Miracle-dz/UniFAR-FTUs huggingface dataset:
Combining Global and Local Surrogate Models to Accelerate Evolutionary Optimization

In this paper, we present a novel surrogate-assisted evolutionary optimization framework for solving computationally expensive problems. The proposed framework uses computationally cheap hierarchical surrogate models constructed through online learning to replace the exact computationally expensive objective functions during evolutionary search. At the first level, the framework employs a data-parallel Gaussian process based global surrogate model to filter the evolutionary algorithm (EA) population of promising individuals. Subsequently, these potential individuals undergo a memetic search in the form of Lamarckian learning at the second level. The Lamarckian evolution involves a trust-region enabled gradient-based search strategy that employs radial basis function local surrogate models to accelerate convergence. Numerical results are presented on a series of benchmark test functions and on an aerodynamic shape design problem. The results obtained suggest that the proposed optimization framework converges to good designs on a limited computational budget. Furthermore, it is shown that the new algorithm gives significant savings in computational cost when compared to the traditional evolutionary algorithm and other surrogate assisted optimization frameworks
Pharmacotherapeutics knowledge of some nonemergency and emergency conditions among medical undergraduates in an Indian medical college

Objectives: To assess pharmacotherapeutics (PT) knowledge of second professional medical undergraduates. Materials and Methods: It is a questionnaire-based cross-sectional study. The questionnaire was designed to objectively assess the current level of knowledge of PT acquired by the second MBBS students in a medical college in India. Thirty Type-A multiple choice questions (MCQs) related with the PT of common and important medical conditions and some emergency conditions were administered to 125 participants. Grading of knowledge was also done as poor, average, and good both subjectively and objectively. Descriptive statistics were used to analyze responses. Association of PT knowledge with respect to mode of admission in a medical college was analyzed with Chi-square test. Results: MCQs related with PT of nonemergency conditions were responded correctly by 9.8–77.7% of participants. MCQs related with PT of some emergency conditions were responded correctly by 17–66.1% of participants. No statistically significant association was observed in PT knowledge with respect to mode of admission. Conclusion: Gross deficiency in the PT knowledge can potentially and adversely affect future rational prescribing skills. PT knowledge about common medical conditions should be emphasized during undergraduate training program.
On Model Parallelization and Scheduling Strategies for Distributed Machine Learning

Distributed machine learning has typically been approached from a data parallel perspective, where big data are partitioned to multiple workers and an algorithm is executed concurrently over different data subsets under various synchronization schemes to ensure speed-up and/or correctness. A sibling problem that has received relatively less attention is how to ensure efficient and correct model parallel execution of ML algorithms, where parameters of an ML program are partitioned to different workers and undergone concurrent iterative updates. We argue that model and data parallelisms impose rather different challenges for system design, algorithmic adjustment, and theoretical analysis. In this paper, we develop a system for model-parallelism, STRADS, that provides a programming abstraction for scheduling parameter updates by discovering and leveraging changing structural properties of ML programs. STRADS enables a flexible tradeoff between scheduling efficiency and fidelity to intrinsic dependencies within the models, and improves memory efficiency of distributed ML. We demonstrate the efficacy of model-parallel algorithms implemented on STRADS versus popular implementations for topic modeling, matrix factorization, and Lasso.
FlowVisor‐based cost‐aware VN embedding in OpenFlow networks

Software‐defined network has emerged as a promising network technology to simplify the network management and enable innovation through network programmability. With the help of FlowVisor, network virtualization is achieved in software‐defined networks. We mainly focus on investigating how to embed virtual network requests with different network sizes (small, regular, and large) in a cost‐efficient way. However, the features of FlowVisor and limitations of OpenFlow switches, such as the presence of a central controller, the limited flow space resource, and the out‐of‐band bandwidth requirement, bring new challenges. In this paper, we first formulate the FlowVisor‐enabled cost‐aware virtual network embedding issue as an integer linear programming problem. Then, we propose two embedding algorithms: a heuristic algorithm LF‐OVNE and a meta‐heuristic algorithm CA‐CVNC‐EPSO. Meanwhile, a separate step is taken to select a cost‐aware controller for each slice. Finally, we evaluate our algorithms and compare the embedding performance with the existing algorithms. The simulation results show that our algorithms perform the online virtual network embedding in a more cost‐efficient way. Copyright © 2016 John Wiley & Sons, Ltd.
Endophytic and rhizospheric bacterial communities isolated from the medicinal plants Echinacea purpurea and Echinacea angustifolia

In this work we analyzed the composition and structure of cultivable bacterial communities isolated from the stem/leaf and root compartments of two medicinal plants, Echinacea purpurea (L.) Moench and Echinacea angustifolia (DC.) Hell, grown in the same soil, as well as the bacterial community from their rhizospheric soils. Molecular PCR-based techniques were applied to cultivable bacteria isolated from the three compartments of the two plants. The results showed that the two plants and their respective compartments were characterized by different communities, indicating a low degree of strain sharing and a strong selective pressure within plant tissues. Pseudomonas was the most highly represented genus, together with Actinobacteria and Bacillus spp. The presence of distinct bacterial communities in different plant species and among compartments of the same plant species could account for the differences in the medicinal properties of the two plants. [Int Microbiol 2014; 17(3):165-174]
Exploratory Search Missions for TREC Topics

We report on the construction of a new query log corpus that consists of 150 exploratory search missions, each of which corresponds to one of the topics used at the TREC Web Tracks 2009–2011. Involved in the construction was a group of 12 professional writers, hired at the crowdsourcing platform oDesk, who were given the task to write essays of 5000 words length about these topics, thereby inducing genuine information needs. The writers used a ClueWeb09 search engine for their research to ensure reproducibility. Thousands of queries, clicks, and relevance judgments were recorded. This paper overviews the research that preceded our endeavors, details the corpus construction, gives quantitative and qualitative analyses of the data obtained, and provides original insights into the querying behavior of writers. With our work we contribute a missing building block in a relevant evaluation setting in order to allow for better answers to questions such as: “What is the performance of today’s search engines on exploratory search? ” and “How can it be improved? ” The corpus will be made publicly available.
An Empirical Analysis of Stock and Bond Market Liquidity

We study the joint time-series of daily liquidity in government bond and stock markets over the period 1991 to 1998. Innovations in liquidity are positively and significantly correlated across stock and bond markets. Further, order imbalances in the stock market impact bond and stock liquidity, even after controlling for order imbalances in the bond market. Both results suggest the existence of a common liquidity factor in stock and bond markets. We consider monetary conditions and mutual fund flows as sources of order flow and as primitive determinants of liquidity. Monetary expansion enhances stock market liquidity during crises. U.S. government bond funds see higher inflows and equity funds see higher outflows during financial crises, and these flows are associated with decreased liquidity in stock and bond markets. Our results establish a link between “macro” liquidity, or money flows, and “micro” or transactions liquidity.
Dynamics of the Hippocampus During Encoding and Retrieval of Face-Name Pairs

The medial temporal lobe (MTL) is critical in forming new memories, but how subregions within the MTL carry out encoding and retrieval processes in humans is unknown. Using new high-resolution functional magnetic resonance imaging (fMRI) acquisition and analysis methods, we identified mnemonic properties of different subregions within the hippocampal circuitry as human subjects learned to associate names with faces. The cornu ammonis (CA) fields 2 and 3 and the dentate gyrus were active relative to baseline only during encoding, and this activity decreased as associations were learned. Activity in the subiculum showed the same temporal decline, but primarily during retrieval. Our results demonstrate that subdivisions within the hippocampus make distinct contributions to new memory formation.
Genomics Comparative microRNA Pro fi ling of Prostate Carcinomas with Increasing Tumor Stage by Deep Sequencing

MicroRNAs (miRNA) posttranscriptionally regulate gene expression and are important in tumorigenesis. Previous deep sequencing identified the miRNA profile of prostate carcinoma versus nonmalignant prostate tissue. Here, we generated miRNA expression profiles of prostate carcinoma by deep sequencing, with increasing tumor stage relative to corresponding nonmalignant and healthy prostate tissue, and detected clearly changed miRNA expression patterns. The miRNA profiles of the healthy and nonmalignant tissues were consistent with our previous findings, indicating a high fidelity of the method employed. In the tumors, quantitative real-time PCR (qRT-PCR) analysis of 40 paired samples of prostate carcinoma versus normal tissue revealed significant upregulation ofmiR-20a,miR-148a, miR-200b, andmiR-375 and downregulation ofmiR-143 andmiR-145. Hereby,miR-375 increased from normal to organ-confined tumors (pT2 pN0), slightly decreased in tumors with extracapsular growth (pT3 pN0), but was then expressed again at higher levels in lymph node metastasizing (pN1) tumors. The sequencing data for miR-375 were confirmed by Northern blotting and qRT-PCR. The regulation for other selected miRNAs could, however, not be confirmed by qRT-PCR in individual tumor stages.MiR-200b, in addition to miR-200c and miR-375 reduced the expression of SEC23A. Interestingly, miR-375, found by sequencing in pT2 upregulated by us and others in tumor versus normal tissue, andmiR-15a, found by sequencing in pT2 and pT3 and in the metastasizing tumors, target the phosphatases PHLPP1 and PHLPP2, respectively. PHLPP1 and PHLPP2 dephosphorylate members of the AKT family of signal transducers, thereby inhibiting cell growth. Coexpression of miR-15a and miR-375 resulted in downregulation of PHLPP1/2 and strongly increased prostate carcinoma cell growth. Implications: These genomic data reveal relevant miRNAs in prostate cancer that may have biomarker and therapeutic potential. Mol Cancer Res; 12(2); 250–63. 2013 AACR.
Novel approaches to characterize age‐related remodelling of the dermal‐epidermal junction in 2D, 3D and in vivo

The dermal‐epidermal junction (DEJ) forms epidermal protrusions down into the dermis (rete ridges) and dermal projections up into the epidermis (dermal papillae). Usually visualized in two‐dimensions (2D), our knowledge of how the DEJ changes with ageing is limited. We aimed to characterize how this structure exists in 3D and changes with age.
Lactobacilli and bile salt hydrolase in the murine intestinal tract

Mice that have a complex intestinal microflora but that do not harbor lactobacilli were used to determine the contribution of lactobacilli to the total bile salt hydrolase activity in the murine intestinal tract. Bile salt hydrolase activity in the ileal contents of these mice was reduced 86% in the absence of lactobacilli and by greater than 98% in the absence of lactobacilli and enterococci compared with samples from conventional mice. Bile salt hydrolase activities were lower in ileal and cecal contents from lactobacillus-free mice colonized with enterococci than in samples from lactobacillus-free mice colonized with lactobacilli. Bile salt hydrolase activity in the duodena, jejuna, ilea, and ceca of reconstituted lactobacillus-free mice colonized by lactobacilli was similar to that in samples from the intestinal tracts of conventional mice. We conclude from these studies that lactobacilli are the main contributors to total bile salt hydrolase activity in the murine intestinal tract.
Amplifying and Linearizing Apical Synaptic Inputs to Cortical Pyramidal Cells

Intradendritic electrophysiological recordings reveal a bewildering repertoire of complex electrical spikes and plateaus that are difficult to reconcile with conventional notions of neuronal function. In this paper we argue that such dendritic events are just an exuberant expression of a more important mechanism - a proportional current amplifier whose primary task is to offset electrotonic losses. Using the example of functionally important synaptic inputs to the superficial layers of an anatomically and electrophysiologically reconstructed layer 5 pyramidal neuron, we derive and simulate the properties of conductances that linearize and amplify distal synaptic input current in a graded manner. The amplification depends on a potassium conductance in the apical tuft and calcium conductances in the apical trunk.
High Tunability in (111)‐Oriented Relaxor Pb0.8Ba0.2ZrO3 Thin Film with Antiferroelectric and Ferroelectric Two‐Phase Coexistence

Using a sol-gel method Pb0.8Ba0. 2ZrO3 (PBZ) thin film with a thickness of ~320 nm was fabricated on Pt(111)/TiOx/SiO2/Si substrate. The analysis results of XRD, SEM, and dielectric properties revealed that this thin film is a (111)-oriented nano-scaled antiferroelectric and ferroelectric two-phase coexisted relaxor. Calculations of dielectric tunability (η) and figure-of-merit (FOM) at room temperature display a maximum value of 75% at E = 560 kV/cm and ~236, respectively. High-temperature stability (η > 75% and FOM > 230 at 560 kV/cm in the range from 300 to 380 K) and high breakdown dielectric strength (leakage current < 1 nA at 598 kV/cm) make the PBZ thin film to be an attractive material for applications of tunable devices.
Acute Hypoglycemia Induces Retinal Cell Death in Mouse

Background Glucose is the most important metabolic substrate of the retina and maintenance of normoglycemia is an essential challenge for diabetic patients. Glycemic excursions could lead to cardiovascular disease, nephropathy, neuropathy and retinopathy. A vast body of literature exists on hyperglycemia namely in the field of diabetic retinopathy, but very little is known about the deleterious effect of hypoglycemia. Therefore, we decided to study the role of acute hypoglycemia in mouse retina. Methodology/Principal Findings To test effects of hypoglycemia, we performed a 5-hour hyperinsulinemic/hypoglycemic clamp; to exclude an effect of insulin, we made a hyperinsulinemic/euglycemic clamp as control. We then isolated retinas from each group at different time-points after the clamp to analyze cells apoptosis and genes regulation. In parallel, we used 661W photoreceptor cells to confirm in vivo results. We showed herein that hypoglycemia induced retinal cell death in mouse via caspase 3 activation. We then tested the mRNA expression of glutathione transferase omega 1 (Gsto1) and glutathione peroxidase 3 (Gpx3), two genes involved in glutathione (GSH) homeostasis. The expression of both genes was up-regulated by low glucose, leading to a decrease of reduced glutathione (GSH). In vitro experiments confirmed the low-glucose induction of 661W cell death via superoxide production and activation of caspase 3, which was concomitant with a decrease of GSH content. Moreover, decrease of GSH content by inhibition with buthionine sulphoximine (BSO) at high glucose induced apoptosis, while complementation with extracellular glutathione ethyl ester (GSHee) at low glucose restored GSH level and reduced apoptosis. Conclusions/Significance We showed, for the first time, that acute insulin-induced hypoglycemia leads to caspase 3-dependant retinal cell death with a predominant role of GSH content.
Pregnancy-specific Glycoprotein 1 Induces Endothelial Tubulogenesis through Interaction with Cell Surface Proteoglycans*

Pregnancy-specific β1 glycoproteins (PSGs) are the most abundant fetal proteins in the maternal bloodstream in late pregnancy. They are secreted by the syncytiotrophoblast and are detected around day 14 postfertilization. There are 11 human PSG genes, which encode a family of proteins exhibiting significant conservation at the amino acid level. We and others have proposed that PSGs have an immune modulatory function. In addition, we recently postulated that they are proangiogenic due to their ability to induce the secretion of VEGF-A and the formation of tubes by endothelial cells. The cellular receptor(s) for human PSGs remain unknown. Therefore, we conducted these studies to identify the receptor for PSG1, the highest expressed member of the family. We show that removal of cell surface glycosaminoglycans (GAGs) by enzymatic or chemical treatment of cells or competition with heparin completely inhibited binding of PSG1. In addition, PSG1 did not bind to cells lacking heparan or chondroitin sulfate on their surface, and binding was restored upon transfection with all four syndecans and glypican-1. Importantly, the presence of GAGs on the surface of endothelial cells was required for the ability of PSG1 to induce tube formation. This finding indicates that the PSG1-GAG interaction mediates at least some of the PSG1 proposed functions.
Failure of aseptic revision total knee arthroplasties

Background and purpose — In Norway, the proportion of revision knee arthroplasties increased from 6.9% in 1994 to 8.5% in 2011. However, there is limited information on the epidemiology and causes of subsequent failure of revision knee arthroplasty. We therefore studied survival rate and determined the modes of failure of aseptic revision total knee arthroplasties. Method — This study was based on 1,016 aseptic revision total knee arthroplasties reported to the Norwegian Arthroplasty Register between 1994 and 2011. Revisions done for infections were not included. Kaplan-Meier and Cox regression analyses were used to assess the survival rate and the relative risk of re-revision with all causes of re-revision as endpoint. Results — 145 knees failed after revision total knee arthroplasty. Deep infection was the most frequent cause of re-revision (28%), followed by instability (26%), loose tibial component (17%), and pain (10%). The cumulative survival rate for revision total knee arthroplasties was 85% at 5 years, 78% at 10 years, and 71% at 15 years. Revision total knee arthroplasties with exchange of the femoral or tibial component exclusively had a higher risk of re-revision (RR = 1.7) than those with exchange of the whole prosthesis. The risk of re-revision was higher for men (RR = 2.0) and for patients aged less than 60 years (RR = 1.6). Interpretation — In terms of implant survival, revision of the whole implant was better than revision of 1 component only. Young age and male sex were risk factors for re-revision. Deep infection was the most frequent cause of failure of revision of aseptic total knee arthroplasties.
Small nonpolypoid carcinomas of the large intestine

Two small carcinomas of the colon were examined, one an intramucosal carcinoma and the other a small carcinoma invading the submucosa. Serial sections did not reveal any adenomatous hyperplasia or polyps in the vicinity. The colonoscopist must be aware of the potential clinical importance of any small mucosal excrescence. Although several studies have indicated that most colonic carcinomas develop from an adenomatous polyp, some carcinomas apparently arise de novo. Further study of the epidemiologic, etiologic, and prognostic factors relating to these apparently uncommon lesions is indicated.
Declining Rates of Fatal and Nonfatal Intracerebral Hemorrhage: Epidemiological Trends in Australia

Background A recent systematic review of epidemiological studies reported intracerebral hemorrhage (ICH) incidence and mortality as unchanged over time; however, comparisons between studies conducted in different health services obscure assessment of trends. We explored trends in ICH rates in a large, representative population in New South Wales, Australia's most populous state (≈7.3 million). Methods and Results Adult hospitalizations with a principal ICH diagnosis from 2001 to 2009 were linked to death registrations through to June 30, 2010. Trends for overall, fatal, and nonfatal ICH rates within 30 days and fatal rates for 30‐day survivors at 365 days were calculated. There were 11 332 ICH patient admissions meeting eligibility criteria, yielding a crude hospitalization rate of 25.2 per 100 000 (age‐standardized rate: 17.2). Age‐ and sex‐adjusted overall rates significantly declined by an average of 1.6% per year (P=0.03). Fatal ICH declined by an average of 2.6% per year (P=0.004). For 30‐day survivors, a nonsignificant decline of 2.3% per year in fatal ICH at 365 days was estimated (P=0.17). Male sex and birth in the Oceania region and Asia were associated with an increased ICH risk, although this depended on age. Approximately 12% of ICH admissions would be prevented if the socioeconomic circumstances of the population equated with those of the least disadvantaged. Conclusions Overall and fatal ICH rates have fallen in this large Australian population. Improvements in cardiovascular prevention and acute care may explain declining rates. There was no evidence of an increase in devastated survivors because the longer term mortality of 30‐day survivors has not increased over time.