Miracle-dz/UniFAR-FTUs huggingface dataset:
General function evaluation in a STPC setting via piecewise linear approximation

While in theory any computable functions can be evaluated in a Secure Two Party Computation (STPC) framework, practical applications are often limited for complexity reasons and by the kind of operations that the available cryptographic tools permit. In this paper we propose an algorithm that, given a function f() and an interval belonging to its domain, produces a piecewise linear approximation f() that can be easily implemented in a STPC setting. Two different implementations are proposed: the first one relies completely on Garbled Circuit (GC) theory, while the second one exploits a hybrid construction where GC and Homomorphic Encryption (HE) are used together. We show that from a communication complexity perspective the full-GC implementation is preferable when the input and output variables are represented with a small number of bits, otherwise the hybrid solution is preferable.
In situ monitoring of 3D in vitro cell aggregation using an optical imaging system

Bioreactor systems that maintain cells and tissues in suspension are increasingly popular for culturing 3D constructs to avoid the loss of in vivo cell function associated with traditional 2D culture methods. There is a need for the online monitoring of such systems to provide better understanding and control of the processes involved and to prevent the disruption of these processes caused by offline sampling and endpoint analysis. We describe a system for the imaging and analysis of cell aggregation, over long periods, within a high aspect rotating vessel (HARV). The system exploits side illumination, using an adjustable beam pattern, to restrict the detected light to that scattered by the cell aggregates, thus eliminating the need for the fluorescent labeling of the cells. The in situ aggregation of mammalian cells (MCF‐7 breast carcinoma cells) was monitored over an 8 h period and image sequences showing the growth and motion of the aggregates within the bioreactor were obtained. Detailed size and population data have been derived characterizing the development of the aggregates during this time. We show how the number of resolvable aggregates increases to reach a peak and then declines as these aggregates merge. Once formed, remaining aggregates are found to consolidate to form more tightly packed bodies, typically reducing in cross‐sectional area by one third. These results provide the basis for the development of an automated feedback system to control the growth of 3D cell cultures for repeatable, reliable, and quality controlled experimentation. Biotechnol. Bioeng. 2008;100: 159–167. © 2007 Wiley Periodicals, Inc.
Using acoustic telemetry monitoring techniques to quantify movement patterns and site fidelity of sharks and giant trevally around French frigate shoals and Midway Atoll

The Northwestern Hawaiian Islands (NWHI) host a variety of large vertebrate animals including seabirds, green sea turtles (Chelonia mydas), Hawaiian monk seals (Monanchus schauislandi), and large teleost fish such as trevally (Family Carangidae) and several species of sharks. The air-breathing vertebrates have been the subjects of relatively continuous and well-funded research programs over the past several decades, and many aspects of their biology in the NWHI have been documented fairly well. However, studies directed at understanding the biology and ecology of large teleost fishes and sharks in the NWHI have lagged substantially behind research conducted on birds, turtles and seals. In the summer of 000, an array of autonomous acoustic receivers was deployed at French Frigate Shoals (FFS) in the NWHI as part of a project investigating the movement patterns of tiger sharks (Galeocerdo cuvier) within the atoll, particularly in relation to the high seasonal abundance of potential prey (birds, turtles, seals). Shortly after the establishment of the initial array of monitors in 000, additional monitors were deployed in an effort to monitor the movements of Galapagos sharks (Carcharhinus galapagensis) at FFS, particularly at locations where monk seal pups had been preyed upon by these sharks. The scope of the monitoring study was further expanded to Midway Atoll during summer of 001 to monitor movements of Galapagos sharks near seal haul-out beaches and to examine survivorship and behavior of giant trevally (Caranx ignobilis) captured and released in a commercial sport fishing operation conducted within the Midway National Wildlife Refuge. For each study, experimental animals were captured and surgically fitted with long-life, individually-coded acoustic transmitters. During nearly years of acoustic monitoring at FFS and years of monitoring at Midway, a total of over 45,000 detections of sharks and fish with transmitters were recorded on acoustic monitors. These data enable an assessment of long-term movement patterns of these large predators within the NWHI. Each species investigated demonstrated somewhat repeated and predictable behavioral patterns that provide a basis for improved understanding of determinants of behavior and for enhanced management of these animals and prey (birds, seals, turtles) with which they may interact. _____________________________________________________ 1Dept. of Biological Sciences, California State University, Long Beach, 1250 Bellflower Blvd., Long Beach, CA 0 0 USA, E-mail: clowe@csulb.edu Dept. of Biological Sciences, Univ. of Rhode Island, 100 Flagg Rd, Kingston, RI 02881 USA Hawaii Institute of Marine Biology, PO Box 1346, Kaneohe, HI 96744 USA
Evaluating the Reference and Representation of Domain Concepts in APIs

As libraries are the most widespread form of software reuse, the usability of their APIs substantially influences the productivity of programmers in all software development phases. In this paper we develop a framework to characterize domain-specific APIs along two directions: 1) how can the API users reference the domain concepts implemented by the API; 2) how are the domain concepts internally represented in the API. We define metrics that allow the API developer for example to assess the conceptual complexity of his API and the non-uniformity and ambiguities introduced by the API's internal representations of domain concepts, which makes developing and maintaining software that uses the library difficult and error-prone. The aim is to be able to predict these difficulties already during the development of the API, and based on this feedback be able to develop better APIs up front, which will reduce the risks of these difficulties later.
A tutorial on predictive repetitive control

It is well known that in order to track a periodic reference signal or reject a periodic disturbance signal, the dominant frequency components of the reference or the disturbance signal need to be incorporated in the predictive control system design, leading to the so called predictive repetitive control systems. With the assumption of input disturbance acting on the system, there are two mainstream approaches to predictive repetitive control where the first is to embed a disturbance model into the predictive controller and the second is to estimate the disturbance model via an observer. The two approaches are different in their design and implementation. This tutorial paper will give an overview of both approaches and evaluate their performance via simulation studies.
Immunomodulating peptides for food allergy prevention and treatment

ABSTRACT Among the most promising strategies currently assayed against IgE-mediated allergic diseases stands the possibility of using immunomodulating peptides to induce oral tolerance toward offending food allergens or even to prevent allergic sensitization. This review focuses on the beneficial effects of food derived immunomodulating peptides on food allergy, which can be directly exerted in the intestinal tract or once being absorbed through the intestinal epithelial barrier to interact with immune cells. Food peptides influence intestinal homeostasis by maintaining and reinforcing barrier function or affecting intestinal cell-signalling to nearby immune cells and mucus secretion. In addition, they can stimulate cells of the innate and adaptive immune system while supressing inflammatory responses. Peptides represent an attractive alternative to whole allergens to enhance the safety and efficacy of immunotherapy treatments. The conclusions drawn from curative and preventive experiments in murine models are promising, although there is a need for more pre-clinical studies to further explore the immunomodulating strategy and its mechanisms and for a deeper knowledge of the peptide sequence and structural requirements that determine the immunoregulatory function.
Integrating Ecosystem Services in Historically Polluted Areas: Bioremediation Techniques for Soils Contaminated by Heavy Metals

Bioremediation of soils contaminated by heavy metals is based on the use of specially selected plants able to reduce the hazards of toxic metals. Depending on the mode of action on the heavy metals existing in the soil and the place where the action takes place, the following mechanisms for soil phytoremediation are distinguished: phytostabilization, phytoextraction, phytoimobilization, rhizofiltration, or evapotranspiration. These mechanisms are complex and include the plant ability to reduce the mobility and bioavailability of heavy metals and other pollutants, to extract large amounts of heavy metals from the soil or to evaporate water together with various pollutants already reached in the rhizosphere. Decontamination of polluted soils by using bioaccumulative plants is proposed as an environmental-friendly alternative to the traditional physicochemical methods, being a sustainable method with a great potential in the terms of environmental protection and cost management.
Attentional Preparation for a Lateralized Visual Distractor: Behavioral and fMRI Evidence

Attending to the location of an expected visual target can lead to anticipatory activations in spatiotopic occipital cortex, emerging before target onset. But less is known about how the brain may prepare for a distractor at a known location remote from the target. In a psychophysical experiment, we found that trial-to-trial advance knowledge about the presence of a distractor in the target-opposite hemifield significantly reduced its behavioral cost. In a subsequent functional magnetic resonance imaging experiment with similar task and stimuli, we found anticipatory activations in the occipital cortex contralateral to the expected distractor, but no additional target modulation, when participants were given advance information about a distractor's subsequent presence and location. Several attention-related control structures (frontal eye fields and superior parietal cortex) were active during attentional preparation for all trials, whereas the left superior prefrontal and right angular gyri were additionally activated when a distractor was anticipated. The right temporoparietal junction showed stronger functional coupling with occipital regions during preparation for trials with an isolated target than for trials with a distractor expected. These results show that anticipation of a visual distractor at a known location, remote from the target, can lead to (1) a reduction in the behavioral cost of that distractor, (2) preparatory modulation of the occipital cortex contralateral to the location of the expected distractor, and (3) anticipatory activation of distinct parietal and frontal brain structures. These findings indicate that specific components of preparatory visual attention may be devoted to minimizing the impact of distractors, not just to enhancements of target processing.
WITHDRAWN: Gabapentin for acute and chronic pain.

BACKGROUND February 2009: The authors are aware of unpublished trial data for Gabapentin which could affect the results of this review. This information together with that from trials published since 2005, will be considered when this review is updated in 2009.Anticonvulsant drugs have been used in the management of pain since the 1960s. The clinical impression is that they are useful for chronic neuropathic pain, especially when the pain is lancinating or burning. OBJECTIVES To evaluate the analgesic effectiveness and adverse effects of gabapentin for pain management in clinical practice. SEARCH STRATEGY Randomised trials of gabapentin in acute, chronic or cancer pain were identified by MEDLINE (1966 to Nov 2004), EMBASE (1994 to Nov 2004), SIGLE (1980 to Jan 2004) and the Cochrane Central Register of Controlled Trials (CENTRAL) (The Cochrane Library, Issue 4, 2004). Additional studies were identified from the reference list of the retrieved papers, and by contacting investigators. Date of most recent search: January 2004. SELECTION CRITERIA Randomised trials reporting the analgesic effects of gabapentin in participants with subjective pain assessment as either the primary or a secondary outcome. DATA COLLECTION AND ANALYSIS Data were extracted by two independent review authors, and trials were quality scored. Numbers-needed-to-treat-to-benefit (NNTs) were calculated, where possible, from dichotomous data for effectiveness, adverse effects and drug-related study withdrawal. MAIN RESULTS Fourteen reports describing 15 studies of gabapentin were considered eligible (1468 participants). One was a study of acute pain. The remainder included the following conditions: post-herpetic neuralgia (two studies), diabetic neuropathy (seven studies), a cancer related neuropathic pain (one study) phantom limb pain (one study), Guillain Barré syndrome (one study), spinal chord injury pain (one study) and various neuropathic pains (one study). The study in acute post-operative pain (70 participants) showed no benefit for gabapentin compared to placebo for pain at rest.In chronic pain, the NNT for improvement in all trials with evaluable data is 4.3 (95% CI 3.5 to 5.7). Forty two percent of participants improved on gabapentin compared to 19% on placebo. The number needed to harm (NNH) for adverse events leading to withdrawal from a trial was not significant. Fourteen percent of participants withdrew from active arms compared to 10% in placebo arms. The NNH for minor harm was 3.7 (95% CI 2.4 to 5.4). The NNT for effective pain relief in diabetic neuropathy was 2.9 (95% CI 2.2 to 4.3) and for post herpetic neuralgia 3.9 (95% CI 3 to 5.7). AUTHORS' CONCLUSIONS There is evidence to show that gabapentin is effective in neuropathic pain. There is limited evidence to show that gabapentin is ineffective in acute pain.
Gene–Environment Interaction in Yeast Gene Expression

The effects of genetic variants on phenotypic traits often depend on environmental and physiological conditions, but such gene–environment interactions are poorly understood. Recently developed approaches that treat transcript abundances of thousands of genes as quantitative traits offer the opportunity to broadly characterize the architecture of gene–environment interactions. We examined the genetic and molecular basis of variation in gene expression between two yeast strains (BY and RM) grown in two different conditions (glucose and ethanol as carbon sources). We observed that most transcripts vary by strain and condition, with 2,996, 3,448, and 2,037 transcripts showing significant strain, condition, and strain–condition interaction effects, respectively. We expression profiled over 100 segregants derived from a cross between BY and RM in both growth conditions, and identified 1,555 linkages for 1,382 transcripts that show significant gene–environment interaction. At the locus level, local linkages, which usually correspond to polymorphisms in cis-regulatory elements, tend to be more stable across conditions, such that they are more likely to show the same effect or the same direction of effect across conditions. Distant linkages, which usually correspond to polymorphisms influencing trans-acting factors, are more condition-dependent, and often show effects in different directions in the two conditions. We characterized a locus that influences expression of many growth-related transcripts, and showed that the majority of the variation is explained by polymorphism in the gene IRA2. The RM allele of IRA2 appears to inhibit Ras/PKA signaling more strongly than the BY allele, and has undergone a change in selective pressure. Our results provide a broad overview of the genetic architecture of gene–environment interactions, as well as a detailed molecular example, and lead to key insights into how the effects of different classes of regulatory variants are modulated by the environment. These observations will guide the design of studies aimed at understanding the genetic basis of complex traits.
Towards a MOLGENIS Based Computational Framework

High-throughput bioinformatics research is complex and requires the combination of multiple experimental approaches each producing large amounts of diverse data. The analysis and evaluation of these data are equally complex requiring specific integrations of various software components into complex workflows. The challenge is to provide less technically involved bioinformaticians with simple interfaces to specify the workflow of commands they need while at the same time scale up to hundreds of jobs to get the terabytes of genetic data processed by recent methods. Here, we present a computational framework for bioinformatics which enables data and workflow management in a distributed computational environment. Firstly, we propose a new data model to specify workflow execution logic on available network resources and components. Our model extends existing generic workflow and bioinformatics models to describe workflows compactly and unambiguously. Secondly, we present the implementation of our computational framework, which is constructed as a computational cloud for bioinformatics using open source off-the-shelf components. Finally, we demonstrate applications of the framework on complex real-world bioinformatics tasks.
Decision Manifolds: Classification Inspired by Self-Organization

We present a classifier algorithm that approximates the decision surface of labeled data by a patchwork of separating hyperplanes. The hyperplanes are arranged in a way inspired by how Self-Organizing Maps are trained. We take advantage of the fact that the boundaries can often be approximated by linear ones connected by a low-dimensional nonlinear manifold. The resulting classifier allows for a voting scheme that averages over neighboring hyperplanes. Our algorithm is computationally efficient both in terms of training and classification. Further, we present a model selection framework for estimation of the paratmeters of the classification boundary, and show results for artificial and real-world data sets.
Considerations for Focused Surgical Intervention in the Presence of Adult Spinal Deformity

Study Design. Case studies, literature review. Objectives. The goal of this review is to raise awareness and stimulate contributions on this topic. Summary of Background Data. Surgical management of adult patients presenting with intractable back and leg pain in conjunction with spinal deformity often raises the question of need for curve arthrodesis. Meticulous patient assessment is essential in determining if the deformity underlies patient symptoms. If so, then the deformity must be stabilized according to criteria established in the literature. However, when patient evaluation suggests that the deformity is not the source of symptoms, other surgical options may be considered. These include limited decompression without fusion or decompression with short fusion limited only to the site of pathology. Materials and Methods. Three cases are presented illustrating situations where decompression alone or decompression with short fusion was indicated. Results. When an adult spinal deformity is stable and is not the source of symptoms, symptomatic relief may be provided through limited decompression within the curve but without curve arthrodesis. Similarly, symptomatic pathology arising from levels adjacent to or remote from the deformity may be addressed with short-segment decompression and fusion. Conclusions. This brief and limited communication reviews some of the pertinent issues and provides several examples of selective surgical treatment options without curve arthrodesis in patients with deformity. These options are typically much smaller surgical undertakings, particularly in adult patients who generally have complicating comorbidities. Little has been published to guide surgical management for these conditions.
Detecting shifts in diversity limits from molecular phylogenies: what can we know?

Large complete species-level molecular phylogenies can provide the most direct information about the macroevolutionary history of clades having poor fossil records. However, extinction will ultimately erode evidence of pulses of rapid speciation in the deep past. Assessment of how well, and for how long, phylogenies retain the signature of such pulses has hitherto been based on a—probably untenable—model of ongoing diversity-independent diversification. Here, we develop two new tests for changes in diversification ‘rules’ and evaluate their power to detect sudden increases in equilibrium diversity in clades simulated with diversity-dependent speciation and extinction rates. Pulses of diversification are only detected easily if they occurred recently and if the rate of species turnover at equilibrium is low; rates reported for fossil mammals suggest that the power to detect a doubling of species diversity falls to 50 per cent after less than 50 Myr even with a perfect phylogeny of extant species. Extinction does eventually draw a veil over past dynamics, suggesting that some questions are beyond the limits of inference, but sudden clade-wide pulses of speciation can be detected after many millions of years, even when overall diversity is constrained. Applying our methods to existing phylogenies of mammals and angiosperms identifies intervals of elevated diversification in each.
Dielectric properties of graphene-filled epoxy nanocomposite with enhanced thermal conductivity

The development of advanced dielectric materials with high thermal conductivity is of crucial importance in modern electronic and power equipment systems. Herein, multilayer graphene nanosheets/epoxy nanocomposites with enhanced thermal conductivity were fabricated by solution blended processes. It was found that the incorporation of graphene nanosheets had little impact on thermogravimetric properties of epoxy composite but had a certain effect on glass transition temperature (Tg), which increased by 4.63 °C with the incorporation of 0.1 wt. % graphene nanosheets. The incorporation of graphene nanosheets also increased dielectric constant and loss as well as DC conductivity in different ranges. At 25 C and 50 Hz, in contrast with the neat epoxy composite, dielectric constant increased by 36.87 % with incorporation of 0.5 wt. % graphene nanosheets. The thermal conductivity and diffusivity increased by 34.59 % and 24.37 % respectively with the incorporation of 0.5 wt. % graphene nanosheets. The incorporation of uniformly dispersed graphene nanosheets into polymer matrix as thermal conductive fillers paves a way to expand the application of polymer materials in electronic packaging fields.