Miracle-dz/UniFAR-FTUs huggingface dataset:
Local DNA hypomethylation activates genes in rice endosperm

Cytosine methylation silences transposable elements in plants, vertebrates, and fungi but also regulates gene expression. Plant methylation is catalyzed by three families of enzymes, each with a preferred sequence context: CG, CHG (H = A, C, or T), and CHH, with CHH methylation targeted by the RNAi pathway. Arabidopsis thaliana endosperm, a placenta-like tissue that nourishes the embryo, is globally hypomethylated in the CG context while retaining high non-CG methylation. Global methylation dynamics in seeds of cereal crops that provide the bulk of human nutrition remain unknown. Here, we show that rice endosperm DNA is hypomethylated in all sequence contexts. Non-CG methylation is reduced evenly across the genome, whereas CG hypomethylation is localized. CHH methylation of small transposable elements is increased in embryos, suggesting that endosperm demethylation enhances transposon silencing. Genes preferentially expressed in endosperm, including those coding for major storage proteins and starch synthesizing enzymes, are frequently hypomethylated in endosperm, indicating that DNA methylation is a crucial regulator of rice endosperm biogenesis. Our data show that genome-wide reshaping of seed DNA methylation is conserved among angiosperms and has a profound effect on gene expression in cereal crops.
Peripapillary nerve fiber layer thickness measurement reproducibility using optical coherence tomography.

OBJECTIVE To assess reproducibility of quadrantic and clock hour sectors of retinal nerve fiber layer thickness in normal eyes using optical coherence tomography. MATERIALS AND METHODS Normal eyes of healthy volunteers meeting eligibility criteria were imaged by two inexperienced operators. Six 360 degrees circular scans with a diameter of 3.4 mm centered on the optic disc were obtained during each scanning session, and a baseline image was formed using 3 high-quality images defined by the software. Images were obtained on three different days within a 4-week period. Variance and coefficient of variation (CV) were calculated for quadrantic and retinal nerve fiber layer clock hour sectors obtained from the baseline image. RESULTS Five normal eyes were scanned. Intraoperator reproducibility was high. The mean (+/- SD) CV for total retinal nerve fiber layer thickness was 5.3 +/- 3.82% and 4.33 +/- 3.7% for operators 1 and 2, respectively. Interoperator reproducibility was good with statistically similar variance for all quadrantic and clock hour retinal nerve fiber layer parameters (P = .42 to .99). The nasal retinal nerve fiber layer was the most variable sector for both operators (mean CV: 10.42% and 7.83% for operators 1 and 2, respectively). Differences in mean total, nasal, temporal, and superior retinal nerve fiber layer thickness were not statistically significant between operators for all eyes; however, for inferior retinal nerve fiber layer thickness, there was a significant (P = .0007) difference between operators in one eye. CONCLUSION Peripapillary retinal nerve fiber layer thickness assessments using optical coherence tomography have good intraoperator and interoperator reproducibility. Inexperienced operators can generate useful measurement data with acceptable levels of variance.
Adoptive immunotherapy with vaccine-primed lymph node cells secondarily activated with anti-CD3 and interleukin-2.

PURPOSE In preclinical studies, we have reported the ability to induce immune T cells in lymph nodes (LN) primed by in vivo vaccination with tumor cells admixed with a bacterial adjuvant. These LN cells can be activated and expanded ex vivo for the successful immunotherapy of established tumors. We have applied these methods to generate vaccine-primed LN in patients with advanced melanoma and renal cell cancer (RCC) for therapy. MATERIALS AND METHODS Irradiated autologous tumor cells admixed with bacille Calmette-Guérin (BCG) were used to vaccinate patients. Seven days later, draining LN were removed for activation with anti-CD3 monoclonal antibody (mAb) followed by expansion in interleukin-2 (IL-2). Activated LN cells were administered intravenously (IV) with the concomitant administration of IL-2. RESULTS A total of 23 patients were evaluated (11 melanoma and 12 RCC). Vaccine-primed LN were expanded ex vivo with a mean of 8.4 x 10(10) cells administered per patient. Among 20 patients assessed, 15 demonstrated minimal cytotoxicity of autologous tumor cells by the activated LN cells, with the remaining mediating nonspecific cytotoxicity. By contrast, a majority of the activated LN cells showed highly specific release of granulocyte-macrophage colony-stimulating factor (GM-CSF) and interferon gamma (IFN-gamma) to autologous but not allogeneic tumor stimulation. This tumor-specific cytokine release was found to be major histocompatibility complex (MHC) class I-restricted, which indicates the involvement of CD8+ cells. Among 11 melanoma patients, one had a partial tumor response. Among 12 RCC patients, two had complete and two partial responses. A trend (P = .066) between the enhancement of delayed-type hypersensitivity (DTH) reactivity to autologous tumor after therapy and tumor regression was observed. CONCLUSION Tumor vaccines can be used to induce immunologically specific T-cell responses against melanoma and RCC in draining LN. Anti-CD3/IL-2 activation of primed LN cells can be reliably performed for clinical therapy and appears to have activity in patients with metastatic RCC.
Framework For Cost Modeling A Supply Chain

Researchers are interested in value chain analysis to identify the different opportunities for cost savings. The literature have been narrow in scope and addressed specific problems; however none has addressed the need for a general framework that can be used as a standard template in the supply chain cost management and optimization, though Dekker and Goor (2000) said that the goal was to develop a model that would allow direct comparison of specific activities between firms, such as warehousing activities costs. There was no indication in the literature of a cost model that can identify all costs and cost drivers through the supply chain. Some firms built models to analyze the effect of changes in activities but only with limited activities such as logistics. The purpose of this research is to create a general framework that can express the cost data for the partners of the supply chain in similar terms. The framework will layout the common activities identified within the firm and the relationship of these activities between the partners of the supply chain, and the framework will identify the effect of changes in activities on other partners within the supply chain. Cost information will help in making decisions about pricing, outsourcing, capital expenditures, and operational efficiency. The framework will be able to track cost through the chain, which will improve the flexibility of the supply chain to respond to rapidly changing technology. The framework
Choosing fertilization method by analyzing sperm morphology or by performing swim‐up preparation

Background. Evaluation of sperm morphology has been used as a screening method for choosing between intracytoplasmic sperm injection (ICSI) and conventional in vitro fertilization (IVF). However, sperm morphology analysis is a time‐consuming and often subjective scoring method, and may lead to an unnecessarily large proportion of invasive and costly ICSI treatments. The aim of this study was to evaluate if the yield after swim‐up preparation could be of advantage over sperm morphology evaluation for choosing fertilization method. Material and methods. In the first part of the study 53 split cycles with less than 5% normal forms in the ejaculate were retrospectively evaluated. Part 2 is a prospective evaluation including 357 cycles where the number of sperm available after a standardized swim‐up procedure was used for choosing fertilization method. In all cycles where ≤1 million sperm were obtained after swim‐up, conventional IVF was performed. Results. In the first part no statistically significant difference in fertilization rates was found for IVF and ICSI respectively (59.2% versus 64.7%). Four IVF cycles ended up in total fertilization failure (TFF) while in no ICSI cycle was TFF obtained. In the second part 8.9% TFF was obtained in the poor sperm morphology group compared to 1.3% in the good morphology group. These TFF corresponded to 1% of all our treatment cycles. Conclusion. The present strategy reduced ICSI treatments by 10%, thereby reducing the cost and workload. It can be discussed if an increase of TFF in absolute number of eight is balanced by a reduced workload of 100 ICSI treatments.
School Failure : An Exploratory Observational Study in Omani Schoolgirls

The objective of this study was to find the prevalence and psychosocial correlates of school failure among schoolgirls in Muscat and its suburbs in a randomly selected cohort of 708 girls from three state elementary schools (grades 1 –6). Students were examined with various parameters to elicit some of their behavioral, cognitive and social correlates of school failure. Socio-demographic information was sought from relevant sources. Objective assessment measures were administered to the subjects including Arabic versions of the short form of Conners’ Teacher Rating Scale (CTRS) to measure hyperactivity, and Raven’s Progressive Matrices (RPM) as a measure of intelligence. Previous years’ school performance data on all subjects were examined and those with a history of school failure (inability to pass the grades) were identified. In addition, the indices of all students’ performance in Arabic and Mathematics in the first semester were obtained. Based upon the above data, girls who scored 15 on CTRS constituted the hyperactive group; 5-8 points/12 in RPM represented average intelligence group, scores of < 50% in Arabic and/or Mathematics in the first semester were considered as the poor current semester performers, and the girls who failed one year or more during the previous years were constituted the “previously school failing” group. Approximately 23% (n=161) of the subjects had one year or more of school failures. The school-failure-group manifested more behavioral problems than the rest such as hyperactivity and aggression. Larger family size and lower parental education significantly predicted school failure. Indices of intellectual functioning among those with a history of school failure were comparatively lower than their consistently successful counterparts. The present study suggests that various psychosocial pathology other than mere lack of intelligence correlate with the observed high levels of school failure in Omani girls. These psychosocial correlates dovetail with previous studies conducted elsewhere, and need to be addressed for effective remedial interventions.
Depressed mononuclear leukocyte chemotaxis in thermally injured patients.

Microbial infection is the leading cause of morbidity and mortality in thermally injured patients. Since normal mononuclear leukocytes (MNL) function is essential in host defense, the chemotactic response of MNL from 25 thermally injured patients was evaluated in vitro. Patients with burns involving <20% total body surface had normal MNL chemotaxis, while MNL from patients with burns ≽20% had significantly depressed chemotaxis. This defect was most pronounced in patients with burns ≽40% and in those who died. Analysis of the data as a function of time revealed that patients who died generally had depressed chemotaxis immediately postburn and that their cells showed no functional improvement with time. In contrast, surviving patients with burns ≽40% initially had normal MNL chemotaxis which decreased significantly at approximately day 15 post burn, reached a nadir about day 45, and gradually returned to normal. Since the average burn size of these two groups was very similar, these data suggest that the early chemotactic response of MNL after a burn may be a predictive index of clinical outcome. Thirteen of the 25 patients developed infections and in all but one case depressed MNL chemotaxis preceded the septic event. Sera from patients with depressed MNL chemotaxis contained a cell-directed chemotactic inhibitor which was heat stable (56°C, 30 min), non-dialyzable and distinct from the sulfadiazine used for topical therapy. These studies document that depressed MNL chemotaxis occurs as a consequence of serious thermal trauma, that this defect may be due to a serum inhibitor and that abnormal MNL chemotaxis may contribute to septic morbidity and mortality in severely burned patients.
Basal forebrain neurons in the dementia of Parkinson disease

Demented patients with Parkinson disease share certain neuropathological and neurochemical features with patients suffering from Alzheimer disease. Recently, loss of cholinergic neurons in the basal forebrain, particularly the nucleus basalis of Meynert, has been implicated in the pathophysiology of Alzheimer disease. The present investigation of 12 patients with Parkinson disease demonstrates that the demented patients with this disease also show a selective loss of cells in the nucleus basalis of Meynert, thus providing an important link between the dementias of Alzheimer disease and Parkinson disease.
Employee Turnover Intentions in the Hospitality Industry

Employee Turnover Intentions in the Hospitality Industry by Bettye Holston-Okae EMBA, Texas Woman’s University, 2011 MS, Jackson State University, 2001 BS, Mississippi Valley State University, 1999 Doctoral Study Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Business Administration Walden University May 2017 Abstract Employee turnover is detrimental to organizational performance and profitability, leadingEmployee turnover is detrimental to organizational performance and profitability, leading to loss of diverse financial and intellectual resources and assets. Grounded in the motivation-hygiene theory, the purpose of this correlational study was to examine the relationship between employee turnover intention and job satisfaction, employee compensation, employee engagement, employee motivation, and work environment. The population consisted of lowto mid-level hospitality employees residing in Western Georgia, Central Mississippi, and North Central Texas, over the age of 18, and employed in the hospitality industry. A convenience sample of 156 participants completed the Compensation Scale, Job Satisfaction Scale, Utrecht Work Employee Engagement Scale, Work Extrinsic and Intrinsic Motivation Scale, Work Environment Scale, and Turnover Intention Scale via an online survey. Multiple linear regression analyses and Pearsonproduct correlation coefficients were used to predict employee turnover. The 5 predictors accounted for approximately 36% of the variance in turnover intention and the result was statistically significant, (R2 =.36, F (5, 105) = 11.57, p < . 001). The correlation between motivation and turnover intention was not significant. The findings may contribute to positive social change by increasing the potential to provide hospitality leaders with a foundation for future research on job satisfaction, employee compensation, employee engagement, employee motivation, work environment, and turnover intentions. These improvement may lead to the formulation of strategies and policies of business practices to reduce turnover intentions. Employee Turnover Intentions in the Hospitality Industry by Bettye Holston-Okae EMBA, Texas Woman’s University, 2011 MS, Jackson State University, 2001 BS, Mississippi Valley State University, 1999 Doctoral Study Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Business Administration
Dynamic module replacement in a distributed programming system

The replacement of parts of software systems is an important aspect of programming methodology. Most of the research in this area has centered around support for modular construction and the clear separation of interface from implementation. The emphasis has been on producing easily modified static program structures. With recent increased interest in distributed systems, attention has been focused on a class of applications for which this approach to modifiability is insufficient. These are applications involving long-running, distributed computations with long-term, on-line state information. In the context of the Argus programming system, we examine a method of supporting dynamic modification of software for this class of applications. We determine the appropriate granularity of replacement in relation to the module structure of the language, examine the constraints imposed on dynamic replacement by the need to ensure behavioral consistency across replacements, and then analyze functional requirements for a replacement mechanism.
A prescient recovery approach for disjoint MSNs

In Mobile Sensor Networks (MSNs), limited transmission range of the sensor nodes requires nodes to collaborate with each other in order to send their data to the Base Station (BS) which acts as a gateway between the network and the remote user. However, nodes may fail arbitrarily due to battery depletion, hardware malfunction, or an external damage. Such failures may partition the network into multiple disjoint segments isolated from the rest of the network. To restore network connectivity, network topology can be restructured by employing node mobility. However, mobility incurs excessive energy consumption and must be limited to avoid further failures and extend the network lifetime. In this paper, we present a distributed mobility-based approach to restore network connectivity while minimizing the movement cost as well as the number of nodes to be relocated. While determining the movement target, we consider the former locations of the upstream nodes but designate an alternative spot for movement to avoid possible risks caused the failure and to minimize the movement cost. The experiment results indicate that the proposed approach outperforms the approaches currently used in terms of total movement distance, maximum movement distance and the number of relocated nodes.
Engineering interchain disulfide bonds into conserved framework regions of Fv fragments: improved biochemical characteristics of recombinant immunotoxins containing disulfide-stabilized Fv.

Using molecular modeling technology, we have recently identified two positions in conserved framework regions of antibody Fv fragments (Fvs) that are distant from CDRs, and potentially can be used to make recombinant Fv fragments in which the unstable VH and VL heterodimer is stabilized by an interchain disulfide bond inserted between structurally conserved framework positions. A disulfide bond has been introduced at one of these positions, VH44-VL105, and shown to stabilize various Fvs that retain full binding and specificity. Recombinant immunotoxins, e.g. B3(dsFv)-PE38KDEL in which this disulfide-stabilized Fv moiety is connected to a truncated form of Pseudomonas exotoxin (PE; PE38KDEL) which contains the translocation and ADP ribosylation domains, are indistinguishable in binding and specificity from its single-chain immunotoxin counterparts. We have now analyzed the alternative position, (VH111-VL48), predicted by the modeling methodology, for disulfide stabilization of mAb B3(Fv) by producing a recombinant immunotoxin with such disulfide-stabilized (ds) Fv. This immunotoxin was also very active and retained full specificity to B3 antigen-positive cells. However, it was 2- to 3-fold less active than the VH44-VL105 dsFv-molecule. We also tested various biochemical features of VH44-VL105 and VH111-VL48 dsFv immunotoxins and compared them with the corresponding single-chain immunotoxin. We found the dsFv immunotoxins were more stable in human serum and more resistant to thermal and chemical denaturation than the single chain (sc) Fv immunotoxin. Because dsFv immunotoxins and dsFvs have full activity and specificity and improved stability, they may be more useful than scFv immunotoxins as therapeutic and diagnostic agents.
The Grammar of Graphics

Examples are discussed to show the differences among discriminant analysis, logistic regression, and multiple regression. Chapter 6, “Multivariate Analysis of Variance,” presents advantages of multivariate analysis of variance (MANOVA) over univariate analysis of variance (ANOVA), discusses assumptions of MANOVA, and assesses validations of MANOVA assumptions and model estimation. The authors also discuss post hoc tests of MANOVA and multivariate analysis of covariance. Chapter 7, “Conjoint Analysis,” explains what conjoint analysis does and how it is different from other multivariate techniques. Guidelines of selecting attributes, models, and methods of data collection are presented. Chapter 8, “Cluster Analysis,” studies objectives, roles, and limitations of cluster analysis. Two basic concepts: similarity and distance are discussed. The authors also discuss details of five most popular hierarchical algorithms (singlelinkage, complete-linkage, average-linkage, centroid method, Ward’s method) and three nonhierarchical algorithms (the sequential threshold method, the parallel threshold method, and the optimizing procedure). Profiles of clusters and guidelines for cluster validation are studied as well. Chapter 9, “Multidimensional Scaling and Correspondence Analysis,” introduces two interdependence techniques to display the relationships in the data. The book describes clearly and intuitively the differences between the two techniques and how these two techniques are performed. Chapters 10–12 cover topics in SEM. Chapter 10, “Structural Equation Modeling: An Introduction,” introduces SEM and related concepts such as exogenous, endogenous constructs, and so on, points out the differences between SEM and other multivariate techniques, overviews the decision process of SEM. Chapter 11, “Confirmatory Factor Analysis,” explains the differences between exploratory and confirmatory factor analysis, discusses how to construct, validate, and assess the goodness of fit of a measurement model in SEM by confirmatory factor analysis. Chapter 12, “Testing a Structural Model,” presents some methods of SEM in examining the relationships between latent constructs. The book is an excellent book for people in management and marketing. For the Technometrics audience, this book does not have much flavor of physical, chemical, and engineering sciences. For example, partial least squares, a very popular method in Chemometrics, is discussed but not as detailed as other techniques in the book. Furthermore, due to the amount of materials covered in the book, it might be inappropriate for someone who is new to multivariate analysis.
Wozu Kasusrektion auszeichnen bei Präpositionen?

Die Identifizierung von Kasus bei kasustragenden, deklinierbaren Wörtern (Pronomen, Artikel, Nomen, Adjektive) ist eine entscheidende Anforderung an die Sprachverarbeitung für flektierende Sprachen wie Deutsch. Neben grundlegenden syntaktischen Funktionen (Subjekte im Nominativ, Objekte im Akkusativ, Dativ oder Genitiv), welche vom Verb regiert werden und nominalen Modifikatoren im Genitiv sind Präpositionen mit ihren Rektionseigenschaften kasusbestimmend bzw. kasusregierend. Im folgenden Beispiel sind alle Präpositionen und alle kasustragenden Wörter mit entsprechenden Kasus-Tags markiert1: