Miracle-dz/UniFAR-FTUs huggingface dataset:
Prohead RNA: a noncoding viral RNA of novel structure and function

Prohead RNA (pRNA) is an essential component of the powerful Φ29‐like bacteriophage DNA packaging motor. However, the specific role of this unique RNA in the Φ29 packaging motor remains unknown. This review examines pRNA as a noncoding RNA of novel structure and function. In order to highlight the reasons for exploring the structure and function of pRNA, we (1) provide an overview of Φ29‐like bacteriophage and the Φ29 DNA packaging motor, including putative motor mechanisms and structures of its component parts; (2) discuss pRNA structure and possible roles for pRNA in the Φ29 packaging motor; (3) summarize pRNA self‐assembly; and (4) describe the prospective therapeutic applications of pRNA. Many questions remain to be answered in order to connect what is currently known about pRNA structure to its novel function in the Φ29 packaging motor. The knowledge gained from studying the structure, function, and sequence variation in pRNA will help develop tools to better navigate the conformational landscapes of RNA. WIREs RNA 2016, 7:428–437. doi: 10.1002/wrna.1330
Interpretability and Definability in the Recursively Enumerable Degrees

We investigate definability in R, the recursively enumerable Turing degrees, using codings of standard models of arithmetic (SMAs) as a tool. First we show that an SMA can be interpreted in R without parameters. Building on this, we prove that the recursively enumerable T‐degrees satisfy a weak form of the bi‐interpretability conjecture which implies that all jump classes Lown and Highn−1 n ⩾ 2 are definable in R without parameters and, more generally, that all relations on R that are definable in arithmetic and invariant under the double jump are actually definable in R. This partially answers Soare's Question 3.7 (R. Soare, Recursively enumerable sets and degrees (Springer, Berlin, 1987), Chapter XVI). 1991 Mathematics Subject Classification: primary 03D25, 03D35; secondary 03D30.
Comparative Analysis of Codon Usage Bias Patterns in Microsporidian Genomes

The sub-3 Mbp genomes from microsporidian species of the Encephalitozoon genus are the smallest known among eukaryotes and paragons of genomic reduction and compaction in parasites. However, their diminutive stature is not characteristic of all Microsporidia, whose genome sizes vary by an order of magnitude. This large variability suggests that different evolutionary forces are applied on the group as a whole. In this study, we have compared the codon usage bias (CUB) between eight taxonomically distinct microsporidian genomes: Encephalitozoon intestinalis, Encephalitozoon cuniculi, Spraguea lophii, Trachipleistophora hominis, Enterocytozoon bieneusi, Nematocida parisii, Nosema bombycis and Nosema ceranae. While the CUB was found to be weak in all eight Microsporidia, nearly all (98%) of the optimal codons in S. lophii, T. hominis, E. bieneusi, N. parisii, N. bombycis and N. ceranae are fond of A/U in third position whereas most (64.6%) optimal codons in the Encephalitozoon species E. intestinalis and E. cuniculi are biased towards G/C. Although nucleotide composition biases are likely the main factor driving the CUB in Microsporidia according to correlation analyses, directed mutational pressure also likely affects the CUB as suggested by ENc-plots, correspondence and neutrality analyses. Overall, the Encephalitozoon genomes were found to be markedly different from the other microsporidians and, despite being the first sequenced representatives of this lineage, are uncharacteristic of the group as a whole. The disparities observed cannot be attributed solely to differences in host specificity and we hypothesize that other forces are at play in the lineage leading to Encephalitozoon species.
Association of androgen receptor GGN repeat length polymorphism and male infertility in Khuzestan, Iran

Background: Androgens play critical role in secondary sexual and male gonads differentiations such as spermatogenesis, via androgen receptor. The human androgen receptor (AR) encoding gene contains two regions with three nucleotide polymorphic repeats (CAG and GGN) in the first exon. Unlike the CAG repeats, the GGN has been less studied because of technical difficulties, so the functional role of these polymorphic repeats is still unclear. Objective: The goal of this study was to investigate any relationship between GGN repeat length in the first exon of AR gene and idiopathic male infertility in southwest of Iran. Materials and Methods: This is the first study on GGN repeat of AR gene in infertile male in Khuzestan, Iran. We used polymerase chain reaction (PCR) and polyacrylamide gel electrophoresis to categorize GGN repeat lengths in 72 infertile and 72 fertile men. Afterwards we sequenced the PCR products to determine the exact length of GGN repeat in each category. Our samples included 36 azoospermic and 36 oligozoospermic men as cases and 72 fertile men as control group. Results: We found that the numbers of repeats in the cases range from 18 to 25, while in the controls this range is from 20 to 28. The results showed a significant relation between the length of GGN repeat and fertility (p=0.015). The most frequent alleles were alleles with 24 and 25 repeats respectively in case and control groups. On the other hand no significant differences were found between Arab and non-Arab cases by considering GGN repeat lengths (p=0.234). Conclusion: Due to our results, there is a significant association between the presence of allele with 24 repeats and susceptibility to male infertility. Therefore this polymorphism should be considered in future studies to clarify etiology of disorders related to androgen receptor activity.
Exploring the measurement of collaborative problem solving using a human-agent educational game

Collaborative problem solving (CPS) is a process that relies on both cognitive and social skills contributions by those involved in the joint activity. If a student is matched with a problematic group of peers, then there will be no valid measurement of the CPS skills. In the human-agent settings, CPS skills are measured by pairing each individual student with a computer agent or agents that can be programmed to act as team members with varying characteristics relevant to different CPS skills and contexts. This paper describes current research on measuring CPS skills through human-agent interactions in a prototype of a collaborative educational game.
Holocene optimum events inferred from subglacial sediments at Tschierva Glacier, Eastern Swiss Alps

This study investigates the subglacial sedimentary archive at Tschierva Glacier, Eastern Swiss Alps. Subfossil wood remains found at the retreating glacier tongue indicate that their emergence results from recent transport from an upvalley basin. A confluence-basin-like structure was found to exist by georadar measurements underneath the present glacier. In combination with high resolution age determinations based on dendrochronology and radiocarbon dating it is implied that a retreated Tschierva Glacier allowed vegetation growth and sediment accumulation in that basin. Three periods of glacier recession were detected, which occurred around 9200 cal yr BP, from 7450 to 6650 cal yr BP and from 6200 to 5650 cal yr BP. These periods are called Holocene optimum events (HOE). Accordingly, an equilibrium line rise 4220m compared to the reference period from 1960 to 1985 was inferred from digital elevation models of former glacier extents. Since glacier mass balance depends on summer (June–July–August) temperature and precipitation, an equilibrium line altitude (ELA) rise of 220m implies a summer temperature increase of about 1.8 1C assuming unchanged precipitation during the dated HOE. Alternative calculations point to probable temperature increase in a broad interval between +1.0 1C taking into account a precipitation change of 250mm/a to +2.5 1C with +250mm/a precipitation change, supporting earlier paleotemperature estimates. It is proposed that higher mean summer insolation caused a stronger seasonality during the mid-Holocene as compared to late Holocene conditions. r 2007 Elsevier Ltd. All rights reserved.
Boredom at work: what, why, and what then?

: The emotion of state boredom is experienced by nearly everyone from time to time. The workplace may predispose to episodes of boredom when autonomy is low, tasks lack personal meaning or are too simple or too complex, and performers find that attention is effortful or their minds wander. Bored individuals attempt to down-regulate their negative emotional state in a variety of ways, some of which are helpful and others harmful to themselves and/or the organization.
Metaphor's validity in marketing research

Using metaphor is widespread in management and marketing because it provides creativity. However, metaphor's validity is seldom investigated. This article offers an analysis of the validity of metaphor using three steps: (1) analysis of the metaphor's source concept, (2) analysis of the metaphor's aptness, and (3) analysis of the process of metaphor generation. These three steps have been applied to investigate the validity of two very well-known metaphors in marketing: product life cycle and brand personality. Results show these two metaphors lack validity when analyzed using the three steps. © 2009 Wiley Periodicals, Inc.
Post-mastectomy radiotherapy can improve survival in breast cancer patients aged 35 years or younger with four or more positive nodes but not in one to three positive nodes

Introduction This retrospective study investigated the clinical value of post-mastectomy radiotherapy (PMRT) in female Chinese breast cancer patients aged 35 years or younger with positive axillary lymph nodes after mastectomy. Methods We performed an analysis of clinical pathological data from 221 female Chinese breast cancer patients aged 35 years or younger treated between 1998 and 2007. Patients were diagnosed with positive axillary lymph nodes and underwent mastectomy. PMRT was delivered to 92 patients. Results The median follow-up was 61 months. The 5-year locoregional recurrence-free survival (LRFS), distant metastasis-free survival (DMFS), disease-free survival (DFS), and overall survival (OS) were 84.1%, 65.2%, 61.4%, and 77.2%, respectively. Univariate survival analysis (P=0.003) and multivariate analysis (P<0.001) both suggested that PMRT is an independent prognostic factor of LRFS. PMRT positively affected LRFS (P=0.003), but had no significant impact on DMFS (P=0.429), DFS (P=0.146), and OS (P=0.750). PMRT improved LRFS (P=0.001), DFS (P=0.017), and OS (P=0.042) in patients with four or more positive nodes, but no survival benefit was observed in patients with one to three positive nodes (P>0.05). Conclusion PMRT can improve survival in breast cancer patients aged 35 years or younger with four or more positive nodes but not in those with one to three positive nodes.
Shikimate Accumulation in Sunflower, Wheat, and Proso Millet after Glyphosate Application

Abstract Experiments were conducted to examine the utility of a spectrophometric leaf disc assay for detecting shikimate accumulation after glyphosate application in sunflower, proso millet, and wheat. The assay was conducted on both greenhouse- and field-grown plants. Glyphosate was applied at five rates ranging from 840 to 53 g ae ha−1. Shikimate accumulation data were generated at 1, 4, 7, and 14 d after application (DAA). Sunflower accumulated shikimate more rapidly and at lower glyphosate rates than the other two species. At 14 DAA, glyphosate at the two highest rates remained detectable in all three species. Plants receiving lower glyphosate doses (210, 105, and 53 g ae ha−1) had begun to grow out of the injury, or at least the shikimate levels in the plants were no longer significantly different than that present in the untreated controls. This spectrophotometric assay is both rapid and simple, with respect to other means of detecting shikimate, and it can be used to detect glyphosate drift. For it to be used by crop managers, samples from potentially drift-affected crops should be taken as soon as possible after the suspected drift event or immediately after the appearance of glyphosate injury. Nomenclature: Glyphosate; proso millet, Panicum miliaceum L. ‘Sunup’; sunflower, Helianthus annus L. ‘Triumph 765C’; wheat, Triticum aestivum, L. ‘Stak-Tite N25550’.
Sámi language teachers’ professional identities explained through narratives about language acquisition

Abstract Conducted in northern Finland, this study examines Sámi language teachers’ professional identities through their narratives of language acquisition. We focus on how teachers’ professional identities are shaped by their language acquisition process. The results are based on the narratives of nine North, Inari and Skolt Sámi language teachers. Two aspects of teachers’ narratives were significantly linked to their identities as Sámi language teachers: (1) their backgrounds (indigenous/non-indigenous) and (2) their language acquisition experiences (acquired Sámi language in childhood/adulthood). Indigenous teachers appeared to express their professional identities strongly despite their challenging acquisition experiences and were inclined to work towards the future of Sámi languages. In addition, non-indigenous teachers were willing to further the development of Sámi languages although they are not indigenous, which perhaps contributes towards the future of Sámi languages. Teachers narrated complex thoughts about language acquisition and their professional identity and helped develop indigenous language education in their respective indigenous communities. We recommend that teachers’ in pre-service and service education should prepare and support indigenous language teachers by sharing knowledge about multilingual education practices and coping skills, particularly to help the latter manage varied tasks and heterogeneous contexts. Thus, this research study shows that both teachers’ language acquisition experiences and their current work situations shape their professional identity.
Understanding the neurobiological basis of reading disorders in aphasia and predicting patients' responses to reading therapy

This thesis investigated cognitive abilities and brain regions associated with reading impairments in chronic aphasic patients with central alexia (CA). Moreover, analyses on cognitive abilities and brain lesion-site were conducted to determine whether these may predict patients’ outcomes in response to a computerised reading therapy called iReadMore. First, a review of the literature was undertaken. This included reading models and reading impairments in aphasia, neuroanatomical basis of reading, executive function in aphasia, computerised-based aphasia treatments, transcranial direct current stimulation in language therapies, and individual factors that influence aphasia recovery and patients’ response to therapy. Second, iReadMore was described and its therapeutic effect on a group of patients (n=23) was reported. Then, behavioural and neuroimaging methods implemented in this thesis were described. The first experimental chapter explored the cognitive profile of CA patients. Moreover, it included principal component analysis and voxel-based-morphometry conducted to study which brain regions are associated with reading patterns underlying patients’ remaining abilities. Here results showed that preserved white matter deep to the lingual gyrus was related to semantic abilities in reading. This region has not been related before. The second experimental chapter aimed to identify what patients’ demographic information, cognitive abilities and brain lesions explain their response to iReadMore. In this study, it is demonstrated for the first time, that lesion-site is determinant in patients’ response to therapy and also that therapy response in new patients is predictable. The final chapter investigated structural brain changes in response to iReadMore. Here a quantitative MRI protocol was implemented to study biomarkers associated with reading improvement. Results showed that iron content increases in two regions infrequently associated with reading, the left superior frontal gyrus and the supplementary motor area bilateral, when patients respond positively to the therapy. Finally, a general discussion and suggestions of new studies were provided.
Diet-Microbiota Interactions and Their Implications for Healthy Living

It is well established that diet influences the health of an individual and that a diet rich in plant-based foods has many advantages in relation to the health and well-being of an individual. What has been unclear until recently is the large contribution of the gut microbiota to this effect. As well as providing basic nutritional requirements, the long-term diet of an animal modifies its gut microbiota. In adults, diets that have a high proportion of fruit and vegetables and a low consumption of meat are associated with a highly diverse microbiota and are defined by a greater abundance of Prevotella compared to Bacteroides, while the reverse is associated with a diet that contains a low proportion of plant-based foods. Furthermore, it is becoming increasingly clear that the effect of the microbial ecology of the gut goes beyond the local gut immune system and is implicated in immune-related disorders, such as IBS, diabetes and inflamm-ageing. In this review, we investigate the evidence that a balanced diet leads to a balanced, diverse microbiota with significant consequences for healthy ageing by focusing on conditions of interest.
Nanoscale homogeneity and degradation process of two dimensional atomically thin hexagonal boron nitride dielectric stacks

In this paper we analyze the reliability of atomically thin hexagonal boron nitride (A-BN) dielectric stacks subjected to electrical stresses. The 2D insulating stacks are grown by chemical vapor deposition, meaning that (unlike exfoliated nanosheets) they can cover large areas and are suitable for the fabrication of scalable devices using photolithography tools. By comparing HfO2 and A-BN stacks with similar equivalent oxide thickness we find that the 2D dielectric shows a striking stable conduction when subjected to sequences of ramped voltage stresses, indicating that it is much more stable versus electrical-field-induced defects. These results point A-BN as superb dielectric for electronic devices.
A retrospective look at PD projects

W h i l e m o d e r n m e t h o d s f o r i n f o r m a t i o n s y s t e m d e v e l o p m e n t g e n e r a l l y a c c e p t t h a t u s e r s s h o u l d b e i n v o l v e d in s o m e w a y [15], t h e f o r m o f t h e i n v o l v e m e n t d i f f e r s c o n s i d e r a b l y . M o s t l y , u s e r s a r e v i e w e d a s r e l a t i v e l y p a s s i v e s o u r c e s o f i n f o r m a t i o n , a n d t h e i n v o l v e m e n t is r e g a r d e d a s " f u n c t i o n a l , " in t h e s e n s e t h a t i t s h o u l d y i e l d b e t t e r s y s t e m r e q u i r e m e n t s a n d i n c r e a s e d a c c e p t a n c e b y u s e r s .
Learning from the Case: A Grounded Account of Best Value Practice from within Easington District Council

Abstract: The thesis provides a grounded account of Best Value (BV) practice from within the setting of Easington District Council (1974-2009); formally recognised as an 'excellent' local authority by the Audit Commission in a Comprehensive Performance Assessment completed in 2003. Introduced by the Local Government Act 1999, BV replaced the previous Conservative regime of Compulsory Competitive Tendering (CCT). A regime which was criticised as relegating the import of quality in favour of a robust emphasis on the financial cost of local public service delivery. In contrast, conceived by the newly elected Labour government in May 1997, BV was intended to ensure "continuous improvement in both the quality and cost of services". Initially at the forefront of New Labour's improvement and modernisation agenda for local government, the 'test' of BV was intended to "be the hallmark of the modern council" (DETR 1998: 64). Informed by personal experience, the aim of the thesis is to acknowledge the human accomplishment of BV as a collaborative process as achieved through the culturally evolved meaning making frames enacted by both elected members and paid employees working in the context of a local authority setting. The thesis provides a description of the local authority as situated in place and of that placedness as providing a bounded sense of reality determining the interpretation and implementation of national policy frameworks – specifically, BV. Achieved by way of combination of an analysis of local authority documents, observational methods and semi-structured interviews the thesis examines the complexity of the contemporary local authority organisational form and presents an argument for a more nuanced approach in appreciating the interactions which inform the underlying accomplishment of specific performance outcomes by the local authority.
Mortality at 1 year for the direct comparison of tirofiban and abciximab during percutaneous coronary revascularization: do tirofiban and ReoPro give similar efficacy outcomes at trial 1-year follow-up.

AIMS Compared with placebo, abciximab has been associated with mortality reduction at late follow-up. The TARGET trial was performed to test whether tirofiban and abciximab provide similar efficacy outcomes among patients undergoing non-emergent, stent-based percutaneous coronary intervention. We report here the 1-year mortality of the study population. METHODS AND RESULTS In 18 countries at 149 hospitals, 4,809 patients undergoing elective or urgent stent implantation were randomly assigned a bolus and infusion of tirofiban or abciximab. Ischaemic events were assessed at 30 days and 6 months and mortality was assessed at 1 year. We previously reported that abciximab was superior to tirofiban considering the composite rate of death or myocardial infarction at 30 days among all patients and at 6 months among those with an acute coronary syndrome (ACS). At 1-year follow-up death occurred in 46 (1.9%) patients who received tirofiban and 42 (1.7%) patients who received abciximab (hazard ratio 1.10, 95% CI 0.72-1.67; P=0.660). Mortality rates for patients with ACS were 2.3% with tirofiban vs. 2.2% with abciximab (hazard ratio 1.03, 95% CI 0.64-1.67; P=0.897) and those without ACS were 1.4 vs. 1.0% (hazard ratio 1.32, 95% CI 0.56-3.13; P=0.530). CONCLUSION At 1 year, tirofiban provided a similar level of survival benefit compared with abciximab.
Inhibition of Experimental Periodontitis by a Topical Boron-based Antimicrobial

AN0128 is a boron-containing compound with antibacterial and anti-inflammatory properties. To test its potential effectiveness in treating periodontal disease, we induced experimental periodontitis in the rat by placing ligatures and assessed the impact of AN0128 and positive and negative controls by micro-CT and histologic measurements. The formation of an inflammatory infiltrate was measured in hematoxylin-and-eosin-stained sections. Daily application of AN0128 (1%) compared with controls reduced bone loss by 38 to 44% (P < 0.05), while vehicle alone had no effect (P > 0.05). The reduction in bone loss with AN0128 was similar to that achieved with a NSAID, ketorolac, and Total toothpaste containing triclosan. AN0128 also reduced the level of gingival inflammation 42% compared with the ligature only (P < 0.05), whereas vehicle alone had no effect (P > 0.05). The results indicate that AN0128 significantly reduces the formation of an inflammatory infiltrate and reduces bone loss, measured histologically and by micro-CT.