Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcript Profiling in the chl 1-5 Mutant of Arabidopsis Reveals a Role of the Nitrate Transporter NRT 1 . 1 in the Regulation of Another Nitrate Transporter , NRT 2

Arabidopsis thaliana mutants deficient for the NRT1.1 NO3 transporter display complex phenotypes, including lowered NO3 uptake, altered development of nascent organs, and reduced stomatal opening. To obtain further insight at the molecular level on the multiple physiological functions of NRT1.1, we performed large-scale transcript profiling by serial analysis of gene expression in the roots of the chl1-5 deletion mutant of NRT1.1 and of the Columbia wild type. Several hundred genes were differentially expressed between the two genotypes, when plants were grown on NH4NO3 as N source. Among these genes, the N satiety-repressed NRT2.1 gene, encoding a major component of the root high-affinity NO3 transport system (HATS), was found to be strongly derepressed in the chl1-5 mutant (as well as in other NRT1.1 mutants). This was associated with a marked stimulation of the NO3 HATS activity in the mutant, suggesting adaptive response to a possible N limitation resulting from NRT1.1 mutation. However, derepression of NRT2.1 in NH4NO3-fed chl1-5 plants could not be attributed to lowered production of N metabolites. Rather, the results show that normal regulation of NRT2.1 expression is strongly altered in the chl1-5 mutant, where this gene is no more repressible by high N provision to the plant. This indicates that NRT1.1 plays an unexpected but important role in the regulation of both NRT2.1 expression and NO3 HATS activity. Overexpression of NRT2.1 was also found in wild-type plants supplied with 1 mM NH4 plus 0.1 mM NO3 , a situation where NRT1.1 is likely to mediate very low NO3 transport. Thus, we suggest that it is the lack of NRT1.1 activity, rather than the absence of this transporter, that derepresses NRT2.1 expression in the presence of NH4. Two hypotheses are discussed to explain these results: (1) NRT2.1 is upregulated by a NO3 demand signaling, indirectly triggered by lack of NRT1.1-mediated uptake, which overrides feedback repression by N metabolites, and (2) NRT1.1 plays a more direct signaling role, and its transport activity generates an unknown signal required for NRT2.1 repression by N metabolites. Both mechanisms would warrant that either NRT1.1 or NRT2.1 ensure significant NO3 uptake in the presence of NH4 in the external medium, which is crucial to prevent the detrimental effects of pure NH4 nutrition.
Journal of Health Global

Spatial distribution and deployment of community–based distributors implementing integrated community case management (iCCM): Geographic information system (GIS) mapping study in three South Sudan states Aim In late 2012 and in conjunction with South Sudan' s Ministry of Health – National Malaria Control Program, PSI (Population Services International) conducted a comprehensive mapping exercise to assess geographical coverage of its integrated community case management (iCCM) program and consider scope for expansion. The operational research was designed to provide evidence and support for low–cost mapping and monitoring systems, demonstrating the use of technology to enhance the quality of programming and to allow for the improved allocation of resources through appropriate and need–based deployment of community–based distributors (CBDs). Methods The survey took place over the course of three months and program staff gathered GPS (global positioning system) data, along with demographic data, for over 1200 CBDs and 111 CBD supervisors operating in six counties in South Sudan. Data was collated, cleaned and quality assured, input into an Excel database, and subsequently uploaded to geographic information system (GIS) for spatial analysis and map production. Results The mapping results showed that over three–quarters of CBDs were deployed within a five kilometer radius of a health facility or another CBD, contrary to program planning and design. Other characteristics of the CBD and CBD supervisor profiles (age, gender, literacy) were more closely matched with other regional programs. Conclusions The results of this mapping exercise provided a valuable insight into the contradictions found between a program " deployment plan " and the realities observed during field implementation. It also highlighted an important need for program implementers and nation-al–level strategy makers to consider the natural and community–driv-en diffusion of CBDs, and take into consideration the strength of the local health facilities when developing a deployment plan.
Dental Arch Relationships on Three-Dimensional Digital Study Models and Conventional Plaster Study Models for Patients with Unilateral Cleft Lip and Palate

Objective To determine if three-dimensional (3D) digital study models could replace plaster study models for the evaluation of dental arch relationships for patients with unilateral cleft lip and palate. Design Observational study involving plaster study models from a records archive Setting U.K. National Health Service. Patients, Participants Thirty sets of study models of 5-year-old patients with unilateral cleft lip and palate were identified and scanned to produce 3D digital study models by ESM Digital Solutions Ltd. (Swords, Co. Dublin, Ireland) using an R250 Orthodontic Study Model Scanner (3Shape A/S, Copenhagen, Denmark). Interventions None. Main Outcome Measure(s) The plaster and 3D digital study models were scored using the 5-year-olds' and modified Huddart Bodenham indices and analyzed using the Friedman test (p < .05) and two-way ANOVA, respectively. Intra-observer and interobserver reproducibility were calculated from the 5-year-olds' index data using the weighted kappa statistic for both the plaster and 3D digital models. Results Intra-observer and interobserver reproducibility were good (0.62 to 0.83 and 0.64 to 0.78, respectively). There were no statistically significant differences between the scores for the 3D digital study models when compared to the plaster study models for either the 5-year-olds' index (p = .12) or for the modified Huddart Bodenham index (p = .506). Conclusions Three-dimensional digital models are a valid alternative to traditional plaster study models for the evaluation of dental arch relationships in patients with unilateral cleft lip and palate.
Delta One T Cells for Immunotherapy of Chronic Lymphocytic Leukemia: Clinical-Grade Expansion/Differentiation and Preclinical Proof of Concept

Purpose: The Vδ1+ subset of γδ T lymphocytes is a promising candidate for cancer immunotherapy, but the lack of suitable expansion/differentiation methods has precluded therapeutic application. We set out to develop and test (preclinically) a Vδ1+ T-cell–based protocol that is good manufacturing practice compatible and devoid of feeder cells for prompt clinical translation. Experimental design: We tested multiple combinations of clinical-grade agonist antibodies and cytokines for their capacity to expand and differentiate (more than 2–3 weeks) Vδ1+ T cells from the peripheral blood of healthy donors and patients with chronic lymphocytic leukemia (CLL). We characterized the phenotype and functional potential of the final cellular product, termed Delta One T (DOT) cells, in vitro and in vivo (xenograft models of CLL). Results: We describe a very robust two-step protocol for the selective expansion (up to 2,000-fold in large clinical-grade cell culture bags) and differentiation of cytotoxic Vδ1+ (DOT) cells. These expressed the natural cytotoxicity receptors, NKp30 and NKp44, which synergized with the T-cell receptor to mediate leukemia cell targeting in vitro. When transferred in vivo, DOT cells infiltrated tumors and peripheral organs, and persisted until the end of the analysis without showing signs of loss of function; indeed, DOT cells proliferated and produced abundant IFNγ and TNFα, but importantly no IL17, in vivo. Critically, DOT cells were capable of inhibiting tumor growth and preventing dissemination in xenograft models of CLL. Conclusions: We provide a clinical-grade method and the preclinical proof of principle for application of a new cellular product, DOT cells, in adoptive immunotherapy of CLL. Clin Cancer Res; 22(23); 5795–804. ©2016 AACR.
Periconceptional nutrient intakes and risks of conotruncal heart defects.

BACKGROUND Few inquiries into periconceptional nutrition, other than folate, and risk of heart defects exist. We investigated the observed association between conotruncal heart defects and periconceptional vitamin use, as well as potential associations with other dietary nutrients. METHODS Data derived from a population-based, case-control study of fetuses and liveborn infants among California births between July 1999 and June 2004; 76% of eligible case mothers and 77% of eligible control mothers were interviewed. Cases included 140 with d-transposition of great arteries (dTGA), and 163 with tetralogy of Fallot (TOF). Total number of controls was 698. Use of vitamins was elicited by questionnaire for the periconceptional period. Dietary nutrient intake was elicited by a well-known food frequency questionnaire. RESULTS The odds ratio for dTGA associated with supplemental vitamin use was 1.0 (95% confidence interval [CI], 0.7-1.5) and for TOF was 0.9 (95% CI, 0.6-1.3). We observed increased risks associated with lower dietary intakes of linoleic acid, total carbohydrate, and fructose for dTGA, whereas decreased risks were observed for lower intakes of total protein and methionine for TOF. Lower dietary intake of several micronutrients-namely folate, niacin, riboflavin, and vitamins B(12), A, and E, even after simultaneous adjustment for other studied nutrients-was associated with increased risk of dTGA but not TOF. These associations were observed among women who did not use vitamin supplements periconceptionally. Analytic consideration of several potential confounders did not reveal alternative interpretations of the results. CONCLUSION Evidence continues to accumulate to show that nutrients, particularly folate, influence risks of structural birth defects. Our results extend observations that other nutrients may also be important in heart development.
An Acknowledgment-Based Scheme to Defend Against Cooperative Black Hole Attacks in Optimized Link State Routing Protocol

In this paper, we address the problem of cooperative black hole attack, one of the major security issues in mobile ad hoc networks. The aim of this attack is to force nodes in the network to choose hostile nodes as relays to disseminate the partial topological information, thereby exploiting the functionality of the routing protocol to retain control packets. In optimized link state routing (OLSR) protocol, if a cooperative black hole attack is launched during the propagation of topology control (TC) packets, the topology information will not be disseminated to the whole network which may lead to routing disruption. In this paper, we investigate the effects of the cooperative black hole attack against OLSR, in which two colluding MPR nodes cooperate in order to disrupt the topology discovery. Then we propose an acknowledgment based technique that overcomes the shortcomings of the OLSR protocol, and makes it less vulnerable to such attacks by identifying and then isolating malicious nodes in the network. The simulation results of the proposed scheme show high detection rate under various scenarios.
A novel algorithm for mobile station location estimation with none line of sight error using robust least M-estimation

A novel algorithm for the mobile station (MS) location estimation with none line of sight (NLOS) error in wireless network is proposed in this paper. In the proposed algorithm, the MS location estimation problem is formulated as a simple linear approximation problem in vector space with the data corrupted by the NLOS errors. The M-estimator is employed to eliminate the NLOS errors, and a recursive algorithm is developed to solve the M-estimation normal equations. Compared to the conventional algorithms, the proposed algorithm does not rely on the prior knowledge of the statistical model of the measurement noise. Another advantage is that the proposed algorithm can track the slow moment of MS due to the recursive nature, which is hardly to achieve in other algorithms. The algorithm also possesses low arithmetic complexity. Effectiveness of the proposed algorithm is verified by the numerical simulations.
Development of a mortality prediction formula due to sepsis/severe sepsis in a medical intensive care unit

Background: Although sepsis is one of the leading causes of mortality in hospitalized patients, information regarding early predictive factors for mortality and morbidity is limited. Materials and Methods: Patients fulfilling the Infectious Disease Society of America criteria of sepsis within the medical intensive care unit (ICU) were included over two years. Apart from baseline hematological, biochemical, and metabolic parameters, Acute Physiology and Chronic Health Evaluation II (APACHE II), Simplified Acute Physiology Score II and III (SAPS II and SAPS III), and Sequential Organ Function Assessment (SOFA) scores were calculated on day 1 of admission. Patients were followed till death or discharge from the ICU. Results: One hundred patients were enrolled over two years (54% males). The overall mortality was 53%, (69.5% in females, 38.8% in males (P < 0.01). Mortality was 65.7%, 55.7%, and 33.3% in patients with septic shock, severe sepsis, and sepsis, respectively. Patients who died were significantly older than the survivors (mean age, 57.37 ± 20.42 years and 44.29 ± 15.53 years respectively, P < 0.01). Nonsurvivors were significantly more anemic and had higher APACHE II, SAPS II, SAPS III, and SOFA scores. The presence of acute respiratory distress syndrome and renal dysfunction were associated with higher mortality (75% and 70.2%, respectively). There was no significant difference in the duration of mechanical ventilation or ICU stay between survivors and nonsurvivors. On multivariate analysis, significant predictors of mortality with odds ratio greater than 2 included the presence of anemia, SAPS II score greater than 35, SAPS III score greater than 47, and SOFA score greater than 6 at day 1 of admission. Conclusion: Several demographic and laboratory parameters as well as composite critical illness scoring systems are reliable early predictors of mortality in sepsis. A sepsis mortality prediction formula (AIIMS Sepsis Score) based on SAPS II, SAPS III, and SOFA scores and hemoglobin has greater predictive power than these scoring methods individually. Routine use of critical illness scoring systems and a composite mortality prediction formula may provide useful early prognostic information in sepsis/severe sepsis.
A Virtual Space Vector Modulation Technique for the Reduction of Common-Mode Voltages in Both Magnitude and Third-Order Component

A virtual space vector modulation technique reducing both magnitude and third-order harmonic component of the common-mode voltage (CMV) in a two-level voltage-source inverter (VSI) is proposed in this paper. The presented method employs a set of virtual space vectors constructed from original stationary space vectors to conduct modulation. Since the created virtual vectors have the lowest instantaneous and zero average CMVs, both the magnitude and third-order harmonic component of the generated CMV are reduced, contributing to better overall CMV performance and common-mode filter design in VSI applications. Three variants of the proposed modulation method using different virtual space vector combinations are presented. The concept of the virtual space vector modulation technique demonstrated with two-level inverter in this paper can also be extended to multilevel inverters. Simulation and experimental results, as well as comparisons with existing methods are provided to verify the proposed technique.
System Identification for Internal Combustion Engine Model

A parametric and non-parametric identification of internal combustion engine (ICE) model using recursive least squares (RLS) and neuro-fuzzy modeling (ANFIS) approach are introduced in this paper. The analytical model of an internal combustion engine is excited by pseudorandom binary sequence (PRBS) input which gives random signals to make sure the information of the system covers large range of frequencies. The input and output data obtained from the simulation of the analytical model is used for the identification of the system. The simplest polynomial form, auto-regressive, external input (ARX) model structure is chosen and the performance of the system is validated by mean square error (MSE) and correlation tests. Although, both methods capable to represent the dynamic of the system very well, it is demonstrated that ANFIS gives better results than RLS in terms of mean squares error between actual and prediction.
Prediction of penetration Rate and cost with Artificial Neural Network for Alhafaya Oil Field

Prediction of penetration rate (ROP) is important process in optimization of drilling due to its crucial role in lowering drilling operation costs. This process has complex nature due to too many interrelated factors that affected the rate of penetration, which make difficult predicting process. This paper shows a new technique of rate of penetration prediction by using artificial neural network technique. A three layers model composed of two hidden layers and output layer has built by using drilling parameters data extracted from mud logging and wire line log for Alhalfaya oil field. These drilling parameters includes mechanical (WOB, RPM), hydraulic (HIS), and travel transit time (DT). Five data set represented five formations gathered from five drilled wells were involved in modeling process.Approximatlly,85 % of these data were used for training the ANN models, and 15% to assess their accuracy and direction of stability. The results of the simulation showed good matching between the raw data and the predicted values of ROP by Artificial Neural Network (ANN) model. In addition, a good fitness was obtained in the estimation of drilling cost from ANN method when compared to the raw data.
Consequences of increased temperature and CO2 for phytoplankton community structure in the Bering Sea

Global climate change is predicted to have large effects on the ocean that could cause shifts in current algal community structure, major nutrient cycles, and carbon export. The Bering Sea is already experiencing changes in sea surface temperature (SST), unprecedented algal blooms, and alterations to trophic level dynamics. We incubated phytoplankton communities from 2 Bering Sea regimes under conditions of elevated SST and/or partial pressure of carbon dioxide (pCO2) similar to predicted values for 2100. In our 'greenhouse ocean' simulations, maximum biomass-normalized photosynthetic rates increased 2.6 to 3.5 times and community composition shifted away from diatoms and towards nanophytoplankton. These changes were driven largely by elevated tempera- ture, with secondary effects from increased pCO2. If these results are indicative of future climate responses, community shifts towards nanophytoplankton dominance could reduce the ability of the Bering Sea to maintain the productive diatom-based food webs that currently support one of the world's most productive fisheries.
The curse of simultaneity

Typical models of strategic interactions in computer science use simultaneous move games. However, in applications simultaneity is often hard or impossible to achieve. In this paper, we study the robustness of the Nash Equilibrium when the assumption of simultaneity is dropped. In particular we propose studying the sequential price of anarchy: the quality of outcomes of sequential versions of games whose simultaneous counterparts are prototypical in algorithmic game theory. We study different classes of games with high price of anarchy, and show that the subgame perfect equilibrium of their sequential version is a much more natural prediction, ruling out unreasonable equilibria, and leading to much better quality solutions. We consider three examples of such games: Cost Sharing Games, Unrelated Machine Scheduling Games and Consensus Games. For Machine Cost Sharing Games, the sequential price of anarchy is at most O(log(n)), an exponential improvement of the O(n) price of anarchy of their simultaneous counterparts. Further, the subgame perfect equilibrium can be computed by a polynomial time greedy algorithm, and is independent of the order the players arrive. For Unrelated Machine Scheduling Games we show that the sequential price of anarchy is bounded as a function of the number of jobs n and machines m (by at most O(m2n)), while in the simultaneous version the price of anarchy is unbounded even for two players and two machines. For Consensus Games we observe that the optimal outcome for generic weights is the unique equilibrium that arises in the sequential game. We also study the related Cut Games, where we show that the sequential price of anarchy is at most 4. In addition we study the complexity of finding the subgame perfect equilibrium outcome in these games.
Metabolic syndrome, peripheral vascular disease and coronary artery disease: A concise review

Metabolic syndrome has a very strong association with both forms of cardiovascular (CV) disease - coronary artery disease and peripheral vascular disease. There is also a marked interrelationship between the two forms of CV disease. When one form of CV disease is present, the other should be strongly suspected and the possible occurrence of associated vascular events should be clinically evaluated. When three of the five major components that define metabolic syndrome are present, the clinical evidence indicates that one or both forms of CV disease are present, at least in incipient form. To give maximum clinical benefit to the patient at risk, the clinician must be aware of these associations, look for them and institute the measures that can reduce the risk of progression.
Periodontal repair in surgically created intrabony defects in dogs: influence of the number of bone walls on healing response.

BACKGROUND The objective of this study was to histologically evaluate periodontal healing following flap surgery in intrabony periodontal defects to determine the influence of the number of bone walls on periodontal regeneration. METHODS One-, 2-, and 3-wall intrabony periodontal defects were surgically produced at the proximal aspect of mandibular premolars in either right or left jaw quadrants in six beagle dogs. Mucoperiosteal flaps were positioned and sutured to their presurgery position following defect preparation. The animals were euthanized at 8 weeks post-surgery, and block sections of the defect sites were collected for histologic and histometric analysis. RESULTS Bone and cementum regeneration was positively correlated to the number of bone walls limiting the intrabony periodontal defects. The junctional epithelium averaged (+/- SD) 1.5 +/- 0.2, 1.2 +/- 0.3, and 0.9 +/- 0.2 mm for the 1-, 2-, and 3-wall defects, respectively, with the 3-wall defects being significantly different from the 1-wall defects (P <0.05). Cementum regeneration averaged 1.2 +/- 0.6, 2.0 +/- 0.6, and 2.8 +/- 0.5 mm for the 1-, 2-, and 3-wall defects, respectively; all groups were significantly different from each other (P <0.05). Bone regeneration averaged 1.5 +/- 0.5, 1.7 +/- 0.6, and 2.3 +/- 0.5 mm for the 1-, 2-, and 3-wall defects, respectively, with the 3-wall defects being significantly different from the 1-wall defects (P <0.05). CONCLUSIONS The results suggest that the number of bone walls is a critical factor determining treatment outcomes in intrabony periodontal defects. One- and 3-wall intrabony defects appear to be reproducible models to evaluate candidate technologies for periodontal regeneration.