Miracle-dz/UniFAR-FTUs huggingface dataset:
Optimal Distance Bounds on Time-Series Data

Most data mining operations include an integral search component at their core. For example, the performance of similarity search or classification based on Nearest Neighbors is largely dependent on the underlying compression and distance estimation techniques. As data repositories grow larger, there is an explicit need not only for storing the data in a compressed form, but also for facilitating mining operations directly on the compressed data. Naturally, the quality or tightness of the estimated distances on the compressed objects directly affects the search performance. We motivate our work within the setting of search engine weblog repositories, where keyword demand trends over time are represented and stored as compressed timeseries data. Search and analysis over such sequence data has important applications for the search engines, including discovery of important news events, keyword recommendation and efficient keyword-to-advertisement mapping. We present new mechanisms for very fast search operations over the compressed time-series data, with specific focus on weblog data. An important contribution of this work is the derivation of optimally tight bounds on the Euclidean distance estimation between compressed sequences. Since our methodology is applicable to sequential data in general, the proposed technique is of independent interest. Additionally, our distance estimation strategy is not tied to a specific compression methodology, but can be applied on top of any orthonormal based compression technique (Fourier, Wavelet, PCA, etc). The experimental results indicate that the new optimal bounds lead to a significant improvement in the pruning power of search compared to previous state-of-the-art, in many cases eliminating more than 80% of the candidate search sequences.
Clinical manifestations and beta cell function in Swedish diabetic children have remained unchanged during the last 25 years

The incidence of type 1 diabetes in childhood has doubled in Sweden during the last decades. Environmental factors may cause a different disease process, residual beta cell function and clinical manifestation. Insulin therapy has become more intensive. The aim of this study was to examine the clinical characteristics at onset, C‐peptide secretion during the first years after diagnosis and if there was any secular trends during the last 25 years.
A hybrid graphical model for robust feature extraction from video

We consider a visual scene analysis scenario where objects (e.g. people, cars) pass through the viewing field of a static camera and need to be detected and segmented from the background. For this purpose, we introduce a hybrid dynamic Bayesian network and derive an expectation propagation (EP) algorithm for robust estimation of object shapes and appearance statistics. We demonstrate the viability of the approximation on an object detection task from real videos, where objects' smooth shapes are segmented from the background. The model is readily extendible to multi-object multi-camera scenarios and can be coupled in a transparent and consistent way with a hierarchical model for object identification under uncertainty.
Anemia in Children with Down Syndrome

Background. Iron deficiency anemia impacts on cognitive development. The objective of this study was to determine the prevalence of anemia and iron deficiency in children with Down syndrome and identify risk factors for anemia. Methods. We conducted a prolective cross-sectional study of children attending a multidisciplinary Down syndrome medical center. One hundred and forty nine children with Down syndrome aged 0–20 years were enrolled in the study. Information obtained included a medical history, physical and developmental examination, nutritional assessment, and the results of blood tests. Results. Of the patients studied, 8.1% were found to have anemia. Among the 38 children who had iron studies, 50.0% had iron deficiency. In a multivariate analysis, Arab ethnicity and low weight for age were significantly associated with anemia. Gender, height, the presence of an eating disorder, and congenital heart disease were not risk factors for anemia. Conclusions. Children with Down syndrome are at risk for anemia and iron deficiency similar to the general population. Children with Down syndrome should be monitored for anemia and iron deficiency so that prompt intervention can be initiated.
Nano-titanium dioxide bioreactivity with human alveolar type-I-like epithelial cells: Investigating crystalline phase as a critical determinant

Abstract There can be significant variability between bioreactivity studies of nanomaterials that are apparently the same, possibly reflecting differences in the models used and differing sources of experimental material. In this study, we have generated two crystal forms of titanium dioxide nanoparticles (nano-TiO2), pure anatase and pure rutile to address the hypothesis that the bioreactivity of these nanoparticles with human alveolar epithelium will depend on their crystal phase. We used a human alveolar type-I-like epithelial cell model (TT1; generated in-house from primary human alveolar epithelial type II cells); these cells cover 95% of the alveolar epithelial surface area and are an important target cell for inhaled nanomaterials. Using literature as a guide, we hypothesised that pure anatase nano-TiO2 would display greater bioreactivity with TT1 cells in comparison to pure rutile nano-TiO2. However, we found the profile and pattern of inflammatory mediator release was similar between these two nano-TiO2 formats, although pure rutile treatment caused a small, but consistently greater, response for IL-6, IL-8 and MCP-1. Interestingly, the temporal induction of oxidative stress (increased reactive oxygen species levels and depleted glutathione) varied markedly between the different nano-TiO2 formats. We have shown that a combination of using nanomaterials synthesised specifically for toxicological study and the use of a highly relevant, reproducible human lung cell model, offers a useful approach to delineating the physicochemical properties of nanomaterials that may be important in their cellular reactivity.
Detecting race conditions in large programs

The race condition checker \rcc{} statically identifies potential races in concurrent Java programs. This paper describes improvements to \rcc{} that enable it to be used on large, realistic programs. These improvements include not only extensions to the underlying analysis, but also an annotation inference algorithm and a user interface to help programmers understand warnings generated by the tool. Experience with programs containing up to 500,000 lines of code indicate that it is an effective tool for identifying races in large-scale software systems.
A Study on Stroke Rehabilitation through Task-Oriented Control of a Haptic Device via Near-Infrared Spectroscopy-Based BCI

This paper presents a study in task-oriented approach to stroke rehabilitation by controlling a haptic device via near-infrared spectroscopy-based brain-computer interface (BCI). The task is to command the haptic device to move in opposing directions of leftward and rightward movement. Our study consists of data acquisition, signal preprocessing, and classification. In data acquisition, we conduct experiments based on two different mental tasks: one on pure motor imagery, and another on combined motor imagery and action observation. The experiments were conducted in both offline and online modes. In the signal preprocessing, we use localization method to eliminate channels that are irrelevant to the mental task, as well as perform feature extraction for subsequent classification. We propose multiple support vector machine classifiers with a majority-voting scheme for improved classification results. And lastly, we present test results to demonstrate the efficacy of our proposed approach to possible stroke rehabilitation practice.
Managing approximate models in evolutionary aerodynamic design optimization

Approximate models have to be used in evolutionary optimization when the original fitness function is computationally very expensive. Unfortunately, the convergence property of the evolutionary algorithm is unclear when an approximate model is used for fitness evaluation because approximation errors are involved in the model. What is worse, the approximate model may introduce false optima that lead the evolutionary algorithm to a wrong solution. To address this problem, individual and generation based evolution control are introduced to ensure that the evolutionary algorithm using approximate fitness functions will converge correctly. A framework for managing approximate models in generation-based evolution control is proposed. This framework is well suited for parallel evolutionary optimization in which evaluation of the fitness function is time-consuming. Simulations on two benchmark problems and one example of aerodynamic design optimization demonstrate that the proposed algorithm is able to achieve a correct solution as well as a significantly reduced computation time.
A Syntactic Analysis Method of Long Japanese Sentences Based on the Detection of Conjunctive Structures

This paper presents a syntactic analysis method that first detects conjunctive structures in a sentence by checking parallelism of two series of words and then analyzes the dependency structure of the sentence with the help of the information about the conjunctive structures. Analysis of long sentences is one of the most difficult problems in natural language processing. The main reason for this difficulty is the structural ambiguity that is common for conjunctive structures that appear in long sentences. Human beings can recognize conjunctive structures because of a certain, but sometimes subtle, similarity that exists between conjuncts. Therefore, we have developed an algorithm for calculating a similarity measure between two arbitrary series of words from the left and the right of a conjunction and selecting the two most similar series of words that can reasonably be considered as composing a conjunctive structure. This is realized using a dynamic programming technique. A long sentence can be reduced into a shorter form by recognizing conjunctive structures. Consequently, the total dependency structure of a sentence can be obtained by relatively simple head-dependent rules. A serious problem concerning conjunctive structures, besides the ambiguity of their scopes, is the ellipsis of some of their components. Through our dependency analysis process, we can find the ellipses and recover the omitted components. We report the results of analyzing 150 Japanese sentences to illustrate the effectiveness of this method.
General Selection Criteria for Mobile Location in NLoS Situations

This paper presents a new mobile station (MS) localization method using round trip time (RTT) measurements in the UMTS-FDD [1]. Three or more base stations (BS) performing RTT measurements of a signal from a mobile station (MS) are necessary for its localization. However, when some of the measurements are from non-line-of-sight (NLoS) paths, the location errors can be very large. We propose a method that takes into account possible large RTT error measurements caused by NLoS. To this end, the new method measures the best coherence between the RTT estimates and allows the mobile to select the three most reliable measures. This method does not depend on a particular distribution of the NLoS error and allows the selection of the least dasianoisypsila RTT when all measurements are of LoS type. Theoretical analysis is provided to assess the performance gain of our proposed algorithm and validated by realistic simulation results.
Hepcidin‐dependent and hepcidin‐independent regulation of erythropoiesis in a mouse model of anemia of chronic inflammation

Increased hepcidin antimicrobial peptide correlates with hypoferremia and anemia in various disease states, but its requirement for anemia of inflammation has not been adequately demonstrated. Anemia of inflammation is usually described as normocytic and normochromic, while diseases associated with over expression of hepcidin, alone, are often microcytic and hypochromic. These differences in erythrocyte parameters suggest anemia in many inflammatory states may not be fully explained by hepcidin‐mediated iron sequestration. We used turpentine‐induced sterile abscesses to model chronic inflammation in mice with targeted disruption of Hepcidin 1 [Hepc1 (−/−)] or its positive regulator, Interleukin‐6 [IL‐6 (−/−)], to determine whether these genes are required for features characteristic of anemia of inflammation. Although hemoglobin levels did not decline in Hepc1 (−/−) mice with sterile abscesses, erythrocyte numbers were significantly reduced compared to untreated Hepc1 (−/−) mice. In contrast, both hemoglobin concentration and erythrocyte number declined significantly in wild type and IL‐6 (−/−) mice with sterile abscesses. Both Hepc1 (−/−) and IL‐6 (−/−) mice had increased erythrocyte mean cell volume and mean cell hemoglobin following sterile abscesses, while wild types had no change. Thus, IL‐6 (−/−) mice with sterile abscesses exhibit an intermediate phenotype between wild type and Hepc1 (−/−). Our results demonstrate the requirement of Hepc1 for the development of anemia in this rodent model. Simultaneously, our results demonstrate hepcidin‐independent effects of inflammation on the suppression of erythropoiesis. Our results suggest chronic anemia associated with inflammation may benefit from interventions protecting erythrocyte number in addition to anti‐hepcidin interventions aimed at enhancing iron availability. Am. J. Hematol. 89:470–479, 2014. © 2014 Wiley Periodicals, Inc.
The Connection Between Selective Referrals for Radical Cystectomy and Radical Prostatectomy and Volume–Outcome Effects

This study delineates the roles of “selective referrals” and “practice makes perfect” in the hospital procedure volume and in-hospital mortality association for radical cystectomy and radical prostatectomy. This is a retrospective analysis of the Nationwide Inpatient Sample (years 2000-2004). All hospitalizations with primary procedure codes for radical cystectomy and radical prostatectomy were selected. The association between hospital procedure volume and in-hospital mortality was examined using generalized estimating equations and by instrumental variables approaches. There was an inverse association between hospital procedure volume and in-hospital mortality for radical cystectomy (odds ratio = 0.57; 95% confidence interval = 0.38-0.87; P < .05). Results from the 2-stages least squares regression approach suggested that receiving treatment in high-volume hospitals decreased the probability of in-hospital mortality by 0.02 points, compared with 0.01 points using the ordinary least squares regression approach. Outcomes following radical cystectomy appear to be driven by “practice makes perfect. ”
The Resting Electrophysiological Profile in Adults With ADHD and Comorbid Dysfunctional Anger

Although dysfunctional anger is not a Diagnostic and Statistical Manual of Mental Disorders (Fourth Edition, Text Revision [DSM-IV-TR]) diagnosis, it sometimes presents as a primary clinical complaint and as a comorbid feature in a subset of adults with attention-deficit/hyperactivity disorder (ADHD). No known studies have examined electroencephalographic (EEG) profiles in adults with comorbid dysfunctional anger and ADHD (ADHD + anger). Resting EEG was recorded in 14 ADHD + anger adults (11 males) and 14 controls. Relative power was assessed at standard frequencies, as was frontal absolute α power asymmetry. A modest increase was noted in β1 power in the ADHD + anger group. Unexpectedly, relatively decreased left (or increased right) frontocortical activity (α assessed) was noted in the ADHD + anger group, which was also characterized by a more diffuse θ/β ratio scalp distribution. Nonmedicated ADHD + anger adults exhibited modest resting cortical hyperarousal, consistent with the findings in a subset of children with ADHD characterized by anger-associated problems. The unexpected frontal α asymmetry may reflect enhanced activity of frontal inhibitory mechanisms.
Some factors affecting the production of second generation ethanol from eucalyptus, sugarcane bagasse and sugarcane straw

vi RESUMO . viii GENERAL INTRODUCTION . 1 LITERATURE CITED . 4 Assessment of chemical transformations in eucalyptus, sugarcane bagasse and straw during hydrothermal, dilute acid and alkaline pretreatments . 6 ABSTRACT . 6. 6 RESUMO . 6
Cognitive remediation of attention deficits following acquired brain injury: A systematic review and meta-analysis.

BACKGROUND Attention deficits are common after acquired brain injury (ABI) and adversely impact academic, vocational and social outcomes. The role of cognitive interventions in post-ABI attention rehabilitation remains unclear. OBJECTIVE To evaluate effectiveness of cognitive interventions in treating attention deficits following ABI and to explore differences in treatment effect between ABI etiologies. METHODS MEDLINE, EMBASE, PsycINFO and CENTRAL databases were searched for randomized controlled trials (RCTs). Studies were selected by three reviewers. Study quality was assessed using Cochrane Collaboration tool for RCTs. Effect sizes (Hedge's g) for each attentional domain were meta-analyzed with subgroup analysis by ABI etiology. RESULTS Twelve RCTs with 584 participants were included, representing individuals with stroke, traumatic brain injury (TBI) and CNS-impacting malignancy. Cognitive rehabilitation improved divided attention in stroke survivors (g 0.67; 95% confidence interval, 0.35-0.98; p < 0.0001) but not other ABI populations. Sustained, selective and alternating attention, and inhibition were not significantly improved in any ABI population. Follow-up data showed no evidence of long-term benefit. CONCLUSION Cognitive rehabilitation resulted in short-term improvements in divided attention following stroke, but not after TBI or CNS-impacting malignancy. Cognitive interventions did not significantly improve other attentional domains in participants with stroke, TBI or CNS-impacting malignancy.
DDBJ new system and service refactoring

The DNA data bank of Japan (DDBJ, http://www.ddbj.nig.ac.jp) maintains a primary nucleotide sequence database and provides analytical resources for biological information to researchers. This database content is exchanged with the US National Center for Biotechnology Information (NCBI) and the European Bioinformatics Institute (EBI) within the framework of the International Nucleotide Sequence Database Collaboration (INSDC). Resources provided by the DDBJ include traditional nucleotide sequence data released in the form of 27 316 452 entries or 16 876 791 557 base pairs (as of June 2012), and raw reads of new generation sequencers in the sequence read archive (SRA). A Japanese researcher published his own genome sequence via DDBJ-SRA on 31 July 2012. To cope with the ongoing genomic data deluge, in March 2012, our computer previous system was totally replaced by a commodity cluster-based system that boasts 122.5 TFlops of CPU capacity and 5 PB of storage space. During this upgrade, it was considered crucial to replace and refactor substantial portions of the DDBJ software systems as well. As a result of the replacement process, which took more than 2 years to perform, we have achieved significant improvements in system performance.
In Vitro Susceptibilities of Yeast Species to Fluconazole and Voriconazole as Determined by the 2010 National China Hospital Invasive Fungal Surveillance Net (CHIF-NET) Study

ABSTRACT We conducted active, laboratory-based surveillance for isolates from patients with invasive infections across China from August 2009 to July 2010. DNA sequencing methods were used to define species, and susceptibility to fluconazole and voriconazole was determined by the Clinical and Laboratory Standards Institute M44-A2 disk diffusion method but using up-to-date clinical breakpoints or epidemiological cutoff values. Candida spp. made up 90.5% of the 814 yeast strains isolated, followed by Cryptococcus neoformans (7.7%) and other non-Candida yeast strains (1.7%). Bloodstream isolates made up 42.9% of the strains, isolates from ascitic fluid made up 22.1%, but pus/tissue specimens yielded yeast strains in <5% of the cases. Among the Candida isolates, Candida albicans was the most common species from specimens other than blood (50.1%) but made up only 23% of the bloodstream isolates (P < 0.001). C. parapsilosis complex species were the most common Candida isolates from blood (33.2%). Uncommon bloodstream yeast strains included Trichosporon spp. , C. pelliculosa, and the novel species C. quercitrusa, reported for the first time as a cause of candidemia. Most (>94%) of the isolates of C. albicans, C. tropicalis, and the C. parapsilosis complex were susceptible to fluconazole and voriconazole, as were all of the Trichosporon strains; however, 12.2% of the C. glabrata sensu stricto isolates were fluconazole resistant and 17.8% had non-wild-type susceptibility to voriconazole. Seven C. tropicalis strains were cross-resistant to fluconazole and voriconazole; six were from patients in the same institution. Resistance to fluconazole and voriconazole was seen in 31.9% and 13.3% of the uncommon Candida and non-Candida yeast strains, respectively. Causative species and azole susceptibility varied with the geographic region. This study provided clinically useful data on yeast strains and their antifungal susceptibilities in China.
High-Resolution Crystal Structure of the Subclass B3 Metallo-β-Lactamase BJP-1: Rational Basis for Substrate Specificity and Interaction with Sulfonamides

ABSTRACT Metallo-β-lactamases (MBLs) are important enzymatic factors in resistance to β-lactam antibiotics that show important structural and functional heterogeneity. BJP-1 is a subclass B3 MBL determinant produced by Bradyrhizobium japonicum that exhibits interesting properties. BJP-1, like CAU-1 of Caulobacter vibrioides, overall poorly recognizes β-lactam substrates and shows an unusual substrate profile compared to other MBLs. In order to understand the structural basis of these properties, the crystal structure of BJP-1 was obtained at 1.4-Å resolution. This revealed significant differences in the conformation and locations of the active-site loops, determining a rather narrow active site and the presence of a unique N-terminal helix bearing Phe-31, whose side chain binds in the active site and represents an obstacle for β-lactam substrate binding. In order to probe the potential of sulfonamides (known to inhibit various zinc-dependent enzymes) to bind in the active sites of MBLs, the structure of BJP-1 in complex with 4-nitrobenzenesulfonamide was also obtained (at 1.33-Å resolution), thereby revealing the mode of interaction of these molecules in MBLs. Interestingly, sulfonamide binding resulted in the displacement of the side chain of Phe-31 from its hydrophobic binding pocket, where the benzene ring of the molecule is now found. These data further highlight the structural diversity shown by MBLs but also provide interesting insights in the structure-function relationships of these enzymes. More importantly, we provided the first structural observation of MBL interaction with sulfonamides, which might represent an interesting scaffold for the design of MBL inhibitors.