Miracle-dz/UniFAR-FTUs huggingface dataset:
Telomeres, histone code, and DNA damage response

Genomic stability is maintained by telomeres, the end terminal structures that protect chromosomes from fusion or degradation. Shortening or loss of telomeric repeats or altered telomere chromatin structure is correlated with telomere dysfunction such as chromosome end-to-end associations that could lead to genomic instability and gene amplification. The structure at the end of telomeres is such that its DNA differs from DNA double strand breaks (DSBs) to avoid nonhomologous end-joining (NHEJ), which is accomplished by forming a unique higher order nucleoprotein structure. Telomeres are attached to the nuclear matrix and have a unique chromatin structure. Whether this special structure is maintained by specific chromatin changes is yet to be thoroughly investigated. Chromatin modifications implicated in transcriptional regulation are thought to be the result of a code on the histone proteins (histone code). This code, involving phosphorylation, acetylation, methylation, ubiquitylation, and sumoylation of histones, is believed to regulate chromatin accessibility either by disrupting chromatin contacts or by recruiting non-histone proteins to chromatin. The histone code in which distinct histone tail-protein interactions promote engagement may be the deciding factor for choosing specific DSB repair pathways. Recent evidence suggests that such mechanisms are involved in DNA damage detection and repair. Altered telomere chromatin structure has been linked to defective DNA damage response (DDR), and eukaryotic cells have evolved DDR mechanisms utilizing proficient DNA repair and cell cycle checkpoints in order to maintain genomic stability. Recent studies suggest that chromatin modifying factors play a critical role in the maintenance of genomic stability. This review will summarize the role of DNA damage repair proteins specifically ataxia-telangiectasia mutated (ATM) and its effectors and the telomere complex in maintaining genome stability.
Cross-media Retrieval by Learning Rich Semantic Embeddings of Multimedia

Cross-media retrieval aims at seeking the semantic association between different media types. Most existing methods paid much attention on learning mapping functions or finding the optimal spaces, but neglected how people accurately cognize images and texts. This paper proposes a brain inspired cross-media retrieval framework to learn rich semantic embeddings of multimedia. Different from directly using off-the-shelf image features, we combine the visual and descriptive senses for an image from the view of human perception via a joint model, called multi-sensory fusion network (MSFN). A topic model based TextNet maps texts into the same semantic space as images according to their shared ground truth labels. Moreover, in order to overcome the limitations of insufficient data for training neural networks and less complexity in text form, we introduce a large-scale image-text dataset, called Britannica dataset. Extensive experiments show the effectiveness of our framework for different lengths of texts on three benchmark datasets as well as Britannica dataset. Most of all, we report the best known average results of Img2Text and Text2Img compared with several state-of-the-art methods.
SUMO-1 Modification Regulates the DNA Binding Activity of Heat Shock Transcription Factor 2, a Promyelocytic Leukemia Nuclear Body Associated Transcription Factor*

Heat shock transcription factor 2 (HSF2) is a transcription factor that regulates heat shock protein gene expression, but the mechanisms regulating the function of this factor are unclear. Here we report that HSF2 is a substrate for modification by the ubiquitin-related protein SUMO-1 and that HSF2 colocalizes in cells with SUMO-1 in nuclear granules. Staining with anti-promyelocytic leukemia antibodies indicates that these HSF2-containing nuclear granules are PML bodies. Our results identify lysine 82 as the major site of SUMO-1 modification in HSF2, which is located in a “wing” within the DNA-binding domain of this protein. Interestingly, SUMO-1 modification of HSF2 results in conversion of this factor to the active DNA binding form. This is the first demonstration that SUMO-1 modification can directly alter the DNA binding ability of a transcription factor and reveals a new mechanism by which SUMO-1 modification can regulate protein function.
Assessment of the non-linear behaviour of plastic ankle foot orthoses by the finite element method

Abstract The stiffness characteristics of plastic ankle foot orthoses (AFOs) are studied through finite element modelling and stress analysis. Particular attention is given to the modelling and prediction of non-linear AFO behaviour, which has been frequently observed in previous experimental studies but not fully addressed analytically. Both large deformation effects and material non-linearity are included in the formulation and their individual influence on results assessed. The finite element program is subsequently applied to the simulation of a series of tests designed to investigate the relation between AFO trimline location and stiffness for moderate and large rotations. Through careful consideration and identification of key modelling parameters, the developed finite element solution proves to be a reliable and effective alternative means of assessing variations of a typical plastic AFO design so that particular patient requirements could be met, in the long term.
Temporal patterns of gene expression in developing maize endosperm identified through transcriptome sequencing

Significance In flowering plants, double fertilization gives rise to an embryo and the endosperm, an absorptive storage structure that supports embryogenesis and seedling germination. In cereal grains, endosperm comprises a large proportion of the mature seed, contains large amounts of carbohydrates and proteins, and is an important source of food, feed, and industrial raw materials. This study provides a comprehensive profile of the genes expressed in the early developing endosperm in maize. We also show how a series of temporal programs of gene expression correlate with progressive functional and cellular specializations. Endosperm is a filial structure resulting from a second fertilization event in angiosperms. As an absorptive storage organ, endosperm plays an essential role in support of embryo development and seedling germination. The accumulation of carbohydrate and protein storage products in cereal endosperm provides humanity with a major portion of its food, feed, and renewable resources. Little is known regarding the regulatory gene networks controlling endosperm proliferation and differentiation. As a first step toward understanding these networks, we profiled all mRNAs in the maize kernel and endosperm at eight successive stages during the first 12 d after pollination. Analysis of these gene sets identified temporal programs of gene expression, including hundreds of transcription-factor genes. We found a close correlation of the sequentially expressed gene sets with distinct cellular and metabolic programs in distinct compartments of the developing endosperm. The results constitute a preliminary atlas of spatiotemporal patterns of endosperm gene expression in support of future efforts for understanding the underlying mechanisms that control seed yield and quality.
Risk of aortic aneurysm surgery as assessed by preoperative gated heart pool scan

Gated heart pool scan measuring left ventricular ejection fraction (LVEF) was performed preoperatively in 72 patients presenting for elective repair of abdominal aortic aneurysm. Patients with a positive cardiac history were more likely to have a LVEF of ⩽45 per cent (P < 0·001). The operative mortality rate was 4 per cent. Each of three patients who died had a LVEF ⩽35 per cent and developed cardiac failure which led to renal failure. Five other patients developed cardiac failure manifested by acute pulmonary oedema during the early postoperative period. There was no statistically significant association between a positive cardiac history and the occurrence of postoperative cardiac failure or death. However, patients with a LVEF of ⩽45 per cent were more likely to develop postoperative cardiac failure (P = 0·004) while patients with a LVEF of >35 per cent had a greater chance of dying (P < 0·001). No patient died with a LVEF > 35 per cent. Preoperative evaluation of LVEF can select patients at high risk of cardiac death from repair of abdominal aortic aneurysm. Such patients could be followed conservatively if they remain asymptomatic and the aneurysm does not enlarge. If operation is considered mandatory, patients with a low LVEF should receive intensive perioperative monitoring with enhancement of ventricular performance.
Phonemic priming in the lexical decision task : Evidence for graphemic dependence

Length TP date Supervisor x Effective date ^987 Telephone number (^5) 572"* 1684 MASTERS DEGREE DATA 5. Full name of University conferring degree Rice M* A* 6. Abbreviation for degree awarded University 7. Date degree awarded 3785 TITLE DATA 8. Title of thesis exactly as it appears on title page and abstract (Please attach a copy of your title page.) Phonemic priming in the lexical decision task: 9. Subject categ&J^à^9^feiLC^£â^fe^if(0//jfêffl§i}â(^Ç lce Main Field y°gy Sub Field Experimental COPYRIGHT DÀTA 10. If your thesis has been previously published, please enter here the copyright notice as it appeared in the published edition. PAGING Preliminary Text Unnumbered TOTAL PAGES. Remarks: 11. Please file, on my behalf, an application for registration of a claim of U.S. copyright in my thesis as outlined in the Copyright Authorization Section on the reverse side of the agreement form. a. yes fefno^ (Circle one) If you answer YES, please complete Items 12-14 and sign the authorization section on the reverse side of the agreement form. 12. Year thesis was completed 13. Has registration for your unpublished thesis, or for an èarlier version of the thesis been made with the Copyricht Office? a. yes If yes, by whom? (Circle one) Previous registration number Year 14.1 authorize University Microfilms International to act on my behalf and grant to the Library of Congress nonexclusive permission to reproduce and distribute copies of my thesis solely for the use of the blind and physically tyatyücapped. (See Item 14 on Agreement Form Instructio If yes, sign here. “(Author’s Sigriatu Please check the method of reproduction you are authorizing. Phonorecords only aille (or similar tactile symbols) copies only_ Braille copies and phonorecords REPRINTS 15. Please send me reprints of my abstract. (Minimum order 100 copies) First set of 100 $20.00 Additional sets of 100 @ $5.00 each set Enclosed please find my check for Please Note: Reprints are not mailed until the abstract appears in Masters Abstracts, which is generally four months after we receive the material from your graduate school.
Danish research-active clinical nurses overcome barriers in research utilization.

AIM The aim of this study was to examine whether there was a difference between clinical nurses who were research-active, and clinical nurses who were nonresearch-active in utilization of research. A further aim was to identify the most significant barriers faced by a group of Danish clinical nurses in their use of research. BACKGROUND Discrepancy between the improved quality of research results and the lack of implementing them was the starting point for a series of studies which showed the types of barriers clinical nurses found especially cumbersome when applying the research results of other researchers. This study investigates whether the clinical nurses' own engagement in research had any impact on their perception of research utilization. METHODOLOGY The study had an exploratory and descriptive design. Seventy-nine Danish clinical nurses participated and semi-structured interviewing was used as the research method. FINDINGS There was a statistically significant difference between the research-active and nonresearch-active nurses on various variables. The study showed that, to a larger extent, research-active nurses used evidence-based knowledge and were generally more internationally orientated. Furthermore, two important barriers for research utilization were identified by all 79 clinical nurses included in the study, i.e. 90% of the nurses explained that the quantity of research results was overwhelming, and 75% of them found that they were unable to evaluate the quality of the research. CONCLUSIONS Clinical nurses, who were research-active themselves, experienced more success in overcoming some of the barriers, which existed in applying research to practice. The research potential found amongst clinical nurses in Denmark needed to be further supported through training and guidance in research methodology, establishing introductory stipends and part-time research positions. By doing so, some of the barriers affecting research utilization and the so-called theory-practice gap might be reduced. Further empirical studies, based on Giddens theory of sociological reflectivity, might see clinical nurses in a more serious light and simultaneously perceive them as producers of knowledge.
Application of induction heating processes of metal deformation

The paper considers the problem of design and operation of the induction heating system, which includes an induction heating unit (INU), a power supply and electronic control system and is intended for heating metal under deformation. Moreover, the INU is considered in a single complex with equipment for metal pressure treatment (OMD) with the aim of obtaining extreme process and economic indicators of operation of the process complex as a whole. The focus is on the study of deformation of aluminum and its alloys. The paper discusses the most common types of hot deformation — pressing and rolling. Moreover, in the latter case, electric, vibration and acoustic processes are considered simultaneously with electromagnetic and thermal ones. In this case, the emphasis is on power supply of powerful heating complexes enabling rolling and extrusion of large workpieces at 50 Hz INU operating frequency. All theoretical conclusions have been confirmed by experiments at full-scale equipment; physical simulation occurred at 2500 Hz. In relation to continuous operation of INU various designs with discrete and continuous advancement of the blanks, the algorithm provides an optimal control in a standard mode, a maximum productivity and minimum total loss rate for a stationary and transient operation mode of the heating-deformation process respectively.
Early-stage glottic cancer: oncological results and margins in laser cordectomy.

OBJECTIVES To assess local control of early-stage glottic cancer by laser cordectomy in comparison with previously published external partial laryngectomy series and to determine the relevance of histological margins in glottic cancers excised with laser cordectomy. DESIGN Retrospective review of laser cordectomy for carcinoma in situ (Tis) and stage T1 glottic cancer from January 1991 to January 2004. SETTING University hospital. PATIENTS Fifty-two patients with Tis or T1 glottic cancer. INTERVENTION Endoscopic laser cordectomy, classified using the system proposed by the European Laryngeal Society Working Committee. MAIN OUTCOME MEASURES Local control after initial surgery and after salvage compared with a published historical control group, according to the type of cordectomy performed and the histological margins of the removed specimen. RESULTS Sixteen patients with Tis, 30 with T1a tumors, and 6 with T1b tumors were followed up for an average of 38 months. Type I cordectomy was the most common procedure used to treat Tis, and type II and type III were the most common for treating T1a and T1b tumors. Of 6 recurrences, 4 were treated with laser cordectomy and 2 were treated with external partial laryngectomy. The rate of laryngeal preservation was 100%. There were 3 recurrences despite histologically clear margins. Three (17%) of 18 patients with suspicious margins developed recurrences. The rate of local control with single intervention (46 [89%] of 52) was lower than with partial external laryngectomy. However, 46 (89%) of 52 patients ultimately had less tissue removed by laser than would have been removed by external partial laryngectomy. CONCLUSIONS Laser cordectomy provides excellent local control and laryngeal preservation. Close follow-up of patients with positive or suspicious margins is an alternative to further routine treatment.
A portable device for intercepting and retransmission of infrared modulated signals

Infrared modulated signals are widely used in remote controls of common household appliances, as well as in business and public places. However, the transmission is not encrypted in any form, and can easily be intercepted and stored for future control of the appliance. This paper explains the functioning of a portable device which can intercept infrared (IR) signals and retransmit them when needed. The device was designed to include multiple functions, have a small number of buttons, and also to be portable, making it a functional keyring. As an added feature, the device can emit an infrared jamming signal, disabling any other user's commands. Finally, we created a small, low power, reliable device that can easily duplicate infrared codes. This makes the device a portable IR security penetration tool that can take over an appliance or disable its remote control.
Modeling Stock Market Volatility in Emerging Markets: Evidence from India

This study models the volatility present in the inter day returns in the stock of the two major national indices of India. Sensitive Index or Sensex related to Bombay Stock Exchange (BSE) and Nifty associated with National Stock Exchange (NSE). The objective is to model the phenomena of volatility clustering and persistence of shock using asymmetric GARCH family of models. Research showed that EGARCH model successfully models the Sensex (BSE) data whereas it is GJR-GARCH which was able to explain conditional variance in the returns from Nifty (NSE).
Improvement in Liver Histology Is Associated With Reduction in Dyslipidemia in Children With Nonalcoholic Fatty Liver Disease

Objectives: Nonalcoholic fatty liver disease (NAFLD), the most common cause of liver disease among US children, may be associated with cardiovascular disease (CVD) risk. The present study sought to determine the prevalence of dyslipidemia in children with NAFLD and assess dyslipidemia by liver histology and histologic changes. Methods: Individuals in the Treatment of NAFLD in Children (TONIC) trial were included (N = 173). In the TONIC trial, children with NAFLD were randomized to vitamin E, metformin, or placebo for 96 weeks. Nonalcoholic steatohepatitis (NASH) improved in 56 children. Change in lipid levels from baseline and 96 weeks was compared between patients with and without histologic improvement and with and without NASH. Results: Dyslipidemia was frequent, with low high-density lipoprotein (HDL) (<40 mg/dL) in 61.8%, hypertriglyceridemia (≥130 mg/dL) in 50.3%, hypercholesterolemia (≥200 mg/dL) in 23.7%, elevated low-density lipoprotein (LDL) (≥130 mg/dL) in 21.5%, elevated non-HDL cholesterol (non-HDL-C) (≥145 mg/dL) in 35.2%, and triglycerides/HDL >3.0 in 57.2% of patients. Histologic improvement was associated with significant decreases in cholesterol (−11.4 mg/dL vs −1.9 mg/dL, P = 0.04), LDL (−11.2 mg/dL vs −2.1 mg/dL, P = 0.04), and non-HDL-C (−8.8 mg/dL vs 0.5 mg/dL, P = 0.03) compared with those without improvement. Children with NASH resolution had significant decreases in cholesterol (−10.0 mg/dL vs −0.9 mg/dL, P = 0.02) and non-HDL-C (−7.3 mg/dL vs 1.1 mg/dL, P = 0.01) compared with those without NASH resolution. There was no improvement in triglycerides, HDL level, or triglycerides/HDL ratio in either group. Conclusions: Dyslipidemia is frequent in children with NAFLD. NASH resolution and histologic improvement are associated with improvements in some forms of dyslipidemia.
Neuromechanical adaptations during a robotic powered exoskeleton assisted walking session

Objective: To evaluate gait parameters and neuromuscular profiles of exoskeleton-assisted walking under Max Assist condition during a single-session for; (i) able bodied (AB) individuals walking assisted with (EXO) and without (non-EXO) a powered exoskeleton, (ii) non-ambulatory SCI individuals walking assisted with a powered exoskeleton. Design: Single-session. Setting: Motion analysis laboratory. Participants: Four AB individuals and four individuals with SCI. Interventions: Powered lower extremity exoskeleton. Outcome Measures: Temporal-spatial parameters, kinematics, walking velocity and electromyography data. Results: AB individuals in exoskeleton showed greater stance time and a significant reduction in walking velocity (P < 0.05) compared to non-EXO walking. Interestingly, when the AB individuals voluntarily assisted the exoskeleton movements, they walked with an increased velocity and lowered stance time to resemble that of slow walking. For SCI individuals, mean percent stance time was higher and walking velocity was lower compared to all AB walking conditions (P < 0.05). There was muscle activation in several lower limb muscles for SCI group. For AB individuals, there were similarities among EXO and non-EXO walking conditions however there were differences in several lower limb EMGs for phasing of muscle activation. Conclusion: The data suggests that our AB individuals experienced reduction in walking velocity and muscle activation amplitudes while walking in the exoskeleton and moreover with voluntary control there is a greater temporal-spatial response of the lower limbs. Also, there are neuromuscular phasic adaptions for both AB and SCI groups while walking in the exoskeleton that are inconsistent to non-EXO gait muscle activation.
Cytokine concentrations in bronchoalveolar lavage fluid of patients with systemic sclerosis.

OBJECTIVE The pathophysiology of pulmonary fibrosis in patients with systemic sclerosis (SSc) is poorly understood, but a number of recent studies have demonstrated an inflammatory process involving the lower respiratory tract. The objective of the present study was to determine the concentrations of several cytokines in the bronchoalveolar lavage (BAL) fluid of patients with SSc and to assess whether the enhanced expression of certain cytokines is associated with the presence of alveolitis. METHODS BAL was performed on patients with SSc (with or without alveolitis) and on normal control subjects. Lyophilized BAL fluid samples were assayed by enzyme-linked immunosorbent assay for tumor necrosis factor alpha (TNF alpha), interleukin-1alpha (IL-1alpha), IL-4, IL-6, IL-8, macrophage inflammatory protein 1alpha (MIP-1alpha), and RANTES. RESULTS There were significant differences between groups in the BAL fluid concentrations of TNF alpha (P = 0.0005, with levels in SSc patients with alveolitis higher than those in normal controls), IL-8 (P = 0.006, with levels in both SSc groups higher than those in normal controls), MIP-1alpha (P = 0.009, with levels in SSc patients with alveolitis higher than those in SSc patients without alveolitis and than those in normal controls), and RANTES (P = 0.03, with levels in SSc patients without alveolitis higher than those in normal controls). With the exception of RANTES, the highest levels were detected in SSc patients with alveolitis. CONCLUSION Each of these cytokines, either alone or in combination, may play an important role in the pathogenesis of pulmonary fibrosis in SSc.