Miracle-dz/UniFAR-FTUs huggingface dataset:
Sirt3 prevents maternal obesity-associated oxidative stress and meiotic defects in mouse oocytes

Maternal obese environment has been reported to induce oxidative stress and meiotic defects in oocytes, however the underlying molecular mechanism remains unclear. Here, using mice fed a high fat diet (HFD) as an obesity model, we first detected enhanced reactive oxygen species (ROS) content and reduced Sirt3 expression in HFD oocytes. We further observed that specific depletion of Sirt3 in control oocytes elevates ROS levels while Sirt3 overexpression attenuates ROS production in HFD oocytes, with significant suppression of spindle disorganization and chromosome misalignment phenotypes that have been reported in the obesity model. Candidate screening revealed that the acetylation status of lysine 68 on superoxide dismutase (SOD2K68) is dependent on Sirt3 deacetylase activity in oocytes, and acetylation-mimetic mutant SOD2K68Q results in almost threefold increase in intracellular ROS. Moreover, we found that acetylation levels of SOD2K68 are increased by ∼80% in HFD oocytes and importantly, that the non-acetylatable-mimetic mutant SOD2K68R is capable of partially rescuing their deficient phenotypes. Together, our data identify Sirt3 as an important player in modulating ROS homeostasis during oocyte development, and indicate that Sirt3-dependent deacetylation of SOD2 plays a protective role against oxidative stress and meiotic defects in oocytes under maternal obese conditions.
Spatial Outsourcing for Location-based Services

The embedding of positioning capabilities in mobile devices and the emergence of location-based applications have created novel opportunities for utilizing several types of multidimensional data through spatial outsourcing. In this setting, a data owner (DO) delegates its data management tasks to a location-based service (LBS) that processes queries originating from several clients/subscribers. Because the LBS is not the real owner of the data, it must prove (to each client) the correctness of query output using an authenticated structure signed by the DO. Currently there is very narrow selection of multidimensional authenticated structures, among which the VR-tree is the best choice. Our first contribution is the MR-tree, a novel index suitable for spatial outsourcing. We show, analytically and experimentally, that the MR-tree outperforms the VR-tree, usually by orders of magnitude, on all performance metrics, including construction cost, index size, query and verification overhead. Motivated by the fact that successive queries by the same mobile client exhibit locality, we also propose a synchronized caching technique that utilizes the results of previous queries to reduce the size of the additional information sent to the client for verification purposes.
Bias in Template-to-Product Ratios in Multitemplate PCR

ABSTRACT Bias introduced by the simultaneous amplification of specific genes from complex mixtures of templates remains poorly understood. To explore potential causes and the extent of bias in PCR amplification of 16S ribosomal DNAs (rDNAs), genomic DNAs of two closely and one distantly related bacterial species were mixed and amplified with universal, degenerate primers. Quantification and comparison of template and product ratios showed that there was considerable and reproducible overamplification of specific templates. Variability between replicates also contributed to the observed bias but in a comparatively minor way. Based on these initial observations, template dosage and differences in binding energies of permutations of the degenerate, universal primers were tested as two likely causes of this template-specific bias by using 16S rDNA templates modified by site-directed mutagenesis. When mixtures of mutagenized templates containing AT- and GC-rich priming sites were used, templates containing the GC-rich permutation amplified with higher efficiency, indicating that different primer binding energies may to a large extent be responsible for overamplification. In contrast, gene copy number was found to be an unlikely cause of the observed bias. Similarly, amplification from DNA extracted from a natural community to which different amounts of genomic DNA of a single bacterial species were added did not affect relative product ratios. Bias was reduced considerably by using high template concentrations, by performing fewer cycles, and by mixing replicate reaction preparations.
Human CD4+ T cell recent thymic emigrants are identified by protein tyrosine kinase 7 and have reduced immune function

CD4+ recent thymic emigrants (RTEs) comprise a clinically and immunologically important T cell population that indicates thymic output and that is essential for maintaining a diverse αβ–T cell receptor (TCR) repertoire of the naive CD4+ T cell compartment. However, their frequency and function are poorly understood because no known surface markers distinguish them from older non-RTE naive CD4+ T cells. We demonstrate that protein tyrosine kinase 7 (PTK7) is a novel marker for human CD4+ RTEs. Consistent with their recent thymic origin, human PTK7+ RTEs contained higher levels of signal joint TCR gene excision circles and were more responsive to interleukin (IL)-7 compared with PTK7− naive CD4+ T cells, and rapidly decreased after complete thymectomy. Importantly, CD4+ RTEs proliferated less and produced less IL-2 and interferon-γ than PTK7− naive CD4+ T cells after αβ-TCR/CD3 and CD28 engagement. This immaturity in CD4+ RTE effector function may contribute to the reduced CD4+ T cell immunity observed in contexts in which CD4+ RTEs predominate, such as in the fetus and neonate or after immune reconstitution. The ability to identify viable CD4+ RTEs by PTK7 staining should be useful for monitoring thymic output in both healthy individuals and in patients with genetic or acquired CD4+ T cell immunodeficiencies.
The Transfer of Object Learning after Training with Multiple Exemplars

Object recognition improves with training. This training effect only partially generalizes to untrained images of the trained objects (new exemplars, orientation,…). The aim of this study is to investigate whether and to what extent the learning transfer improves when participants are trained with more exemplars of an object. Participants were trained to recognize two sets of stimuli using a backward masking paradigm. During training with the first set, only one exemplar of each object was presented. The second set was trained using four exemplars of each object. After 3 days of training, participants were tested on all the trained exemplars and a completely new exemplar of the same objects. In addition, recognition performance was compared to a set of completely new objects. For the objects of which four exemplars were used during training, participants showed more generalization toward new exemplars compared to when they were only trained with one exemplar. Part of the generalization effect extended to completely new objects. In conclusion, more variation during training leads to more generalization toward new visual stimuli.
The pharmacological costs of complete liver resections in unselected advanced colorectal cancer patients: a review of published Phase II and III trials

The pharmacological costs of regimens used as front-line therapy in advanced colorectal cancer patients and their impact on the liver resection rates have not been considered. In this paper, we made a review of published randomized Phase II and III trials that reported the liver resection rates following upfront chemotherapy and linked this outcome to the pharmacological costs of drugs used. The costs are calculated based on the price at Pharmacy of our Hospital in Legnago (Italy), and as a measure of activity, we used the number of patients needed to treat to get one complete liver resection. Number needed to treat is highly variable among the different trials according to patient’s characteristics, tumor biology and the efficacy of chemotherapy administered. The range of activity is greatly amplified when the costs are compared.
Do surfaces of positive electrostatic potential on different halogen derivatives in molecules attract? like attracting like!

Coulomb's law states that like charges repel, and unlike charges attract. However, it has recently been theoretically revealed that two similarly charged conducting spheres will almost always attract each other when both are in close proximity. Using multiscale first principles calculations, we illustrate practical examples of several intermolecular complexes that are formed by the consequences of attraction between positive atomic sites of similar or dissimilar electrostatic surface potential on interacting molecules. The results of the quantum theory of atoms in molecules and symmetry adapted perturbation theory support the attraction between the positive sites, characterizing the F•••X (X = F, Cl, Br) intermolecular interactions in a series of 20 binary complexes as closed‐shell type, although the molecular electrostatic surface potential approach does not (a failure! ). Dispersion that has an r−6 dependence, where r is the equilibrium distance of separation, is found to be the sole driving force pushing the two positive sites to attract. © 2017 Wiley Periodicals, Inc.
Coherence of VCSEL's for holographic interconnects

Temporal and spatial coherence measurements were conducted on the emission from AlGaAs-GaAs vertical-cavity surface-emitting lasers (VCSEL's). Results of both CW and pulsed conditions from devices of 8- and 15-/spl mu/m diameter are reported. Coherence length of 0.6 mm for multi-mode and /spl sim/75 cm for single-mode were obtained. Thermal chirp reduces the single-mode coherence to 16 mm for 5 ns pulses. For holograms smaller than 0.6 mm in size the density of information that can be read by the VCSEL's is diffraction-limited by the size of the holographic element. <<ETX>>
Analysis of sampling techniques for association rule mining

In this paper, we present a comprehensive theoretical analysis of the sampling technique for the association rule mining problem. Most of the previous works have concentrated only on the empirical evaluation of the effectiveness of sampling for the step of finding frequent itemsets. To the best of our knowledge, a theoretical framework to analyze the quality of the solutions obtained by sampling has not been studied. Our contributions are two-fold. First, we present the notions of ε-close frequent itemset mining and ε-close association rule mining that help assess the quality of the solutions obtained by sampling. Secondly, we show that both the frequent items mining and association rule mining problems can be solved satisfactorily with a sample size that is independent of both the number of transactions size and the number of items. Let θ be the required support, ε the closeness parameter, and 1/h the desired bound on the probability of failure. We show that the sampling based analysis succeeds in solving both ε-close frequent itemset mining and ε-close association rule mining with a probability of at least (1 - 1/h) with a sample of size S = O(1/ε2θ [Δ + log h/(1 - ε)θ]), where Δ is the maximum number of items present in any transaction. Thus, we establish that it is possible to speed up the entire process of association rule mining for massive databases by working with a small sample while retaining any desired degree of accuracy. Our work gives a comprehensive explanation for the well known empirical successes of sampling for association rule mining.
TRYGVE HAAVELMO AND THE EMERGENCE OF CAUSAL CALCULUS

Haavelmo was the first to recognize the capacity of economic models to guide policies. This paper describes some of the barriers that Haavelmo’s ideas have had (and still have) to overcome and lays out a logical framework that has evolved from Haavelmo’s insight and matured into a coherent and comprehensive account of the relationships between theory, data, and policy questions. The mathematical tools that emerge from this framework now enable investigators to answer complex policy and counterfactual questions using simple routines, some by mere inspection of the model’s structure. Several such problems are illustrated by examples, including misspecification tests, nonparametric identification, mediation analysis, and introspection. Finally, we observe that economists are largely unaware of the benefits that Haavelmo’s ideas bestow upon them and, to close this gap, we identify concrete recent advances in causal analysis that economists can utilize in research and education.
Physicochemical and Sensory Characteristics of Whey-based White Cheese Supplemented with Whole Milk Powder

Aims: The aim of the study is to manufacture and determine the physicochemical and sensory characteristics of white cheese from whey supplemented with milk powder. Methodology: Cheese was manufactured from whey left after mozzarella cheese manufacture Conclusion: The concentration of whole milk powder affected all physicochemical characteristics of cheese except total solids and ash contents, while the storage period affected all physicochemical characteristics except fat content and pH of cheese.
Anticonvulsant properties of the ketogenic diet in mice.

An animal model for study of the anticonvulsant properties of the ketogenic diet is described. A high fat diet (70% lipid) based on raw pork sausage and casein is ingested and tolerated moderately well by mice. Pups weaned onto the diet at age 16 days exhibited significant resistance to maximal electroshock and hydration threshold electroshock, as well as some protection against the tonic extensor phase of bicuculline-induced seizures, when challenged 10 days later at age 26 days. At this time the animals revealed a mean total blood ketone body concentration of 2.56 mM (controls, 0.30 mM). No protection against threshold electroshock or pentylenetetrazol-induced convulsions was observed. Protection against maximal electroshock, as well as ketonemia, disappeared within 3.5 hours of initiation of standard sustenance. Pups fed the high fat diet (or starved) for only one day at age 25 days did not exhibit increased resistance to experimental convulsions and were not as ketonemic as animals which had ingested the diet for 10 days. Similar negative results were obtained when adult mice were fed the ketogenic diet for 10 days. Results are discussed in terms of utilization of ketone bodies for cerebral energy metabolism.
Can citation analysis of Web publications better detect research fronts?

We present evidence that in some research fields, research published in journals and reported on the Web may collectively represent different evolutionary stages of the field, with journals lagging a few years behind the Web on average, and that a "two-tier" scholarly communication system may therefore be evolving. We conclude that in such fields, (a) for detecting current research fronts, author co-citation analyses (ACA) using articles published on the Web as a data source can outperform traditional ACAs using articles published in journals as data, and that (b) as a result, it is important to use multiple data sources in citation analysis studies of scholarly communication for a complete picture of communication patterns. Our evidence stems from comparing the respective intellectual structures of the XML research field, a subfield of computer science, as revealed from three sets of ACA covering two time periods: (a) from the field's beginnings in 1996 to 2001, and (b) from 2001 to 2006. For the first time period, we analyze research articles both from journals as indexed by the Science Citation Index (SCI) and from the Web as indexed by CiteSeer. We follow up by an ACA of SCI data for the second time period. We find that most trends in the evolution of this field from the first to the second time period that we find when comparing ACA results from the SCI between the two time periods already were apparent in the ACA results from CiteSeer during the first time period.
A Lysine at the C-Terminus of an Odorant-Binding Protein is Involved in Binding Aldehyde Pheromone Components in Two Helicoverpa Species

Odorant-binding proteins (OBPs) are soluble proteins, whose role in olfaction of insects is being recognized as more and more important. We have cloned, expressed and purified an OBP (HarmOBP7) from the antennae of the moth Helicoverpa armigera. Western blot experiments indicate specific expression of this protein in the antennae of adults. HarmOBP7 binds both pheromone components Z-11-hexadecenal and Z-9-hexadecenal with good affinity. We have also performed a series of binding experiments with linear aldehydes, alcohols and esters, as well as with other compounds and found a requirement of medium size for best affinity. The affinity of OBP7, as well as that of a mutant lacking the last 6 residues does not substantially decrease in acidic conditions, but increases at basic pH values with no significant differences between wild-type and mutant. Binding to both pheromone components, instead, is negatively affected by the lack of the C-terminus. A second mutant, where one of the three lysine residues in the C-terminus (Lys123) was replaced by methionine showed reduced affinity to both pheromone components, as well as to their analogues, thus indicating that Lys123 is involved in binding these compounds, likely forming hydrogen bonds with the functional groups of the ligands.
A randomized controlled trial of in-patient treatment for anorexia nervosa in medically unstable adolescents

Background Anorexia nervosa (AN) is a serious disorder incurring high costs due to hospitalization. International treatments vary, with prolonged hospitalizations in Europe and shorter hospitalizations in the USA. Uncontrolled studies suggest that longer initial hospitalizations that normalize weight produce better outcomes and fewer admissions than shorter hospitalizations with lower discharge weights. This study aimed to compare the effectiveness of hospitalization for weight restoration (WR) to medical stabilization (MS) in adolescent AN. Method We performed a randomized controlled trial (RCT) with 82 adolescents, aged 12–18 years, with a DSM-IV diagnosis of AN and medical instability, admitted to two pediatric units in Australia. Participants were randomized to shorter hospitalization for MS or longer hospitalization for WR to 90% expected body weight (EBW) for gender, age and height, both followed by 20 sessions of out-patient, manualized family-based treatment (FBT). Results The primary outcome was the number of hospital days, following initial admission, at the 12-month follow-up. Secondary outcomes were the total number of hospital days used up to 12 months and full remission, defined as healthy weight (>95% EBW) and a global Eating Disorder Examination (EDE) score within 1 standard deviation (s.d.) of published means. There was no significant difference between groups in hospital days following initial admission. There were significantly more total hospital days used and post-protocol FBT sessions in the WR group. There were no moderators of primary outcome but participants with higher eating psychopathology and compulsive features reported better clinical outcomes in the MS group. Conclusions Outcomes are similar with hospitalizations for MS or WR when combined with FBT. Cost savings would result from combining shorter hospitalization with FBT.
Implementation of a Respiratory Therapist-Driven Protocol for Neonatal Ventilation: Impact on the Premature Population

OBJECTIVE. The purpose of this work was to evaluate the impact of the implementation of a ventilation protocol driven by registered respiratory therapists on respiratory outcomes of premature infants with birth weight ≤1250 g. METHODS. A ventilation protocol driven by a registered respiratory therapist was developed by a multidisciplinary group and implemented in our unit in July 2004. A retrospective review of 301 inborn infants with birth weight ≤1250 g who were mechanically ventilated was performed. Ninety-three infants were ventilated before the ventilation protocol (before), 109 in the first year (after 1) and 99 during the second year (after 2) after the ventilation protocol implementation. Data were collected with a predefined form. RESULTS. The baseline characteristics of the population were similar among the 3 groups, except for a significant smaller number of male infants in the first year after the protocol implementation. The significant differences among the 3 periods were as follows: (1) time of first extubation attempt; (2) duration of mechanical ventilation; and (3) rate of extubation failure (40%, 26%, and 20%). There was no difference in the rate of air leaks, patent ductus arteriosus ligation, necrotizing enterocolitis, bronchopulmonary dysplasia, or death. There was a significant decrease in the combined rates of intraventricular hemorrhage grades III to IV and/or periventricular leukomalacia (31%, 18%, and 4%) after the protocol implementation. CONCLUSIONS. In this study, we were able to demonstrate for the first time a significant improvement on the weaning time and duration of mechanical ventilation with the implementation of a ventilation protocol driven by a registered respiratory therapist in the premature population. Based on our experience, other institutions can customize ventilation protocols to their local practice. However, a prospective, randomized, controlled study should be planned to evaluate long-term outcomes such as BPD and neurodevelopment.
The immunoglobulin superfamily in Caenorhabditis elegans and Drosophila melanogaster

Hobert et al. ([Hobert et al., 2004][1]) have made a number of criticisms on our paper ([Vogel et al., 2003][2]). In the following paragraphs we give our replies to these criticisms. In a number of cases, the comments do provide useful corrections to the paper. Nevertheless, the major conclusions of
Control Space Reduction and Real-Time Accurate Modeling of Continuum Manipulators Using Ritz and Ritz–Galerkin Methods

To address the challenges with real-time accurate modeling of multisegment continuum manipulators in the presence of significant external and body loads, we introduce a novel series solution for variable-curvature Cosserat rod static and Lagrangian dynamic methods. By combining a modified Lagrange polynomial series solution, based on experimental observations, with Ritz and Ritz–Galerkin methods, the infinite modeling state space of a continuum manipulator is minimized to geometrical position of a handful of physical points (in our case two). As a result, a unified easy to implement vector formalism is proposed for the nonlinear impedance and configuration control. We showed that by considering the mechanical effects of highly elastic axial deformation, the model accuracy is increased up to 6%. The proposed model predicts experimental results with 6%–8% (4–6 mm) mean error for the Ritz–Galerkin method in static cases and 16%–20% (12–14 mm) mean error for the Ritz method in dynamic cases, in planar and general three-dimensional motions. Comparing to five different models in the literature, our approximate solution is shown to be more accurate with the smallest possible number of modeling states and suitable for real-time modeling, observation, and control applications.