Miracle-dz/UniFAR-FTUs huggingface dataset:
Blending Learning and Inference in Conditional Random Fields

Conditional random fields maximize the log-likelihood of training labels given the training data, e.g., objects given images. In many cases the training labels are structures that consist of a set of variables and the computational complexity for estimating their likelihood is exponential in the number of the variables. Learning algorithms relax this computational burden using approximate inference that is nested as a sub-procedure. In this paper we describe the objective function for nested learning and inference in conditional random fields. The devised objective maximizes the log-beliefs -- probability distributions over subsets of training variables that agree on their marginal probabilities. This objective is concave and consists of two types of variables that are related to the learning and inference tasks respectively. Importantly, we afterwards show how to blend the learning and inference procedure and effectively get to the identical optimum much faster. The proposed algorithm currently achieves the state-of-the-art in various computer vision applications.
Neuroimaging in Dementia

Abstract Although the diagnosis of dementia still is primarily based on clinical criteria, neuroimaging is playing an increasingly important role. This is in large part due to advances in techniques that can assist with discriminating between different syndromes. Magnetic resonance imaging remains at the core of differential diagnosis, with specific patterns of cortical and subcortical changes having diagnostic significance. Recent developments in molecular PET imaging techniques have opened the door for not only antemortem but early, even preclinical, diagnosis of underlying pathology. This is vital, as treatment trials are underway for pharmacological agents with specific molecular targets, and numerous failed trials suggest that earlier treatment is needed. This article provides an overview of classic neuroimaging findings as well as new and cutting-edge research techniques that assist with clinical diagnosis of a range of dementia syndromes, with an emphasis on studies using pathologically proven cases.
Top Altmetric Scores in the Parkinson’s Disease Literature

A new class of social web-based metrics for scholarly publications (altmetrics) has surfaced as a complement to traditional citation-based metrics. Our aim was to study and characterize those recent papers in the field of Parkinson’s disease which had received the highest Altmetric Attention Scores and to compare this attention measure to the traditional metrics. The top 20 papers in our analysis covered a variety of topics, mainly new disease mechanisms, treatment options and risk factors for the development of PD. The main media sources for these high attention papers were news items and Twitter. The papers were published predominantly in high impact journals, suggesting a correlation between altmetrics and conventional metrics. One paper published in a relatively modest journal received a significant amount of attention, reflecting that public attention does not always parallel the traditional metrics. None of the most influential papers in PD, as reviewed by Ponce and Lozano (2011) made it to our list, suggesting that recent publications receive higher attention scores, and that altmetrics may omit older, seminal work in the field.
Mechanical properties and microstructures of resistance spot welded DP980 steel joints using pulsed current pattern

Abstract Dual phase 980 MPa grade (DP980) steel sheets were resistance spot welded using a pulsed current, and the effects of the pulsed current on the strength properties of the joints were investigated. The pulsed current improved the mechanical properties of the joints in cross tensile tests. In situ observations during tear tests revealed that the ductility of the nugget was improved and that the propagation of cracks into the nugget was inhibited when the pulsed current was used. Microstructural observations and electron probe microanalysis (EPMA) of the nugget showed that the segregation of phosphorus at the nugget was reduced in the joint welded using the pulsed current, suggesting that the pulsed current improved the ductility of the nugget by altering their microstructures.
Role of magnesium sulfate in neuroprotection in acute ischemic stroke

Aims: To study the effect of intravenous magnesium sulfate infusion on clinical outcome of patients of acute stroke. Materials and Methods: Sixty consecutive cases of acute ischemic stroke hospitalised within 24 h of an episode of stroke were taken as subjects. All subjects underwent a computed tomography head, and those found to have evidence of bleed/space-occupying lesions were excluded from the study. The subjects taken up for the study were divided into two groups of 30 subjects each. Both the groups received the standard protocol management for acute ischemic stroke. Subjects of Group 1 additionally received intravenous magnesium sulfate as initial 4 g bolus dose over 15 min followed by 16 g as slow infusion over the next 24 h. In all the subjects of the two study groups, serum magnesium levels were estimated at the time of admission (Day 0), Day 1 and Day 2 of hospitalization using an atomic absorption spectrometer. Statistical Analysis Used: Scandinavian stroke scores were calculated on Day 3, day of discharge and Day 28. Paired t-test was employed for comparison of stroke scores on Day 3, day of discharge and Day 28 within the same group and the unpaired t-test was used for the intergroup comparison, i.e. comparison of stroke scores of control group with corresponding stroke scores of magnesium group. Results: Comparison of stroke scores on Day 3 and day of discharge, on the day of discharge and Day 28 and on Day 3 and Day 28 in the magnesium group produced a t-value of 5.000 and P <0.001, which was highly significant. However, the comparison of the mean stroke scores between the magnesium and the control groups on Day 3, day of discharge and Day 28 yielded a P-value of >0.05, which was not significant. Conclusions: The study failed to document a statistical significant stroke recovery in spite of achieving a significant rise in serum magnesium level, more than that necessary for neuroprotection, with an intravenous magnesium sulfate regime.
Identification of Arabidopsis thaliana phloem RNAs provides a search criterion for phloem-based transcripts hidden in complex datasets of microarray experiments.

SUMMARY Phloem-mobile signals play a major role in plant nutrition, development and communication. In the latter context, phloem-mobile RNAs have been associated with signalling between plant tissues. In this study, we focused on the identification of transcripts in the shoot phloem of the model plant Arabidopsis thaliana. To isolate transcripts expressed in phloem parenchyma cells and in companion cell-sieve element complexes, we used laser microdissection coupled to laser pressure catapulting (LMPC). Mobile transcripts in sieve elements were isolated from leaf phloem exudates. After optimization of sampling and fixation, RNA of high quality was isolated from both sources. The modifications to the RNA amplification procedure described here were well suited to production of RNA of sufficient yield and quality for microarray experiments. Microarrays hybridized with LMPC-derived phloem tissue or phloem sap RNA allowed differentiation between phloem-expressed and mobile transcript species. Using this set of phloem transcripts and comparing them with microarrays derived from databases of light, hormone and nutrient treatment experiments, we identified phloem-derived RNAs as mobile, potential long-distance signals. Our dataset thus provides a search criterion for phloem-based signals hidden in the complex datasets of microarray experiments. The availability of these comprehensive phloem transcript profiles will facilitate reverse-genetic studies and forward-genetic screens for phloem and long-distance RNA signalling mutants.
ALOJA-ML: A Framework for Automating Characterization and Knowledge Discovery in Hadoop Deployments

This article presents ALOJA-Machine Learning (ALOJA-ML) an extension to the ALOJA project that uses machine learning techniques to interpret Hadoop benchmark performance data and performance tuning; here we detail the approach, efficacy of the model and initial results. The ALOJA-ML project is the latest phase of a long-term collaboration between BSC and Microsoft, to automate the characterization of cost-effectiveness on Big Data deployments, focusing on Hadoop. Hadoop presents a complex execution environment, where costs and performance depends on a large number of software (SW) configurations and on multiple hardware (HW) deployment choices. Recently the ALOJA project presented an open, vendor-neutral repository, featuring over 16.000 Hadoop executions. These results are accompanied by a test bed and tools to deploy and evaluate the cost-effectiveness of the different hardware configurations, parameter tunings, and Cloud services. Despite early success within ALOJA from expert-guided benchmarking, it became clear that a genuinely comprehensive study requires automation of modeling procedures to allow a systematic analysis of large and resource-constrained search spaces. ALOJA-ML provides such an automated system allowing knowledge discovery by modeling Hadoop executions from observed benchmarks across a broad set of configuration parameters. The resulting empirically-derived performance models can be used to forecast execution behavior of various workloads; they allow a-priori prediction of the execution times for new configurations and HW choices and they offer a route to model-based anomaly detection. In addition, these models can guide the benchmarking exploration efficiently, by automatically prioritizing candidate future benchmark tests. Insights from ALOJA-ML's models can be used to reduce the operational time on clusters, speed-up the data acquisition and knowledge discovery process, and importantly, reduce running costs. In addition to learning from the methodology presented in this work, the community can benefit in general from ALOJA data-sets, framework, and derived insights to improve the design and deployment of Big Data applications.
Coffee, CYP1A2 genotype, and risk of myocardial infarction.

CONTEXT The association between coffee intake and risk of myocardial infarction (MI) remains controversial. Coffee is a major source of caffeine, which is metabolized by the polymorphic cytochrome P450 1A2 (CYP1A2) enzyme. Individuals who are homozygous for the CYP1A2*1A allele are "rapid" caffeine metabolizers, whereas carriers of the variant CYP1A2*1F are "slow" caffeine metabolizers. OBJECTIVE To determine whether CYP1A2 genotype modifies the association between coffee consumption and risk of acute nonfatal MI. DESIGN, SETTING, AND PARTICIPANTS Cases (n = 2014) with a first acute nonfatal MI and population-based controls (n = 2014) living in Costa Rica between 1994 and 2004, matched for age, sex, and area of residence, were genotyped by restriction fragment-length polymorphism polymerase chain reaction. A food frequency questionnaire was used to assess the intake of caffeinated coffee. MAIN OUTCOME MEASURE Relative risk of nonfatal MI associated with coffee intake, calculated using unconditional logistic regression. RESULTS Fifty-five percent of cases (n = 1114) and 54% of controls (n = 1082) were carriers of the slow *1F allele. For carriers of the slow *1F allele, the multivariate-adjusted odds ratios (ORs) and 95% confidence intervals (CIs) of nonfatal MI associated with consuming less than 1, 1, 2 to 3, and 4 or more cups of coffee per day were 1.00 (reference), 0.99 (0.69-1.44), 1.36 (1.01-1.83), and 1.64 (1.14-2.34), respectively. Corresponding ORs (95% CIs) for individuals with the rapid *1A/*1A genotype were 1.00, 0.75 (0.51-1.12), 0.78 (0.56-1.09), and 0.99 (0.66-1.48) (P = .04 for gene x coffee interaction). For individuals younger than the median age of 59 years, the ORs (95% CIs) associated with consuming less than 1, 1, 2 to 3, or 4 or more cups of coffee per day were 1.00, 1.24 (0.71-2.18), 1.67 (1.08-2.60), and 2.33 (1.39-3.89), respectively, among carriers of the *1F allele. The corresponding ORs (95% CIs) for those with the *1A/*1A genotype were 1.00, 0.48 (0.26-0.87), 0.57 (0.35-0.95), and 0.83 (0.46-1.51). CONCLUSION Intake of coffee was associated with an increased risk of nonfatal MI only among individuals with slow caffeine metabolism, suggesting that caffeine plays a role in this association.
Acylsucrose-Producing Tomato Plants Forces Bemisia tabaci to Shift Its Preferred Settling and Feeding Site

Background The whitefly Bemisia tabaci (Genn.) causes dramatic damage to plants by transmitting yield-limiting virus diseases. Previous studies proved that the tomato breeding line ABL 14-8 was resistant to B. tabaci, the vector of tomato yellow leaf curl disease (TYLCD). This resistance is based on the presence of type IV glandular trichomes and acylsucrose production. These trichomes deter settling and probing of B. tabaci in ABL 14-8, which reduces primary and secondary spread of TYLCD. Methodology/Principal Findings Whitefly settlement preference was evaluated on the adaxial and abaxial leaf surfaces of nearly-isogenic tomato lines with and without B. tabaci-resistance traits, ‘ABL 14-8 and Moneymaker’ respectively, under non-choice and free-choice conditions. In addition, the Electrical Penetration Graph technique was used to study probing and feeding activities of B. tabaci on the adaxial and abaxial leaf surfaces of the same genotypes. B. tabaci preferred to settle on the abaxial than on the adaxial surface of ‘Moneymaker’ leaves, whereas no such preference was observed on ABL 14-8 tomato plants at the ten-leaf growth stage. Furthermore, B. tabaci preferred to feed on the abaxial than on the adaxial leaf surface of ‘Moneymarker’ susceptible tomato plants as shown by a higher number of sustained phloem feeding ingestion events and a shorter time to reach the phloem. However, B. tabaci standard probing and feeding behavior patterns were altered in ABL 14-8 plants and whiteflies were unable to feed from the phloem and spent more time in non-probing activities when exposed to the abaxial leaf surface. Conclusions/Significance The distorted behavior of B. tabaci on ABL 14-8 protects tomato plants from the transmission of phloem-restricted viruses such as Tomato yellow leaf curl virus (TYLCV), and forces whiteflies to feed on the adaxial side of leaves where they feed less efficiently and become more vulnerable to natural enemies.
Chemical and Mechanistic Toxicology Evaluation of Exon Skipping Phosphorodiamidate Morpholino Oligomers in mdx Mice

AVI-4658 is a phosphorodiamidate morpholino oligomer (PMO) designed to induce skipping of dystrophin exon 51 and restore its expression in patients with Duchenne muscular dystrophy (DMD). Preclinically, restoration of dystrophin in the dystrophic mdx mouse model requires skipping of exon 23, achieved with the mouse-specific PMO, AVI-4225. Herein, we report the potential toxicological consequences of exon skipping and dystrophin restoration in mdx mice using AVI-4225. We also evaluated the toxicological effects of AVI-4658 in both mdx and wild-type mice. In both studies, animals were dosed once weekly for 12 weeks up to the maximum feasible dose of 960 mg/kg per injection. Both AVI-4658 and AVI-4225 were well-tolerated at all doses. Findings in AVI-4225-treated animals were generally limited to mild renal tubular basophilia/vacuolation, without any significant changes in renal function and with evidence of reversing. No toxicity associated with the mechanism of action of AVI-4225 in a dystrophic animal was observed.
Polycyclic aromatic hydrocarbon metabolite levels and pediatric allergy and asthma in an inner‐city cohort

Miller RL, Garfinkel R, Lendor C, Hoepner L, Li Z, Romanoff L, Sjodin A, Needham L, Perera FP, Whyatt RM. Polycyclic aromatic hydrocarbon metabolite levels and pediatric allergy and asthma in an inner‐city cohort. Pediatr Allergy Immunol 2010: 21: 260–267. © 2009 John Wiley & Sons A/S
Coordination to manage dependencies between logistics service providers and shippers: An environmental perspective

Purpose – Although it has been suggested that shippers’ demands regarding environmental practices appear to have an impact on the environmental work of LSPs, limited attention has been given to environmental practices in the relationships between LSPs and shippers. The purpose of this paper is to explore how dependencies between LSPs and shippers can influence the way in which environmental practices are coordinated in the relationships between them. Design/methodology/approach – Four dyadic case studies, each consisting of one LSP and one shipper, provide the empirical basis for this paper. Findings – Two types of dependencies are suggested as having an influence over the coordination of environmental practices in LSP-shipper relationships: dependence between LSPs and shippers as such; and dependence with regard to specific environmental practices. In addition, the environmental ambition of the actors is found to be of relevance when LSPs and shippers coordinate environmental practices between them. Base.
X-ray studies of supernova remnants: A different view of supernova explosions

The unprecedented spatial and spectral resolutions of Chandra have revolutionized our view of the X-ray emission from supernova remnants. The excellent datasets accumulated on young, ejecta-dominated objects like Cas A or Tycho present a unique opportunity to study at the same time the chemical and physical structure of the explosion debris and the characteristics of the circumstellar medium sculpted by the progenitor before the explosion. Supernova remnants can thus put strong constraints on fundamental aspects of both supernova explosion physics and stellar evolution scenarios for supernova progenitors. This view of the supernova phenomenon is completely independent of, and complementary to, the study of distant extragalactic supernovae at optical wavelengths. The calibration of these two techniques has recently become possible thanks to the detection and spectroscopic follow-up of supernova light echoes. In this paper, I review the most relevant results on supernova remnants obtained during the first decade of Chandra and the impact that these results have had on open issues in supernova research.
Hole Expansion of Dual‐phase and Complex‐phase AHS Steels ‐ Effect of Edge Conditions

Hole expansion is one of the most important properties describing the formability of steel sheets, especially those used in automotive industry. In order to determine and emphasize the influence of hole edge conditions and hole surface quality on the results of standardized hole expansion tests, different hole preparation methods such as hole punching, hole drilling and wire cutting were applied to the industrially produced dual–phase and complex–phase steel grades DP800 and CP800. Results of hole expansion testing were discussed with respect to the impact of deformation introduced into the material during the hole preparation and to the material microstructure and mechanical properties. The damage characteristics of every method as well as the fracture surfaces were investigated in detail via light optical microscopy (LOM) as well as scanning electron microscopy (SEM). Qualitative and quantitative analyses of microstructure combined with microhardness measurements were used for the interpretation of the results and are correlated with the mechanical properties and the formability characteristics of the investigated steel grades.
Transcriptomic and Functional Analysis of NaCl-Induced Stress in Enterococcus faecalis

The robust physiology of Enterococcus faecalis facilitates tolerance to various stresses. We here report the transcriptional response of E. faecalis V583 to growth in the presence of 6.5% NaCl. Among the early responses observed was an immediate down-regulation of mscL, accompanied by an up-regulation of genes predicted to be involved in uptake of extracellular potassium and glycine betaine. The high NaCl concentration also induced expression of chaperons and cell envelope related traits, such as the enterococcal polysaccharide antigen (epa) locus. Functional genetic analysis revealed reduced salt stress resistance in both epaB and epaE mutants. The reduced salt resistance phenotype associated with the epaB mutant was restored by complementation, hence demonstrating a role of Epa in the physiological robustness of E. faecalis. Furthermore, we demonstrate that Epa confers increased resistance towards multiple cell envelope stress-inducing factors. Accordingly, these findings delineate a potential link between the robust nature of E. faecalis and its ability to perform as a human pathogen, and provide a new perspective on the mechanisms by which Epa contributes to virulence. Notably, the high NaCl concentration also resulted in strict repression of the gelE-sprE operon and impaired gelatinase activity. We demonstrate that NaCl antagonize the GBAP-pheromone dependent induction in a concentration dependent manner.
Perspectives on Sexual and Reproductive Health Sample Selection Attitudes and Intentions of Future Health Care Providers toward Abortion Provision

attending the University of Washington and their intention to provide abortion services in their practices. The primary outcome of this study was students' intention to incorporate abortion into their practice. Secondary outcomes were willingness to seek abortion training and attitudes toward advanced clinical practitioner provision of abortion services. On the basis of previous work, we hypothesized that students in medical programs, those in women's health–oriented programs and those who spent their first 15 years of life in an urban area would be more likely than others to intend to provide abortions, once age, sex and religion are controlled for. Also, we predicted that students would be more willing to perform medical abortions than surgical abortions, because medical abortions are limited to first-trimester terminations of pregnancy. Students enrolled in the University of Washington School of Medicine, physician assistant program (MEDEX) or School of Nursing were eligible to participate. We selected our sample on the basis of student availability within each program. First-and second-year nursing and MEDEX students were offered the survey, as were second-year medical students; first-year medical students were not eligible to participate because they were geographically dispersed in CONTEXT: Induced abortion is one of the most common procedures performed among women in the United States. However, 87% of all counties had no abortion provider in 2000, and little is known about the attitudes and intentions of future health care providers, including advanced clinical practitioners, regarding abortion provision. METHODS: During March 2002, first-and second-year students in health sciences programs (i.e., medicine, physician assistant and nursing) at the University of Washington were anonymously surveyed. Univariate, bivariate and multi-variate analyses were used to determine students' attitudes and intentions regarding provision of abortion services. RESULTS: Of the 312 students who completed the survey, 70% supported the availability of legal abortion under any circumstances. Thirty-one percent intended to provide medical abortion in their practice, and 18% planned to offer surgical abortion. Fifty-two percent of all respondents agreed that advanced clinical practitioners should be able to provide medical abortion, and 37% agreed that they should be able to provide surgical abortion services; however, greater proportions of advanced clinical practitioners (45–83%) than of medical students (21–43%) expressed such support. Sixty-four percent of all respondents were willing to attend a program whose curriculum requires abortion training. CONCLUSIONS: Although it may not be possible to require abortion training for every future health care provider, making abortion a standard …