-signalling pathway, which plays a crucial role in regulating cell fate and maintaining tissue homeostasis. Deregulation of the Wnt/β-catenin pathway is characteristic in the development of major types of cancer, where accumulation of β-catenin promotes cancer cell proliferation and renewal. β-catenin gene expression is facilitated through recruitment of co-activators such as histone acetyltransferases CBP/p300; however, the mechanism of their interaction is not fully understood. Here we investigate the interaction between the C-terminal transactivation domain of β-catenin and CBP/p300. Using a combination of pulldown assays, isothermal titration calorimetry, and nuclear resonance spectroscopy we determine the disordered C-terminal region of β-catenin binds promiscuously to the TAZ1 and TAZ2 domains of CBP/p300. We then map the interaction site of the C-terminal β-catenin transactivation domain onto TAZ1 and TAZ2 using chemical-shift perturbation studies. Luciferase-based gene reporter assays indicate Asp750-Leu781 is critical to β-catenin gene activation, and mutagenesis revealed that acidic and hydrophobic residues within this region are necessary to maintain TAZ1 binding. These results provide a mechanistic understanding of Wnt/β-catenin gene regulation that underlies cell development and provide a framework to develop methods to block β-catenin dependent signalling in the future.
Patterns in Nature Forming Patterns in Minds : An Evaluation of an Introductory Physics Unit

This Thesis is brought to you for free and open access. It has been accepted for inclusion in Dissertations and Theses by an authorized administrator of PDXScholar. For more information, please contact pdxscholar@pdx.edu. Recommended Citation Sheaffer, Christopher Ryan, "Patterns in Nature Forming Patterns in Minds : An Evaluation of an Introductory Physics Unit" (2013). Dissertations and Theses. Paper 925.
Black & ABD: Investigating the "All but Dissertation" Stage of the Doctoral Program among Black Graduate Students

Abstract:The purpose of this qualitative study is to identify barriers experienced by Black "All but dissertation" (ABD) students while working to complete the dissertation phase of doctoral education. A heuristic phenomenological approach was adopted to collect and analyze the experiences of ten current and former students in EdD and PhD programs. The study's findings indicate that Black doctoral students feel disconnected from the doctoral process once they reach ABD status. Findings also showed that Black ABD students described positive experiences with external supports yet negative experiences involving program changes, guidance, feedback, and the racialized nature of graduate school experience. The findings have implications for the identification and amelioration of problematic individual, programmatic, or institutional practices that impede doctoral degree completion.
Seven Cs for Tweens: Design Principles for Children Aged 10-13 in the Urban Landscape

Abstract:Outdoor play is critical for the wellbeing of children. In cities, access to unsupervised outdoor play is limited by a host of obstacles. Many of these limiting factors can be mitigated by environmental design. The following identifies seven design principles for urban public landscapes that support play for "tweens" (children 10 to 13 years old). We developed these principles using a mixed methodology that included a literature review, an analysis of qualitive interview transcripts with tweens, and a precedent study of playable urban landscapes. The Seven Cs for Tweens principles include: connectivity, community, cues, character, child agency, challenge, and comfort.
Mother–Child Language Style Predicts Internalizing Behaviors in Children Exposed to Intimate Partner Violence

Abstract:Exposure to intimate partner violence (IPV) is associated with children's internalizing and externalizing problems. IPV is thought to impair mothers' ability to scaffold young children's emotion regulation through coregulated interactions. Mother–child language style matching (LSM) is an index of coregulation that has yet to be examined in IPV-exposed samples. We hypothesized that LSM would mediate the association between IPV and children's behavioral problems. Participants were 194 mother–child dyads. IPV was assessed annually when children were ages 1–4. LSM was derived from speech during a free-play interaction at age 4, and children's behavior problems were assessed concurrently and again at age 10. Chronic IPV exposure in early life was associated with lower levels of mother–child LSM. LSM also mediated the association between IPV and later internalizing problems. These findings provide evidence that mother–child LSM may be a useful index of parent–child interaction quality in the context of IPV.
A control algorithm for statistically stationary large‐eddy simulations of thermally stratified boundary layers

Large‐eddy simulations (LESs) of thermally stratified atmospheric boundary layers (ABLs) typically involve imposed heating or cooling at the ground surface, leading to slowly varying temperature distributions in the domain. While for some applications an interpretation of the resulting fields as quasi‐stationary is possible, there are certain applications for which the slow temporal variations are a serious drawback. An example occurs when using LES for a systematic analysis of effects of large wind farms on atmospheric heat fluxes, where analysis of stationary statistics greatly facilitates understanding. In order to obtain statistically stationary temperature fields in LES of thermally stratified boundary layers, in this article we introduce a control algorithm, and test its effectiveness for various levels of surface heating and cooling. The method uses a ‘proportional‐integral’ (PI) control algorithm, designed to keep constant the horizontally averaged temperature in a computational fringe layer placed above the ABL region of interest. For flows driven by a geostrophic wind, another controller is used to adjust the mean flow angle within the ABL at a specified height to achieve a prescribed direction. This is done by controlling a source term (in the form of an additional Coriolis force) in the momentum equations. This term is deactivated once the statistics become stationary and the flow aligns with the desired direction. Together, these two control schemes enable very long‐time simulations of thermally stratified heated or cooled boundary layers displaying fully stationary distributions of mean velocity and temperature.
Biochemical acclimation, stomatal limitation and precipitationpatterns underlie decreases in photosynthetic stimulation of soybean(<i>Glycine max</i>) at elevated [CO<sub>2</sub>] and temperatures under fully open airfield conditions

The net effect of elevated [CO2] and temperature on photosynthetic acclimation and plant productivity is poorly resolved. We assessed the effects of canopy warming and fully open air [CO2] enrichment on (1) the acclimation of two biochemical parameters that frequently limit photosynthesis (A), the maximum carboxylation capacity of Rubisco (Vc,max) and the maximum potential linear electron flux through photosystem II (Jmax), (2) the associated responses of leaf structural and chemical properties related to A, as well as (3) the stomatal limitation (l) imposed on A, for soybean over two growing seasons in a conventionally managed agricultural field in Illinois, USA. Acclimation to elevated [CO2] was consistent over two growing seasons with respect to Vc,max and Jmax. However, elevated temperature significantly decreased Jmax contributing to lower photosynthetic stimulation by elevated CO2. Large seasonal differences in precipitation altered soil moisture availability modulating the complex effects of elevated temperature and CO2 on biochemical and structural properties related to A. Elevated temperature also reduced the benefit of elevated [CO2] by eliminating decreases in stomatal limitation at elevated [CO2]. These results highlight the critical importance of considering multiple environmental factors (i.e. temperature, moisture, [CO2]) when trying to predict plant productivity in the context of climate change. © 2014 Elsevier Ireland Ltd. All rights reserved.
Hot regions of non-interfering crossovers coexist with a non-uniformly interfering pathway in Arabidopsis thaliana

In most organisms that have been studied, crossovers formed during meiosis exhibit interference: nearby crossovers are rare. Here we provide an in-depth study of crossover interference in Arabidopsis thaliana , examining crossovers genome-wide in over 1500 backcrosses for both male and female meiosis. This unique data set allows us to take a two-pathway modeling approach based on superposing a fraction p of non-interfering crossovers and a fraction (1-p) of interfering crossovers generated using the Gamma model characterized by its interference strength nu . Within this framework, we fit the two-pathway model to the data and compare crossover interference strength between chromosomes and then along chromosomes. We find that the interfering pathway has markedly higher interference strength nu in female than male meiosis and also that male meiosis has a higher proportion p of non-interfering crossovers. Furthermore, we test for possible intra -chromosomal variations of nu and p . Our conclusion is that there are clear differences between left and right arms as well as between central and peripheral regions. Finally, statistical tests unveil a genome-wide picture of small scale heterogeneities, pointing to the existence of hot regions in the genome where COs form preferentially without interference.
Instability-driven Oscillations of Active Microfilament Supplemental Material

We discretize the filament’s centerline into n + 1 vertices r1, . , rn+1 and n straight edges `i = ri+1 − ri, where i = 1, . , n, in the spirit of [1] and [2]; see Fig. 1. The unit tangent to edge i is defined as ti = `i/`i where `i = ‖`i‖. Inextensibility is enforced weakly by considering large tensile stiffness S = EA along the filament’s centerline. That is to say, t is allowed to experience slight extension or compression, inducing a local axial strain si = (`i/ˆ̀i)ti − d3, where ˆ̀i is a strain-free reference configuration length. The linear velocities v1, . vn+1 are assigned to vertices. The body frames are naturally assigned to edges, so is the rotation matrix Q; we let {d1,i,d2,i,d3,i = ti} and Qi denote
Effects of Commercial Prebiotic and Probiotics of Diet on Performance of Laying Hens, Egg Traits and Some Blood Parameters

Aims: This study was conducted to evaluate the influence of adding commercial probiotics and prebiotic to diet on performance of laying hens, egg traits and some blood parameters. Study Design: Data of feed intake (FI), egg production (EP), egg mass (EM), and calculated feed conversion ratio (FCR) were analyzed based on completely randomized design using GLM procedure of SAS. Place and Duration of Study: All procedures used in this 7-week experiment were approved by the "Animal Ethics Committee of Razi University" and complied with the "Guidelines for the Care and Use of Animals in Research". Methodology: Five iso-caloric and iso-nitrogenous diets (ME =2720 Kcal/Kg and CP=150 g/kg) including basal diet (control) and basal diet supplemented by probiotics (PrimaLac®, A-Max and Yeasture) and prebiotic (Fermacto) were formulated. A total number of 90 Lohmann LSL-Lite laying hens were randomly divided in 15 cages (n=6). The experimental probiotics or prebiotic to diets. Conclusion: Using Primalac, Fermacto, A-Max and Yeasture did not have beneficial effects on performance of laying hens. However, the effects of probiotics and prebiotic on suboptimal circumstances should be investigated in future.
Relationship of the In ammatory Diet Status and Dietary Intake with Antimalarial Treatment in Systemic Lupus Rrythematosus: A Cross-Sectional Study

Mónica R. Meza-Meza Universidad de Guadalajara Centro Universitario de Ciencias de la Salud Nitin Shivappa University of South Carolina Margarita Montoya-Buelna Universidad de Guadalajara Centro Universitario de Ciencias de la Salud José Francisco Muñoz-Valle Universidad de Guadalajara Centro Universitario de Ciencias de la Salud James R. Hébert University of South Carolina Barbara Vizmanos-Lamotte Universidad de Guadalajara Centro Universitario de Ciencias de la Salud Isela Parra-Rojas Universidad Autonoma de Guerrero Bertha Campos-López Universidad de Guadalajara Centro Universitario de Ciencias de la Salud Sergio Cerpa-Cruz Hospital Civil de Guadalajara Unidad Hospitalaria Fray Antonio Alcalde Ulises De la Cruz-Mosso (  ulises_cdm@hotmail.com ) University of Guadalajara https://orcid.org/0000-0003-4579-2294
A Single-snapshot Compressed Sensing Technique for Source Localization in Underwater Transportation

In order to obtain the accurate localization results for underwater transportation (such as surface vessels), a single-snapshot compressed sensing technique is proposed in this paper. The source localization problem in underwater transportation is considered as a sparsity representation problem and solved by general-purpose convex toolbox CVX. Different from most of the subspace-based direction-of-arrival (DOA) estimation methods, there is no need to reconstruct the cross-correlation matrix in our proposed algorithm and its performance will not degrade when the snapshot number is small. Simulation results demonstrate the validity and feasibility of our proposed method.
Semantic Segmentation Based Field Detection Using Drones

Smart agriculture has been garnering attention to improve the efficiency of works. For example, advanced technologies such as drones and Artificial Intelligence (AI) may reduce labor, increase productivity, and grow high-quality crops. The aim of our study is to photograph fields of green onions from the sky using drones, then to predict the harvest time and observe the growth situation using AI image analysis. Therefore, in this paper, we proposed basic technology for area section classification of each field by using segmentation method using deep learning to analyze the cultivation situation of each field.
Identification of Transparent and Specular Reflective Glass Planes in TLS Data with Intensity Values

When setting up a terrestrial laser scanner near the target building and performing 3D measurement, the return measurements get corrupted because of the reflectivity and transparency of the glass objects. The discrimination of reflections and indoor points from the outdoor environment is a challenging task. As the first step of removing these erroneous measurements, it is important to detect these glass planes framed in the building façade. In this study, we propose an unsupervised segmentation approach in combination with the threshold of Gaussian distribution to extract transparent and reflective glass planes from point clouds with intensity attributes. For practical validation, our approach is evaluated on two scan points of a building with many glass components.
A 26–31 GHz Linearized Wideband CMOS LNA Using Post-Distortion Technique

This paper presents a modified post-distortion (PD) linearization technique for cascode common-gate low noise amplifiers (CG-LNAs) working at high frequencies up to millimeter-wave band. This technique utilizes an auxiliary transistor together with an inter-stage inductor to suppress the third order distortion without degrading gain. The input third order intercept point (IIP3) of the linearized CG-LNA is improved by a factor of up to 12 dB. For demonstration, an mm-wave differential CG-LNA was fabricated based on a 65-nm CMOS process. It achieves 2.4–10.6 dBm IIP3, 9.6–12 dB gain, 5.0–5.45 dB NF over 26–31 GHz and consumes 14.4 mW from a 1.2 V supply.
ST18 Enhances PV-IgG-Induced Loss of Keratinocyte Cohesion in Parallel to Increased ERK Activation

Pemphigus is an autoimmune blistering disease targeting the desmosomal proteins desmoglein (Dsg) 1 and Dsg3. Recently, a genetic variant of the Suppression of tumorigenicity 18 (ST18) promoter was reported to cause ST18 up-regulation, associated with pemphigus vulgaris (PV)-IgG-mediated increase in cytokine secretion and more prominent loss of keratinocyte cohesion. Here we tested the effects of PV-IgG and the pathogenic pemphigus mouse anti-Dsg3 antibody AK23 on cytokine secretion and ERK activity in human keratinocytes dependent on ST18 expression. Without ST18 overexpression, both PV-IgG and AK23 induced loss of keratinocyte cohesion which was accompanied by prominent fragmentation of Dsg3 immunostaining along cell borders. In contrast, release of pro-inflammatory cytokines such as IL-1α, IL-6, TNFα, and IFN-γ was not altered significantly in both HaCaT and primary NHEK cells. These experiments indicate that cytokine expression is not strictly required for loss of keratinocyte cohesion. Upon ST18 overexpression, fragmentation of cell monolayers increased significantly in response to autoantibody incubation. Furthermore, production of IL-1α and IL-6 was enhanced in some experiments but not in others whereas release of TNF-α dropped significantly upon PV-IgG application in both EV- and ST18-transfected HaCaT cells. Additionally, in NHEK, application of PV-IgG but not of AK23 significantly increased ERK activity. In contrast, ST18 overexpression in HaCaT cells augmented ERK activation in response to both c-IgG and AK23 but not PV-IgG. Because inhibition of ERK by U0126 abolished PV-IgG- and AK23-induced loss of cell cohesion in ST18-expressing cells, we conclude that autoantibody-induced ERK activation was relevant in this scenario. In summary, similar to the situation in PV patients carrying ST18 polymorphism, overexpression of ST18 enhanced keratinocyte susceptibility to autoantibody-induced loss of cell adhesion, which may be caused in part by enhanced ERK signaling.
Clothing Recommendation Based on Deep Learning

Nowadays, with massive growth of e-commerce platforms, more and more consumers are buying clothes online, but consumers are often confused when choosing clothes. At this time, the clothing recommendation system acts as a bridge between consumers and stores. Through a recommendation system, it can recommend clothing that consumers are interested in, and help the store to improve turnover as well as solve many problems in people's lives. For this study, we design a deep multi-branch network based clothing recommendation system, and add channel attention for feature enhancement. We also utilize gender prediction to improve our clothing recommendation results. The effectiveness of our proposed method is verified through our experimental results.