Miracle-dz/UniFAR-FTUs huggingface dataset:
University of Groningen Metacognition in the Prisoner's Dilemma Stevens, Christopher; Taatgen, Niels; Cnossen, Fokeltje

In this paper, we show ACT-R agents capable of metacognitive reasoning about opponents in the repeated prisoner’s dilemma. Two types of metacognitive agent were developed and compared to a non-metacognitive agent and two fixed-strategy agents. The first type of metacognitive agent (opponent-perspective) takes the perspective of the opponent to anticipate the opponent’s future actions and respond accordingly. The other metacognitive agent (modeler) predicts the opponent’s next move based on the previous moves of the agent and the opponent. The modeler agent achieves better individual outcomes than a non-metacognitive agent and is more successful at encouraging cooperation. The opponent perspective agent, by contrast, fails to achieve these outcomes because it lacks important information about the opponent. These simple agents provide insights regarding modeling of metacognition in more complex tasks.
TMIX: Temporal model for indexing XML documents

Different models have been proposed recently for representing temporal data, tracking historical information and retrieving temporal queries results efficiently. We consider the problem of indexing temporal XML documents. In particular, we propose an indexing scheme that uses a summary structure and a matrix that captures the structural relationships as well as time intervals inside a temporal XML document. We introduce an algorithm to efficiently process all types of temporal queries with any depth using our newly proposed index. We show that our proposed index out-performs the state of the art indices in terms of both query processing time and support for different temporal query types.
The active metabolic rate predicts a male spider's proximity to females and expected fitness

Conspicuous traits, such as weaponry and body size, are often correlated with fitness. By contrast, we understand less about how inconspicuous physiological traits affect fitness. Not only is linking physiology directly to fitness a challenge, but in addition, behavioural studies most often focus on resting or basal metabolic rates, resulting in a poor understanding of how active metabolic rates affect fitness. Here we use the golden orb-web spider (Nephila plumipes), a species for which proximity to a female on the web predicts a male's paternity share, to examine the role of resting and active metabolic rates in fitness. Using a semi-natural experimental set-up, we show that males closer to a female have higher active metabolic rates than males further from females. This higher metabolic activity is paralleled by increased citrate synthase activity, suggesting greater mitochondrial densities. Our results link both higher active metabolic rates and increased citrate synthase activity with fitness. Coupled with the behaviour and life history of N. plumipes, these results provide insight into the evolution of physiological systems.
The AHL- and BDSF-Dependent Quorum Sensing Systems Control Specific and Overlapping Sets of Genes in Burkholderia cenocepacia H111

Quorum sensing in Burkholderia cenocepacia H111 involves two signalling systems that depend on different signal molecules, namely N-acyl homoserine lactones (AHLs) and the diffusible signal factor cis-2-dodecenoic acid (BDSF). Previous studies have shown that AHLs and BDSF control similar phenotypic traits, including biofilm formation, proteolytic activity and pathogenicity. In this study we mapped the BDSF stimulon by RNA-Seq and shotgun proteomics analysis. We demonstrate that a set of the identified BDSF-regulated genes or proteins are also controlled by AHLs, suggesting that the two regulons partially overlap. The detailed analysis of two mutually regulated operons, one encoding three lectins and the other one encoding the large surface protein BapA and its type I secretion machinery, revealed that both AHLs and BDSF are required for full expression, suggesting that the two signalling systems operate in parallel. In accordance with this, we show that both AHLs and BDSF are required for biofilm formation and protease production.
Implications of Heterogeneity in Multiple Myeloma

Multiple myeloma is the second most common hematologic malignancy in the world. Despite improvement in outcome, the disease is still incurable for most patients. However, not all myeloma are the same. With the same treatment, some patients can have very long survival whereas others can have very short survival. This suggests that there is underlying heterogeneity in myeloma. Studies over the years have revealed multiple layers of heterogeneity. First, clinical parameters such as age and tumor burden could significantly affect outcome. At the genetic level, there are also significant heterogeneity ranging for chromosome numbers, genetic translocations, and genetic mutations. At the clonal level, there appears to be significant clonal heterogeneity with multiple clones coexisting in the same patient. At the cell differentiation level, there appears to be a hierarchy of clonally related cells that have different clonogenic potential and sensitivity to therapies. These levels of complexities present challenges in terms of treatment and prognostication as well as monitoring of treatment. However, if we can clearly delineate and dissect this heterogeneity, we may also be presented with unique opportunities for precision and personalized treatment of myeloma. Some proof of concepts of such approaches has been demonstrated.
Activity of Minocycline Against Acinetobacter calcoaceticus Var. anitratus (Syn. Herellea vaginicola) and Serratia Marcescens

The activity of minocycline and tetracycline against 23 isolates of Acinetobacter calcoaceticus var. anitratus (syn. Herellea vaginicola) and 178 strains of Serratia marcescens was determined by disk and microdilution methods. The results indicate that minocycline is highly active against this species of Acinetobacter, all but one strain being inhibited by 0.007 μg of the antibiotic per ml. Tetracycline was also active, though to a lesser degree, against A. calcoaceticus. Of the 178 strains of S. marcescens tested, only seven (3.9%) had a minimum inhibitory concentration of 2 μg or less of minocycline per ml. Tetracycline was less active than minocycline against S. marcescens; with 2 μg of tetracycline per ml, only 2 of 152 (1.3%) strains were inhibited. At concentrations of 8 and 16 μg of minocycline per ml, which can be achieved in the urine with the usual doses, 44.9 and 63.5% of S. marcescens strains were inhibited, which implies its possible usefulness for the therapy of urinary tract infection due to this organism.
Purification and properties of inducible penicillin beta-lactamase isolated from Pseudomonas maltophilia

Two types of beta-lactamase were found in the cell-free extract from Pseudomonas maltophilia GN12873. One was an inducible penicillin beta-lactamase, and the other was an inducible cephalosporin beta-lactamase. The purified penicillin beta-lactamase gave a single protein band on polyacrylamide gel electrophoresis. The isoelectric point was 6.9, and the approximate molecular weight was 118,000 by gel filtration and 26,000 by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, suggesting that this enzyme consisted of four subunits. For the hydrolysis of penicillin G, the optimal pH was 8.0 and the optimal temperature was 35 degrees C. The enzyme activity was inhibited by cephamycin derivatives, carpetimycins A and B, iodine, and HgCl2, but not by clavulanic acid. Furthermore, beta-lactamase activity was almost completely inhibited by EDTA but was recovered by the addition of zinc ion. The enzyme showed a unique substrate profile, hydrolyzing N-formimidoyl thienamycin at a significant rate.
Diversity and distribution of food plants: Implications for conservation of the critically endangered Hainan gibbon

An understanding of the diversity and distribution patterns of Hainan gibbon (Nomascushainanus) foods is essential to its conservation. We used data from plots in various successional stages and Pinusmerkusii plantations (PF) of Bawangling National Nature Reserve (BNNR) to compare variations in food species diversity and composition amongst forest types. A total of 85 food species and 16,882 food plants individuals were found across forest types. Habitat-exclusive food species were most abundant in old growth natural forest (OGF), followed by mid-aged natural secondary forest (MSF). We did not find exclusive species in PF. For all food species, as well as each stem size class, PF displayed a lower species richness and abundance and, in addition, less similar species composition in each age class compared to secondary forests. The highest stem density and species richness were found in MSF. The abundance of food trees was higher in MSF and OGF than in young natural secondary forest. Results suggested that MSF could serve as an alternative habitat for Hainan gibbons after short-term recovery. Hainan gibbons might be limited to secondary forests older than 25 years old. PF was found to be unsuitable for Hainan gibbons.
Lean Body Mass is a Predictor of the Daily Requirement for Thyroid Hormone in Older Men and Women

Levothyroxine (T4) replacement need in adults with primary hypothyroidism has recently been reported to fall with age. Previous studies have demonstrated that the resting metabolic rate falls with age in euthyroid adults and that this fall is proportional to a reduction in lean body mass (LBM). Since LBM is correlated also with 24‐hour energy expenditure, this study examined the possibility that LBM might be an accurate predictor of T4 requirement. Seventy‐five hypothyroid adults receiving full replacement therapy, ranging in age from 24 to 88 years, were studied retrospectively. Lean body mass was found to be a better predictor of T4 requirement than age or weight for the entire group as well as for subgroups of men and women 51 years old and older. The age‐related reduction in LBM may be responsible for the reported decrease in the rate of fractional thyroxine degradation with age.
Information-Geometric Markov Chain Monte Carlo Methods Using Diffusions

Recent work incorporating geometric ideas in Markov chain Monte Carlo is reviewed in order to highlight these advances and their possible application in a range of domains beyond statistics. A full exposition of Markov chains and their use in Monte Carlo simulation for statistical inference and molecular dynamics is provided, with particular emphasis on methods based on Langevin diffusions. After this, geometric concepts in Markov chain Monte Carlo are introduced. A full derivation of the Langevin diffusion on a Riemannian manifold is given, together with a discussion of the appropriate Riemannian metric choice for different problems. A survey of applications is provided, and some open questions are discussed.
Levosimendan has a prolonged antispasmodic effect in isolated human radial artery bypass grafts and inhibits thrombin-induced aggregation of human platelets in vitro

We have shown that contractions of the human RA grafts are larger than those of the IMA grafts in vitro. This finding supports the higher incidence of severe vasospasm of RA during CABG. We have demonstrated that the 5-HT-induced contractions of human RA graft segments pre-incubated in 0.9% NaCl solution were stable for 120 minutes. Levosimendan, in a therapeutic concentration (0.16 μmol/L), had a prolonged effect (>90 minutes) on the 5-HT-induced tone of the human RA segment. Levosimendan also effectively decreased NA-induced contractions. The colloidal Biseko®solution is effective against both NA- and 5-HT-induced contractions in human RA graft segments. The effect of Biseko®solution on 5-HT-induced contractions lasts for only 45 minutes. The maximal contractile and vasodilating capacities as well as the endothelium-dependent relaxation of RA segments pre-incubated in levosimendan solution were comparable to controls, suggesting that the inodilator does not deteriorate the function of the graft. BKCachannels do not account for the prolonged effect of levosimendan in reducing contraction of RA graft segments. Therapeutic concentrations of levosimendan (≤0.2 μmol/L) reduced thrombin-induced platelet aggregation in vitro. The platelet inhibitory effect of levosimendan is markedly decreased by albumin and significantly enhanced upon increasing the time of pre-incubation. These findings may render the inodilator drug, levosimendan, effective in preventing the spasm of the RA and the thrombotic occlusion of the graft during the intraoperative phase of CABG.
Whole-Exome Sequencing in the Differential Diagnosis of Primary Adrenal Insufficiency in Children

Adrenal insufficiency is a rare, but potentially fatal medical condition. In children, the cause is most commonly congenital and in recent years a growing number of causative gene mutations have been identified resulting in a myriad of syndromes that share adrenal insufficiency as one of the main characteristics. The evolution of adrenal insufficiency is dependent on the variant and the particular gene affected, meaning that rapid and accurate diagnosis is imperative for effective treatment of the patient. Common practice is for candidate genes to be sequenced individually, which is a time-consuming process and complicated by overlapping clinical phenotypes. However, with the availability, and increasing cost effectiveness of whole-exome sequencing, there is the potential for this to become a powerful diagnostic tool. Here, we report the results of whole-exome sequencing of 43 patients referred to us with a diagnosis of familial glucocorticoid deficiency (FGD) who were mutation negative for MC2R, MRAP, and STAR the most commonly mutated genes in FGD. WES provided a rapid genetic diagnosis in 17/43 sequenced patients, for the remaining 60% the gene defect may be within intronic/regulatory regions not covered by WES or may be in gene(s) representing novel etiologies. The diagnosis of isolated or familial glucocorticoid deficiency was only confirmed in 3 of the 17 patients, other genetic diagnoses were adrenal hypo- and hyperplasia, Triple A, and autoimmune polyendocrinopathy syndrome type I, emphasizing both the difficulty of phenotypically distinguishing between disorders of PAI and the utility of WES as a tool to achieve this.
Digital modulation classification using power moment matrices

With the rising number of modulation types used in multi-user and multi-service digital communication systems, the need to find efficient methods for their discrimination in the presence of noise has become increasingly important. We present a new approach based on a pattern recognition method previously applied to word spotting problems in binary images. In this approach, a large number of spatial moments are arranged in a symmetric positive definite matrix for which eigendecomposition and noise subspace processing methods can be applied. The resultant denoised moment matrix has entries which are used in place of the raw moments for improved pattern classification. In this paper, we generalize the moment matrix technique to grey scale images and apply the technique to discrimination between M-ary PSK and QAM constellations in signal space. Invariance to unknown phase angle and signal amplitude is achieved by representing the in-phase and quadrature components of the signal in the complex plane, and computing joint moments of normalized magnitude and phase components.
Elaborating the Role of Natural Products-Induced Autophagy in Cancer Treatment: Achievements and Artifacts in the State of the Art

Autophagy is a homeostatic process that is highly conserved across different types of mammalian cells. Autophagy is able to relieve tumor cell from nutrient and oxidative stress during the rapid expansion of cancer. Excessive and sustained autophagy may lead to cell death and tumor shrinkage. It was shown in literature that many anticancer natural compounds and extracts could initiate autophagy in tumor cells. As summarized in this review, the tumor suppressive action of natural products-induced autophagy may lead to cell senescence, provoke apoptosis-independent cell death, and complement apoptotic cell death by robust or target-specific mechanisms. In some cases, natural products-induced autophagy could protect tumor cells from apoptotic death. Technical variations in detecting autophagy affect data quality, and study focus should be made on elaborating the role of autophagy in deciding cell fate. In vivo study monitoring of autophagy in cancer treatment is expected to be the future direction. The clinical-relevant action of autophagy-inducing natural products should be highlighted in future study. As natural products are an important resource in discovery of lead compound of anticancer drug, study on the role of autophagy in tumor suppressive effect of natural products continues to be necessary and emerging.
Probiotics for treatment of acute diarrhoea in children: randomised clinical trial of five different preparations

Objective To compare the efficacy of five probiotic preparations recommended to parents in the treatment of acute diarrhoea in children. Design Randomised controlled clinical trial in collaboration with family paediatricians over 12 months. Setting Primary care. Participants Children aged 3-36 months visiting a family paediatrician for acute diarrhoea. Intervention Children's parents were randomly assigned to receive written instructions to purchase a specific probiotic product: oral rehydration solution (control group); Lactobacillus rhamnosus strain GG; Saccharomyces boulardii; Bacillus clausii; mix of L delbrueckii var bulgaricus, Streptococcus thermophilus, L acidophilus, and Bifidobacterium bifidum; or Enterococcus faecium SF68. Main outcome measures Primary outcomes were duration of diarrhoea and daily number and consistency of stools. Secondary outcomes were duration of vomiting and fever and rate of admission to hospital. Safety and tolerance were also recorded. Results 571 children were allocated to intervention. Median duration of diarrhoea was significantly shorter (P<0.001) in children who received L rhamnosus strain GG (78.5 hours) and the mix of four bacterial strains (70.0 hours) than in children who received oral rehydration solution alone (115.0 hours). One day after the first probiotic administration, the daily number of stools was significantly lower (P<0.001) in children who received L rhamnosus strain GG and in those who received the probiotic mix than in the other groups. The remaining preparations did not affect primary outcomes. Secondary outcomes were similar in all groups. Conclusions Not all commercially available probiotic preparations are effective in children with acute diarrhoea. Paediatricians should choose bacterial preparations based on effectiveness data. Trial registration number Current Controlled Trials ISRCTN56067537.
A Pipelining Approach to Informed Prefetching in Distributed Multi-level Storage Systems

In this paper, we present an informed prefetching technique called IPODS that makes use of application-disclosed access patterns to prefetch hinted blocks in distributed multi-level storage systems. We develop a prefetching pipeline in IPODS, where an informed prefetching process is divided into a set of independent prefetching steps among multiple storage levels in a distributed system. In the IPODS system, while data blocks are prefetched from hard disks to memory buffers in remote storage servers, data blocks buffered in the servers are prefetched through networks to clients' local cache. We show that these two prefetching steps can be handled in a pipelining manner to improve I/O performance of distributed storage systems. Our IPODS technique differs itself from existing prefetching schemes in two ways. First, IPODS reduces applications' I/O stalls by keeping hinted data in clients' local caches and storage servers' fast buffers (e.g., solid state disks). Second, in a prefetching pipeline, multiple informed prefetching mechanisms semi-dependently coordinate to fetch blocks (1) from low-level (slow) to high-level (fast) storage devices in servers and (2) from high-level devices in servers to clients' local cache. The prefetching pipeline in IPODS judiciously hides network latencies in distributed storage systems, thereby reducing the overall I/O access time in distributed systems. Using a wide range of real-world I/O traces, our experiments show that IPODS can improve noticeably I/O performance of distributed storage systems.
Single Nucleotide Polymorphism rs10919543 in FCGR2A/FCGR3A Region Confers Susceptibility to Takayasu Arteritis in Chinese Population

Background:Takayasu arteritis (TA) is a rare inflammatory arteriopathy of unknown etiology. The aim of this study was to investigate the genetic susceptibility to TA in a Chinese population. Methods:Four single nucleotide polymorphisms (SNPs) those locate in the IL12B region (rs56167332), the MLX region (rs665268), the FCGR2A/FCGR3A locus (rs10919543), and the HLA-B/MICA locus (rs12524487), associated with TA in different population, were genotyped in 123 Chinese TA patients and 147 healthy controls from January 2013 to August 2014. A Chi-square test was used to test for genotype/allele frequencies variants. Results:Among the four SNPs, rs10919543 was found to be significantly associated with TA in the studied population. The GG genotype of rs10919543 at the FCGR2A/FCGR3A locus is a high risk factor (odds ratio [OR] = 6.532, 95% confidence interval [CI] = 2.402 − 17.763, P < 0.001) for TA. Among TA patients, the level of eosinophil granulocytes (Eos) in the peripheral blood was observed to be higher in the GG group of rs10919543 (n = 23, Eos = 0.11 [0.08, 0.17] ×109/L) than the GA + AA group (n = 100, Eos = 0.08 [0.05, 0.13] ×109/L, P = 0.028). No correlation between the genotypes of the other three SNPs and TA patients was observed. Conclusions:Our findings revealed unique genetic pattern in Chinese TA patients that may be partly responsible for the higher risk of TA in this population. FCGR2A/FCGR3A-related immune disorder might contribute to the etiology of TA.
Radar Reflectivity and Altitude Distributions of Lightning as a Function of IC, CG, and HY Flashes: Implications for LNOx Production

Two dimensional (2‐D) histogram distributions of lightning flashes relative to radar reflectivity and altitude were created using a total of 41,180 intercloud/intracloud (IC) flashes, 3,326 cloud‐to‐ground (CG) flashes, and 4,349 hybrid (HY) flashes that originated in multicells; 111,479 IC flashes, 8,588 CG flashes, and 11,699 HY flashes that originated in mesoscale convective systems; and 91,283 IC flashes, 3,023 CG flashes, and 7,872 HY flashes that originated in supercells that occurred over northern Alabama and southern Tennessee. It was shown that although CG flashes initiate and propagate at the same altitude irrespective of storm type, IC flashes could have differences of up to 10 °C, while for HY flashes these differences increased to up to 20 °C relative to storm type. Further, IC, CG, and HY flashes propagated in lower reflectivities than where they initiated, while CG flashes initiated and propagated within higher reflectivities than IC and HY flashes. HY flashes were also twice as large as IC flashes and ~40% larger than CG flashes, and flashes that originated in mesoscale convective systems had larger overall sizes as compared to multicells and supercells. When comparing the new 2‐D histogram distributions to the legacy distributions used for the calculation of lightning‐produced nitrogen oxides (LNOx), it was shown that the new distributions perform much better, with higher Pearson product moment correlation coefficient values and much lower root‐mean‐square errors. These new distributions are thus more appropriate to use when modeling LNOx and will lead to more accurate LNOx estimations than using the legacy distributions.