Miracle-dz/UniFAR-FTUs huggingface dataset:
Quasi-isometries and rigidity of solvable groups

In this note, we announce the first results on quasi-isometric rigidity of non-nilpotent polycyclic groups. In particular, we prove that any group quasi-isometric to the three dimenionsional solvable Lie group Sol is virtually a lattice in Sol. We prove analogous results for groups quasi-isometric to $R \ltimes R^n$ where the semidirect product is defined by a diagonalizable matrix of determinant one with no eigenvalues on the unit circle. Our approach to these problems is to first classify all self quasi-isometries of the solvable Lie group. Our classification of self quasi-isometries for $R \ltimes \R^n$ proves a conjecture made by Farb and Mosher in [FM4]. Our techniques for studying quasi-isometries extend to some other classes of groups and spaces. In particular, we characterize groups quasi-isometric to any lamplighter group, answering a question of de la Harpe [dlH]. Also, we prove that certain Diestel-Leader graphs are not quasi-isometric to any finitely generated group, verifying a conjecture of Diestel and Leader from [DL] and answering a question of Woess from [SW],[Wo1]. We also prove that certain non-unimodular, non-hyperbolic solvable Lie groups are not quasi-isometric to finitely generated groups. The results in this paper are contributions to Gromov's program for classifying finitely generated groups up to quasi-isometry [Gr2]. We introduce a new technique for studying quasi-isometries, which we refer to as "coarse differentiation".
Shewanella oneidensis MR-1 Restores Menaquinone Synthesis to a Menaquinone-Negative Mutant

ABSTRACT The mechanisms underlying the use of insoluble electron acceptors by metal-reducing bacteria, such as Shewanella oneidensis MR-1, are currently under intensive study. Current models for shuttling electrons across the outer membrane (OM) of MR-1 include roles for OM cytochromes and the possible excretion of a redox shuttle. While MR-1 is able to release a substance that restores the ability of a menaquinone (MK)-negative mutant, CMA-1, to reduce the humic acid analog anthraquinone-2,6-disulfonate (AQDS), cross-feeding experiments conducted here showed that the substance released by MR-1 restores the growth of CMA-1 on several soluble electron acceptors. Various strains derived from MR-1 also release this substance; these include mutants lacking the OM cytochromes OmcA and OmcB and the OM protein MtrB. Even though strains lacking OmcB and MtrB cannot reduce Fe(III) or AQDS, they still release a substance that restores the ability of CMA-1 to use MK-dependent electron acceptors, including AQDS and Fe(III). Quinone analysis showed that this released substance restores MK synthesis in CMA-1. This ability to restore MK synthesis in CMA-1 explains the cross-feeding results and challenges the previous hypothesis that this substance represents a redox shuttle that facilitates metal respiration.
Generating High-Coverage Semantic Orientation Lexicons From Overtly Marked Words and a Thesaurus

Sentiment analysis often relies on a semantic orientation lexicon of positive and negative words. A number of approaches have been proposed for creating such lexicons, but they tend to be computationally expensive, and usually rely on significant manual annotation and large corpora. Most of these methods use WordNet. In contrast, we propose a simple approach to generate a high-coverage semantic orientation lexicon, which includes both individual words and multi-word expressions, using only a Roget-like thesaurus and a handful of affixes. Further, the lexicon has properties that support the Polyanna Hypothesis. Using the General Inquirer as gold standard, we show that our lexicon has 14 percentage points more correct entries than the leading WordNet-based high-coverage lexicon (SentiWordNet). In an extrinsic evaluation, we obtain significantly higher performance in determining phrase polarity using our thesaurus-based lexicon than with any other. Additionally, we explore the use of visualization techniques to gain insight into the our algorithm beyond the evaluations mentioned above.
Targeting Class IA PI3K Isoforms Selectively Impairs Cell Growth, Survival, and Migration in Glioblastoma

The phosphoinositide 3-kinase (PI3K)/Akt/mammalian target of rapamycin (mTOR) pathway is frequently activated in human cancer and plays a crucial role in glioblastoma biology. We were interested in gaining further insight into the potential of targeting PI3K isoforms as a novel anti-tumor approach in glioblastoma. Consistent expression of the PI3K catalytic isoform PI3K p110α was detected in a panel of glioblastoma patient samples. In contrast, PI3K p110β expression was only rarely detected in glioblastoma patient samples. The expression of a module comprising the epidermal growth factor receptor (EGFR)/PI3K p110α/phosphorylated ribosomal S6 protein (p-S6) was correlated with shorter patient survival. Inhibition of PI3K p110α activity impaired the anchorage-dependent growth of glioblastoma cells and induced tumor regression in vivo. Inhibition of PI3K p110α or PI3K p110β also led to impaired anchorage-independent growth, a decreased migratory capacity of glioblastoma cells, and reduced the activation of the Akt/mTOR pathway. These effects were selective, because targeting of PI3K p110δ did not result in a comparable impairment of glioblastoma tumorigenic properties. Together, our data reveal that drugs targeting PI3K p110α can reduce growth in a subset of glioblastoma tumors characterized by the expression of EGFR/PI3K p110α/p-S6.
COCA: a secure distributed online certification authority

COCA is a fault-tolerant and secure online certification authority that has been built and deployed both in a local area network and in the Internet. Extremely weak assumptions characterize environments in which COCA's protocols execute correctly: no assumption is made about execution speed and message delivery delays; channels are expected to exhibit only intermittent reliability; and with 3t + 1 COCA servers up to t may be faulty or compromised. COCA is the first system to integrate a Byzantine quorum system (used to achieve availability) with proactive recovery (used to defend against mobile adversaries which attack, compromise, and control one replica for a limited period of time before moving on to another). In addition to tackling problems associated with combining fault-tolerance and security, new proactive recovery protocols had to be developed. Experimental results give a quantitative evaluation for the cost and effectiveness of the protocols.
MUCILAGE-MODIFIED4 Encodes a Putative Pectin Biosynthetic Enzyme Developmentally Regulated by APETALA2, TRANSPARENT TESTA GLABRA1, and GLABRA2 in the Arabidopsis Seed Coat1

The Arabidopsis seed coat epidermis undergoes a complex process of differentiation that includes the biosynthesis and secretion of large quantities of pectinaceous mucilage, cytoplasmic rearrangement, and secondary cell wall biosynthesis. Mutations in MUM4 (MUCILAGE-MODIFIED4) lead to a decrease in seed coat mucilage and incomplete cytoplasmic rearrangement. We show that MUM4 encodes a putative NDP-l-rhamnose synthase, an enzyme required for the synthesis of the pectin rhamnogalacturonan I, the major component of Arabidopsis mucilage. This result suggests that the synthesis of monosaccharide substrates is a limiting factor in the biosynthesis of pectinaceous seed coat mucilage. In addition, the reduced cytoplasmic rearrangement observed in the absence of a key enzyme in pectin biosynthesis in mum4 mutants establishes a causal link between mucilage production and cellular morphogenesis. The cellular phenotype seen in mum4 mutants is similar to that of several transcription factors (AP2 [APETALA2], TTG1 [TRANSPARENT TESTA GLABRA1], TTG2 MYB61, and GL2 [GLABRA2]). Expression studies suggest that MUM4 is developmentally regulated in the seed coat by AP2, TTG1, and GL2, whereas TTG2 and MYB61 appear to be regulating mucilage production through alternate pathway(s). Our results provide a framework for the regulation of mucilage production and secretory cell differentiation.
Hardware acceleration of transactional memory on commodity systems

The adoption of transactional memory is hindered by the high overhead of software transactional memory and the intrusive design changes required by previously proposed TM hardware. We propose that hardware to accelerate software transactional memory (STM) can reside outside an unmodified commodity processor core, thereby substantially reducing implementation costs. This paper introduces Transactional Memory Acceleration using Commodity Cores (TMACC), a hardware-accelerated TM system that does not modify the processor, caches, or coherence protocol. We present a complete hardware implementation of TMACC using a rapid prototyping platform. Using this hardware, we implement two unique conflict detection schemes which are accelerated using Bloom filters on an FPGA. These schemes employ novel techniques for tolerating the latency of fine-grained asynchronous communication with an out-of-core accelerator. We then conduct experiments to explore the feasibility of accelerating TM without modifying existing system hardware. We show that, for all but short transactions, it is not necessary to modify the processor to obtain substantial improvement in TM performance. In these cases, TMACC outperforms an STM by an average of 69% in applications using moderate-length transactions, showing maximum speedup within 8% of an upper bound on TM acceleration. Overall, we demonstrate that hardware can substantially accelerate the performance of an STM on unmodified commodity processors.
Attitudes towards and perceptions about contraceptive use among married refugee women of Somali descent living in Finland

Objectives To assess attitudes towards and perceptions about contraceptive use among married refugee women of Somali descent living in Finland. Method A sample of 100 married refugee women of Somali descent (18–50 years of age) were invited to participate in a study on contraceptive use in Finland (30 women refused). Qualitative and quantitative methods were used to collect the data. Questionnaire of the first data set was written in the Somali language. Interviews were conducted in the Somali language. Results The attitudes and opinions of these women towards contraceptive use (73% did not use contraceptives, 27% did use them) were connected with religious beliefs and issues involving marital relations. Religious or gender issues did not seem to influence those who used contraception. Conclusions The findings indicated that the majority of the married refugee women of Somali descent living in Finland did not use contraception. The process of starting the use of contraception was possible because of an access to good reproductive health care and family planning services, changes in life situations, and adaptations to Finnish social and cultural norms.
The effects of selected flavonoids on cytochromes P450 in rat liver and small intestine

The effects of selected flavonoids on cytochromes P450 in rat liver and small intestine In recent years, the consumption and use of dietary supplements containing concentrated phytochemicals (e.g. flavonoids) increased dramatically. Flavonoids, as foreign compounds (xenobiotics), have great potential to modulate the activity of cytochrome P450s (CYPs), xenobiotic-metabolizing enzymes involved in the activation and detoxification of food and environmental carcinogens. Thus, the aim of this study was to investigate the effects of model glycosylated and deglycosylated flavonoids on CYPs in rat liver and small intestine, as the two main organs responsible for xenobiotic metabolism, after p.o. administration by gastric gavages. The effects of two glycosylated flavonoids (isoquercitrin, rutin) and their aglycone (quercetin) on CYPs were determined using Western blotting technique and specific activity assays with alkyl-resorufin derivatives. In liver microsomes, a considerable increase of all the measured marker activities (EROD, MROD, PROD) was observed only after isoquercitrin treatment. To evaluate the effects of flavonoids on CYPs along small intestine, the tissue was dissected into proximal (near pylorus), middle and distal parts. Of all the tested compounds, isoquercitrin was the most efficient CYP inducer, namely in the middle part of small intestine. Obtained data demonstrate the different effects of flavonoid glycosides and aglycone on CYP expression in rat liver and small intestine. Since these phytochemicals are xenobiotics, and thus they can increase the human risk of cancer development, their consumption in large quantities should be carefully considered.
Made to measure: Bespoke landmarks for 24-hour, all-weather localisation with a camera

This paper is about camera-only localisation in challenging outdoor environments, where changes in lighting, weather and season cause traditional localisation systems to fail. Conventional approaches to the localisation problem rely on point-features such as SIFT, SURF or BRIEF to associate landmark observations in the live image with landmarks stored in the map; however, these features are brittle to the severe appearance change routinely encountered in outdoor environments. In this paper, we propose an alternative to traditional point-features: we train place-specific linear SVM classifiers to recognise distinctive elements in the environment. The core contribution of this paper is an unsupervised mining algorithm which operates on a single mapping dataset to extract distinct elements from the environment for localisation. We evaluate our system on 205km of data collected from central Oxford over a period of six months in bright sun, night, rain, snow and at all times of the day. Our experiment consists of a comprehensive N-vs-N analysis on 22 laps of the approximately 10km route in central Oxford. With our proposed system, the portion of the route where localisation fails is reduced by a factor of 6, from 33.3% to 5.5%.
Effect of Preterm Birth on Postnatal Apolipoprotein and Adipocytokine Profiles

Background: Critical metabolic changes preparing for ex utero life may occur at the fetal age of approximately 28-32 weeks, and preterm birth <28 weeks postmenstrual age (PMA) may affect these pathways. Children born <28 weeks often have poorer outcomes possibly due to a major shift in metabolism, including nutritional supply and a shift in lipid-transporting particles and lipid profile. This shift may occur in apolipoprotein and adipocytokine levels, which may influence metabolism. Objective: To determine whether there is a shift in apolipoprotein and adipocytokine levels in neonates born at a gestational age (GA) of 28 and 32 weeks, respectively. Methods: Blood samples from 47 infants (GA 32 weeks, n = 30 and GA 28 weeks, n = 17) were collected at birth and, in the GA28 group, also at PMA 32 weeks. Apolipoproteins A-1, A-2, B, C-2, C-3, and E were analyzed, as well as adiponectin and leptin levels. Results: Serum levels of apolipoproteins A-1, C-2, C-3, and E were lower at birth in the GA28 group compared to the GA32 group. Adiponectin and leptin levels were low at birth in the GA28 group. In the GA28 group 4 weeks after birth, leptin levels were still low, whereas adiponectin levels had increased to levels similar to those found at birth in the GA32 group. Apolipoprotein A-1, C-2, C-3, and E levels were negatively correlated with days receiving total parenteral nutrition. Conclusion: There are significant differences in apolipoprotein and adipocytokine levels, which can be associated with GA and birth weight. The impact of these changes on neonatal and future morbidity remains to be determined.
Performance Study of Multithreaded MPI and OpenMP Tasking in a Large Scientific Code

With a large variety and complexity of existing HPC machines and uncertainty regarding exact future Exascale hardware, it is not clear whether existing parallel scientific codes will perform well on future Exascale systems: they can be largely modified or even completely rewritten from scratch. Therefore, now it is important to ensure that software is ready for Exascale computing and will utilize all Exascale resources well. Many parallel programming models try to take into account all possible hardware features and nuances. However, the HPC community does not yet have a precise answer whether, for Exascale computing, there should be a natural evolution of existing models interoperable with each other or it should be a disruptive approach. Here, we focus on the first option, particularly on a practical assessment of how some parallel programming models can coexist with each other. This work describes two API combination scenarios on the example of iPIC3D [26], an implicit Particle-in-Cell code for space weather applications written in C++ and MPI plus OpenMP. The first scenario is to enable multiple OpenMP threads call MPI functions simultaneously, with no restrictions, using an MPI THREAD MULTIPLE thread safety level. The second scenario is to utilize the OpenMP tasking model on top of the first scenario. The paper reports a step-by-step methodology and experience with these API combinations in iPIC3D; provides the scaling tests for these implementations with up to 2048 physical cores; discusses occurred interoperability issues; and provides suggestions to programmers and scientists who may adopt these API combinations in their own codes.
Contact Heat Evoked Potentials (CHEPs) in Patients with Mild-Moderate Alzheimer's Disease and Matched Control--A Pilot Study.

OBJECTIVE Clinical studies have found that patients with Alzheimer's disease report pain of less intensity and with a lower affective response, which has been thought to be due to altered pain processing. The authors wished to examine the cerebral processing of non-painful and painful stimuli using somatosensory evoked potentials and contact heat evoked potentials in patients with Alzheimer's disease and in healthy elderly controls. DESIGN Case-control study SETTING AND SUBJECTS Twenty outpatients with mild-moderate Alzheimer's disease and in 17 age- and gender-matched healthy controls were included METHOD Contact heat evoked potentials and somatosensory evoked potentials were recorded in all subjects. Furthermore, warmth detection threshold and heat pain threshold were assessed. Patients and controls also rated quality and intensity of the stimuli. RESULTS The authors found no difference on contact heat evoked potential amplitude (P = 0.59) or latency of N2 or P2 wave (P = 0.62 and P = 0.75, respectively) between patients and controls. In addition, there was no difference in regard to pain intensity scores or pain quality. The patients and controls had similar warmth detection threshold and heat pain threshold. Somatosensory evoked potentials, amplitude, and latency were within normal range and similar for the two groups. CONCLUSIONS The findings suggest that the processing of non-painful and painful stimuli is preserved in patients with mild to moderate Alzheimer's disease.
An investigation of the antiplatelet effects of succinobucol (AGI-1067)

Abstract Succinobucol is a phenolic antioxidant with anti-inflammatory and antiplatelet effects. Given the importance of oxidant stress in modulating platelet–platelet and platelet–vessel wall interactions, the aim of this study was to establish if antioxidant activity was responsible for the antiplatelet activity of succinobucol. Platelet aggregation in response to collagen and adenosine diphosphate (ADP) was studied in rabbit whole blood and platelet-rich plasma using impedance aggregometry. The effect of oxidant stress on aggregation, platelet lipid peroxides, and vascular tone was studied by incubating platelets, washed platelets or preconstricted rabbit iliac artery rings respectively with a combination of xanthine and xanthine oxidase (X/XO). To study the effect of succinobucol in vivo, anaesthetized rats were injected with up to 150 mg/kg succinobucol and aggregation measured in blood removed 15 mins later. Succinobucol (10−5–10−4 M) significantly attenuated platelet aggregation to collagen and ADP in whole blood and platelet-rich plasma. X/XO significantly increased aggregation to collagen and platelet lipid peroxides and this was reversed by succinobucol. Addition of X/XO to denuded rabbit iliac arteries caused a dose-dependent relaxation which was significantly inhibited by succinobucol. In vivo administration up to 150 mg/kg had no effect on heart rate or mean arterial blood pressure but significantly inhibited platelet aggregation to collagen ex vivo. In conclusion, succinobucol displays anti-platelet activity in rabbit and rat blood and reverses the increase in platelet aggregation in response to oxidant stress.
Population genomics of wild and laboratory zebrafish (Danio rerio)

Understanding a wider range of genotype–phenotype associations can be achieved through ecological and evolutionary studies of traditional laboratory models. Here, we conducted the first large‐scale geographic analysis of genetic variation within and among wild zebrafish (Danio rerio) populations occurring in Nepal, India, and Bangladesh, and we genetically compared wild populations to several commonly used lab strains. We examined genetic variation at 1832 polymorphic EST‐based single nucleotide polymorphisms (SNPs) and the cytb mitochondrial gene in 13 wild populations and three lab strains. Natural populations were subdivided into three major mitochondrial DNA clades with an average among‐clade sequence divergence of 5.8%. SNPs revealed five major evolutionarily and genetically distinct groups with an overall FST of 0.170 (95% CI 0.105–0.254). These genetic groups corresponded to discrete geographic regions and appear to reflect isolation in refugia during past climate cycles. We detected 71 significantly divergent outlier loci (3.4%) and nine loci (0.5%) with significantly low FST values. Valleys of reduced heterozygosity, consistent with selective sweeps, surrounded six of the 71 outliers (8.5%). The lab strains formed two additional groups that were genetically distinct from all wild populations. An additional subset of outlier loci was consistent with domestication selection within lab strains. Substantial genetic variation that exists in zebrafish as a whole is missing from lab strains that we analysed. A combination of laboratory and field studies that incorporates genetic variation from divergent wild populations along with the wealth of molecular information available for this model organism provides an opportunity to advance our understanding of genetic influences on phenotypic variation for a vertebrate species.