Miracle-dz/UniFAR-FTUs huggingface dataset:
Assembly of Microparticles to Patterned Trenches Using the Depletion Volume Effect

In this paper, we demonstrate that 20 μm microbeads can be preferentially assembled into substrate trenches of similar width by employing a polymer (depletant) that induces the depletion volume effect (depletion attraction). In previous works, we proved that this strategy is useful to assemble mesoscale parts in a site-specific manner. Here, we show that it is also applicable to assemble functional parts, such as fluorescent particles, into trenches engraved on the surface of two- and three-dimensional template components. A convenient advantage of this strategy is that it is independent of material properties for assembling mesoscale functional components into desired patterns.
Interventions for English Language Learners: effects of Reading Recovery® on reading achievement.

English Language Learners (ELLs) in the United States have been plagued by low reading achievement, high dropout rates, and overrepresentation in special education. One researched-based reading intervention, Reading Recovery®, has a large body of research supporting its effectiveness for native speakers as well as a few studies demonstrating its effectiveness for ELLs. However, there is limited research comparing the rates of progress of native English speakers with those of ELLs as well as exploring if there is a difference in outcomes between students at different English language proficiency levels. The research questions that guided this investigation are: 1) How do the reading achievement outcomes of English Language Learners receiving the intervention Reading Recovery® compare to the outcomes of native English speakers receiving the same intervention in grade one of a large diverse urban school district? 2) What is the relationship between the reading achievement outcomes and proficiency levels of English Language Learners as determined by the Reading Recovery® language proficiency intake assessment? This study employed a quantitative methodology to compare the reading achievement outcomes of students receiving the intervention Reading Recovery® in a large, urban district from 2004-2013. The analysis in this study suggests that Reading Recovery® was actually more effective for ELLs. Based on the results of this research study, it is recommended that access be expanded and that all low reading performing ELLs that meet the selection criteria, regardless of English proficiency, be considered for Reading Recovery®.
Modeling the mobility of glyphosate from two contrasting agricultural soils in laboratory column experiments

Abstract Glyphosate (GLP) currently is one of the most widely used herbicides worldwide. The persistence of GLP and its major metabolite, aminomethylphosphonic acid (AMPA) in the environment has been described by other authors. This study was aimed at comparing the GLP and AMPA behavior in sandy and loamy sand soils after spiking with enhanced (445 µg g−1) concentrations of GLP in herbicide KLINIK® (Nufarm, Austria) and bioaugmentation followed by 40 days weathering and a consistent three-stage leaching in a laboratory column experiment. Soil samples were obtained from mineral topsoil (0–10 cm) within former agricultural lands where soil parent material was formed by glacigenic deposits. The total amount of GLP and AMPA collected during three leaching stages was significantly (p<.05) higher from columns with sandy soil, compared to loamy sand soil. Bioaugmentation resulted in considerably lower concentrations of AMPA in leachates, especially in the sets with sandy soil (p=.01). Leachates were tested using FTIR spectroscopy and Daphnia magna. Statistical analysis of the changes in Ntot, Ctot, K+, Mg2+, Al3+, Ca2+, Mn2+ and Fe3+ concentrations in soils after the leaching experiment revealed that the loamy sand soil was likely to be more sensitive to the addition of GLP and bioaugmentation than sandy soil.
Characterization of functional relationships of R-loops with gene transcription and epigenetic modifications in rice

We conducted genome-wide identification of R-loops followed by integrative analyses of R-loops with relation to gene expression and epigenetic signatures in the rice genome. We found that the correlation between gene expression levels and profiled R-loop peak levels was dependent on the positions of R-loops within gene structures (hereafter named “genic position”). Both antisense only (ASO)-R-loops and sense/antisense (S/AS)-R-loops sharply peaked around transcription start sites (TSSs), and these peak levels corresponded positively with transcript levels of overlapping genes. In contrast, sense only (SO)-R-loops were generally spread over the coding regions, and their peak levels corresponded inversely to transcript levels of overlapping genes. In addition, integrative analyses of R-loop data with existing RNA-seq, chromatin immunoprecipitation sequencing (ChIP-seq), DNase I hypersensitive sites sequencing (DNase-seq), and whole-genome bisulfite sequencing (WGBS or BS-seq) data revealed interrelationships and intricate connections among R-loops, gene expression, and epigenetic signatures. Experimental validation provided evidence that the demethylation of both DNA and histone marks can influence R-loop peak levels on a genome-wide scale. This is the first study in plants that reveals novel functional aspects of R-loops, their interrelations with epigenetic methylation, and roles in transcriptional regulation.
NMR and Molecular Modeling Reveal Specificity of the Interactions between CXCL14 and Glycosaminoglycans.

CXCL14, chemokine (C-X-C motif) ligand 14, is a novel highly conserved chemokine with unique features. Despite exhibiting the typical chemokine fold, it has a very short N-terminus of just two amino acid residues responsible for chemokine receptor activation. CXCL14 actively participates in homeostatic immune surveillance of skin and mucosae, is linked to metabolic disorders, fibrotic lung diseases, and possesses strong anti-angiogenic properties in early tumor development. In this work, we investigated the interaction of CXCL14 with various glycosaminoglycans (GAGs) by NMR spectroscopy, microscale thermophoresis, analytical heparin affinity chromatography, and in silico approaches to understand the molecular basis of GAG-binding. We observed different GAG binding modes specific for the GAG type used in the study. In particular, the CXCL14 epitope for heparin suggests a binding pose distinguishable from the ones of the other GAGs investigated (hyaluronic acid, chondroitin sulfate-A/C, -D, dermatan sulfate. This observation is also supported by computational methods that included molecular docking, molecular dynamics and free energy calculations. Based on our results, we suggest that distinct GAG sulfation patterns confer specificity beyond simple electrostatic interactions usually considered to represent the driving forces in protein-GAG interactions. The CXCL14-GAG system represents a promising approach to investigate the specificity of GAG protein interactions, which represents an important topic for developing the rational approaches to novel strategies in regenerative medicine.
THE INTEGRATED SOFTWARE RELIABILITY GROWTH MODELS FOR VARIABLE POTENTIAL ERRORS USING TIME-VARYING LEARNING EFFECTS WITH CHANGE-POINTS

Recently, various software reliability growth models (SRGMs) have been proposed to assess software reliability. Some important issues in these models include the S-curve or exponential testing behaviour, the change-points in process performance, estimation of the parameters, variations in potential errors, and learning eﬀects in the testing process. This paper provides an integrated SRGM with time-varying learning eﬀects to deal with multiple situations of software testing/debugging, based on the non-homogeneous Poisson process (NHPP) to satisfy both S-shaped and exponential-shaped types simultaneously. An exponential learning function is adopted to describe the learning eﬀects varied with time, and a sine function is also adopted to point out the change-points for the testing environment and the various potential errors. The results show better ﬁt than those of other models with actual data sets. This study also veriﬁes the eﬀectiveness of the proposed model with R 2 , mean square error, and RRMS and LSE. criteria. The proposed model not only provides good numerical prediction performance for several diﬀerent kinds of data but also explains the testing/debugging behaviour of the testing staﬀ, the learning eﬀects of the testing project itself, and the changes in the testing environment necessary to improve software system testing and management.
A Stress-Responsive NAC Transcription Factor from Tiger Lily (LlNAC2) Interacts with LlDREB1 and LlZHFD4 and Enhances Various Abiotic Stress Tolerance in Arabidopsis

Our previous studies have indicated that a partial NAC domain protein gene is strongly up-regulated by cold stress (4 °C) in tiger lily (Lilium lancifolium). In this study, we cloned the full-length of this NAC gene, LlNAC2, to further investigate the function of LlNAC2 in response to various abiotic stresses and the possible involvement in stress tolerance of the tiger lily plant. LlNAC2 was noticeably induced by cold, drought, salt stresses, and abscisic acid (ABA) treatment. Promoter analysis showed that various stress-related cis-acting regulatory elements were located in the promoter of LlNAC2; and the promoter was sufficient to enhance activity of GUS protein under cold, salt stresses and ABA treatment. DREB1 (dehydration-responsive binding protein1) from tiger lily (LlDREB1) was proved to be able to bind to the promoter of LlNAC2 by yeast one-hybrid (Y1H) assay. LlNAC2 was shown to physically interact with LlDREB1 and zinc finger-homeodomain ZFHD4 from the tiger lily (LlZFHD4) by bimolecular fluorescence complementation (BiFC) assay. Overexpressing LlNAC2 in Arabidopsis thaliana showed ABA hypersensitivity and enhanced tolerance to cold, drought, and salt stresses. These findings indicated LlNAC2 is involved in both DREB/CBF-COR and ABA signaling pathways to regulate stress tolerance of the tiger lily.
The d16HER2 Splice Variant: A Friend or Foe of HER2-Positive Cancers?

Human epidermal growth factor receptor 2 (ERBB2 or HER2) amplification/overexpression is associated with a particularly aggressive molecular subtype of breast cancer (BC), characterized by a poor prognosis, increased metastatic potential, and disease recurrence. As only approximately 50% of HER2-positive patients respond to HER2-targeted therapies, greater knowledge of the biology of HER2 and the mechanisms that underlie drug susceptibility is needed to improve cure rates. Evidence suggests that the coexistence of full-length, wild-type HER2 (wtHER2) and altered forms of HER2—such as carboxy-terminus-truncated fragments, activating mutations, and splice variants—significantly increases the heterogeneity of HER2-positive disease, affecting its biology, clinical course, and treatment response. In particular, expression of the d16HER2 splice variant in human HER2-positive BC has a crucial pathobiological function, wherein the absence of sixteen amino acids from the extracellular domain induces the formation of stable and constitutively active HER2 homodimers on the tumor cell surface. Notably, the d16HER2 variant significantly influences the initiation and aggressiveness of tumors, cancer stem cell properties, epithelial–mesenchymal transition (EMT), and the susceptibility of HER2-positive BC cells to trastuzumab compared with its wtHER2 counterpart, thus constituting a novel and potentially clinically useful biomarker. The aims of this review are to summarize the existing evidence regarding the pathobiological functions of the d16HER2 variant and discuss its current and future value with regard to risk assessment and treatment choices in HER2-positive disease.
Review-Microwave Radar Sensing Systems for Search and Rescue Purposes

This paper presents a survey of recent developments using Doppler radar sensor in searching and locating an alive person under debris or behind a wall. Locating a human and detecting the vital signs such as breathing rate and heartbeat using a microwave sensor is a non-invasive technique. Recently, many hardware structures, signal processing approaches, and integrated systems have been introduced by researchers in this field. The purpose is to enhance the accuracy of vital signs’ detection and location detection and reduce energy consumption. This work concentrates on the representative research on sensing systems that can find alive people under rubble when an earthquake or other disasters occur. In this paper, various operating principles and system architectures for finding survivors using the microwave radar sensors are reviewed. A comparison between these systems is also discussed.
Differential Impacts of Citrus Thrips Across Sweet Orange and Mandarin Species

Abstract Several domesticated Citrus species are grown as major commercial crops in California. Despite this, farmers currently use a single set of management practices, originally created for sweet oranges (Citrus sinensis (L.) Osbeck [Sapindales: Rutaceae]), for both sweet oranges and all mandarin species. Mandarins, primarily Citrus reticulata Blanco, Citrus clementina hort. ex Tanaka, and Citrus unshiu Marcovitch, comprise almost 25% of California citrus acreage, and little work has been done to assess host–pest interactions for these species. Citrus thrips (Scirtothripscitri Moulton [Thysanoptera: Thripidae]) are one of the main pests in California citrus and are major targets for early spring, “petal fall” insecticide applications. We used mixed species citrus blocks to test the influence of Citrus species, including C. sinensis, C. reticulata, C. clementina, and C. unshiu, on 1) citrus thrips densities following petal fall; 2) citrus thrips-induced scarring on both the calyx and stylar ends of fruit; and 3) fruit deformation. Citrus sinensis and C. unshiu had relatively high citrus thrips densities and scarring levels, whereas C. reticulata had lower densities of citrus thrips and scarring levels. The age structure of citrus thrips populations also varied across Citrus species. Fruit deformity associated with citrus thrips scarring was found on all Citrus species examined. Scarring on the stylar-end of fruit, a previously largely ignored location of citrus thrips scarring, was found to be common in C. reticulata. It is clear from our work that species-specific management guidelines for citrus thrips are needed in sweet oranges and mandarins.
Functionalization of the TMEM175 p.M393T variant as a risk factor for Parkinson disease

Abstract Multiple genome-wide association studies (GWAS) in Parkinson disease (PD) have identified a signal at chromosome 4p16.3; however, the causal variant has not been established for this locus. Deep investigation of the region resulted in one identified variant, the rs34311866 missense SNP (p.M393T) in TMEM175, which is 20 orders of magnitude more significant than any other SNP in the region. Because TMEM175 is a lysosomal gene that has been shown to influence α-synuclein phosphorylation and autophagy, the p.M393T variant is an attractive candidate, and we have examined its effect on TMEM175 protein and PD-related biology. After knocking down each of the genes located under the GWAS peak via multiple shRNAs, only TMEM175 was found to consistently influence accumulation of phosphorylated α-synuclein (p-α-syn). Examination of the p.M393T variant showed effects on TMEM175 function that were intermediate between the wild-type (WT) and knockout phenotypes, with reduced regulation of lysosomal pH in response to starvation and minor changes in clearance of autophagy substrates, reduced lysosomal localization, and increased accumulation of p-α-syn. Finally, overexpression of WT TMEM175 protein reduced p-α-syn, while overexpression of the p.M393T variant resulted in no change in α-synuclein phosphorylation. These results suggest that the main signal in the chromosome 4p16.3 PD risk locus is driven by the TMEM175 p.M393T variant. Modulation of TMEM175 may impact α-synuclein biology and therefore may be a rational therapeutic strategy for PD.
Reflexives and tree unification grammar

Although there has been a great deal of research into identifying the constraints responsible for the distribution of reflexive pronouns (like himself, herself, themselves), accounts of reflexivisation are often based entirely on syntactic factors. Furthermore, it is usually assumed that a reflexive and its antecedent (ie. the noun phrase to which a reflexive pronoun 'refers') must be from the same sentence, and the anaphoric relationship between a reflexive and its antecedent is often established based on a complete structural analysis of the sentence containing them. In this thesis, we propose a treatment of reflexives in which an anaphoric relationship between pronoun and antecedent can be established based on information contained in partial structures associated with linguistic expressions. There is no need to obtain a complete structural analysis before performing anaphora resolution, and information obtained from anaphora resolution can be used to constrain possible analyses. In presenting an account for the distribution of locally bound reflexives in English and of long distance reflexives in Icelandic, we will see that the same general treatment will be applicable to local as well as non-local reflexive anaphoric phenomena. Our first goal is to establish the constraints that are relevant for the distribution of reflexive pronouns. Then a declarative unification-based linguistic framework will be introduced in which these constraints can be stated. Within a declarative framework, constraints can be stated independent from any processing strategy. The basic grammar structures of this framework will be partial specifications of trees, and the framework will require only a single grammar rule to combine these partial specifications. Finally, we will illustrate how various phenomena associated with reflexive pronouns can be accounted for in this framework. We will provide an account for the distribution of reflexives appearing in complement clauses, picture-noun constructions, possessives, unbounded dependency constructions, prepositional phrases, and constructions where reflexives can have either 'sloppy' or 'strict' readings.
Examining the Association between Weapon Carrying on School Property and Suicide Attempt among Adolescents in the United States

ABSTRACT Suicidal behaviors among adolescents in the United States are the second leading cause of death and has been steadily increasing over the years. Although access to and possession of a weapon may facilitate the transition from suicidal ideation to a suicide attempt, few studies have examined the association between weapon carrying and suicide attempts among adolescents. The objective of this study was to examine the association between weapon carrying on school property and suicide attempt among adolescents. Data for this study came from the 2017 Youth Risk Behavior Surveillance System. A sample of 14,547 adolescents aged 14–18 years old (50.5% female) was analyzed using logistic regression. Of the 14,547 adolescents, 4% carried a weapon on school property, and 7.7% attempted suicide during the past 12 months. In the multivariate logistic regression, adolescents who reported carrying a weapon on school property had more than double the odds of attempting suicide when compared to their counterparts who did not carry a weapon on school property. Other significant predictors of suicide attempt include sexual minority, history of forced sexual intercourse, school bullying and cyberbullying victimization, feeling sad or hopeless, and substance use. Examining the association between weapon carrying and suicide attempt among adolescents would contribute to early identification of adolescents who are likely to engage in suicidal behaviors.
Goal-setting behaviour in massive open online courses

Massive Open Online Courses (MOOCs) represent a new and increasingly popular model of online learning course where the learner’s ability sets their learning goals and the emphasis is on creating new knowledge rather than on ’working through structured course materials’. This study set out to investigate the skills and attributes learners need to possess to participate effectively in a MOOC, and in particular: ‘How do participants plan and reflect upon their learning goals within the Change 11 MOOC? ’ Participants for this primarily qualitative study were recruited from the Change 11 course cohort. Participants were first invited to complete a self-report instrument to establish a measure of their self-regulation. Semi-structured in-depth interviews (n=27) exploring goal-setting and other learning behaviours were then conducted. Anonymised interviews were analysed and a combination of pre-defined and emergent codes used to categorise the data. Interview data was then analysed against the SR scores derived from the survey instrument. Findings from the study highlight that learners with different self-regulated learning profiles differ in their approach to goal setting and learning in a MOOC, but that other factors are also important with the topic and precise format of the course in particular mediating individual approaches to goal-setting. These findings can help practitioners design more supportive learning environments and learning designs which take account of different learner approaches to goal-setting in MOOCs which, while presently under-researched, are rapidly gaining prominence as a mechanism for delivering learning online.
Analysis on Characteristics of ZnO Surface Acoustic Wave with and without Micro-Structures

In this paper, we fabricate a surface acoustic wave (SAW) device with micro-structures on a zinc oxide (ZnO) thin film and measure its signal response. The manufacturing processes of the SAW device include the fabrication of micro-structures of a SAW element and its interdigital transducer by silicon micro-machining and the fabrication of a thin film of ZnO by RF magnetron sputtering. We, then, measure the SAW properties. This research investigates the properties of sputtered thin films for various amounts of O2/(Ar + O2) using Zn and ZnO targets. Regardless of target, the growth rate of the ZnO thin film decreases as the oxygen content increases. When the SAW is sputtered ZnO thin film using 30% oxygen, the digital signal of the SAW has better performance. The measurement signal of the SAW with micro-structures is similar to that without micro-structures.
Artery of Percheron Stroke: Imaging and Clinical Findings

The thalamus has a complex arterial blood supply from small end arteries arising from the P1 and P2 segments of the posterior cerebral artery (PCA) and the posterior communicating artery. There are four classically described thalamic vascular territories: anterior, paramedian, inferolateral, and posterior. An anatomic variant of the paramedian thalamic arterial supply is called the artery of Percheron (AOP). The AOP is a single perforating blood vessel that supplies the bilateral paramedian thalami, usually from the P1 segment of either PCA with variable contribution to the ventral midbrain. It has an estimated prevalence of approximately 10% based on a small cadaveric study, but the true prevalence is unknown. Occlusion of the AOP results in bilateral paramedian thalamic infarcts with variable midbrain involvement. It is seen in 0.1% to 0.3% of all stroke patients, and may account for up to 20% of thalamic strokes. Acutely, these patients present with varied signs and symptoms depending on the infarct size and specific thalamic and midbrain structures involved. The most common symptoms include a triad of alteredmental status ranging from drowsiness to coma, vertical gaze palsy, and memory