Miracle-dz/UniFAR-FTUs huggingface dataset:
Architecture of a mediator for a bioinformatics database federation

Developments in our ability to integrate and analyze data held in existing heterogeneous data resources can lead to an increase in our understanding of biological function at all levels. However, supporting ad hoc queries across multiple data resources and correlating data retrieved from these is still difficult. To address this, we are building a mediator based on the functional data model database, P/FDM, which integrates access to heterogeneous distributed biological databases. Our architecture makes use of the existing search capabilities and indexes of the underlying databases, without infringing on their autonomy. Central to our design philosophy is the use of schemas. We have adopted a federated architecture with a five-level schema, arising from the use of the ANSI-SPARC three-level schema to describe both the existing autonomous data resources and the mediator itself. We describe the use of mapping functions and list comprehensions in query splitting, producing execution plans, code generation, and result fusion. We give an example of cross-database querying involving data held locally in P/FDM systems and external data in SRS.
Biomimetic synthesis of proline-derivative templated mesoporous silica for increasing the brain distribution of diazepam and improving the pharmacodynamics of nimesulide

Abstract Herein a new kind of proline-derivative templated mesoporous silica with curved channels (CMS) was biomimetically synthesized and applied as carrier to improve the drug dissolution and bioavailability of hydrophobic diazepam (DZP) and nimesulide (NMS). Drugs can be incorporated into CMS with high efficiency; during this process, they successfully transformed to amorphous phase. As a result, the dissolution rate of DZP and NMS was significantly improved. Biodistribution study confirmed that CMS converted DZP distribution in mice with the tendency of lung targeting and brain targeting. At 45 min postadministration, the concentrations of DZP in plasma, lung and brain were 8.57-fold, 124.94-fold and 19.55-fold higher from 1:3 DZP/CMS sample than that of pure DZP sample, respectively. At 90 min postadministration, the content of DZP in brain was 62.31-fold higher for 1:3 DZP/CMS sample than that of pure DZP. Besides, the anti-inflammatory and analgesic effects of 1:3 NMS/CMS were systematic evaluated using mouse ankle swelling test (MAST), mouse ear swelling test (MEST) and mouse writhing test (MWT). The results indicated that after incorporating into CMS, the therapeutic effects of NMS were obviously improved, and the inhibition rates of 1:3 NMS/CMS in all pharmacodynamics tests varied from 102.2% to 904.3%.
Circulating biomarkers of dairy fat and risk of incident stroke in U.S. men and women in 2 large prospective cohorts.

BACKGROUND Previous observational studies of self-reported dairy product consumption and stroke risk have reported mixed findings. Few studies have used circulating biomarkers that provide objective measures of dairy fat intake. OBJECTIVES We tested the hypothesis that the circulating biomarkers of dairy fat, pentadecanoic acid (15:0), heptadecanoic acid (17:0), and trans palmitoleate (trans 16:1n-7), were associated with lower incidence of stroke, especially ischemic stroke. Secondarily, we evaluated 14:0, which is obtained from dairy products and beef, and also endogenously synthesized. DESIGN In participants from 2 large US cohorts (the Health Professionals Follow-Up Study: 51,529 men; the Nurses' Health Study: 121,700 women) with stored blood samples in 1993-1994 (n = 18,225) and 1989-1990 (n = 32,826), respectively, we prospectively identified 594 incident stroke cases (median follow-up: 8.3 y) and matched them 1:1 to risk-set-sampled control subjects by age, sex, race, and smoking. Total plasma and red blood cell (RBC) fatty acids were measured by using gas-liquid chromatography. Covariates were assessed by using validated questionnaires. Stroke events and subtypes were adjudicated by using medical records or other supporting documentation. We used conditional logistic regression to estimate associations of fatty acids with incident stroke, and cohort-specific findings were combined by inverse-variance weights. RESULTS After adjustment for demographic characteristics, lifestyle, cardiovascular disease risk factors, diet, and other circulating fatty acids, no significant associations with total stroke were seen for plasma 15:0 (pooled HR for highest compared with lowest quartiles: 0.85; 95% CI: 0.54, 1.33), 17:0 (0.99; 0.67, 1.49), trans 16:1 n-7 (0.89; 0.55, 1.45), or 14:0 (1.05; 0.62, 1.78). Results were similar for ischemic and hemorrhagic stroke subtypes, for RBC fatty acids, and in several different sensitivity analyses. CONCLUSION In 2 large prospective cohorts, circulating biomarkers of dairy fat were not significantly associated with stroke.
The Oswestry Disability Index.

STUDY DESIGN The Oswestry Disability Index (ODI) has become one of the principal condition-specific outcome measures used in the management of spinal disorders. This review is based on publications using the ODI identified from the authors' personal databases, the Science Citation Index, and hand searches of Spine and current textbooks of spinal disorders. OBJECTIVES To review the versions of this instrument, document methods by which it has been validated, collate data from scores found in normal and back pain populations, provide curves for power calculations in studies using the ODI, and maintain the ODI as a gold standard outcome measure. SUMMARY OF BACKGROUND DATA It has now been 20 years since its original publication. More than 200 citations exist in the Science Citation Index. The authors have a large correspondence file relating to the ODI, that is cited in most of the large textbooks related to spinal disorders. METHODS All the published versions of the questionnaire were identified. A systematic review of this literature was made. The various reports of validation were collated and related to a version. RESULTS Four versions of the ODI are available in English and nine in other languages. Some published versions contain misprints, and many omit the scoring system. At least 114 studies contain usable data. These data provide both validation and standards for other users and indicate the power of the instrument for detecting change in sample populations. CONCLUSIONS The ODI remains a valid and vigorous measure and has been a worthwhile outcome measure. The process of using the ODI is reviewed and should be the subject of further research. The receiver operating characteristics should be explored in a population with higher self-report disabilities. The behavior of the instrument is incompletely understood, particularly in sensitivity to real change.
The Nizza secure-system architecture

The trusted computing bases (TCBs) of applications running on today's commodity operating systems have become extremely large. This paper presents an architecture that allows to build applications with a much smaller TCB. It is based on a kernelized architecture and on the reuse of legacy software using trusted wrappers. We discuss the design principles, the architecture and some components, and a number of usage examples
HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot

The growth in the number of completely sequenced microbial genomes (bacterial and archaeal) has generated a need for a procedure that provides UniProtKB/Swiss-Prot-quality annotation to as many protein sequences as possible. We have devised a semi-automated system, HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes), that uses manually built annotation templates for protein families to propagate annotation to all members of manually defined protein families, using very strict criteria. The HAMAP system is composed of two databases, the proteome database and the family database, and of an automatic annotation pipeline. The proteome database comprises biological and sequence information for each completely sequenced microbial proteome, and it offers several tools for CDS searches, BLAST options and retrieval of specific sets of proteins. The family database currently comprises more than 1500 manually curated protein families and their annotation templates that are used to annotate proteins that belong to one of the HAMAP families. On the HAMAP website, individual sequences as well as whole genomes can be scanned against all HAMAP families. The system provides warnings for the absence of conserved amino acid residues, unusual sequence length, etc. Thanks to the implementation of HAMAP, more than 200 000 microbial proteins have been fully annotated in UniProtKB/Swiss-Prot (HAMAP website: http://www.expasy.org/sprot/hamap).
Synthesis of Au nanoclusters supported upon a TiO_2 nanotube array

Gold nanoclusters were successfully deposited in the interior of TiO_2 nanotubes fabricated as ordered arrays. This approach is a useful fabrication platform for miniature planar fuel cells, gas sensors, and heterogeneous catalysts. A pressure impregnation process was used to inject the titania and Au precursors into mesoporous alumina. After thermal treatment, Au nanoclusters were well-dispersed on the interior walls of nanotubular TiO_2. The TiO_2 nanotubes were shown by x-ray diffraction to be entirely anatase. Transmission electron microscopy imaging confirmed that 80% of the Au particles were 4.1 nm ± 2.0 nm in diameter. This material exhibited catalytic CO oxidation activity at low temperatures.
Failure-aware kidney exchange

Most algorithmic matches in fielded kidney exchanges do not result in an actual transplant. In this paper, we address the problem of cycles and chains in a proposed match failing after the matching algorithm has committed to them. We show that failure-aware kidney exchange can significantly increase the expected number of lives saved (i) in theory, on random graph models; (ii) on real data from kidney exchange match runs between 2010 and 2012; (iii) on synthetic data generated via a model of dynamic kidney exchange. From the computational viewpoint, we design a branch-and-price-based optimal clearing algorithm specifically for the probabilistic exchange clearing problem and show that this new solver scales well on large simulated data, unlike prior clearing algorithms.
Outpatient vs. comprehensive first-episode psychosis services, a 5-year follow-up of Soteria Nacka

Three years experience of an outpatient unit for first-episode psychosis showed that most of the patients at some point became hospitalized in a psychiatric ward with discontinuity in care as a consequence. Adding “need-adapted” inpatient care in the form of a small and calm crisis home guaranteed continuity in approach and treatment, as the same caregivers staffed the inpatient and outpatient parts of Soteria. Information on early signs of psychosis was given to other units of the psychiatric clinic and to general practitioners. As the organization was considerably changed from that point of time, the patients could be divided into two separate groups. The aim of the present study was to follow the patients in the two groups for 5 years, comparing the outcome. The results showed that easily accessible need-adapted treatment with integrated overnight care might be advantageous for first-episode psychotic patients. The duration of untreated psychosis was shorter and the outcome better.
An English Part of Speech Tagging Method Based on Maximum Entropy

As part of speech is a fundamental step in syntactic parsing and machine translation, this paper proposes an English part of speech tagging method based on maximum entropy, and this issue is very crucial for natural language processing. The proposed part of speech tagging system is made up of two steps, that is, (a) Training process and (b) Tagging process. Maximum Entropy estimation is able to compute Probability Density Function of the random variables, and in this paper, we solve the problem of tagging part of speech for English by tackling an optimization problem using maximum entropy. Using the ISO-639-1 code: EN dataset, a series of experiments are conducted. Finally, experimental results prove that the proposed method is very effective to tag part of speech for English.
The Effect of the May 2003 Dividend Tax Cut on Corporate Dividend Policy: Empirical and Survey Evidence

We analyze the impact of the May 2003 dividend tax cut on corporate dividend policy. First, we find that while there was a temporary increase in dividend initiations, this increase was not long-lasting. While dividend payments were increased right after the tax change, there was a larger and more pronounced increase in repurchases during the same time period. Second, we survey 328 financial executives to determine the effects of the May 2003 dividend tax cut. We find that the tax cut led to initiations and dividend increases at some firms. However, executives say that among the factors that affect dividend policy, the tax rate reduction is less important than the stability of future cashflows, cash holdings, and the historic level of dividends. Tax effects have roughly the same importance as attracting institutional investors and the availability of profitable investments. We also find that press releases only occasionally mention the dividend tax cut as the reason for an initiation. Overall we conclude that the dividend tax reduction had only a second-order impact of payout policy.
Display power reduction for mobile closed-source games

With the rapid development of mobile games, power consumption and battery life of mobile platforms become a crucial problem, therefore, saving power for display which consumes a lot of power without decreasing the user experience becomes necessary. Content-centric techniques are most commonly used to save display power. However, they cannot be applied to closed-source games as they need to modify the game images. In this paper, we explore a backlight power model and propose a novel method to make a trade-off between the game image quality and display power. Different from content-centric methods, based on the proposed trade-off model, we propose a backlight dimming algorithm which maintains the user game experience using game-state information and saves display power for mobile games without modifying any game image. We implement the proposed trade-off model and backlight dimming policy in a contemporary mobile platform where the evaluation results show that, maintaining a specific game image quality level, our policy can save system power up to 10.43% compared with the static policy without decreasing games' performances.
EVIDENCE FOR STRONG HOST CLONE-PARASITE SPECIES INTERACTIONS IN THE DAPHNIA MICROPARASITE SYSTEM

Abstract Organisms are often confronted with multiple enemy species. Defenses against different parasite species may be traded off against each other. However, if resistance is based on (potentially costly) general defense mechanisms, it may be positively correlated among parasites. In an experimental study, we confronted 19 clones from one Daphnia magna population with two bacterial and three microsporidian parasite species. All parasites were isolated from the same pond as the hosts. Host clones were specific in their susceptibility towards different parasite species, and parasite species were host-clone specific in their infectivity, spore production, and virulence, resulting in highly significant host-parasite interactions. Since the Daphnia's resistance to different parasite species showed no obvious correlation, neither general defense mechanisms nor trade-offs in resistance explain our findings. None of the Daphnia clones were resistant to all parasite species, and the average level of resistance was quite similar among clones. This may reflect a cost of defense, so that the cumulative cost of being resistant to all parasite species might be too high.
Data fusion based framework for the recognition of Isolated Handwritten Kannada Numerals

combining classifiers appears as a natural step forward when a critical mass of knowledge of single classifier models has been accumulated. Although there are many unanswered questions about matching classifiers to real-life problems, combining classifiers is rapidly growing and enjoying a lot of attention from pattern recognition and machine learning communities. For any pattern classification task, an increase in data size, number of classes, dimension of the feature space and interclass separability affect the performance of any classifier. It is essential to know the effect of the training dataset size on the recognition performance of a feature extraction method and classifier. In this paper, an attempt is made to measure the performance of the classifier by testing the classifier with two different datasets of different sizes. In practical classification applications, if the number of classes and multiple feature sets for pattern samples are given, a desirable recognition performance can be achieved by data fusion. In this paper, we have proposed a framework based on the combined concepts of decision fusion and feature fusion for the isolated handwritten Kannada numerals classification. The proposed method improves the classification result. From the experimental results it is seen that there is an increase of 13.95% in the recognition accuracy.
RAPID MANUFACTURING OF EMBEDDED MICROCHANNELS FROM A SINGLE LAYERED SU-8, AND DETERMINING THE DEPENDENCE OF SU-8 YOUNG'S MODULUS ON

This paper presents an innovative methodology for rapid manufacturing embedded microchannels. The presented technology is based on a direct-write technique using a scanning laser system to pattern a single layered SU-8. It greatly simplifies the processes for embedded microchannels fabrication and differs from the previous work that was fimdamentaltlly limited by the third dimension (perpendicular to the surface) processing capability. This paper also describes the underlying theory and method to determine the Young’s modulus of exposed SU-8 by using a laser acoustic microscopy system. The laser-based ultrasonic technique offers a non-contact, nondestructive means of evaluation and materials characterization. It allows for local inspection of material properties within the field of view of the microscope.
Multilingual Word Sense Disambiguation and Entity Linking for Everybody

In this paper we present a Web interface and a RESTful API for our state-of-the-art multilingual word sense disambiguation and entity linking system. The Web interface has been developed, on the one hand, to be user-friendly for non-specialized users, who can thus easily obtain a first grasp on complex linguistic problems such as the ambiguity of words and entity mentions and, on the other hand, to provide a showcase for researchers from other fields interested in the multilingual disambiguation task. Moreover, our RESTful API enables an easy integration, within a Java framework, of state-of-the-art language technologies. Both the Web interface and the RESTful API are available at http://babelfy.org
Hypnotic and Waking Suggestibility : A Historical Review In the 1920 ’ s researchers

The history of the most enduring experimental design in hypnosis research is reviewed. More than 75 years of research converge to indicate that: 1) all of the phenomena produced in hypnosis by suggestion also can be produced by suggestion without the induction of hypnosis, 2) the induction of hypnosis produces a relatively small increase in responsiveness to suggestion, and 3) hypnotic and waking suggestion are highly correlated, in many cases rivalling the reliability of the suggestibility measure. The importance of these data to both clinical and experimental hypnosis is emphasized.
The Membrane Lipoprotein LppX of Paenibacillus sp. Strain W-61 Serves as a Molecular Chaperone for Xylanase of Glycoside Hydrolase Family 11 during Secretion across the Cytoplasmic Membrane

ABSTRACT Paenibacillus sp. strain W-61, which can utilize xylan as the sole source of carbon and energy, produces extracellular xylanases 1 and 3 (Xyn1 and Xyn3) and cell surface xylanase 5. In this study we found that lppX, immediately downstream of xyn1, encodes a lipoprotein located on the outer layer of the cytoplasmic membrane and that the LppX lipoprotein is essential for the secretion of active Xyn1 across the cytoplasmic membranes. In Escherichia coli, wild-type LppX was destined for the inner layer of the outer membrane. Mutant LppX(C19A), in which Cys-19, a possible lipomodification residue, is replaced with Ala, was located in the periplasm without being anchored to the membranes. Another mutant, LppX(S20D S21D), with substitutions of Asp for Ser-20 and Ser-21 (conversion to an Asp-Asp signal for sorting to the inner membrane), resided on the outer layer of the inner membrane, demonstrating that LppX has the sorting property of a lipoprotein. E. coli harboring both xyn1 and lppX secreted active Xyn1 into the periplasm. In contrast, E. coli carrying xyn1 alone failed to do so, accumulating inactive Xyn1 in the cytoplasmic membranes. Exogenous LppX(C19A) liberated the inactive Xyn1, which had been stagnating in the inner membrane, into the medium as an active enzyme. Thus, we propose that LppX is a novel type of lipoprotein that assists Xyn1 in making the proper fold necessary for traveling across the cytoplasmic membranes to be secreted as an active enzyme.
Towards Energy Efficient Duty-Cycled Networks: Analysis, Implications and Improvement

Duty cycling mode is widely adopted in wireless sensor networks to save energy. Existing duty-cycling protocols cannot well adapt to different data rates and dynamics, resulting in a high energy consumption in real networks. Improving those protocols may require global information or heavy computation and thus may not be practical, leading to many empirical parameters in real protocols. To fill the gap between the application requirement and protocol performance, in this paper, we analyze the energy consumption for duty cycled sensor networks with different data rates. Our analysis shows that existing protocols cannot lead to an efficient energy consumption in various scenarios. Based on the analysis, we design a light-weight adaptive duty-cycling protocol (LAD), which reduces the energy consumption under different data rates and protocol dynamics. LAD can adaptively adjust the protocol parameters according to network conditions such as data rate and achieve an optimal energy efficiency. To make LAD practical in real network, we further pre-calculate optimal parameters offline and store them on sensor nodes, which significantly reduces the computation time. We theoretically validate the performance improvement of the protocol. We implement the protocol in TinyOS and extensively evaluate it on 40 TelosB nodes. The evaluation results show the energy consumption can be reduced by 28.2-40.1 percent compared with state-of-the-art protocols. Results based on data from a 1,200-node operational network further show the effectiveness and scalability of the design.