Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptional Responses of Treponema denticola to Other Oral Bacterial Species

The classic organization by Socransky and coworkers categorized the oral bacteria of the subgingival plaque into different complexes. Treponema denticola, Porphyromonas gingivalis and Tannerella forsythia are grouped into the red complex that is highly correlated with periodontal disease. Socransky's work closely associates red with orange complex species such as Fusobacterium nucleatum and Prevotella intermedia but not with members of the other complexes. While the relationship between species contained by these complexes is in part supported by their ability to physically attach to each other, the physiological consequences of these interactions and associations are less clear. In this study, we employed T. denticola as a model organism to analyze contact-dependent responses to interactions with species belonging to the same complex (P. gingivalis and T. forsythia), the closely associated orange complex (using F. nucleatum and P. intermedia as representatives) and the unconnected yellow complex (using Streptococcus sanguinis and S. gordonii as representatives). RNA was extracted from T. denticola alone as well as after pairwise co-incubation for 5 hrs with representatives of the different complexes, and the respective gene expression profiles were determined using microarrays. Numerous genes related to motility, metabolism, transport, outer membrane and hypothetical proteins were differentially regulated in T. denticola in the presence of the tested partner species. Further analysis revealed a significant overlap in the affected genes and we identified a general response to the presence of other species, those specific to two of the three complexes as well as individual complexes. Most interestingly, many predicted major antigens (e.g. flagella, Msp, CTLP) were suppressed in responses that included red complex species indicating that the presence of the most closely associated species induces immune-evasive strategies. In summary, the data presented here provide an in-depth understanding of the transcriptional responses triggered by contact-dependent interactions between microorganisms inhabiting the periodontal pocket.
Lithospheric Structure Beneath the Alboran Basin: Results from 3D Gravity Modeling and Tectonic Relevance

A three-dimensional gravity modeling combined with integrated heat flow and elevation modeling is conducted to map out the crustal and lithospheric mantle thickness in the Alboran Basin, in the westernmost Mediterranean. A “sediment”-corrected Bouguer anomaly has been derived using a depth-to-the-basement map and densities determined from well logs and seismic data. The gravity effect of the base of the lithosphere has been removed from the sediment-corrected Bouguer anomaly to obtain a “crustal” Bouguer anomaly, which has been inverted for crustal thickness. The resulting lithospheric structure is further constrained by elevation data under the assumption of local isostasy. The low residual elevation anomalies obtained (±100 m in average) suggest that the area is in local isostasy, particularly the medium- and long-wavelength topography features. Variations in crustal thickness range from 36 km underneath the Betic and Rif Chains to <12 km beneath the easternmost part of the Alboran Sea Basin, in the transition to the South Balearic Basin. In western Alboran the Moho lies at a rather constant depth of ∼18 km, deepening sharply toward the Gibraltar Strait down to 30–32 km. The base of the lithosphere shallows from 140 km depth in the Gibraltar Strait to <45 km depth in the easternmost Alboran Sea. Lithospheric thinning penetrates to the southeastern side of the Iberian margin crosscutting topographic highs of the central and eastern Betic Chain. Our results favor mantle delamination produced by detachment and subsequent peeling away of the lithospheric mantle rather than convective removal of the lithospheric mantle either by orogenic collapse or detachment and sinking of a lithospheric slab.
Three-Dimensional Stability of Slopes and Excavations

Three-dimensional (3D) limit analysis of stability of slopes is presented. Such analyses are not common, because of the difficulties in constructing three-dimensional mechanisms of failure in frictional soils. A class of admissible rotational mechanisms is considered in this paper. The failure surface has the shape of a curvilinear cone (‘horn'), with upper and lower contours defined by log-spirals; all radial cross-sections of the surface are circular. In the special case of cohesive soils (undrained behaviour), the shape of the failure surface reduces to a torus. An alternative failure surface is generated when the axis of rotation intersects the circle that generates the surface. The 3D mechanism is further modified with a plane-strain central insert to ensure the transition to a plane-strain mechanism if no restraint is placed on the slope width. Also, the spherical failure surface considered in the literature is re-examined. The critical height of slopes with finite width is determined, and the resul.
Travelling ionospheric disturbances effect on the single station location accuracy

In this paper we present the results of experimental observation from October till November 2016. Variations in angles-of-arrival (AoA) on two mid-latitude paths with different orientation were calculated and the average accuracy of single-station location (SSL) was estimated. The comparison of obtained data with radio channel simulation results was conducted in terms of naturally disturbed ionosphere in the presence of travelling ionospheric disturbances (TID).
Surgery is the best intervention for severe coronary artery disease

For the past two decades coronary artery bypass grafting has been the standard treatment for patients with severe multivessel ischaemic heart disease.1 In the past few years, however, it has been increasingly challenged by percutaneous coronary intervention. Indeed, in many parts of the developed world percutaneous coronary intervention is done twice as often as coronary artery bypass grafting. Why has this change in practice occurred? I believe that it is not evidence based, does not represent best value for money, and that patients are not appropriately informed of its limitations. Coronary artery bypass grafting is probably the most intensively studied surgical procedure, with follow up data extending over 20 years.2 It is highly effective in relieving the symptoms of ischaemic heart disease and improving life expectancy in patients with certain anatomical patterns of disease; these benefits are magnified in patients with more severe disease and with impaired left ventricular function.1 Furthermore, coronary artery bypass grafting is remarkably safe. Improvements in medical, anaesthetic, and surgical management have ensured that hospital mortality has remained around 2% over the past decade despite the treatment being used in older and sicker patients.3 On the other hand, …
Preterm Birth, Intrauterine Infection, and Fetal Inflammation

Preterm birth (PTB) (delivery before 37 weeks’ gestation) is a leading cause of neonatal death and disease in industrialized and developing countries alike. Infection (most notably in high-risk deliveries occurring before 28 weeks’ gestation) is hypothesized to initiate an intrauterine inflammatory response that plays a key role in the premature initiation of labor as well as a host of the pathologies associated with prematurity. As such, a better understanding of intrauterine inflammation in pregnancy is critical to our understanding of preterm labor and fetal injury, as well as on-going efforts to prevent PTB. Focusing on the fetal innate immune system responses to intrauterine infection, the present paper will review clinical and experimental studies to discuss the capacity for a fetal contribution to the intrauterine inflammation associated with PTB. Evidence from experimental studies to suggest that the fetus has the capacity to elicit a pro-inflammatory response to intrauterine infection is highlighted, with reference to the contribution of the lung, skin, and gastrointestinal tract. The paper will conclude that pathological intrauterine inflammation is a complex process that is modified by multiple factors including time, type of agonist, host genetics, and tissue.
Assembly intermediates of the mouse muscle nicotinic acetylcholine receptor in stably transfected fibroblasts

We have used fibroblast clones expressing muscle nicotinic acetylcholine receptor alpha and gamma, and alpha and delta subunits to measure the kinetics of subunit assembly, and to study the properties of the partially assembled products that are formed. We demonstrate by coimmunoprecipitation that assembly intermediates in fibroblasts coexpressing alpha and delta subunits are formed in a time-dependent manner. The alpha and gamma- and the alpha and delta-producing transfected cells form complexes that, when labeled with 125I-alpha- bungarotoxin, migrate in sucrose gradients at 6.3S, a value consistent with a hetero-dimer structure. An additional peak at 8.5S is formed from the alpha and gamma subunits expressed in fibroblasts suggesting that gamma may have more than one binding site for alpha subunit. The stability and specificity of formation of these partially assembled complexes suggests that they are normal intermediates in the assembly of acetylcholine receptor. Comparison of the binding of 125I-alpha- bungarotoxin to intact and detergent-extracted fibroblasts indicate that essentially all of the binding sites are retained in an intracellular pool. The fibroblast delta subunit has the electrophoretic mobility in SDS-PAGE of a precursor that does not contain complex carbohydrates. In addition, alpha gamma and alpha delta complexes had lectin binding properties expected of subunits lacking complex oligosaccharides. Therefore, fibroblasts coexpressing alpha and gamma or alpha and delta subunits produce discrete assembly intermediates that are retained in an intracellular compartment and are not processed by Golgi enzymes.
Learning Structural Dependencies of Words in the Zipfian Tail

Using semi-supervised EM, we learn finegrained but sparse lexical parameters of a generative parsing model (a PCFG) initially estimated over the Penn Treebank. Our lexical parameters employ supertags, which encode complex structural information at the pre-terminal level, and are particularly sparse in labeled data -- our goal is to learn these for words that are unseen or rare in the labeled data. In order to guide estimation from unlabeled data, we incorporate both structural and lexical priors from the labeled data. We get a large error reduction in parsing ambiguous structures associated with unseen verbs, the most important case of learning lexico-structural dependencies. We also obtain a statistically significant improvement in labeled bracketing score of the treebank PCFG, the first successful improvement via semi-supervised EM of a generative structured model already trained over large labeled data.
Desho grass (Pennisetum pedicellatum) for livestock feed, grazing land and soil and water management on small-scale farms

Description: • Desho is an indigenous grass of Ethiopia belonging to the family of Poaceae (Welle et al. 2006; Smith 2010) • It is a perennial grass which has an extensive root system that anchors well with the soil (SLM Ethiopia) • It has a high biomass production capacity 30–109 t/ha (Ecocrop 2010) • It grows upright with the potential of reaching 90– 120 cm based on soil fertility (SLM Ethiopia; Shiferaw et al. 2011) • It can grow anywhere from 1500–2800 masl with optimum elevation over 1700 masl on medium to low soil fertility (SLM Ethiopia) Uses: • A year round livestock fodder (SLM Ethiopia) • For erosion control through strip planting (SLM Ethiopia; Welle et al. 2006) • To rehabilitate degraded land (SLM Ethiopia; Smith 2010) • To improve grazing land management (Danano 2007) • As silage for dry season feed
School Health Promotion Policy in Nova Scotia: A Case Study

In response to the growing concern of children’s health, many local governments have responded by implementing health promotion policies that support a health promoting schools (or comprehensive school health) approach. The purpose of this study is to explore the context and nature of policies that relate to health promoting schools in Nova Scotia. The results revealed that a number of policy initiatives had been developed (N= 348) at the provincial level (n=53) and across school districts (n=295). The policy scan demonstrated that there were many supportive policies at different levels of jurisdiction but incongruence of priorities and enforcement practices between the province and school districts. To optimize the impact of health promotion policies, different levels of jurisdictions need to work together and support the implementation of policies that support a health promoting schools approach. Compte tenu des inquietudes croissantes entourant la sante des enfants, plusieurs paliers de gouvernements se sont dotes de politiques de promotion de la sante a l’ecole qui souscrivent a l’approche des ecoles axees sur la promotion de la sante (aussi appelee l’approche de sante globale dans les ecoles). Cette etude s’est interessee a l’encadrement et a la nature des politiques qui sous-tendent l’approche des ecoles axees sur la promotion de la sante en Nouvelle-Ecosse. Les resultats ont demontre que plusieurs projets d’elaboration de politiques ont ete lances (N= 348) a l’echelle provinciale (n=53) et au niveau des districts scolaires (n=295). Un survol de ces politiques a revele que meme si chaque palier de gouvernement s’est dote de politiques favorables en ce sens, leurs priorites et leurs modes d’application varient selon qu’elles relevent de la province ou des districts scolaires. Pour maximiser l’impact de ces politiques sur la promotion de la sante, la province et les districts scolaires doivent collaborer et appuyer l’implantation de politiques au service de l’approche des ecoles axees sur la promotion de la sante.
Acute epididymitis

Acute epididymitis is characterized by testicular pain and tender swelling of the epididymis. The symptoms are usually unilateral and develop over a few days. It should be distinguished from chronic epididymitis, which causes persistent testicular pain often with no epididymal swelling. In clinical trials acute epididymitis is not usually diagnosed unless the history is <6 weeks [1,2]. Acute epididymitis is caused by a broad range of infections and less commonly by other in ̄ammatory processes.
Polycystic ovarian syndrome: a follow-up study on fertility and menstrual pattern in 149 patients 15-25 years after ovarian wedge resection.

BACKGROUND The aim of this study was to evaluate fertility and menstrual pattern in women with polycystic ovarian syndrome (PCOS) 15-25 years after ovarian wedge resection (OWR). METHODS AND RESULTS The diagnosis was based on the combination of ovarian pathology and symptoms. The 149 patients, all primarily treated at a university teaching hospital, were studied three times by means of a questionnaire up to 25 years after surgery. Kaplan-Meier analysis showed a cumulative rate of spontaneous pregnancies of 76%, increasing to 88% when induced pregnancies were included. The cumulated live birth rate was 78%. A bootstrap simulation indicated that 69.5% would develop post-operative adhesions, which could impede pregnancy in 13.4%. In the majority of the patients a regular menstrual pattern was restored up to 25 years after OWR. CONCLUSION The results of OWR in PCOS are favourable to most modern treatments. Laparoscopic electrocautery of the ovaries is the only method equally successful, and, by being less invasive, it has made OWR history in the treatment of PCOS.
A Constitutively Active Form of the Protein Kinase p90Rsk1 Is Sufficient to Trigger the G2/M Transition in Xenopus Oocytes*

The protein kinase p90Rsk has previously been implicated as a key target of the MAPK pathway during M phase of meiosis II in Xenopus oocytes. To determine whether Rsk is a mediator of MAPK for stimulation of the G2/M transition early in meiosis I, we sought to generate a form of Rsk that would be constitutively active in resting, G2 phase oocytes. Initial studies revealed that an N-terminal truncation of 43 amino acids conferred enhanced specific activity on the enzyme in G2 phase, and stability was highest if the C terminus was not truncated. The full-length enzyme is known to be activated by phosphorylation at five sites. Two of these sites and flanking residues were replaced with either aspartic or glutamic acid, and Tyr699 was mutated to alanine. The resulting construct, termed fully activated (FA) Rsk, had constitutive activity in G2 phase, with a specific activity equivalent to that of wild type Rsk in M phase. In eight independent experiments ∼45% of oocytes expressing FA-Rsk underwent germinal vesicle breakdown (GVBD, the G2/M transition) in the absence of progesterone, and this effect could be observed even in the presence of the MAPK kinase inhibitor U0126. Moreover, the specific activity of FA-Rsk in vivo was unaffected by U0126. In oocytes that did not undergo GVBD with FA-Rsk expression, subsequent treatment with progesterone resulted in a very rapid rate of GVBD even in the presence of U0126 to inhibit the endogenous MAPK/Rsk pathway. These results indicate that Rsk is the mediator of MAPK effects for the G2/M transition in meiosis I and in a subpopulation of oocytes Rsk is sufficient to trigger the G2/M transition.
Nurses' Workplace Distress and Ethical Dilemmas in Tanzanian Health Care

The aim of this study was to describe Tanzanian nurses' meaning of and experiences with ethical dilemmas and workplace distress in different care settings. An open question guide was used and the study focused on the answers that 29 registered nurses supplied. The theme, `Tanzanian registered nurses' invisible and visible expressions about existential conditions in care', emerged from several subthemes as: suffering from (1) workplace distress; (2) ethical dilemmas; (3) trying to maintaining good quality nursing care; (4) lack of respect, appreciation and influence; and (5) a heavy workload that did not prevent registered nurses from struggling for better care for their patients. The analysis shows that, on a daily basis, nurses find themselves working on the edge of life and death, while they have few opportunities for doing anything about this situation. Nurses need professional guidance to gain insight and be able to reflect on their situations, so that they do not become overloaded with ethical dilemmas and workplace distress.
The performance of TCP/IP for networks with high bandwidth-delay products and random loss

This paper examines the performance of TCP/IP, the Internet data transport protocol, over wide-area networks (WANs) in which data traffic could coexist with real-time traffic such as voice and video. Specifically, we attempt to develop a basic understanding, using analysis and simulation, of the properties of TCP/IP in a regime where: (1) the bandwidth-delay product of the network is high compared to the buffering in the network and (2) packets may incur random loss (e.g., due to transient congestion caused by fluctuations in real-time traffic, or wireless links in the path of the connection). The following key results are obtained. First, random loss leads to significant throughput deterioration when the product of the loss probability and the square of the bandwidth-delay product is larger than one. Second, for multiple connections sharing a bottleneck link, TCP is grossly unfair toward connections with higher round-trip delays. This means that a simple first in first out (FIFO) queueing discipline might not suffice for data traffic in WANs. Finally, while the Reno version of TCP produces less bursty traffic than the original Tahoe version, it is less robust than the latter when successive losses are closely spaced. We conclude by indicating modifications that may be required both at the transport and network layers to provide good end-to-end performance over high-speed WANs.
CARS: a new code generation framework for clustered ILP processors

Clustered ILP processors are characterized by a large number of non-centralized on-chip resources grouped into clusters. Traditional code generation schemes for these processors consist of multiple phases for cluster assignment, register allocation and instruction scheduling. Most of these approaches need additional re-scheduling phases because they often do not impose finite resource constraints in all phases of code generation. These phase-ordered solutions have several drawbacks, resulting in the generation of poor performance code. Moreover the iterative/back-tracking algorithms used in some of these schemes have large turning times. In this paper we present CARS, a code generation framework for Clustered ILP processors, which combines the cluster assignment, register allocation, and instruction scheduling phases into a single code generation phase, thereby eliminating the problems associated with phase-ordered solutions. The CARS algorithm explicitly takes into account all the resource constraints at each cluster scheduling step to reduce spilling and to avoid iterative re-scheduling steps. We also present a new on-the-fly register allocation scheme developed for CARS. We describe an implementation of the proposed code generation framework and the results of a performance evaluation study using the SPEC95/2000 and MediaBench benchmarks.
Determination of Nitrate and Nitrite Content of Dietary Supplements Using Ion Chromatography

Following the discovery of nitrite and nitrate as pro-drugs of the vasorelaxant nitric oxide, many studies have reported enhanced athletic performance following intake of these ions either intravenously or as a food supplement. The primary aim of this study was to develop a new accurate, reliable and robust ion chromatography based method. The newly developed method was applied to selected foodstuffs in powdered and/or juice form to measure levels of nitrate and nitrite. In addition to the commonly used beetroot juice, an initial HPLC-based screen of a range of foods identified spinach powder with very high nitrate and nitrite content. As a result of the initial screening, branded beetroot juice, concentrated beetroot juice and spinach powder were analysed using a new extraction method followed by a newly developed and validated ion chromatographic determination of nitrate and nitrite levels. The new ion chromatography based assay showed higher efficiency and better recovery than the HPLC approach. Significant inter-batch variations were found in levels of nitrate and nitrite in the beetroot juice and concentrated beetroot juice samples tested. In contrast spinach powder could provide a homogenous source of nitrate and nitrate for physiological studies. In summary, the new assay is rapid and efficient facilitating rigorous analyses of nitrate and nitrite levels prior to investigations requiring intake of foodstuffs containing these nitric oxide precursors.
IMMUNOCHEMICAL AND COLLAGEN‐BINDING PROPERTIES OF FIBRONECTIN *

Fibronectin (also called SFA,'.' LETS galactoprotein a,5 CSP,(' Z p r ~ t e i n , ~ C l g , ' CA F.9 and C A P " . " ) , a cell surface and plasma protein,'i2 has many interesting biologic properties, such as nonexistence in surfaces of transformed ce~~s4 . s . 7 . 12-14 and interaction with fibrin15 and collagen. '6 Thesc properties have made it the subject o f m u c h current research. It still remains a protein in search of a function, especially in regard to its plasma form, but the evidence available suggests that it may function in the attachment of cells t o the extracellular matrix. '. '' I n this paper, we will briefly summarize some of our past work and present some new data on the immunochemical properties and detection of fibroncctin and its interaction with structural proteins, such a s collagen and fibrin.