Miracle-dz/UniFAR-FTUs huggingface dataset:
On quantitative versions of theorems due to

This paper is another case study in the program of logically analyzing proofs to extract new (typically effective) information (‘proof mining’). We extract explicit uniform rates of metastability (in the sense of T. Tao) from two ineffective proofs of a classical theorem of F.E. Browder on the convergence of approximants to fixed points of nonexpansive mappings as well as from a proof of a theorem of R. Wittmann which can be viewed as a nonlinear extension of the mean ergodic theorem. The first rate is extracted from Browder’s original proof that is based on an application of weak sequential compactness (in addition to a projection argument). Wittmann’s proof follows a similar line of reasoning and we adapt our analysis of Browder’s proof to get a quantitative version of Wittmann’s theorem as well. In both cases one also obtains totally elementary proofs (even for the strengthened quantitative forms) of these theorems that neither use weak compactness nor the existence of projections anymore. In this way, the present article also discusses general features of extracting effective information from proofs based on weak compactness. We then extract another rate of metastability (of similar nature) from an alternative proof of Browder’s theorem essentially due to Halpern that already avoids any use of weak compactness. The paper is concluded by general remarks concerning the logical analysis of proofs based on weak compactness as well as a quantitative form of the so-called demiclosedness principle. In a subsequent paper these results will be utilized in a quantitative analysis of Baillon’s nonlinear ergodic theorem.
Transcriptomics of the Interaction between the Monopartite Phloem-Limited Geminivirus Tomato Yellow Leaf Curl Sardinia Virus and Solanum lycopersicum Highlights a Role for Plant Hormones, Autophagy and Plant Immune System Fine Tuning during Infection

Tomato yellow leaf curl Sardinia virus (TYLCSV), a DNA virus belonging to the genus Begomovirus, causes severe losses in tomato crops. It infects only a limited number of cells in the vascular tissues, making difficult to detect changes in host gene expression linked to its presence. Here we present the first microarray study of transcriptional changes induced by the phloem-limited geminivirus TYLCSV infecting tomato, its natural host. The analysis was performed on the midrib of mature leaves, a material naturally enriched in vascular tissues. A total of 2206 genes were up-regulated and 1398 were down-regulated in infected plants, with an overrepresentation of genes involved in hormone metabolism and responses, nucleic acid metabolism, regulation of transcription, ubiquitin-proteasome pathway and autophagy among those up-regulated, and in primary and secondary metabolism, phosphorylation, transcription and methylation-dependent chromatin silencing among those down-regulated. Our analysis showed a series of responses, such as the induction of GA- and ABA-responsive genes, the activation of the autophagic process and the fine tuning of the plant immune system, observed only in TYLCSV-tomato compatible interaction so far. On the other hand, comparisons with transcriptional changes observed in other geminivirus-plant interactions highlighted common host responses consisting in the deregulation of biotic stress responsive genes, key enzymes in the ethylene biosynthesis and methylation cycle, components of the ubiquitin proteasome system and DNA polymerases II. The involvement of conserved miRNAs and of solanaceous- and tomato-specific miRNAs in geminivirus infection, investigated by integrating differential gene expression data with miRNA targeting data, is discussed.
Strong P2X4 purinergic receptor‐like immunoreactivity is selectively associated with degenerating neurons in transgenic rodent models of amyotrophic lateral sclerosis

The distribution of the P2X family of ATP receptors was analyzed in a rat model for amyotrophic lateral sclerosis (ALS) expressing mutated human superoxide dismutase (mSOD1G93A). We showed that strong P2X4 immunoreactivity was selectively associated with degenerating motoneurons (MNs) in spinal cord ventral horn. Degenerating P2X4‐positive MNs did not display apoptotic features such as chromatin condensation, positive TUNEL reaction, or active caspase 3 immunostaining. In contrast, these neurons showed other signs of abnormality, such as loss of the neuronal marker NeuN and recruitment of microglial cells with neuronophagic activity. Similar changes were observed in MNs from the cerebral cortex and brainstem in mSOD1G93A in both rat and mice. In addition, P2X4 immunostaining demonstrated the existence of neuronal degeneration in the locus coeruleus, reticular formation, and Purkinje cells of the cerebellar cortex. It is suggested that abnormal trafficking and proteolytic processing of the P2X4 receptor protein may underlie these changes. J. Comp. Neurol. 506:75–92, 2008. © 2007 Wiley‐Liss, Inc.
Hepatitis B virus infection in Thai children

Summary We studied hepatitis B virus (HBV) transmission among 7416 Thai children from 148 schools in Kamphaeng Phet province, a rural part of northern Thailand. Their age ranged from 2 to 16 years (median 9 years). Between May 1991 and June 1992, 61 of 2593 (2.4%) in the cohort of susceptible children acquired anti‐HBc immunoglobulin. Forty‐seven of the 148 schools had children who acquired anti‐HBc. School seroconversion rates to anti‐HBc varied from 0% to 23%. There was no correlation between percent of carriers in schools and percent of anti‐HBc acquisition. Of the 61 children who acquired anti‐HBc, eight (13%) became HBsAg carriers but only two were symptomatic, for a clinical to subclinical infection ration of 1 : 30. One of the two symptomatic children became an HBsAg carrier. Three (38%) of the eight who were persistently antigenemic developed antibody to hepatitis B virus e antigen. Males were 2.5 times (95% CI 1.4–4.3) more likely to acquire anti‐HBc than females. Risk factors for acquisition of HBc in Thailand over a 9‐month period were examined in a subset of 2412 susceptible children and later in a case‐control study of 22 children who acquired anti‐HBc and 59 age and sex‐matched controls. Risks for acquiring anti‐HBc were male gender and a history of bleeding gums. In comparing this study to an earlier pilot study among 9848 children from the same area in Thailand, the yearly antibody acquisition rate to anti‐HBc among Thai children dropped from 5.7% in 1989 to 2.4% in 1992. A random sample of children in the pilot study showed that 16% were HBsAg positive and 27% had anti‐HBc at the beginning of the study. 34% had markers for either anti‐HBc or HBsAg. 12% were repeatedly positive for HBsAg a year later.
Enhanced proton treatment in mouse tumors through proton irradiated nanoradiator effects on metallic nanoparticles

The impact of protons on metallic nanoparticles (MNPs) produces the potent release of MNP-induced secondary electrons and characteristic x-rays. To determine the ability of secondary radiations to enhance proton treatment, the therapeutic irradiation of tumors was investigated in mice receiving 100–300 mg MNPs/kg intravenously prior to single dose, 10–41 Gy, proton irradiation. A proton beam was utilized to irradiate nanoparticles with a single Bragg peak set to occur inside a tumor volume (fully absorbed) or to occur after the beam had traversed the entire body. The dose-dependent increase in complete tumor regression (CTR) was 37–62% in the fully-absorbed irradiation group or 50–100% in the traversing irradiation group, respectively, compared with the proton-alone control mice (p < 0.01). One year survival was 58–100% versus 11–13% proton alone. The dose-dependent increase of intracellular reactive oxygen species level was 12–36% at 10 Gy compared with the proton-alone control cell. Therapeutic effective drug concentration that led to 100% CTR with a proton dose of 31 Gy was measured either 41 µg Au/g tissue or 59 µg Fe/g tissue. MNP-based proton treatment increased not only percent CTR and survival in vivo but also ROS generation in vitro, suggesting tumor dose enhancement from secondary radiation as one potent pathway of therapeutic enhancement.
Investigation of the effects of game difficulty on the engagement level of patient with brain injury during rehabilitation exercise

Enhancing engagement of patients with brain injury during rehabilitation exercises are beneficial for recovery. The objective of this paper is to investigate the influence of game difficulty levels of exercise on patient’s engagement. Five patients with brain injury were recruited to play a Tetris game using their affected limb in different difficulty levels. During the experiment, the patient’s EMG and EEG were monitored to analyze motor and cognitive engagement respectively. The results showed a significant difference in patient’s engagement in different difficulty levels. Moreover, a positive correlation was identified between motor engagement and cognitive engagement when the cognitive difficulty of the game increased. The indicators are able to represent the actual engagement level of the patients with brain injury during rehabilitation exercise. Proper difficulty level of the cognitive task is not only beneficial for the patient to engage cognitively but can also promote motor engagement.
Development of a Finite Element Digital Human Hand Model

The aim of this research was to develop an anatomically accurate and numerically feasible and stable finite element digital human hand model, which would allow accurate bio-mechanical behavior during movement and grasping. Therefore, correct anatomical geometry of the hand has been defined based on CT images, which has been then used for the definition of the finite element model. Using the finite element software, material properties and boundary conditions have been defined to obtain accurate movement of the bones and deformation of the skin. The result of the conducted research is a developed angle-driven finite element digital human hand model, which is numerically stable. Using the accurate geometry and correct definition of the material properties and boundary conditions, the finite element digital human hand model shows reasonable bio-mechanical behavior under movement.
Conceptualizing and validating the human services integration measure

Abstract Purposes This paper proposes both a model and a measure of human service integration through strategic alliances with autonomous services as one way to achieve comprehensive health and social services for target populations. Theory Diverse theories of integrated service delivery and collaboration were combined reflecting integration along a continuum of care within a service sector, across service sectors and between public, not-for-profit and private sectors of financing services. Methods A measure of human service integration is proposed and tested. The measure identifies the scope and depth of integration for each sector and service that make up a total service network. It captures in quantitative terms both intra and inter sectoral service integration. Results Results are provided using the Human Service Measure in two networks of services involved in promoting Healthy Babies and Healthy Children known to have more and less integration. Conclusions The instrument demonstrated discriminate validity with scores correctly distinguishing the two networks. The instrument does not correlate (r=0.13) with Weiss (2001) measure of partnership synergy confirming that it measures a distinct component of integration. Discussion We recommend the combined use of the proposed measure and the Weiss (2001) measure to more completely capture the scope and depth of integration efforts as well as the nature of the functioning of a service program or network.
Complications of Intralesional Bleomycin in the Treatment of Orbital Lymphatic Malformations

Abstract Purpose: Lymphatic malformations (LM) are associated with significant morbidity, and in the orbit, can lead to vision loss. Treatment of these lesions is complicated by their infiltrative nature, making surgical excision challenging. Bleomycin has been used since the 1970s for sclerosis of LM to reduce the need for or improve the success of surgical excision. This paper reviews the complications associated with intralesional bleomycin in the treatment of orbital LM. Methods: A comprehensive literature search was performed on PubMed. Thirty full-length English articles were reviewed. Results: The pathophysiology and imaging characteristic of LM were first reviewed. The head and neck literature was heavily cited given the dearth of specific orbital data. This review highlights the common techniques and dosages for injection, the overall success rate of this treatment, and its common side effects. The orbital data were then reviewed, and differentiated from the head and neck literature. Conclusion: Sclerotherapy of most LM with bleomycin appears to be safe and effective, but the lack of specific orbital data means we must extrapolate LM data from other fields to orbital LM with caution. Additional research is warranted, though the risk-benefit ratio remains unknown.
Resolving the ‘nitrogen paradox’ of arbuscular mycorrhizas: fertilization with organic matter brings considerable benefits for plant nutrition and growth

Abstract Arbuscular mycorrhizal fungi (AMF) can transfer nitrogen (N) to host plants, but the ecological relevance is debated, as total plant N and biomass do not generally increase. The extent to which the symbiosis is mutually beneficial is thought to rely on the stoichiometry of N, phosphorus (P) and carbon (C) availability. While inorganic N fertilization has been shown to elicit strong mutualism, characterized by improved plant and fungal growth and mineral nutrition, similar responses following organic N addition are lacking. Using a compartmented microcosm experiment, we determined the significance to a mycorrhizal plant of placing a 15N‐labelled, nitrogen‐rich patch of organic matter in a compartment to which only AMF hyphae had access. Control microcosms denied AMF hyphal access to the patch compartment. When permitted access to the patch compartment, the fungus proliferated extensively in the patch and transferred substantial quantities of N to the plant. Moreover, our data demonstrate that allowing hyphal access to an organic matter patch enhanced total plant N and P contents, with a simultaneous and substantial increase in plant biomass. Furthermore, we demonstrate that organic matter fertilization of arbuscular mycorrhizal plants can foster a mutually beneficial symbiosis based on nitrogen transfer, a phenomenon previously thought irrelevant.
Incorporating Efficiency in Evaluation

The trade-o between retrieval eciency and eectiveness naturally arises in various domains of information retrieval research. In this paper, we argue that the users’ reaction to the system eciency should be incorporated into the cascade model of the user behaviour and that an eectiveness-awar e modication of a state-of-the-art evaluation metric can be derived. We propose to base the study on the anonymised browser/toolbar log data, and our preliminary experiments demonstrate that the users’ reaction to the delays observed in the dataset is consistent with one reported previously.
Location-aided distributed primary user identification in a cognitive radio scenario

We address a cognitive radio scenario, where a number of secondary users performs identification of which primary user, if any, is transmitting, in a distributed way and using limited location information. We propose two fully distributed algorithms: the first is a direct identification scheme, and in the other a distributed sub-optimal detection based on a simplified Neyman-Pearson energy detector precedes the identification scheme. Both algorithms are studied analytically in a realistic transmission scenario, and the advantage obtained by detection pre-processing is also verified via simulation. Finally, we give details of their fully distributed implementation via consensus averaging algorithms.
In Vivo and In Vitro Acquisition of Resistance to Voriconazole by Candida krusei

ABSTRACT Candida krusei is an important agent of opportunistic infections that often displays resistance to several antifungals. We describe here the in vivo acquisition of resistance to voriconazole (VRC) by C. krusei isolates recovered from a leukemia patient during a long period of VRC therapy. In order to mimic the in vivo development of VRC resistance, a susceptible C. krusei isolate was exposed daily to 1 μg/ml of VRC in vitro. Interestingly, after 5 days of exposure to VRC, a MIC of 4 μg/ml was achieved; this value remained constant after 25 additional days of treatment with VRC and also after 30 consecutive days of incubation in VRC-free medium. Our objective was to determine the associated molecular resistance mechanisms, such as expression of efflux pump genes and ERG11 gene mutations, among the resistant strains. Synergistic effects between the efflux blocker tacrolimus (FK506) and VRC were found in all of the resistant strains. Moreover, ABC1 gene expression increased over time in both the in vivo- and in vitro-induced resistant strains, in contrast to the ABC2 and ERG11 genes, whose expression was invariably lower and constant. ERG11 gene sequencing showed two different types of mutations, i.e., heterozygosity at T1389T/C, corresponding to synonymous mutations, in C. krusei strains and a missense mutation at position T418C, resulting in a change from Tyr to His, among resistant C. krusei clinical isolates. This study highlights the relevance of ATP-dependent efflux pump (namely, Abc1p) activity in VRC resistance and describes new mutations in the ERG11 gene among resistant C. krusei clinical isolates.
Seed priming with sodium nitroprusside attenuates the effects of water deficit on soybean seedlings

Considering that water deficit is one of the main environmental factors responsible for low soybean yield and that nitric oxide (NO) has been shown to be a fundamental part of plant defense signaling during stress, the aim of the present study was to evaluate the effect of seed priming with nitric oxide on the induction of water deficit tolerance during the initial development of soybean. Thus, seeds were treated with 0 (water only), 50, 100 or 250 μmol. L-1 sodium nitroprusside for 6 hours. Additionally, untreated seeds were used. After drying, the seeds were placed in containers filled with a commercial substrate mixture and vermiculite and irrigated to 100% and 50% field capacity. Biometric and biochemical evaluations (pigment and proline contents) were performed after 14 days. It was concluded that pretreatment of soybean seeds with 50 to 250 μmol. L-1 SNP attenuated the effects of water deficit on stem growth, leaf area, and shoot dry matter and induced carotenoid biosynthesis. The accumulation of proline in the leaves was pronounced in the treatments with 100 and 250 μmol. L-1 SNP, while 100 μmol. L-1 SNP induced proline accumulation in the roots.
Small-molecule inhibition of MLL activity by disruption of its interaction with WDR5

WDR5 (WD40 repeat protein 5) is an essential component of the human trithorax-like family of SET1 [Su(var)3–9 enhancer-of-zeste trithorax 1] methyltransferase complexes that carry out trimethylation of histone 3 Lys4 (H3K4me3), play key roles in development and are abnormally expressed in many cancers. In the present study, we show that the interaction between WDR5 and peptides from the catalytic domain of MLL (mixed-lineage leukaemia protein) (KMT2) can be antagonized with a small molecule. Structural and biophysical analysis show that this antagonist binds in the WDR5 peptide-binding pocket with a Kd of 450 nM and inhibits the catalytic activity of the MLL core complex in vitro. The degree of inhibition was enhanced at lower protein concentrations consistent with a role for WDR5 in directly stabilizing the MLL multiprotein complex. Our data demonstrate inhibition of an important protein–protein interaction and form the basis for further development of inhibitors of WDR5-dependent enzymes implicated in MLL-rearranged leukaemias or other cancers.
Relation of Automatically Extracted Formant Trajectories with Intelligibility Loss and Speaking Rate Decline in Amyotrophic Lateral Sclerosis

Effective monitoring of bulbar disease progression in persons with amyotrophic lateral sclerosis (ALS) requires rapid, objective, automatic assessment of speech loss. The purpose of this work was to identify acoustic features that aid in predicting intelligibility loss and speaking rate decline in individuals with ALS. Features were derived from statistics of the first (F1) and second (F2) formant frequency trajectories and their first and second derivatives. Motivated by a possible link between components of formant dynamics and specific articulator movements, these features were also computed for low-pass and high-pass filtered formant trajectories. When compared to clinician-rated intelligibility and speaking rate assessments, F2 features, particularly mean F2 speed and a novel feature, mean F2 acceleration, were most strongly correlated with intelligibility and speaking rate, respectively (Spearman correlations > 0.70, p < 0.0001). These features also yielded the best predictions in regression experiments (r > 0.60, p < 0.0001). Comparable results were achieved using low-pass filtered F2 trajectory features, with higher correlations and lower prediction errors achieved for speaking rate over intelligibility. These findings suggest information can be exploited in specific frequency components of formant trajectories, with implications for automatic monitoring of ALS.
Cellular diversity within embryonic stem cells: pluripotent clonal sublines show distinct differentiation potential

Embryonic stem cells (ESC), derived from the early inner cell mass (ICM), are constituted of theoretically homogeneous pluripotent cells. Our study was designed to test this concept using experimental approaches that allowed characterization of progenies derived from single parental mouse ESC. Flow cytometry analysis showed that a fraction of ESC submitted to neural differentiation generates progenies that escape the desired phenotype. Live imaging of individual cells demonstrated significant variations in the capacity of parental ESC to generate neurons, raising the possibility of clonal diversity among ESC. To further substantiate this hypothesis, clonal sublines from ESC were generated by limit dilution. Transcriptome analysis of undifferentiated sublines showed marked differences in gene expression despite the fact that all clones expressed pluripotency markers. Sublines showed distinct differentiation potential, both in phenotypic differentiation assays and with respect to gene expression in embryoid bodies. Clones generated from another ESC line also showed individualities in their differentiation potential, demonstrating the wider applicability of these findings. Taken together, our observations demonstrate that pluripotent ESC consist of individual cell types with distinct differentiation potentials. These findings identify novel elements for the biological understanding of ESC and provide new tools with a major potential for their future in vitro and in vivo use.