Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of the Arabinogalactan Protein 31 (AGP31) of Arabidopsis thaliana

Background: AGP31 is a multidomain plant cell wall hydroxyproline-rich glycoprotein. The position of Hyp and the distribution of carbohydrates is unknown. Results: Most Hyp of the Pro-rich domain are isolated within repeated motifs and carry glycans of various sizes. Conclusion: AGP31 glycoforms are very heterogeneous. Significance: This might be the first evidence for new Hyp-O-glycans. Proteins are important actors in plant cell walls because they contribute to their architecture and their dynamics. Among them, hydroxyproline (Hyp)-rich glycoproteins constitute a complex family of O-glycoproteins with various structures and functions. In this study, we characterized an atypical Hyp-rich glycoprotein, AGP31 (arabinogalactan protein 31), which displays a multidomain organization unique in Arabidopsis thaliana, consisting of a short arabinogalactan protein (AGP) motif, a His stretch, a Pro-rich domain, and a C-terminal PAC (PRP-AGP containing Cys) domain. The use of various mass spectrometry strategies was innovative and powerful: it permitted us to locate Hyp residues, to demonstrate the presence of carbohydrates, and to refine their distribution over the Pro-rich domain. Most Hyp were isolated within repeated motifs such as KAOV, KSOV, K(PO/OP)T, K(PO/OP)V, T(PO/OP)V, and Y(PO/OP)T. A few extensin-like motifs with contiguous Hyp (SOOA and SOOT) were also found. The Pro-rich domain was shown to carry Gal residues on isolated Hyp but also Ara residues. The existence of new type Hyp-O-Gal/Ara-rich motifs not recognized by the β-glucosyl Yariv reagent but interacting with the peanut agglutinin lectin was proposed. In addition, the N-terminal short AGP motif was assumed to be substituted by arabinogalactans. Altogether, AGP31 was found to be highly heterogeneous in cell walls because arabinogalactans could be absent, Hyp-O-Gal/Ara-rich motifs of different sizes were observed, and truncated forms missing the C-terminal PAC domain were found, suggesting degradation in muro and/or partial glycosylation prior to secretion.
Multilingual data-driven pronunciation

Automatic pronunciation of unknown words is a hard problem of great importance in speech technology. The difficulty of the problem appears to vary across languages, according to the ‘depth’ of orthography, although there are, as yet, little by way of quantitative comparisons. Early solutions were based on manually-written expert rules but these are expensive to derive and maintain, are entirely language-specific and—according to more recent evaluations using large test sets—do not perform very well (at least for English). By contrast, data-driven methods (which infer pronunciations from a set of examples) require little expert knowledge, can be quickly and easily applied to new languages for which an appropriate set of examples is available, and seem to perform far better than rules. In this paper, we compare the success of data-driven automatic pronunciation for four European languages: English, French, Frisian and German. We also attempt to quantify the difficulty of the problem using the entropy of the association between letters and phonemes found after prior alignment of the various dictionaries.
Social Impact Bonds: The Role of Private Capital in Outcome-Based Commissioning

Abstract Social impact bonds are payment by results contracts that leverage private social investment to cover the up-front expenditure associated with welfare services. The introduction of private principles and actors through outcome-based commissioning has received a great deal of attention in social policy research. However, there has been much less attention given to the introduction of private capital and its relation to more established forms of quasi-marketisation. This paper examines what effect private social investment has on outcome-based commissioning and whether the alternative forms of performance measurement and management, that social impact bonds bring to bear on service operations, demonstrate the capacity to engender: innovation in service delivery; improved social outcomes; future cost savings; and additionality. This paper draws on an in-depth study of four social impact bonds in the UK context, as the welfare regime at the vanguard of this policy development. The findings suggest that the introduction of private capital in outcome-based commissioning has had a number of unique and unintended effects on service providers, operations and outcomes. The paper concludes by considering whether social impact bonds represent a risk or an opportunity for public service reform both in the UK and further afield.
Assessment of Fetal Development Using Cardiac Valve Intervals

An automated method to assess the fetal physiological development is introduced which uses the component intervals between fetal cardiac valve timings and the Q-wave of fetal electrocardiogram (fECG). These intervals were estimated automatically from one-dimensional Doppler Ultrasound and noninvasive fECG. We hypothesize that the fetal growth can be estimated by the cardiac valve intervals. This hypothesis was evaluated by modeling the fetal development using the cardiac intervals and validating against the gold standard gestational age identified by Crown-Rump Length (CRL). Among the intervals, electromechanical delay time, isovolumic contraction time, ventricular filling time and their interactions were selected in a stepwise regression process that used gestational age as the target in a cohort of 57 fetuses. Compared with the gold standard age, the newly proposed regression model resulted in a mean absolute error of 3.8 weeks for all recordings and 2.7 weeks after excluding the low quality recordings. Since Fetal Heart Rate Variability (FHRV) has been proposed in the literature for assessing the fetal development, we compared the performance of gestational age estimation by our new valve-interval based method, vs. FHRV, while assuming the CRL as the gold standard. The valve interval-based method outperformed both the model based on FHRV. Results of evaluation for 30 abnormal cases showed that the new method is less affected by arrhythmias such as tachycardia and bradycardia compared to FHRV, however certain types of heart anomalies cause large errors (more than 10 weeks) with respect to the CRL-based gold standard age. Therefore, discrepancies between the regression based estimation and CRL age estimation could indicate the abnormalities. The cardiac valve intervals have been known to reflect the autonomic function. Therefore the new method potentially provides a novel approach for assessing the development of fetal autonomic nervous system, which may be growth curve independent.
Long-Term Effects of Pneumococcal Conjugate Vaccine on Nasopharyngeal Carriage of S. pneumoniae, S. aureus, H. influenzae and M. catarrhalis

Background Shifts in pneumococcal serotypes following introduction of 7-valent pneumococcal conjugate vaccine (PCV-7) may alter the presence of other bacterial pathogens co-inhabiting the same nasopharyngeal niche. Methodology/Principal Findings Nasopharyngeal prevalence rates of S. pneumoniae, S. aureus, H. influenzae and M. catarrhalis were investigated before, 3 and 4.5 years after introduction of PCV-7 in the national immunisation program in children at 11 and 24 months of age, and parents of 24-month-old children (n≈330/group) using conventional culture methods. Despite a virtual disappearance of PCV-7 serotypes over time, similar overall pneumococcal rates were observed in all age groups, except for a significant reduction in the 11-month-old group (adjusted Odds Ratio after 4.5 years 0.48, 95% Confidence Interval 0.34–0.67). Before, 3 and 4.5 years after PCV-7 implementation, prevalence rates of S. aureus were 5%, 9% and 14% at 11 months of age (3.59, 1.90–6.79) and 20%, 32% and 34% in parents (1.96, 1.36–2.83), but remained similar at 24 months of age, respectively. Prevalence rates of H. influenzae were 46%, 65% and 65% at 11 months (2.22, 1.58–3.13), 52%, 73% and 76% at 24 months of age (2.68, 1.88–3.82) and 23%, 30% and 40% in parents (2.26, 1.58–3.33), respectively. No consistent changes in M. catarrhalis carriage rates were observed over time. Conclusions/Significance In addition to large shifts in pneumococcal serotypes, persistently higher nasopharyngeal prevalence rates of S. aureus and H. influenzae were observed among young children and their parents after PCV-7 implementation. These findings may have implications for disease incidence and antibiotic treatment in the post-PCV era.
Evidence that pinocytosis in lymphoid cells has a low capacity

In contrast to adherent cells, human B and T lymphoblasts, marmoset monkey T lymphoblasts, and mouse T lymphoblasts do not form monolayers and have a poor ability to pinocytose. After a 10-min incubation of lymphoblasts at 37 degrees C, the level of internalized medium reached a plateau. During this time, lymphoblasts pinocytosed 3-4 femtoliters (1 fl = 10(-15) l) of medium per cell as calculated by the quantity of the entrapped pinocytic marker 5(6)-carboxyfluorescein. The levels of pinocytosed liquid did not increase during a subsequent 90-min incubation of cells at 37 degrees C. Adherent HeLa cells took up 27 fl of medium per cell per hour. Other types of adherent cells were reported by others to pinocytose 20 to 90 fl of medium per cell per hour. The process of pinocytosis in lymphoblasts appeared to be reversible since cells which were pre-loaded with carboxyfluorescein and then incubated at 37 degrees C in fresh medium lost the marker almost completely within 40 min. Similar results were obtained with horseradish peroxidase as the pinocytic marker. Further evidence that lymphoblasts have a low capacity for pinocytic internalization relative to adherent cells was obtained from the observation that Namalwa lymphoblasts were approximately 100 times more resistant to the cytotoxic action of the protein toxin gelonin than the adherent HeLa cells. Gelonin is a ribosome-inactivating toxin which is not capable of binding to cells, and its only mode for internalization appears to be pinocytosis. Ribosomes in cell lysates of the two lines were equally sensitive to gelonin. It is speculated that the poor pinocytic ability of lymphoid cells may reflect a fundamental difference between adherent and non-adherent cells and that this may impede the targeting of drugs into lymphoid cells.
The PageRank Citation Ranking : Bringing Order to the Web

The importance of a Web page is an inherently subjective matter, which depends on the readers interests, knowledge and attitudes. But there is still much that can be said objectively about the relative importance of Web pages. This paper describes PageRank, a mathod for rating Web pages objectively and mechanically, effectively measuring the human interest and attention devoted to them. We compare PageRank to an idealized random Web surfer. We show how to efficiently compute PageRank for large numbers of pages. And, we show how to apply PageRank to search and to user navigation.
Investigating the association between tinnitus severity and symptoms of depression and anxiety, while controlling for neuroticism, in a large middle-aged UK population

Abstract Objective: Clinical studies indicate increased risk for depression and anxiety among tinnitus patients. However population data are scarce, and no studies have controlled for neuroticism. We examined associations between tinnitus and symptoms of depression and anxiety in a large UK population, controlling for neuroticism, to explore whether neuroticism, as previously reported, fully explains the association between symptoms of depression and anxiety, and tinnitus. Design: We used the UK Biobank resource. Study sample: 171 728 participants answered hearing questions. Results: Using generalized linear modelling, we examined associations between tinnitus (mild to severe) and symptoms of depression and anxiety. Controlling for neuroticism, patients with severe tinnitus were at increased risk of depression (odds ratio (OR) = 1.27) and anxiety (OR = 1.11) symptoms, compared to those without tinnitus. Conclusions: Although it is not possible to determine whether tinnitus is a predisposing factor to depression, these results suggest an association. We suggest further exploration to determine the clinical significance of this association. Early psychosocial intervention aimed at reducing anxiety and depression in patients at increased risk might influence the extent to which tinnitus is experienced as troubling, and therefore psychological distress associated with it. Likewise, with tinnitus patients, assessment for anxiety/depression should be considered.
Approximating the Satisfiability Threshold for Random k-XOR-formulas

In this paper we study random linear systems with $k > 3$ variables per equation over the finite field GF(2), or equivalently k-XOR-CNF formulas. In a previous paper Creignou and Daudé proved that there exists a phase transition exhibiting a sharp threshold, for the consistency (satisfiability) of such systems (formulas). The control parameter for this transition is the ratio of the number of equations to the number of variables, and the scale for which the transition occurs remains somewhat elusive. In this paper we establish, for any $k > 3$, non-trivial lower and upper estimates of the value of the control ratio for which the phase transition occurs. For $k=3$ we get 0.89 and 0.93, respectively. Moreover, we give experimental results for $k=3$ suggesting that the critical ratio is about 0.92. Our estimates are clearly close to the critical ratio.
Reinforcement learning with limited reinforcement: using Bayes risk for active learning in POMDPs

Partially Observable Markov Decision Processes (POMDPs) have succeeded in planning domains that require balancing actions that increase an agent's knowledge and actions that increase an agent's reward. Unfortunately, most POMDPs are defined with a large number of parameters which are difficult to specify only from domain knowledge. In this paper, we present an approximation approach that allows us to treat the POMDP model parameters as additional hidden state in a "model-uncertainty" POMDP. Coupled with model-directed queries, our planner actively learns good policies. We demonstrate our approach on several POMDP problems.
Attainment of polarity promotes growth factor secretion by retinal pigment epithelial cells: Relevance to age-related macular degeneration

The antiangiogenic and neurotrophic growth factor, pigment epithelial derived factor (PEDF), and the proangiogenic growth factor, vascular endothelial growth factor-A (VEGF), are released from retinal pigment epithelial (RPE) cells where they play a critical role in the pathogenesis of age-related macular degeneration (AMD). Since RPE polarity may be altered in advanced AMD, we studied the effect of polarization of differentiated, human RPE monolayer cultures on expression and secretion of PEDF and VEGF. Polarized RPE demonstrated apical microvilli, expression of tight junction proteins, apical localization of Na/K- ATPase, and high transepithelial resistance (490 ± 17 Ω•cm2). PEDF secretion was about 1000 fold greater than that for VEGF in both polarized and non-polarized cultures. Polarization of the RPE monolayer increased PEDF secretion, which was predominantly apical, by 34 fold (p<0.02) and VEGF secretion, which was predominantly basolateral, by 5.7 fold (p<0.02). Treatment of non-polarized RPE cultures with bone morphogenetic protein-4 (BMP-4) had no effect on PEDF or VEGF secretion, but resulted in a dose-dependent >2-fold increase in basolateral VEGF secretion (p<0.05) in polarized cultures. Our data show that polarity is an important determinant of the level of PEDF and VEGF secretion in RPE and support the contention that loss of polarity of RPE in AMD results in marked loss of neurotrophic and vascular support for the retina potentially leading to photoreceptor loss and blindness.
Brain IGF-1 Receptors Control Mammalian Growth and Lifespan through a Neuroendocrine Mechanism

Mutations that decrease insulin-like growth factor (IGF) and growth hormone signaling limit body size and prolong lifespan in mice. In vertebrates, these somatotropic hormones are controlled by the neuroendocrine brain. Hormone-like regulations discovered in nematodes and flies suggest that IGF signals in the nervous system can determine lifespan, but it is unknown whether this applies to higher organisms. Using conditional mutagenesis in the mouse, we show that brain IGF receptors (IGF-1R) efficiently regulate somatotropic development. Partial inactivation of IGF-1R in the embryonic brain selectively inhibited GH and IGF-I pathways after birth. This caused growth retardation, smaller adult size, and metabolic alterations, and led to delayed mortality and longer mean lifespan. Thus, early changes in neuroendocrine development can durably modify the life trajectory in mammals. The underlying mechanism appears to be an adaptive plasticity of somatotropic functions allowing individuals to decelerate growth and preserve resources, and thereby improve fitness in challenging environments. Our results also suggest that tonic somatotropic signaling entails the risk of shortened lifespan.
Nutrients Can Enhance the Abundance and Expression of Alkane Hydroxylase CYP153 Gene in the Rhizosphere of Ryegrass Planted in Hydrocarbon-Polluted Soil

Plant-bacteria partnership is a promising strategy for the remediation of soil and water polluted with hydrocarbons. However, the limitation of major nutrients (N, P and K) in soil affects the survival and metabolic activity of plant associated bacteria. The objective of this study was to explore the effects of nutrients on survival and metabolic activity of an alkane degrading rhizo-bacterium. Annual ryegrass (Lolium multiflorum) was grown in diesel-contaminated soil and inoculated with an alkane degrading bacterium, Pantoea sp. strain BTRH79, in greenhouse experiments. Two levels of nutrients were applied and plant growth, hydrocarbon removal, and gene abundance and expression were determined after 100 days of sowing of ryegrass. Results obtained from these experiments showed that the bacterial inoculation improved plant growth and hydrocarbon degradation and these were further enhanced by nutrients application. Maximum plant biomass production and hydrocarbon mineralization was observed by the combined use of inoculum and higher level of nutrients. The presence of nutrients in soil enhanced the colonization and metabolic activity of the inoculated bacterium in the rhizosphere. The abundance and expression of CYP153 gene in the rhizosphere of ryegrass was found to be directly associated with the level of applied nutrients. Enhanced hydrocarbon degradation was associated with the population of the inoculum bacterium, the abundance and expression of CYP153 gene in the rhizosphere of ryegrass. It is thus concluded that the combination between vegetation, inoculation with pollutant-degrading bacteria and nutrients amendment was an efficient approach to reduce hydrocarbon contamination.
Avoiding exponential parameter growth in fuzzy systems

For standard fuzzy systems where the input membership functions are defined on a grid on the input space, and all possible combinations of rules are used, there is an exponential growth in the number of parameters of the fuzzy system as the number of input dimensions increases. This "curse of dimensionality" effect leads to problems with design of fuzzy controllers (e.g., how to tune all these parameters), training of fuzzy estimators (e.g., complexity of a gradient algorithm for training, and problems with "over parameterization" that lead to poor convergence properties), and with computational complexity in the implementation for practical problems. We introduce a fuzzy system whose number of parameters grows linearly depending upon the number of inputs, even though it is constructed by using all possible combinations of the membership functions in defining the rules. We prove that this fuzzy system is equivalent to the standard fuzzy system as long as its parameters are specified in a certain way. Then, we show that it still holds the universal approximator property by using the Stone-Welerstrass theorem. Finally, we illustrate the performance of the fuzzy system via an application.
Effect of treating isolated systolic hypertension on the risk of developing various types and subtypes of stroke: the Systolic Hypertension in the Elderly Program (SHEP).

CONTEXT The Systolic Hypertension in the Elderly Program (SHEP) demonstrated that treating isolated systolic hypertension in older patients decreased incidence of total stroke, but whether all types of stroke were reduced was not evaluated. OBJECTIVE To investigate antihypertensive drug treatment effects on incidence of stroke by type and subtype, timing of strokes, case-fatality rates, stroke residual effects, and relationship of attained systolic blood pressure to stroke incidence. DESIGN The SHEP study, a randomized, double-blind, placebo-controlled trial began March 1, 1985, and had an average follow-up of 4.5 years. SETTING AND PARTICIPANTS A total of 4736 men and women aged 60 years or older with isolated systolic hypertension at 16 clinical centers in the United States. INTERVENTIONS Patients were randomly assigned to receive treatment with 12.5 mg/d of chlorthalidone (step 1); either 25 mg/d of atenolol or 0.05 mg/d of reserpine (step 2) could be added (n = 2365); or placebo (n = 2371). MAIN OUTCOME MEASURES Occurrence, type and subtype, and timing of first strokes and stroke fatalities; and change in stroke incidence for participants (whether in active treatment or placebo groups) reaching study-specific systolic blood pressure goal (decrease of at least 20 mm Hg from baseline to below 160 mm Hg) compared with participants not reaching goal. RESULTS A total of 85 and 132 participants in the active treatment and placebo groups, respectively, had ischemic strokes (adjusted relative risk [RR], 0.63; 95% confidence interval [CI], 0.48-0.82); 9 and 19 had hemorrhagic strokes (adjusted RR, 0.46; 95% CI, 0.21-1.02); and 9 and 8 had strokes of unknown type (adjusted RR, 1.05; 95% CI, 0.40-2. 73), respectively. Four subtypes of ischemic stroke were observed in active treatment and placebo group participants, respectively, as follows: for lacunar, n = 23 and n = 43 (adjusted RR, 0.53; 95% CI, 0.32-0.88); for embolic, n = 9 and n = 16 (adjusted RR, 0.56; 95% CI, 0.25-1.27); for atherosclerotic, n = 13 and n = 13 (adjusted RR, 0. 99; 95% CI, 0.46-2.15); and for unknown subtype, n = 40 and n = 60 (adjusted RR, 0.64; 95% CI, 0.43-0.96). Treatment effect was observed within 1 year for hemorrhagic strokes but was not seen until the second year for ischemic strokes. Stroke incidence significantly decreased in participants attaining study-specific systolic blood pressure goals. CONCLUSIONS In this study, antihypertensive drug treatment reduced the incidence of both hemorrhagic and ischemic (including lacunar) strokes. Reduction in stroke incidence occurred when specific systolic blood pressure goals were attained. JAMA. 2000;284:465-471