Miracle-dz/UniFAR-FTUs huggingface dataset:
Altered Patterns of Gene Expression Underlying the Enhanced Immunogenicity of Radiation-Attenuated Schistosomes

Background Schistosome cercariae only elicit high levels of protective immunity against a challenge infection if they are optimally attenuated by exposure to ionising radiation that truncates their migration in the lungs. However, the underlying molecular mechanisms responsible for the altered phenotype of the irradiated parasite that primes for protection have yet to be identified. Methodology/Principal Findings We have used a custom microarray comprising probes derived from lung-stage parasites to compare patterns of gene expression in schistosomula derived from normal and irradiated cercariae. These were transformed in vitro and cultured for four, seven, and ten days to correspond in development to the priming parasites, before RNA extraction. At these late times after the radiation insult, transcript suppression was the principal feature of the irradiated larvae. Individual gene analysis revealed that only seven were significantly down-regulated in the irradiated versus normal larvae at the three time-points; notably, four of the protein products are present in the tegument or associated with its membranes, perhaps indicating a perturbed function. Grouping of transcripts using Gene Ontology (GO) and subsequent Gene Set Enrichment Analysis (GSEA) proved more informative in teasing out subtle differences. Deficiencies in signalling pathways involving G-protein–coupled receptors suggest the parasite is less able to sense its environment. Reduction of cytoskeleton transcripts could indicate compromised structure which, coupled with a paucity of neuroreceptor transcripts, may mean the parasite is also unable to respond correctly to external stimuli. Conclusions/Significance The transcriptional differences observed are concordant with the known extended transit of attenuated parasites through skin-draining lymph nodes and the lungs: prolonged priming of the immune system by the parasite, rather than over-expression of novel antigens, could thus explain the efficacy of the irradiated vaccine.
Constructing Quasi-Cyclic LDPC codes Using a Search Algorithm

This article presents a search algorithm for constructing regular and irregular quasi-cyclic LDPC codes. Code rows and columns are divided into j (column weight) and k (row-weight) or more groups respectively. Rows or columns in a group are connected to the same group and in order of appearance. Grouping of rows and columns forms sub-matrices. The sequential row-column connections order creates a cyclic structure in sub-matrices. The row-column constraint is observed to avoid four-cycles. The proposed algorithm is flexible compared to other methods. It obtains codes over a wide range of girths, rates and lengths. Bit-error rate simulations show that obtained codes have good performance with randomly searched codes performing better that sequentially searched codes.
Multi-Level Support With Respect to Inquiry, Explanations and Regulation During an Inquiry Cycle

Engaging students in inquiry learning without sufficient support often results in poor learning performance. Students need to be supported to benefit from inquiry learning activities (de Jong, 2006; Hmelo-Silver, Duncan, & Chinn, 2007). The main goal of this work is to investigate the effects of supporting regulation using prompts on learning gain and scientific reasoning in a computer-based inquiry learning context offering advanced inquiry support. Does learning gain depend on the extent of inquiry support? Are regulation prompts (e.g. “Compare your result graph with your hypothesis. Are they different from each other? ”) superior in comparison to generic explanation prompts (e.g. “please explain”) with respect to knowledge gain and scientific reasoning? Do students benefit from those additional regulation prompts sustainably? Before these questions were addressed in two experimental studies, an exploratory study revealed problems to engage in (1) deliberate regulation and (2) a tendency to write descriptive explanations lacking scientific reasoning while running experiments in an inquiry cycle. The model-based environment FreeStyler (Hoppe & Gassner, 2002) was adapted to guide a learner through the respective phases of an inquiry cycle and to offer prompts. Results of the main experimental study were able to confirm findings from the pilot study showing an advantage for the regulation group (students receiving regulation prompts) in comparison to the explanation group (students receiving explanation prompts only) with respect to knowledge gain. In addition, it was shown that the regulation group outperformed a basic inquiry group that served as a baseline receiving minimal support in terms of inquiry and no support with respect to explanation and regulation. Moreover, the sustainability of this effect was demonstrated. It was shown that prompts are effective means leading to deeper processing and that explanation prompts should be augmented with regulation prompts. Findings suggest in general that in order to engage learners in inquiry learning, a balance between inquiry support, explanation support, and regulation support is needed.
Network-based virtual personal overlay networks using programmable virtual routers

This article explores the use and adaptation of well established VPN technologies to dynamically network at run time devices and services in personal networks. Virtual personal overlay networks are envisaged as an extension of the basic VPN concept to network PN nodes in a secure manner. User managed and provider provisioned-based overlays are analyzed in terms of scalability, management complexity, and security to select the most appropriate VPON deployment and management framework. The dynamic nature of PNs calls for highly flexible self-configuring and self-adaptive VPON architectures. Programmable edge routers and dynamic tunneling mechanisms can be combined to meet the requirements set by PNs. The virtual router model is used in the provider edge to ease the dynamic deployment and management of VPONs. Results of an implementation and a performance evaluation of the VR concept based on open software routers are reported.
Implicit measures of environmental attitudes: a comparative study

The present investigation aims to inquire about the capacity of three implicit instruments to measure the attitude toward natural and urban environments. One hundred and three students from a Mexican public university participated in the investigation. The implicit instruments used were the affective priming technique, the implicit association test, and the affect misattribution procedure. Further, an explicit scale was used for comparison. The results showed that all instruments converge in the same way; the nature images were viewed as more pleasant compared to the city images. Also, most results indicated good effect size values, observed power, and reliability, with the exception of the affective priming technique, which established low values. In addition, all instruments indicated weak correlations between each other. The results were discussed in terms of the capacity of the instruments to measure environmental attitudes, and also possible theoretical and methodological implications.
Serum Protein Signatures Differentiating Autoimmune Pancreatitis versus Pancreatic Cancer

Autoimmune pancreatitis (AIP) is defined by characteristic lymphoplasmacytic infiltrate, ductal strictures and a pancreatic enlargement or mass that can mimic pancreatic cancer (PaCa). The distinction between this benign disease and pancreatic cancer can be challenging. However, an accurate diagnosis may pre-empt the misdiagnosis of cancer, allowing the appropriate medical treatment of AIP and, consequently, decreasing the number of unnecessary pancreatic resections. Mass spectrometry (MS) and two-dimensional differential gel electrophoresis (2D-DIGE) have been applied to analyse serum protein alterations associated with AIP and PaCa, and to identify protein signatures indicative of the diseases. Patients' sera were immunodepleted from the 20 most prominent serum proteins prior to further 2D-DIGE and image analysis. The identity of the most-discriminatory proteins detected, was performed by MS and ELISAs were applied to confirm their expression. Serum profiling data analysis with 2D-DIGE revealed 39 protein peaks able to discriminate between AIP and PaCa. Proteins were purified and further analysed by MALDI-TOF-MS. Peptide mass fingerprinting led to identification of eleven proteins. Among them apolipoprotein A-I, apolipoprotein A-II, transthyretin, and tetranectin were identified and found as 3.0-, 3.5-, 2-, and 1.6-fold decreased in PaCa sera, respectively, whereas haptoglobin and apolipoprotein E were found to be 3.8- and 1.6-fold elevated in PaCa sera. With the exception of haptoglobin the ELISA results of the identified proteins confirmed the 2D-DIGE image analysis characteristics. Integration of the identified serum proteins as AIP markers may have considerable potential to provide additional information for the diagnosis of AIP to choose the appropriate treatment.
Experimental Models of Renal Disease and the Cardiovascular System

Cardiovascular disease is a leading cause of death among patients with end stage renal failure. Animal models have played a crucial role in teasing apart the complex pathological processes involved. This review discusses the principles of using animal models, the history of their use in the study of renal hypertension, the controversies arising from experimental models of non-hypertensive uraemic cardiomyopathy and the lessons learned from these models, and highlights important areas of future research in this field, including de novo cardiomyopathy secondary to renal transplantation.
The moderating effects of perceived threat to valued job features on career commitment among university professors

This article studies the relationships between perceptions of threats to valued job features, total job (job insecurity), and career commitment among university professors, using the context of post-tenure review policy. It surveys professors from a randomly selected sample of 74 universities that have implemented post-tenure review policies and processes and analyzes their responses using structural equation methods. It tests hypotheses about relationships between perceptions of threats to job features, the total job as a result of post-tenure review policy, and career commitment. It finds that when post-tenure review is perceived as a threat to valued job features such as job autonomy and the total job, it negatively affects measures of affective, continuance, and normative career commitments. The implications of these findings for university administrators, regents, and boards of governors contemplating the development and implementation of post-tenure review policies are discussed.
Laryngeal verrucous carcinoma: A clinicopathologic study and detection of human papillomavirus using polymerase chain reaction

Laryngeal verrucous carcinoma (LVC) is a rare, well‐differentiated variant of squamous carcinoma with a low malignant potential. Human papillomavirus (HPV)–16 DNA has been identified in a small number of LVC and an etiologic relationship has been suggested. A correlative clinical and molecular pathological study was performed in order to determine the prevalence and typing of HPV DNA in LVC. Possible associations between patient and tumor subsets, and the presence of HPV DNA were also investigated. Formalin‐fixed, paraffin‐embedded tissue samples from 29 patients with LVC were examined by polymerase chain reaction (PCR) using DNA primers specific for HPV types 6b/11, 16, and 18. Overall, HPVDNA was detected in 13 (45%) of the cases. Of these, HPV‐16 DNA, HPV‐18 DNA, and both HPV‐16 DNA and HPV‐18 DNA were detected in 4 (14% overall; 31% of positive cases), 4, and 5 (17% overall; 38% of positive cases), respectively. HPV‐6b/11 DNA was not detected in any LVCs. In 16 cases, no HPV DNA was detected. There was a trend toward HPV DNA detection in higher stage tumors. HPV DNA detection was unrelated to patient age, tumor site, or radiotherapeutic responsiveness. The detection of HPV DNA in 45% of LVCs suggests an association between the presence of HPV‐16 DNA and HPV‐18 DNA, and some LVCs.
Exploring articulation in internal activism and public relations theory: A case study

ABSTRACT This paper answers Dozier and Lauzen’s (2000) call for critical theoretical examinations of activism and public relations to provide new perspectives and avoid the paradox inherent in organizational-level analyses. It also fills a literature gap by examining a case of internal activism, Girl Scout members protesting the use of palm oil in Girl Scout cookies, thus blurring organizational boundaries and rejecting Us/Other dichotomies. The basic precepts of the cultural-economic model (Curtin & Gaither, 2005, 2007) are expanded to provide greater heuristic power to the model (Curtin, Gaither, & Ciszek) and to delineate a more nuanced understanding of the public relations/activism relationship.
Dyrk1A Overexpression Inhibits Proliferation and Induces Premature Neuronal Differentiation of Neural Progenitor Cells

Dyrk1A is a member of the mammalian Dyrk [dual-specificity tyrosine-(Y)-phosphorylation regulated kinase] family of protein kinases that is expressed at high levels in the brain, but its role in the development and function of this organ is not well understood. The human DYRK1A gene is located on trisomic chromosome 21 in Down syndrome (DS) patients, leading to its overexpression. Dyrk1A is also overexpressed in animal models of DS and in gene-specific transgenic mice that consistently exhibit cognitive impairment. To elucidate the cellular and molecular mechanisms that are affected by increased levels of Dyrk1A in the developing brain, we overexpressed this kinase in the embryonic mouse neocortex using the in utero electroporation technique. We found that Dyrk1A overexpression inhibits neural cell proliferation and promotes premature neuronal differentiation in the developing cerebral cortex without affecting cell fate and layer positioning. These effects are dependent on the Dyrk1A kinase activity and are mediated by the nuclear export and degradation of cyclin D1. This study identifies specific Dyrk1A-induced mechanisms that disrupt the normal process of corticogenesis and possibly contribute to cognitive impairment observed in DS patients and animal models.
The phonetics of hyper-active feet: Effects of stress priming on speech planning and production

This study employs a stress priming paradigm to investigate sensitivity to metrical structure in speech planning and production in Australian English. Target words with iambic stress were preceded by primes with either congruent or incongruent stress and also embedded in metrical contexts biased towards either persistent foot types (Experiment 1) or variable foot types (Experiment 2). Both naming latency, the time from stimulus presentation to the onset of speech, and phonetic patterns showed sensitivity to metrical manipulations. The paradigm produced stress errors, iambic targets produced as trochees, and variation in vowel formants and syllable duration as a function of metrical context. Patterns in the reaction time data indicated sensitivity to global metrical biases calculated over feet. When the metrical bias was toward persistent feet, iambs were pro- duced more quickly in the congruent stress context. When the metrical bias was reversed, iambs were produced more quickly in the incongruent stress context. This pattern of results supports a speech production model that represents metri- cal structure and allows competition at the metrical level to influence phonetic variability.
Loss of tumor suppressors KAI1 and p27 identifies a unique subgroup of primary melanoma patients with poor prognosis

Primary melanoma, a highly aggressive malignancy, exhibits heterogeneity in biologic behaviors, clinical characteristics, metastasis potential and mortality. The present study sought to identify the molecular signatures that define a subgroup of primary melanomas with high risks of metastasis and mortality. First, we identified the markers that best differentiated metastatic melanomas from primary melanomas by examining the expression of seven previously reported biomarkers (BRAF, Dicer, Fbw7, KAI1, MMP2, p27 and Tip60) in a training cohort consisting of 145 primary melanomas and 105 metastatic melanomas. KAI1 and p27, both tumor suppressors, emerged as best candidates. Loss of both tumor suppressors occurred in the majority (74.29%) of metastatic melanomas. Further, a subset (metastatic like, or “ML”, 33.10%) of primary melanomas also lost these two tumor suppressors. Kaplan-Meier analysis indicated that ML subgroup of primary melanoma patients had much worse 5 year survival compared with other primary melanoma patients (P = 0.002). The result was confirmed in an independent validation cohort with 92 primary melanomas (P = 0.030) and in the combined cohort with 237 melanoma patients (P = 3.00E-4). Additionally, compared to KAI1 and p27 as an individual prognostic marker, the combined signature is more closely associated with melanoma patient survival (P = 0.025, 0.264 and 0.009, respectively). In conclusion, loss of both KAI1 and p27 defines a subgroup of primary melanoma patients with poor prognosis. This molecular signature may help in metastatic melanoma diagnosis and may provide information useful in identifying high-risk primary melanoma patients for more intensive clinical surveillance in the future.
((Re)Gendering Panic: Towards a Critical Sociology of Agoraphobia

Since 1871, when the first psychiatric article on agoraphobia was published, this disease—known variously as panic, panic disorder, agoraphobia with or without panic, and so forth—has had a curious trajectory: beginning with a marked prevalence in men that lasted roughly five decades, the disease was ‘re-gendered’ after the First World War and has persisted as a predominantly female problem ever since. Using the method of discourse analysis and working from the premise that psychiatry is shaped by factors beyond medicine, this paper examines psychiatric reports of agoraphobia since the late nineteenth century to argue that the history of this disease represents more than simply that of an individual psychological/biological disease phenomenon. Rather, it is important to understand agoraphobia in the context of the complex normative social and historical process of its re-gendering.
Links between metabolic plasticity and functional redundancy in freshwater bacterioplankton communities

Metabolic plasticity and functional redundancy are fundamental properties of microbial communities, which shape their response to environmental forcing, and also mediate the relationship between community composition and function. Yet, the actual quantification of these emergent community properties has been elusive, and we thus do not know how they vary across bacterial communities, and their relationship to environmental gradients and to each other. Here we present an experimental framework that allows us to simultaneously quantify metabolic plasticity and functional redundancy in freshwater bacterioplankton communities, and to explore connections that may exists between them. We define metabolic plasticity as the rate of change in single-cell properties (cell wall integrity, cell size, single-cell activity) relative to changes in community composition. Likewise, we define functional redundancy as the rate of change in carbon substrate uptake capacities relative to changes in community composition. We assessed these two key community attributes in transplant experiments where bacterioplankton from various aquatic habitats within the same watershed were transplanted from their original water to waters from other systems that differ in their main resources. Our results show that metabolic plasticity is an intrinsic property of bacterial communities, whereas the expression of functional redundancy appears to be more dependent on environmental factors. Furthermore, there was an overall strong positive relationship between the level of functional redundancy and of metabolic plasticity, suggesting no trade-offs between these community attributes but rather a possible co-selection. The apparent continuum in the expression of both functional redundancy and plasticity among bacterial communities and the link between them, in turn suggest that the link between community diversity and function may also vary along a continuum, from being very tight, to being weak, or absent.
Being patient : exploring experiences of, and responses to, social constructions of patient-hood

BEING PATIENT: EXPLORING EXPERIENCING OF AND RESPONSES TO SOCIAL CONSTRUCTIONS OF PATIENT-HOOD The term "patient" is widely used within public and nursing domains. Arguably, the word is assumed to have common meaning across all disciplines. But is this the case? Does the word-label patient contain implicit assumptions and values? What social, political and professional constructions of patient-hood exist? How do people in the position of patient experience and respond to these images? For example, nursing research confirms that nurses actively construct patients based on such characteristics as income, age, gender and social position and that, on the basis of these and similar criteria, nurses make decisions about the worth of individuals and act, in various ways, on those judgments. While this phenomenon has been well-studied, little work has been done to explore how patients experience and respond to popular constructions of patient-hood. In this study, I sought to shift attention away from the dominant discourse of professional perspectives and toward examination of these issues from an emic view ~ that of patients. Using interpretive description, I invited seven people with varying degrees of experience within the health care system to discuss their experiences while in the position of patient. Through this analysis I offer an expanded understanding of how the role of patient is both experienced and responded to. People in the position of patient experience constant threats to self and to personal integrity. These threats included objectification, invisibility against a background of technology, and a lack of value for individuals' contributions as agents in their own health and illness experiences.