Miracle-dz/UniFAR-FTUs huggingface dataset:
Distribution of Typical Freshwater Bacterial Groups Is Associated with pH, Temperature, and Lake Water Retention Time

ABSTRACT The distribution of 15 typical freshwater bacterial groups in 15 diverse lakes in northern Europe was investigated using reverse line blot hybridization. Statistical evaluation of the data in relation to the characteristics of the lakes showed that pH, temperature, and the theoretical hydrological retention time of the lakes were most strongly related to variations in the distribution of bacterial taxa. This suggests that pH and temperature are steering factors in the selection of taxa and supports the notion that communities in lakes with short water turnover times are influenced by the input of bacterial cells from the drainage areas. Within the beta subdivision of the Proteobacteria (Betaproteobacteria), as well as within the divisions Actinobacteria and Verrucomicrobia, different subgroups were associated differently with environmental variables.
Pupil damage after periorbital laser treatment of a port-wine stain.

BACKGROUND The increase in the number of laser treatments has led to an increase in the number of therapy-related adverse effects. Herein we report a case in which long-term adverse effects occurred after periorbital laser treatment of a treatment-resistant port-wine stain using a long-pulsed alexandrite laser without protective eyewear. OBSERVATIONS A 33-year-old woman with a therapy-resistant port-wine stain was treated periorbitally with a 755-nm long-pulsed alexandrite laser after several treatment sessions with the pulsed-dye laser; she was not given protective eye shields. Within a few days of the session, she reported disorders in the motility of her left pupil and a painful sensitivity to light, which was not completely resolved after 12 months of follow-up. CONCLUSIONS We recommend that both patients and operators use protective eyewear with every laser procedure. When treatment is administered near the eye, eye shields should be placed behind the eyelid or a safe distance should be maintained between the laser and the eyeball by treating up to the orbital rim only.
Electrospun TiO2 electrodes for dye-sensitized solar cells

We report the new application of electrospun TiO2 fibres as an electrode for dye-sensitized solar cells (DSSCs). TiO2 fibre electrode was electrospun directly onto a conducting glass substrate from a mixture of titanium(IV) propoxide and poly(vinyl acetate) (PVAc) in dimethyl formamide. The TiO2 fibres are composed of one-dimensionally aligned nanofibrils about 20 nm thick with an islands-in-a-sea morphology, which was obtained from the phase separation of TiO2 gel and PVAc during the solidification process. The porous structure of the electrospun TiO2 electrode was found to be efficiently penetrated by a viscous polymer gel electrolyte. In order to improve the photocurrent generation, we treated the electrospun TiO2 electrode with TiCl4 aqueous solution. The rutile crystal was grown on the surface of anatase TiO2 fibres. An additional TiO2 layer increased the volume fraction of active materials, resulting in an increase of sensitizer adsorption. The energy conversion efficiency obtained from electrospun TiO2 electrodes with a PVDF-HFP gel electrolyte was over 90% of that from a liquid electrolyte system.
Sediment nitrate manipulation using porewater equilibrators reveals potential for N and S coupling in freshwaters

Anthropogenic nitrogen (N) loading to agricultural and populated landscapes has resulted in elevated nitrate (NO3 - ) concentrations in ground water, streams and rivers, ultimately causing problems in coastal marine environments such as eutrophication, hypoxia and harmful algal blooms. Nitrate removal along hydrologic flow paths through landscapes intercepts much of the N before it reaches coastal zones. We used traditional porewater equilibrators in a novel way to add nitrate to the sediment porewater of 8 wetlands in southwestern Michigan. Nitrate losses and changes in porewater chemistry were examined to elucidate N removal processes, with particular focus on the potential coupling of bacterial sulfur (S) oxidation to (1) dissimilatory nitrate reduction to ammonium (DNRA) and (2) denitrification. We hypothesized that, if S oxidizers utilized the added nitrate, porewater sulfide concentrations should decrease and sulfate concentrations should increase. Additionally, if the nitrate is used in DNRA, ammonium concentrations should increase as well. Nitrate additions caused decreases in dissolved hydrogen sulfide and increases in sulfate relative to controls at all sites. Ammonium also tended to increase, though the response was less consistent due to a high background ammonium pool. These results provide evidence that microbial S transforma- tions may play an important role in nitrate removal in these freshwater wetland sediments.
Epidermal Growth Factor Receptor Activation in Glioblastoma through Novel Missense Mutations in the Extracellular Domain

Background Protein tyrosine kinases are important regulators of cellular homeostasis with tightly controlled catalytic activity. Mutations in kinase-encoding genes can relieve the autoinhibitory constraints on kinase activity, can promote malignant transformation, and appear to be a major determinant of response to kinase inhibitor therapy. Missense mutations in the EGFR kinase domain, for example, have recently been identified in patients who showed clinical responses to EGFR kinase inhibitor therapy. Methods and Findings Encouraged by the promising clinical activity of epidermal growth factor receptor (EGFR) kinase inhibitors in treating glioblastoma in humans, we have sequenced the complete EGFR coding sequence in glioma tumor samples and cell lines. We identified novel missense mutations in the extracellular domain of EGFR in 13.6% (18/132) of glioblastomas and 12.5% (1/8) of glioblastoma cell lines. These EGFR mutations were associated with increased EGFR gene dosage and conferred anchorage-independent growth and tumorigenicity to NIH-3T3 cells. Cells transformed by expression of these EGFR mutants were sensitive to small-molecule EGFR kinase inhibitors. Conclusions Our results suggest extracellular missense mutations as a novel mechanism for oncogenic EGFR activation and may help identify patients who can benefit from EGFR kinase inhibitors for treatment of glioblastoma.
Auditory stimuli elicit hippocampal neuronal responses during sleep

To investigate how hippocampal neurons code behaviorally salient stimuli, we recorded from neurons in the CA1 region of hippocampus in rats while they learned to associate the presence of sound with water reward. Rats learned to alternate between two reward ports at which, in 50% of the trials, sound stimuli were presented followed by water reward after a 3-s delay. Sound at the water port predicted subsequent reward delivery in 100% of the trials and the absence of sound predicted reward omission. During this task, 40% of recorded neurons fired differently according to which of the two reward ports the rat was visiting. A smaller fraction of neurons demonstrated onset response to sound/nosepoke (19%) and reward delivery (24%). When the sounds were played during passive wakefulness, 8% of neurons responded with short latency onset responses; 25% of neurons responded to sounds when they were played during sleep. During sleep the short-latency responses in hippocampus are intermingled with long lasting responses which in the current experiment could last for 1–2 s. Based on the current findings and the results of previous experiments we described the existence of two types of hippocampal neuronal responses to sounds: sound-onset responses with very short latency and longer-lasting sound-specific responses that are likely to be present when the animal is actively engaged in the task.
CGDSNPdb: a database resource for error-checked and imputed mouse SNPs

The Center for Genome Dynamics Single Nucleotide Polymorphism Database (CGDSNPdb) is an open-source value-added database with more than nine million mouse single nucleotide polymorphisms (SNPs), drawn from multiple sources, with genotypes assigned to multiple inbred strains of laboratory mice. All SNPs are checked for accuracy and annotated for properties specific to the SNP as well as those implied by changes to overlapping protein-coding genes. CGDSNPdb serves as the primary interface to two unique data sets, the ‘imputed genotype resource’ in which a Hidden Markov Model was used to assess local haplotypes and the most probable base assignment at several million genomic loci in tens of strains of mice, and the Affymetrix Mouse Diversity Genotyping Array, a high density microarray with over 600 000 SNPs and over 900 000 invariant genomic probes. CGDSNPdb is accessible online through either a web-based query tool or a MySQL public login. Database URL: http://cgd.jax. org/cgdsnpdb/
Economic development, income inequality and preferences for redistribution *

Adopting a cross-regional and global perspective, this article critically evaluates one of the core assertions of political economy approaches to welfare—that support for redistribution is inversely related to income. We hypothesize that economic self-interest gives way to more uniform support for redistribution in the interest of ensuring that basic or relative needs are met in less developed and highly unequal societies. To test this hypothesis, we analyze individual-level surveys combined with country-level indicators for more than 50 countries between 1984 and 2004. Our analysis shows that individual-level income does not systematically explain support for redistribution in countries with low levels of economic development or high levels of income inequality. These findings challenge the universality of the assumption of economic self-interest in shaping preferences for redistribution that has been so pervasive in the literature.
On the convergence of the iterative solution of the likelihood equations

To determine the maximum likelihood estimate in case of the iterative solution of the likelihood equations we need a convergence criterion. Usually numerically motivated convergence criteria are used; we propose a statistically motivated convergence criterion. Our criterion reduces the number of iterations tremendously. The iterative algorithm to solve the equations is known to be unstable in the neighborhood of the exact solution. Our method avoids this numerical unstable region. The theory is validated by simulations.
Learning Deep Contextual Attention Network for Narrative Photo Stream Captioning

While image captioning has been extensively studied, the problem of generating narrative descriptions for photo streams still remains under explored. Photo stream captioning is more challenging due to the large visual variance, complicated object context, and sentence-to-sentence coherence in the ordered collection of photos. To deal with these challenges, we propose a novel deep contextual attention network (CAN) to narratively describe photo streams by jointly exploring the rich context among attended regions and the coherence in sentences. The proposed CAN is designed in an encoder-decoder framework: the encoder models visual contexts via region-level bilinear similarity and selectively focuses on the attention areas with salient context; while a novel hierarchical gated recurrent unit (h-GRU) acts as the decoder to effectively preserve the semantic coherence among the generated sentences. As CAN is capable to exploit visual attention and context in the photo stream, the generated story is more semantically coherent than merely concatenating the isolated individual image captions. We conduct experiments on the SIND dataset and show that CAN outperforms the state-of-the-art methods by 3.1%, 8.9%, and 9.1% in terms of BLEU, METEOR and CIDEr, respectively.
UK stroke incidence, mortality and cardiovascular risk management 1999–2008: time-trend analysis from the General Practice Research Database

Objectives Stroke is a major cause of morbidity and mortality. This study aimed to investigate secular trends in stroke across the UK. Design This study aimed to investigate recent trends in the epidemiology of stroke in the UK. The study was a time-trend analysis from 1999 to 2008 within the UK General Practice Research Database. Outcome measures were incidence and prevalence of stroke, stroke mortality, rate of secondary cardiovascular events, and prescribing of pharmacological therapy for primary and secondary prevention of cardiovascular disease. Results The study cohort included 32 151 patients with a first stroke. Stroke incidence fell by 30%, from 1.48/1000 person-years in 1999 to 1.04/1000 person-years in 2008 (p<0.001). Stroke prevalence increased by 12.5%, from 6.40/1000 in 1999 to 7.20/1000 in 2008 (p<0.001). 56-day mortality after first stroke reduced from 21% in 1999 to 12% in 2008 (p<0.0001). Prescribing of drugs to control cardiovascular risk factors increased consistently over the study period, particularly for lipid lowering agents and antihypertensive agents. In patients with atrial fibrillation, use of anticoagulants prior to first stroke did not increase with increasing stroke risk. Conclusion Stroke incidence in the UK has decreased and survival after stroke has improved in the past 10 years. Improved drug treatment in primary care is likely to be a major contributor to this, with better control of risk factors both before and after incident stroke. There is, however, scope for further improvement in risk factor reduction in high-risk patients with atrial fibrillation.
Calcium fluoride for ArF laser lithography: characterization by in-situ transmission and LIF measurements

An experimental setup was established for in situ transmission and laser induced fluorescence (LIF) measurements of CaF2 at 193 nm laser irradiation. The known rapid damage process in CaF2 upon ArF laser irradiation is shown to terminate for all tested samples within 3×104 laser pulses for the applied fluences. Furthermore, it is demonstrated that for typical application values the fluence dependent transmission (FDT) at the end of the rapid damage process is independent of the irradiation history and determined by the specific crystal quality. From the lifetimes and signal strengths of different present fluorescence bands the excitation and recording conditions for LIF investigations are derived. The results of laser induced fluorescence measurements at 193 nm excitation make evident that certain impurities or defects are responsible for the different transmission properties even of high purity CaF2 crystals. Comparing transmission and LIF data a quantitative correlation was found between selected emission bands and ArF laser stability of CaF2 material.
Learning to Rank Image Tags With Limited Training Examples

With an increasing number of images that are available in social media, image annotation has emerged as an important research topic due to its application in image matching and retrieval. Most studies cast image annotation into a multilabel classification problem. The main shortcoming of this approach is that it requires a large number of training images with clean and complete annotations in order to learn a reliable model for tag prediction. We address this limitation by developing a novel approach that combines the strength of tag ranking with the power of matrix recovery. Instead of having to make a binary decision for each tag, our approach ranks tags in the descending order of their relevance to the given image, significantly simplifying the problem. In addition, the proposed method aggregates the prediction models for different tags into a matrix, and casts tag ranking into a matrix recovery problem. It introduces the matrix trace norm to explicitly control the model complexity, so that a reliable prediction model can be learned for tag ranking even when the tag space is large and the number of training images is limited. Experiments on multiple well-known image data sets demonstrate the effectiveness of the proposed framework for tag ranking compared with the state-of-the-art approaches for image annotation and tag ranking.
An adaptive hidden Markov model for indoor OFDM based wireless systems

Detailed physical layer simulation of orthogonal frequency division multiplexing (OFDM) systems requires programs that execute too slowly due to long coherence time of the indoor mobile channel. Evaluation of higher layers of such systems is simplified if suitable models for reproduction of channel errors statistics are available. An adaptive hidden Markov model (HMM) for indoor OFDM based systems that accurately reproduces error statistics of the real system with less computational effort than the exact simulation is presented in this paper. The standard HMM methodology has been modified in order to reproduce the periodicity in the error positions of the OFDM systems. The proposed model is validated by comparison of three statistical parameters: number of errors, length of the errors run and length of the error—free intervals in a frame of bits. Keywords—hidden Markov model, OFDM, multicarrier transmission.
Efficacy for a New Live Attenuated Salmonella Enteritidis Vaccine Candidate to Reduce Internal Egg Contamination

To evaluate the efficacy of a novel attenuated Salmonella Enteritidis (△lon△cpxR) vaccine candidate (JOL919), chickens were immunized through oral and intramuscular routes to reduce egg contamination against S. Enteritidis challenge. Birds were orally immunized with JOL919 on the first day of life and were subsequently boosted in the 6th and 16th weeks through oral (group B) or intramuscular (group C) route, while control birds were unimmunized (group A). The chickens of all groups were challenged intravenously with the virulent S. Enteritidis strain in the 24th week. The immunized groups B and C showed significantly higher plasma IgG and intestinal secretory IgA levels as compared to those of the control group. The lymphocyte proliferation response and CD45+CD3+ T‐cell number in the peripheral blood of the groups B and C were significantly increased. In addition, the egg contamination rates were significantly lower in the group B (0%, 10.7% and 0%) and the group C (3.6%, 14.3% and 3.6%) as compared to the group A (28.6%, 42.8% and 28.6%) in the 1st, 2nd and 3rd weeks post‐challenge. All animals in the groups B and C showed lower organ lesion scores in the liver and spleen and lower bacterial counts in the liver, spleen and ovary at the 3rd week post‐challenge. These results indicate that this vaccine candidate can be an efficient tool for prevention of Salmonella infections by inducing protective humoral and cellular immune responses. In addition, this vaccine did not prevent egg contamination, but did appear to reduce incidence. Booster immunizations, especially via oral administration route, showed an efficient protection against internal egg contamination with S. Enteritidis.
Diversity and plasticity in Rab GTPase nucleotide release mechanism has consequences for Rab activation and inactivation

Ras superfamily GTPase activation and inactivation occur by canonical nucleotide exchange and GTP hydrolysis mechanisms. Despite conservation of active-site residues, the Ras-related Rab GTPase activation pathway differs from Ras and between different Rabs. Analysis of DENND1-Rab35, Rabex-Rab5, TRAPP-Rab1 and DrrA-Rab1 suggests Rabs have the potential for activation by distinct GDP-release pathways. Conserved active-site residues in the Rab switch II region stabilising the nucleotide-free form differentiate these pathways. For DENND1-Rab35 and DrrA-Rab1 the Rab active-site glutamine, often mutated to create constitutively active forms, is involved in GEF mediated GDP-release. By contrast, in Rab5 the switch II aspartate is required for Rabex mediated GDP-release. Furthermore, Rab1 switch II glutamine mutants refractory to activation by DrrA can be activated by TRAPP, showing that a single Rab can be activated by more than one mechanistically distinct GDP-release pathway. These findings highlight plasticity in the activation mechanisms of closely related Rab GTPases. DOI: http://dx.doi. org/10.7554/eLife.01623. 001
Disrupted Expression of CXCL5 in Colorectal Cancer Is Associated with Rapid Tumor Formation in Rats and Poor Prognosis in Patients

Purpose: We isolated a subline (CC531M) from the CC531S rat colon carcinoma cell line, which grows and metastasizes much more rapidly than CC531S. We found, using RNA expression profiling, that one of the major changes in the CC531M cell line was a 5.8-fold reduction of the chemokine CXCL5. The purpose of this study was to determine the effect of CXCL5 expression on colorectal tumor growth and metastasis. Experimental Design: CC531 clones were generated with either knockdown or restored expression of CXCL5. These clones were inoculated in the liver of rats. In addition, in two independent cohorts of colorectal cancer patients, the level of CXCL5 expression was determined and associated to clinical variables. Results: Knockdown of CXCL5 expression in CC531S resulted in rapid tumor growth and increased number of metastasis, whereas restored expression of CXCL5 in CC531M resulted in a return of the “mild” tumor growth pattern of the parental cell line CC531S. In vitro, no difference was found in proliferation rate between clones with either high or low expression of CXCL5, suggesting that environmental interactions directed by CXCL5 determine tumor outgrowth. Finally, the importance of our findings was established for patients with colorectal cancer. We found that low expression of CXCL5 was significantly associated with poor prognosis for colorectal cancer patients. CXCL5 showed a trend (P = 0.05) for a positive correlation with intratumoral CD8+ T-cell infiltration, suggesting a possible explanation for the observed poorer prognosis. Conclusions: Our results show that CXCL5 is important in growth and development of colorectal cancer, implicating a future role in both cancer therapy and diagnosis.
A sequential Bayesian algorithm for surveillance with nonoverlapping cameras

Visual surveillance in wide areas (e.g. airports) relies on sparsely distributed cameras, that is, cameras that observe nonoverlapping scenes. In this setup, multiobject tracking requires reidentification of an object when it leaves one field of view, and later appears at some other. Although similar association problems are common for multiobject tracking scenarios, in the distributed case one has to cope with asynchronous observations and cannot assume smooth motion of the objects. In this paper, we propose a method for human indoor tracking. The method is based on a Dynamic Bayes Network (DBN) as a probabilistic model for the observations. The edges of the network define the correspondences between observations of the same object. Accordingly, we derive an approximate EM-like method for selecting the most likely structure of DBN and learning model parameters. The presented algorithm is tested on a collection of real-world observations gathered by a system of cameras in an office building.