Miracle-dz/UniFAR-FTUs huggingface dataset:
Changes in Gene Expression and Metabolite Profiles in Platanus acerifolia Leaves in Response to Feeding Damage Caused by Corythucha ciliata

The sycamore lace bug, Corythucha ciliata (Say) is a highly invasive pest insect that feeds on sycamore trees (Platanus spp.) worldwide. The interaction between Platanus species and this insect pest has not yet been studied at the molecular level. Therefore, a recent study was conducted to compare the gene expression and metabolite profiles of Platanus acerifolia leaves in response to C. ciliata feeding damage after 24 and 48 h. We employed high throughput RNA sequencing (RNA- seq) to identify a total of 2,828 significantly differentially expressed genes (DEGs) after C. ciliata feeding. In addition, 303 unigenes were found to be up-regulated at both time points. Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that monoterpenoid biosynthesis, the linoleic acid metabolism pathway, and alpha- linolenic acid metabolism were the most prominent pathways among the DEGs. Further analysis of the metabolite profiles showed that nine metabolites were significantly different before and after C. ciliata damage. In addition, we analyzed DEGs detected in the P. acerifolia and C. ciliata interaction using Mapman. The terpene synthase gene family was also identified. We suggest that the results obtained from DEGs and metabolite analysis can provide important information for the identification of genes involved in the P. acerifolia–C. ciliata interaction, which might be necessary for controlling C. ciliata efficiently.
Variability of Executive Function Performance in Preschoolers with Developmental Language Disorder

Abstract Although results vary across individual studies, a large body of evidence suggests that children with developmental language disorder (DLD) have domain-general deficits in executive function compared with peers with typically developing language. Poorer performance for children with DLD has been reported on verbal and nonverbal measures of sustained selective attention, working memory, inhibition, and shifting. However, examination of the variability of task scores among both children with and without DLD reveals a wide range of executive function performance for both groups. Additionally, using executive function scores to classify children into DLD versus typical groups results in classification accuracy that is not clinically useful. This evidence indicates that group-level differences in executive function abilities between children with and without DLD cannot be applied at the individual level. Many children with DLD appear to have intact executive function abilities, which undermines the possibility that poor executive functioning causes language deficits in this population. However, a substantial number of children with DLD also have executive function deficits, and, therefore, therapy approaches with this population should consider both their language and executive function abilities.
Plasma Nanocoatings Developed to Control the Shear Strength of Polymer Composites

All reinforcements for polymer-matrix composites must be coated with a suitable material in the form of a thin film to improve compatibility and interfacial adhesion between the reinforcement and the polymer matrix. In this study, plasma nanotechnology was used to synthetize such functional nanocoatings using pure tetravinylsilane (TVS) and its mixtures with oxygen gas (O2) as precursors. The plasma-coated glass fibers (GFs) were unidirectionally embedded in a polyester resin to produce short composite beams that were analyzed by a short-beam-shear test to determine the shear strength characterizing the functionality of the nanocoatings in a GF/polyester composite. The developed plasma nanocoatings allowed controlling the shear strength between 26.2–44.1 MPa depending on deposition conditions, i.e., the radiofrequency (RF) power and the oxygen fraction in the TVS/O2 mixture. This range of shear strength appears to be sufficiently broad to be used in the design of composites.
Obstructive Sleep Apnoea Contributes to Executive Function Impairment in Young Children with Down Syndrome

ABSTRACT Objective/Background Children with Down syndrome (DS) commonly experience difficulties with executive function (EF). They are also vulnerable to obstructive sleep apnoea (OSA). OSA is associated with EF deficits in typically developing children. A recent study reported an association between OSA and cognitive deficits in 38 school-aged children with DS. We experimentally investigated EF behaviours in young children with DS, and their association with OSA. Participants and Methods Children with DS were recruited to take part in a larger study of OSA (N = 202). Parents of 80 children (50 male) aged 36 to 71 months (M = 56.90, SD = 10.19 months) completed the Behavior Rating Inventory of Executive Function – Preschool Version (BRIEF-P). Of these 80 children, 69 were also successfully studied overnight with domiciliary cardiorespiratory polygraphy to diagnose OSA. Results Obstructive apnoea/hypopnoea index was in the normal range (0–1.49/h) for 28 children but indicated OSA (≥1.5/h) in 41 children. Consistent with previous research, we found a large effect for children experiencing particular weaknesses in working memory, planning and organising, whilst emotional control was a relative strength. OSA was associated with poorer working memory (β = .23, R2 = .05, p = .025), emotional control (β = .20, R2 = .04, p = .047) and shifting (β = .24, R2 = .06, p = .023). Conclusions Findings suggest that known EF difficulties in DS are already evident at this young age. Children with DS already have limited cognitive reserve and can ill afford additional EF deficit associated with OSA. OSA is amenable to treatment and should be actively treated in these children to promote optimal cognitive development.
Inhalation Injury Does Not Influence The Amount of Blood Transfused to Major Burn Patients: A Secondary Analysis from The Transfusion Requirement in Burn Care Evaluation (TRIBE) Study.

INTRODUCTION Patients with major burn injuries typically require numerous blood transfusions. It is not known if an inhalation injury (INHI) directly influences the need for blood transfusion. The purpose of this study was to determine whether INHI increases the amount of blood transfused to major burn patients. METHODS A secondary analysis from the Transfusion Requirement in Burn Care Evaluation (TRIBE) Study was conducted. Patients with INHI were compared to patients without INHI. The number of red blood cell transfusions/day (RBC/day) between INHI and No INHI was analyzed with a multivariable regression. RESULTS Patients with INHI (n = 78) had significantly larger burns (p=0.0004), larger full thickness burns (p=0.0007), greater admission APACHE score (p < 0.0001), higher admission MOD scores (p < 0.0001), and were transfused more RBC/day (p=0.009) than NoINHI patients (n = 267). In the multivariable regression analysis RBC/day was significantly associated with the % TBSA burn (p < 0.0001), age of the patient (p=0.004), the need for more than one day of mechanical ventilation (p < 0.0001), the occurrence of at least one BSI (p = 0.044), and being assigned to the liberal transfusion arm of TRIBE (p< 0.001), but not the presence of INHI (p=0.056). CONCLUSION The null hypothesis that INHI exerts no influence on the amount of blood transfused could not be rejected. Larger burn size, advanced patient age, mechanical ventilation, and BSIs are important determinants of the blood transfusion rate in major burn patients.
PD-L1/PD-1 Expression in Endometrial Clear Cell Carcinoma: A Potential Surrogate Marker for Clinical Trials

Background. Endometrial clear cell carcinoma (ECCC) represents a rare subtype of endometrial cancer. Recently, immunotherapeutic drugs targeting programmed cell death protein 1 (PD-1)/programmed death ligand-1 (PD-L1) was associated with improved survival in several types of cancer (especially in patients with mismatch-repair (MMR)-deficient status). The aim of this study is to evaluate the correlation between the PD-L1/PD-1 axis and clinical and pathological features in strictly defined ECCC diagnosed at our institution. Design. Review of ECCC (diagnosed in the period of 2000 to 2017) identified 23 cases (n = 23) in our institution. The cases were reviewed by 2 gynecological pathologists. Estrogen receptor, progesterone receptor, napsin A, p16, and p53 were also performed so that only pure CCC cases were included. PD-L1 (SP142), PD-1, and MMR antibodies were performed. PD-L1 and PD-1 were scored in both the tumor and the peritumoral lymphocyte infiltration. Clinical and pathological features were recorded to correlate with the expression of the 2 markers. Results. Among the 23 cases, 20 cases were qualified for pure CCC by histology and immunohistochemistry patterns. Regarding PD-1 expression, 6/20 (30%) patients had positive expression in peritumoral lymphocyte infiltration. While 3/20 (15%) cases had PD-L1 either tumoral or peritumoral lymphocytes expression. Loss of MMR expression was present in 1 (5%) of 20 patients. PD-1 and/or PD-L1 expression cases tended to have deeper myometrial invasion and higher stage at presentation. Conclusions. Our results are suggestive of the roles of both PD-1 and PD-L1 in ECCCs as useful therapeutic biomarkers for immunotherapy.
“Closer to the Unfair Reality”: Magnitude and Spatial Analysis of Femicides in Ecuador

During the last 5 years, Ecuador has published a series of progressive laws aiming to protect girls and women against any type of violence. While these efforts are of extreme importance, concerns were raised by national nongovernmental organizations that the official numbers might be biased due to the restricted definition of femicide applied. The main objective of this study was to assess the magnitude and spatial distribution of the femicide rate by province in Ecuador in 2017. Data on cases were collected by a national network of nongovernmental organizations. Age-specific population data were obtained from the National Institute of Statistics for the year 2017. Thematic maps of overall and age-specific femicide rates were also constructed. Moran’s index was used to identify clusters of provinces with similar risks for the occurrence of the outcome. The total number of femicides during 2017 was 155, but age could not be recorded in 9 of those cases. More than one-third of the cases (36.99%) occurred in young women aged 15 to 24 years. The total rate was 1.99/100,000 women. When the femicide definition was restricted to women 15 years and above, the total rate increased to 2.41 cases/100,000. The femicide rate in Orellana boosted to 10.21 cases/100,000 in the age group of 15 years and older, the highest in the country. No pattern of spatial autocorrelation was observed. Femicides in Ecuador is a big public health problem, particularly in certain Amazon provinces. The observed rate for women above the age of 15 years (2.41) places Ecuador among the countries in the Latin American and the Caribbean region with the highest femicide rates. While progressive policies have been implemented in the last years, more educational interventions are needed at all societal levels to eradicate this kind of violence.
Shedding light on autophagy coordinating with cell wall integrity signaling to govern pathogenicity of Magnaporthe oryzae

ABSTRACT Cells are faced with various stresses during their growth and development, and autophagy is a degradative process in which cells can break down their own components to recycle macromolecules and provide energy under these stresses. For pathogenic fungi that utilize cell wall as the first barrier against external stress, the cell wall integrity (CWI) pathway also provides an essential role in responding to these stresses. However, the specific connection between autophagy and CWI remains elusive in either the model fungi including budding yeast Saccharomyces cerevisiae or the rice blast fungus Magnaporthe oryzae. Here, we provided evidence that the endoplasmic reticulum (ER) stress is highly induced during M. oryzae infection and that CWI MAP kinase kinase MoMkk1 (S. cerevisiae Mkk1/2 homolog) was subject to phosphorylation regulation by MoAtg1, the only identified kinase in the core autophagy machinery. We also identified MoMkk1 serine 115 as the MoAtg1-dependent phosphorylation site and this phosphorylation could activate CWI, similar to that by the conserved MAP kinase kinase kinase MoMck1 (S. cerevisiae Bck1 homolog). Together with the first report of MoMkk1 subjects to phosphorylation regulation by MoAtg1, we revealed a new mechanism by which autophagy coordinates with CWI signaling under ER stress, and this MoAtg1-dependent MoMkk1 phosphorylation is essential for the pathogenicity of M. oryzae. Abbreviations: A/Ala: alanine; Atg: autophagy-related; Bck1: bypass of C kinase 1; co-IP: co-immunoprecipitation; CWI: cell wall integrity;DTT: dithiothreitol; ER: endoplasmic reticulum; GFP: green fluorescent protein; Mo: Magnaporthe oryzae; MAPK: mitogen-activated protein kinase; Mkk1: mitogen-activated protein kinase-kinase 1; MS: mass spectrometry; PAS: phagophore assembly site; RFP: red fluorescent protein; RT: room temperature; S/Ser: serine; Slt2: suppressor of the lytic phenotype 2; T/Thr: threonine; UPR: unfolded protein response; Y2H: yeast two-hybrid screen.
Molecular Docking and Molecular Dynamics Studies on Selective Synthesis of α-Amyrin and β-Amyrin by Oxidosqualene Cyclases from Ilex Asprella

Amyrins are the immediate precursors of many pharmaceutically important pentacyclic triterpenoids. Although various amyrin synthases have been identified, little is known about the relationship between protein structures and the constituent and content of the products. IaAS1 and IaAS2 identified from Ilex asprella in our previous work belong to multifunctional oxidosqualene cyclases and can produce α-amyrin and β-amyrin at different ratios. More than 80% of total production of IaAS1 is α-amyrin; while IaAS2 mainly produces β-amyrin with a yield of 95%. Here, we present a molecular modeling approach to explore the underlying mechanism for selective synthesis. The structures of IaAS1 and IaAS2 were constructed by homology modeling, and were evaluated by Ramachandran Plot and Verify 3D program. The enzyme-product conformations generated by molecular docking indicated that ASP484 residue plays an important role in the catalytic process; and TRP611 residue of IaAS2 had interaction with β-amyrin through π–σ interaction. MM/GBSA binding free energy calculations and free energy decomposition after 50 ns molecular dynamics simulations were performed. The binding affinity between the main product and corresponding enzyme was higher than that of the by-product. Conserved amino acid residues such as TRP257; TYR259; PHE47; TRP534; TRP612; and TYR728 for IaAS1 (TRP257; TYR259; PHE473; TRP533; TRP611; and TYR727 for IaAS2) had strong interactions with both products. GLN450 and LYS372 had negative contribution to binding affinity between α-amyrin or β-amyrin and IaAS1. LYS372 and ARG261 had strong repulsive effects for the binding of α-amyrin with IaAS2. The importance of Lys372 and TRP612 of IaAS1, and Lys372 and TRP611 of IaAS2, for synthesizing amyrins were confirmed by site-directed mutagenesis. The different patterns of residue–product interactions is the cause for the difference in the yields of two products.
The classification of LDA model essay based on information gain

In this paper the classification of short essay was improved based on LDA.The information gain of the essay with LDA classification method was put forward.Using the information gain calculation to calculate the text classification vocabulary contribution,to improve "function word" weight,and to filter out "the function word",at last the passage of the filtered was in the LDA theme modeling,and the center vector method was used to establish the text category model.The experimental results prove that with the reducing of function word ratio,classification performance is distinctly improved in the method.
Effect of CT image-based voxel size on EGSnrc Monte Carlo dose calculation

Empirical and semi-empirical routine dose calculation algorithms have been commonly selected for the radiation treatment planning system, though they have limited accuracy for dose distribution calculation. The Monte Carlo method can precisely give the above distributions, but its long CPU time affects clinic application. This paper presents a calculation instance. Namely, based on the CT data of a patient’s head and neck, the Monte Carlo code is used to investigate the effect of different voxel sizes on the accuracy of dose distribution calculation and the computing time.
Characterization of E coli Hfq structure and its RNA binding properties

iii To my family, for their constant love and support. iv ACKNOWLEDGEMENTS There are many people I would like to thank and acknowledge for their support and help during my five-year Ph.D. study. First and foremost, I would like to thank my advisor, Dr Roger Wartell, for his guidance and assistance throughout this chapter of my career. His constantly open door, scientific insight and perspective, and technical guidance have been integral to furthering my scientific education. He also provided knowledgeable recommendations and multi-faceted support in my personal life and bridged me to a culture which I have never experienced. Without him, it would be impossible to accomplish this thesis work. Spiro and Dr. Loren Williams for being on my thesis committee and helpful discussion in structural modeling. for readily helping me with using their fluorimeters, and Dr. Nicholas Hud and his student Swapan Jain for volunteering their time of showing me the RNA radio-labeling. On a personal note, I would like to express my appreciation to the many past and present colleagues in Atlanta and elsewhere, particularly and other fellows in Dr Wartell's lab for getting me through all of my Atlanta ordeals with helping hand and a friendly beverage. Finally I would like to thank my family for their eagerness to support me in any way they could. I can not begin to express the gratitude I have for my parents and siblings v because of their incredible love and support. With visits, emails, phone calls, and joyous holiday getting together, they have inspired and encouraged me in all of my accomplishments and taught me the value of dedication, hard work, patience and faith.
A Person-Centred Approach When Encountering Students With Recurrent Pain: School Nurses’ Experiences

Stress has a negative impact on students’ daily lives and can be associated with recurrent pain. School nurses play a key role in supporting young people with stress-related pain. The purpose of this qualitative interview study was to elucidate school nurses’ experiences of encountering students with recurrent pain when practicing person-centred care. The school nurses were based at public and private schools and worked with students aged 12-19. Data were collected through interviews with 18 school nurses and analyzed with deductive content analysis. The school nurses felt that actively listening to the students’ narratives about daily life with recurrent pain, and co-creation of a health plan, encouraged the students to participate as partners in their own care and strengthened their relation with the students. The application of a person-centred approach in school health care meant that traditional knowledge transfer was replaced with a dialogue that reflects both the student’s and school nurse’s perspective.
Validation of Sedentary Behavior Record Instrument as a Measure of Contextual Information of Sedentary Behavior.

BACKGROUND To establish evidence for the validity of the Sedentary Behavior Record (SBR) instrument using a criterion measure through a proxy of direct observation. METHODS A total of 27 study participants (aged ≥18 y; 15 male) participated in this study. Throughout a 4-day measurement period, each participant recorded their sedentary behavior using the SBR in 10-minute blocks every night. During the measurement period, participants also wore wearable Autographer cameras as a proxy for direct observation. Autographer data were aggregated into 10-minute intervals. To establish evidence of validity, contingency (C) and Kappa (K) coefficients were calculated between the SBR and the Autographer data. For C and K, agreements were determined between 2 measures every cell. The coefficient C was compared across domains, types, and time of day, and K was compared across types of day and times of day. RESULTS Overall, the coefficients C and K were acceptable (C = .70) and substantial (K = .64), respectively. Among all domains, the highest C was reported for work-related sitting (C = .87). Values of C ranged from . 49 to . 91 among all activities; the highest accuracy was for work-related, screen-based sitting. CONCLUSIONS This study suggests that the SBR is an acceptable self-report measure of sedentary behavior in adults.
Lindermyrrhin, a novel 3,4-dihydroisocoumarin from Lindera myrrha roots

Abstract A novel 3,4-dihydroisocoumarin, lindermyrrhin (1), along with three known compounds, quercetin (2), northalifoline (3) and N-formyl-laurolitsine (4) were isolated from the roots of Lindera myrrha. The structure of compound 1 was identified by interpretation of their spectroscopic data as well as comparison with those reported in the literature. The novel compound 1 represents the first 3,4-dihydroisocoumarin bearing a 2-hydroxyisopropyl substituent at C-3. Graphical Abstract
Enhanced web log based recommendation by personalized retrieval

With the rapid development of the Internet and WWW, it is more and more important for people to access quality web information. Thus the problem of enabling users to quickly and accurately find information has become an urgent issue. As one of the basic ways to solve this problem, personalized information services have been focusing on fulfilling the personalized information requirements of different users based on their actual demands, preference characteristics, behaviour patterns, etc. This thesis focuses on enhancing web log based recommendation by personalized retrieval, and its main works and innovations include: • For personalized retrieval, the thesis proposes two models to improve user experience and optimize search performance. The first is a query suggestion model based on query semantics and click-through data. This model calculates the subject relevance between queries, and then combines the semantic information and the relevance of the query-click matrix model as this can effectively eliminate the ambiguity and input errors of reminder queries. The second is a collaborative filtering retrieval model based on local and global features. By the integration of the local and global characteristics of the accessed information, this model overcomes the limitations of a single feature, and increases the degree of application of the retrieval model. • For recommendation by personalized retrieval, we propose two recommendation models based on the web log. The first is based on the user’s atomic retrieval transaction sequence and the browse characteristics. This model decomposes search transactions, and calculates the user’s degree of interest on the search term, which allows users to query information more clearly. Further, it incorporates the user feedback on the search results evaluation value, which overcomes the shortcomings of the model based on content filtering. The second model is based on user interests association findings, which can be used to: find the relationship between resources accessed by users, extract the associations of user interests, and address the problem of user interests isolation.