Miracle-dz/UniFAR-FTUs huggingface dataset:
Glued Matrices and the MRRR Algorithm

During the last ten years, Dhillon and Parlett devised a new algorithm (multiple relatively robust representations (MRRR)) for computing numerically orthogonal eigenvectors of a symmetric tridiagonal matrix $T$ with $\mathcal{O}(n^2)$ cost. It has been incorporated into LAPACK version 3.0 as routine {\sc stegr}. We have discovered that the MRRR algorithm can fail in extreme cases. Sometimes eigenvalues agree to working accuracy and MRRR cannot compute orthogonal eigenvectors for them. In this paper, we describe and analyze these failures and various remedies.
Analyses of Compact Trichinella Kinomes Reveal a MOS-Like Protein Kinase with a Unique N-Terminal Domain

Parasitic worms of the genus Trichinella (phylum Nematoda; class Enoplea) represent a complex of at least twelve taxa that infect a range of different host animals, including humans, around the world. They are foodborne, intracellular nematodes, and their life cycles differ substantially from those of other nematodes. The recent characterization of the genomes and transcriptomes of all twelve recognized taxa of Trichinella now allows, for the first time, detailed studies of their molecular biology. In the present study, we defined, curated, and compared the protein kinase complements (kinomes) of Trichinella spiralis and T. pseudospiralis using an integrated bioinformatic workflow employing transcriptomic and genomic data sets. We examined how variation in the kinome might link to unique aspects of Trichinella morphology, biology, and evolution. Furthermore, we utilized in silico structural modeling to discover and characterize a novel, MOS-like kinase with an unusual, previously undescribed N-terminal domain. Taken together, the present findings provide a basis for comparative investigations of nematode kinomes, and might facilitate the identification of Enoplea-specific intervention and diagnostic targets. Importantly, the in silico modeling approach assessed here provides an exciting prospect of being able to identify and classify currently unknown (orphan) kinases, as a foundation for their subsequent structural and functional investigation.
Fractal and Multi-Scale Fractal Dimension analysis: a comparative study of Bouligand-Minkowski method

Shape is one of the most important visual attributes used to characterize objects, playing a important role in pattern recognition. There are various approaches to extract relevant information of a shape. An approach widely used in shape analysis is the complexity, and Fractal Dimension and Multi-Scale Fractal Dimension are both well-known methodologies to estimate it. This papers presents a comparative study between Fractal Dimension and Multi-Scale Fractal Dimension in a shape analysis context. Through experimental comparison using a shape database previously classified, both methods are compared. Different parameters configuration of each method are considered and a discussion about the results of each method is also presented.
Antiproteinuric efficacy of losartan in comparison with amlodipine in non-diabetic proteinuric renal diseases: a double-blind, randomized clinical trial.

BACKGROUND Proteinuria is a significant independent determinant of the progression of chronic renal diseases. It induces an increased synthesis of angiotensin II, endothelin and profibrogenic growth factors, such as transforming growth factor-beta (TGF-beta), by mesangial and tubular cells. The antiproteinuric effect of angiotensin-converting enzyme inhibitors (ACEIs) in diabetic and non-diabetic nephropathies predicts long-term renoprotection afforded by these drugs. Angiotensin II receptor antagonists are renoprotective in patients with type 2 diabetes, but studies about their effect in non-diabetic proteinuric nephropathies are very scarce. METHODS We randomly assigned 97 patients with non-diabetic nephropathies and proteinuria >1.5 g/24 h to treatment with losartan (50 mg daily) or amlodipine (5 mg daily) for 20 weeks. Doses of the study medications were titrated to achieve a target blood pressure <140/90 mmHg in both groups. Primary outcome was the decrease in the level of 24 h proteinuria. Secondary outcomes were changes in the plasma and urinary levels of TGF-beta. RESULTS The baseline characteristics in both groups were similar. Proteinuria decreased by 32.4% (95% confidence interval -38.4 to -21.8%) after 4 weeks of treatment and by 50.4% (-58.9 to -40.2%) after 20 weeks in the losartan group, whereas no significant proteinuria changes were observed in the amlodipine group (P < 0.001). There was no significant correlation between the level of baseline proteinuria and the proteinuria decrease induced by losartan. Both losartan and amlodipine induced a similar and significant blood pressure reduction. Target blood pressure was achieved with the initial dose of study medication (50 mg daily) in 76% of losartan group patients and in 68% of the amlodipine group patients (5 mg daily). Urinary TGF-beta significantly decreased with losartan (-22.4% of the baseline values after 20 weeks of treatment), whereas it tended to increase with amlodipine (between-group difference P < 0.05). A significant correlation between proteinuria decrease and urinary TGF-beta reduction was found in the losartan group (r = 0.41, P < 0.005). Serum creatinine and serum potassium remained stable during the study in both groups. CONCLUSIONS Losartan induced a drastic decrease in proteinuria accompanied by a reduction in urinary excretion of TGF-beta in patients with non-diabetic proteinuric renal diseases.
A Pair of Fluorescent Resonance Energy Transfer-based Probes for Tyrosine Phosphorylation of the CrkII Adaptor Protein in Vivo * 210

An adaptor protein, CrkII, which is involved in a variety of signaling cascades such as cell growth, migration, and apoptosis, becomes phosphorylated on Tyr221 upon stimulation. Here, we report on a fluorescent resonance energy transfer-based sensor, which consists of CrkII sandwiched with cyan- and yellow-emitting variants of green fluorescent protein. This protein enabled us to monitor rapid and transient phosphorylation of CrkII upon epidermal growth factor stimulation in a living cell. However, rapid diffusion of the probes prevented us from specifying where the phosphorylation started within the cell. To overcome this problem, we fused the CAAX box of Ki-Ras to the carboxyl terminus of this probe and restricted its localization mostly to the plasma membrane. With this modified probe, we found that epidermal growth factor-induced phosphorylation of CrkII was initiated at the peripheral plasma membrane, moving toward the center of the cell. Moreover, this CAAX box-fused probe showed improvement in sensitivity and time resolution of the monitoring of CrkII phosphorylation. Thus, this pair of CrkII probes visualizes dynamic changes in the total and local levels of the tyrosine phosphorylation of CrkII in a living cell.
New Directions in Recommender Systems

Recommender systems are an integral part of how we experience the Web today and they have become so ubiquitous that we do not even notice them anymore. However, today's recommender systems mostly treat items they recommend as black boxes and primarily focus on extracting correlations and co-counts from user behavior data. In this talk I argue that next generation recommender systems will require deep understanding of items being recommended as well as modeling the relationships between those items. I will present examples how auxiliary data about items (descriptions, reviews, product specifications) can be used to improve recommendations.
The Children's Friend Society in Upper Canada, 1833-1837

Large scale, open immigration of unaccompanied dependent children to Canada did not commence until 1869, but it had been advocated for decades and some such immigration to the British North American colonies took place earlier in the century. The first systematic emigration of destitute British children was organized in the 1830s by the Children's Friend Society, which sent about 141 children to the Canadas from 1833 to 1836, at least 70 of whom went to Upper Canada. While the emigration scheme was short lived, it established that such children would be welcomed and that homes and work would be available for them, and it probably helped pave the way for a new wave of older juvenile immigrants in the 1850s, and for the high profile, large scale immigration of young dependent children that began in 1869 and continued for more than half a century.
El contexto urbano y las interacciones sociales: dualidad del espacio de actividades de sectores de ingresos altos y bajos en Concepción, Chile

Este trabajo busca abordar la relacion entre el contexto urbano y las interacciones entre las personas, identificando las dimensiones sociales y espaciales de esa relacion, las que son enfocadas en dos niveles de analisis: el barrio, como base de los hogares de la muestra estudiada; y el individuo, en el contexto de sus redes sociales personales. Este analisis se hace a partir de casos de estudio individuales. La investigacion se basa en un marco teorico interdisciplinar y en datos empiricos recogidos en Concepcion, Chile. Los resultados sugieren la existencia de un espacio de actividades delimitado por los lugares donde los individuos desarrollan sus actividades sociales cotidianas, su entorno cercano. A ello se suma el espacio de movimiento que se conforma por la ruta o trayecto entre el hogar y trabajo de los individuos, y los lugares de interaccion social con sus redes personales. Los analisis revelan la dualidad existente entre el espacio de actividades de sectores de ingresos altos y el de sectores de bajos ingresos, sugiriendo que la integracion socioespacial y problemas concomitantes tiene ribetes mas complejos y multidimensionales que los generalmente abordados en la literatura.
Acute respiratory distress syndrome: frequency, clinical course, and costs of care.

OBJECTIVE To define the occurrence rate of acute respiratory distress syndrome (ARDS) using established criteria in a well-defined general patient population, to study the clinical course of ARDS when patients were ventilated using a "lung-protective" strategy, and to define the total costs of care. DESIGN A 3-yr (1993 through 1995) retrospective descriptive analysis of all patients with ARDS treated in Kuopio University Hospital. SETTING Intensive care unit in the university hospital. PATIENTS Fifty-nine patients fulfilled the definition of ARDS: Pao2/Fio2 <200 mm Hg (33.3 kPa) during mechanical ventilation and bilateral infiltrates on chest radiograph. INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS With a patient data management system, the day-by-day data of hemodynamics, ventilation, respiratory mechanics, gas exchange, and organ failures were collected during the period that Pao2/Fio2 ratio was <200 mm Hg (33.3 kPa). The frequency of ARDS was 4.9 cases/100,000 inhabitants/yr. Pneumonia and sepsis were the most common causes of ARDS. Mean age was 43+/-2 yrs. At the time of lowest Pao2/Fio2, the nonsurvivors had lower arterial and venous oxygen saturations and higher arterial lactate than survivors, whereas there were no differences between the groups in other parameters. Multiple organ dysfunction preceded the worst oxygenation in both the survivors and nonsurvivors. The intensive care mortality was 37%; hospital mortality and mortality after a minimum 8 months of follow-up was 42%. The most frequent cause of death was multiple organ failure. The effective costs of intensive care per survivor were US $73,000. CONCLUSIONS The outcome of ARDS is unpredictable at the time of onset and also at the time of the worst oxygenation. Keeping the inspiratory pressures low (30-35 cm H2O [2.94 to 3.43 kPa]) reduces the frequency of pneumothorax, and might lower the mortality. Most patients are young, and therefore the costs per saved year of life are low.
Conformai wearable monopole antenna backed by a compact EBG structure for body area networks

A compact planar monopole antenna backed by an electromagnetic bandgap (EBG) structure is presented. The antenna is conformal to the human body and is intended for wearable applications in wireless body area networks. It operates at 2.45 GHz, and is fabricated on a 68mm by 38mm by 1.57mm semi-flexible substrate. The performance of the antenna does not degrade with structural bends along both of its axes, thus making it robust to structural deformation. In all cases it maintains a fractional impedance bandwidth in the range of 5%, with a gain ranging from 6.3 to 6.7 dBi. The antenna performance is also insensitive to the antenna location on the human body. For placements of the antenna on the arm, chest and leg, it maintained a 5% impedance bandwidth with radiation efficiencies above 70% and an average gain of 7.3 dBi.
Pervasive Intelligent Routing in Content Centric Delay Tolerant Networks

This paper introduces a Swarm-Intelligence based Routing protocol (SIR) that aims to efficiently route information in content centric Delay Tolerant Networks (CCDTN) also dubbed pocket switched networks. First, this paper formalizes the notion of optimal path in CCDTN and introduces an original and efficient algorithm to process these paths in dynamic graphs. The properties and some invariant features of these optimal paths are analyzed and derived from several real traces. Then, this paper shows how optimal path in CCDTN can be found and used from a fully distributed swarm-intelligence based approach of which the global intelligent behavior (i.e. shortest path discovery and use) emerges from simple peer to peer interactions applied during opportunistic contacts. This leads to the definition of the SIR routing protocol of which the consistency, efficiency and performances are demonstrated from intensive representative simulations.
Does the Neighborhood Area of Residence Influence Non-Attendance in an Urban Mammography Screening Program? A Multilevel Study in a Swedish City

Background and aim The public health impact of population-based mammography screening programs depends on high participation rates. Thus, monitoring participation rates, as well as understanding and considering the factors influencing attendance, is important. With the goal to acquire information on the appropriate level of intervention for increasing screening participation our study aimed to (1) examine whether, over and above individual factors, the neighborhood of residence influences a woman’s mammography non-attendance, and (2) evaluate, whether knowing a woman’s neighborhood of residence would be sufficient to predict non-attendance. Methods We analyze all women invited to mammography screening in 2005–09, residing in the city of Malmö, Sweden. Information regarding mammography screening attendance was linked to data on area of residence, demographic and socioeconomic characteristics available from Statistics Sweden. The influence of individual and neighborhood factors was assessed by multilevel logistic regression analysis with 29,901 women nested within 212 neighborhoods. Results The prevalence of non-attendance among women was 18.3%. After adjusting for individual characteristics, the prevalence in the 212 neighborhoods was 3.6%. Neighborhood of residence had little influence on non-attendance. The multilevel analysis indicates that 8.4% of the total individual differences in the propensity of non-attendance were at the neighborhood level. However, when adjusting for specific individual characteristics this general contextual effect decreased to 1.8%. This minor effect was explained by the sociodemographic characteristic of the neighborhoods. The discriminatory accuracy of classifying women according to their non-attendance was 0.747 when considering only individual level variables, and 0.760 after including neighborhood level as a random effect. Conclusion Our results suggest that neighborhoods of residence in Malmö, Sweden (as defined by small-area market statistics (SAMS) areas) do not condition women’s participation in population based mammography screening. Thus, interventions should be directed to the whole city and target women with a higher risk of non-attendance.
Proteomic and Biochemical Analyses of Human B Cell-derived Exosomes

Exosomes are 60–100-nm membrane vesicles that are secreted into the extracellular milieu as a consequence of multivesicular body fusion with the plasma membrane. Here we determined the protein and lipid compositions of highly purified human B cell-derived exosomes. Mass spectrometric analysis indicated the abundant presence of major histocompatibility complex (MHC) class I and class II, heat shock cognate 70, heat shock protein 90, integrin α4, CD45, moesin, tubulin (α and β), actin, Giα2, and a multitude of other proteins. An α4-integrin may direct B cell-derived exosomes to follicular dendritic cells, which were described previously as potential target cells. Clathrin, heat shock cognate 70, and heat shock protein 90 may be involved in protein sorting at multivesicular bodies. Exosomes were also enriched in cholesterol, sphingomyelin, and ganglioside GM3, lipids that are typically enriched in detergent-resistant membranes. Most exosome-associated proteins, including MHC class II and tetraspanins, were insoluble in 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonic acid (CHAPS)-containing buffers. Multivesicular body-linked MHC class II was also resistant to CHAPS whereas plasma membrane-associated MHC class II was solubilized readily. Together, these data suggest that recruitment of membrane proteins from the limiting membranes into the internal vesicles of multivesicular bodies may involve their incorporation into tetraspanin-containing detergent-resistant membrane domains.
DEMO-II Trial. Aerobic Exercise versus Stretching Exercise in Patients with Major Depression—A Randomised Clinical Trial

Background The effect of referring patients from a clinical setting to a pragmatic exercise intervention for depressive symptoms, cognitive function, and metabolic variables has yet to be determined. Methods Outpatients with major depression (DSM-IV) were allocated to supervised aerobic or stretching exercise groups during a three months period. The primary outcome was the Hamilton depression score (HAM-D17). Secondary outcomes were cognitive function, cardiovascular risk markers, and employment related outcomes. Results 56 participants were allocated to the aerobic exercise intervention versus 59 participants to the stretching exercise group. Post intervention the mean difference between groups was −0.78 points on the HAM-D17 (95% CI −3.2 to 1.6; P = .52). At follow-up, the participants in the aerobic exercise group had higher maximal oxygen uptake (mean difference 4.4 l/kg/min; 95% CI 1.7 to 7.0; P = .001) and visuospatial memory on Rey’s Complex Figure Test (mean difference 3.2 points; 95% CI 0.9 to 5.5; P = .007) and lower blood glucose levels (mean difference 0.2 mmol/l; 95% CI 0.0 to 0.5; P = .04) and waist circumference (mean difference 2.2 cm; 95% CI 0.3 to 4.1; P = .02) compared with the stretching exercise group. Conclusions The results of this trial does not support any antidepressant effect of referring patients with major depression to a three months aerobic exercise program. Due to lower recruitment than anticipated, the trial was terminated prior to reaching the pre-defined sample size of 212 participants; therefore the results should be interpreted in that context. However, the DEMO-II trial does suggest that an exercise program for patients with depression offer positive short-term effects on maximal oxygen uptake, visuospatial memory, fasting glucose levels, and waist circumference. Trial Registration ClinicalTrials.gov NCT00695552
Nucleosome regulatory dynamics in response to TGFβ

Nucleosomes play important roles in a cell beyond their basal functionality in chromatin compaction. Their placement affects all steps in transcriptional regulation, from transcription factor (TF) binding to messenger ribonucleic acid (mRNA) synthesis. Careful profiling of their locations and dynamics in response to stimuli is important to further our understanding of transcriptional regulation by the state of chromatin. We measured nucleosome occupancy in human hepatic cells before and after treatment with transforming growth factor beta 1 (TGFβ1), using massively parallel sequencing. With a newly developed method, SuMMIt, for precise positioning of nucleosomes we inferred dynamics of the nucleosomal landscape. Distinct nucleosome positioning has previously been described at transcription start site and flanking TF binding sites. We found that the average pattern is present at very few sites and, in case of TF binding, the double peak surrounding the sites is just an artifact of averaging over many loci. We systematically searched for depleted nucleosomes in stimulated cells compared to unstimulated cells and identified 24 318 loci. Depending on genomic annotation, 44–78% of them were over-represented in binding motifs for TFs. Changes in binding affinity were verified for HNF4α by qPCR. Strikingly many of these loci were associated with expression changes, as measured by RNA sequencing.
Cloud-Based Approximate Constrained Shortest Distance Queries Over Encrypted Graphs With Privacy Protection

Constrained shortest distance (CSD) querying is one of the fundamental graph query primitives, which finds the shortest distance from an origin to a destination in a graph with a constraint that the total cost does not exceed a given threshold. CSD querying has a wide range of applications, such as routing in telecommunications and transportation. With an increasing prevalence of cloud computing paradigm, graph owners desire to outsource their graphs to cloud servers. In order to protect sensitive information, these graphs are usually encrypted before being outsourced to the cloud. This, however, imposes a great challenge to CSD querying over encrypted graphs. Since performing constraint filtering is an intractable task, existing work mainly focuses on unconstrained shortest distance queries. CSD querying over encrypted graphs remains an open research problem. In this paper, we propose Connor, a novel graph encryption scheme that enables approximate CSD querying. Connor is built based on an efficient, tree-based ciphertext comparison protocol, and makes use of symmetric-key primitives and the somewhat homomorphic encryption, making it computationally efficient. Using Connor, a graph owner can first encrypt privacy-sensitive graphs and then outsource them to the cloud server, achieving the necessary privacy without losing the ability of querying. Extensive experiments with real-world data sets demonstrate the effectiveness and efficiency of the proposed graph encryption scheme.
An expert-guided decision tree construction strategy: an application in knowledge discovery with medical databases

With the steady growth in electronic patient records and clinical medical informatics systems, the data collected for routine clinical use have been accumulating at a dramatic rate. Inter-disciplinary research provides a new generation of computation tools in knowledge discovery and data management is in great demand. In this study, an expert-guided decision tree construction strategy is proposed to offer an user-oriented knowledge discovery environment. The strategy allows experts, based on their expertise and/or preference, to override inductive decision tree construction process. Moreover, by reviewing decision paths, experts could focus on subsets of data that may be clues to new findings, or simply contaminated cases.