Miracle-dz/UniFAR-FTUs huggingface dataset:
New Immunosuppressive Therapies in Uveitis Treatment

Uveitis is an inflammatory process that initially starts in the uvea, but can also affect other adjacent eye structures, and is currently the fourth cause of blindness in developed countries. Corticoids are probably the most widespread treatment, but resorting to other immunosuppressive treatments is a frequent practice. Since the implication of different cytokines in uveitis has been well demonstrated, the majority of recent treatments for this disease include inhibitors or antibodies against these. Nevertheless, adequate treatment for each uveitis type entails a difficult therapeutic decision as no clear recommendations are found in the literature, despite the few protocolized clinical assays and many case-control studies done. This review aims to present, in order, the mechanisms and main indications of the most modern immunosuppressive drugs against cytokines.
Discovery and Directed Evolution of a Glyphosate Tolerance Gene

The herbicide glyphosate is effectively detoxified by N-acetylation. We screened a collection of microbial isolates and discovered enzymes exhibiting glyphosate N-acetyltransferase (GAT) activity. Kinetic properties of the discovered enzymes were insufficient to confer glyphosate tolerance to transgenic organisms. Eleven iterations of DNA shuffling improved enzyme efficiency by nearly four orders of magnitude from 0.87 mM–1 min–1 to 8320 mM–1 min–1. From the fifth iteration and beyond, GAT enzymes conferred increasing glyphosate tolerance to Escherichia coli, Arabidopsis, tobacco, and maize. Glyphosate acetylation provides an alternative strategy for supporting glyphosate use on crops.
A Comparative Study of Supervised Learning Techniques for the Radiative Transfer Equation Inversion

Estimation of the constituents of a gas (e.g. temperature, concentration) from high reso- lution spectroscopic measurements is a fundamental step to control and improve the eciency of com- bustion processes governed by the Radiative Tran- fer Equation (RTE). Typically such estimation is per- formed using thermocouples; however, these sensors are intrusive and must undergo the harsh furnace en- vironment. In this paper, we follow a machine learn- ing approach to learn the relation between the spec- troscopic measurements and gas constituents such as temperature, concentration and length. This is a chal- lenging problem due to the non-linear behavior of the RTE and the high dimensional data obtained from sensor measurements. We perform a comparative study of linear and neural network regression mod- els, using canonical correlation analysis (CCA), prin- cipal component analysis (PCA), reduced rank regres- sion(RRR), and kernel canonical correlation (KCCA) to reduce the dimensionality.
Ranking target objects of navigational queries

Web navigation plays an important role in exploring public interconnected data sources such as life science data. A navigational query in the life science graph produces a result graph which is a layered directed acyclic graph (DAG). Traversing the result paths in this graph reaches a target object set (TOS). The challenge for ranking the target objects is to provide recommendations that re ect the relative importance of the retrieved object, as well as its relevance to the specific query posed by the scientist. We present a metric layered graph PageRank (lgPR) to rank target objects based on the link structure of the result graph. LgPR is a modification of PageRank; it avoids random jumps to respect the path structure of the result graph. We also outline a metric layered graph ObjectRank (lgOR) which extends the metric ObjectRank to layered graphs. We then present an initial evaluation of lgPR. We perform experiments on a real-world graph of life sciences objects from NCBI and report on the ranking distribution produced by lgPR. We compare lgPR with PageRank. In order to understand the characteristics of lgPR, an expert compared the Top K target objects (publications in the PubMed source) produced by lgPR and a word-based ranking method that uses text features extracted from an external source (such as Entrez Gene) to rank publications.
Reply: Glial mitochondropathy in infantile neuroaxonal dystrophy: pathophysiological and therapeutic implications.

Sir, Mitochondrial dysfunction is increasingly being recognized as a therapeutic target in PLA26G-associated neurodegeneration (PLAN). We demonstrated in Drosophila and in human PLA2G6 mutant fibroblasts that loss of normal PLA2G6 activity is associated with increased mitochondrial lipid peroxidation and mitochondrial dysfunction. Furthermore, we identified the therapeutic benefits of deuterated polyunsaturated fatty acids (D-PUFAs) in PLAN, through inhibition of lipid peroxidation. D-PUFAs ameliorated the locomotor deficits in flies lacking the fly orthologue of PLA2G6 ( iPLA2-VIA ), and reversed the mitochondrial abnormalities in patient fibroblasts harbouring pathogenic mutations in PLA2G6 (Kinghorn et al. , 2015). In their Letter to the Editor, Farrar et al. (2016) report abnormal mitochondrial morphology at the ultrastructural level in muscle and cutaneous nerves, as well as in cutaneous Schwann cells of a patient with infantile neuroaxonal dystrophy (INAD) associated with homozygous PLA2G6 mutations. They also observed a selective loss of complex IV of the respiratory chain in skeletal muscle, and they report elevated urine catecholamine levels and serum neuronal specific enolase in their patient. This study is thus supportive of the abnormal mitochondrial morphology observed in the CNS of Drosophila and mouse models of PLA2G6 deficiency (Beck et al. , 2011; Kinghorn et al. , 2015; Kinghorn and Castillo-Quan, 2016). It also provides evidence for the involvement of peripheral nerves outside of the CNS, and that mitochondrial pathology extends beyond neurons to glia. The next step will be to …
Reduction of the HIV Seroconversion Window Period and False Positive Rate by Using ADVIA Centaur HIV Antigen/Antibody Combo Assay

Background Early diagnosis of HIV infection reduces morbidity and mortality. Fourth-generation HIV detection assays are more sensitive because they can detect p24 antigen as well as anti-HIV antibodies. In this study, we evaluated the performance of a new fourth-generation ADVIA Centaur HIV antigen/antibody combo (CHIV) assay (Siemens Healthcare Diagnostics Inc., USA) for early detection of HIV infection and reduction of false positive rate. Methods Four seroconversion panels were included. The third-generation ADVIA Centaur HIV 1/O/2 enhanced (EHIV) assay (Siemens Healthcare Diagnostics Inc., USA) and fourth-generation CHIV assay were used to test each panel for HIV infection. The presence of antigen was confirmed using HIV p24 antigen assay. To evaluate false-positivity and specificity, 54 HIV false-positive and HIV-negative serum samples from 100 hospitalized patients and 600 healthy subjects were included. Results Compared to the EHIV assay, the CHIV assay had a shorter window for three of the seroconversion panels: a difference of 10 days and two bleeds in one panel, and 4 days and one bleed in the other two panels. Only 34 of the 54 (63%) samples known to yield false-positive results by EHIV assay had repeatedly yielded reactive results in the CHIV assay. One of the 600 healthy subjects had a false-positive result with the CHIV assay; thus, the specificity was 99.85% (699/700). CHIV accurately determined the reactive results for the HIV-confirmed serum samples from known HIV patients and Korea Food & Drug Administration (KFDA) panels. Conclusions The new fourth-generation ADVIA Centaur HIV assay is a sensitive and specific assay that shortens the serological window period and allows early diagnosis of HIV infection.
Localization Algorithms for Mobile Wireless Sensor Networks: A Review and Future Scope

Many applications in wireless sensor networks require sensor nodes to obtain their absolute geographical positions. There are various localization algorithms have been recently proposed. Localization – finding the position of individual sensor nodes-remains one of the most difficult research challenges. Many applications based on networked sensors require location awareness; a node must be able to find its location.This paper presents a reviewof some localization algorithms which used different techniques such as CAB, GRAHAM’S SCAN, QUERY MODEL, EVENT TRIGGERED DISTRIBUTED OPTIMIZATION, and BILATERATION.
Multi-threshold image segmentation using histogram thresholding-Bayesian honey bee mating algorithm

Image thresholding is one of the most imperative practices to accomplish image segmentation, image compression and target recognition. This has been widely studied over the past few decades. However, the multilevel thresholding computationally takes more time when the threshold number increases. Hence, this paper proposes a honey bee mating-based algorithm (HBMA) based on Bayesian theorem and the characters of intensity images for image segmentation to save computation time. This kind of HBMA is called as Bayesian Honey Bee Mating Algorithm (BHBMA). Moreover, we adopt a population initialization strategy to make the search more efficient, according to the characters of multilevel thresholding in an image arranged from a low gray level to a high one. Extensive experiments have shown that BHBMA can deliver more effective and efficient results to be applied in complex image processing such as automatic target recognition, compared with state-of-the-art population-based thresholding methods.
csPCR: A computational tool for the simulation of the Polymerase Chain Reaction

Dasu S, Williams A, Fofanov Y, Putonti C. , csPCR: A computational tool for the simulation of the Polymerase Chain Reaction, Online J Bioinformatics, 11 (1): 30-33, 2010. Herein we present a computational simulation package PCR (csPCR) which models the PCR reaction, taking into consideration the issues of specificity, sensitivity, potential mishybridizations throughout the primer sequence as well as at the 3’ end, and primer interactions, including selfcomplementarity and primer-primer interactions. A single target sequence or multiple target sequences can be considered simultaneously in addition to multiple primer sequences; thus a complex community and/or a multiplex assay can be simulated in a manner analogous with the actual experiment. This tool leaves primer design to the user, as there is a wealth of existing programs already available, and rather focuses on simulation of the anticipated amplification and expected agarose gel in addition to providing information about the location(s) of amplification in both text and graphical format. The software is freely available at www.bioinfo. uh.edu/csPCR.
High throughput Byzantine fault tolerance

This paper argues for a simple change to Byzantine fault tolerant (BFT) state machine replication libraries. Traditional BFT state machine replication techniques provide high availability and security but fail to provide high throughput. This limitation stems from the fundamental assumption of generalized state machine replication techniques that all replicas execute requests sequentially in the same total order to ensure consistency across replicas. We propose a high throughput Byzantine fault tolerant architecture that uses application-specific information to identify and concurrently execute independent requests. Our architecture thus provides a general way to exploit application parallelism in order to provide high throughput without compromising correctness. Although this approach is extremely simple, it yields dramatic practical benefits. When sufficient application concurrency and hardware resources exist, CBASE, our system prototype, provides orders of magnitude improvements in throughput over BASE, a traditional BFT architecture. CBASE-FS, a Byzantine fault tolerant file system that uses CBASE, achieves twice the throughput of BASE-FS for the IOZone micro-benchmarks even in a configuration with modest available hardware parallelism.
Telemedicine system for remote blood pressure and heart rate monitoring

In this paper we present the realization of a remote blood pressure and heart rate monitoring system, based on wireless devices, capable to measure and transmit patient's arterial blood pressure and heart rate. The use of the proposed system is suitable for continuous long-time patient monitoring, as a part of a diagnostic procedure. The patient can achieve medical assistance of a chronic condition, or can be supervised during recovery from an acute event or surgical procedure. We use commercially available devices, low power microcontrollers and RF transceivers that perform the measurements and transmit them to the patient monitoring device. The patient monitoring device, in form of a PDA that running a personal heart monitor application, receives the blood pressure systolic and diastolic values and heart rate, activates the alarms when these values exceed the preset limits, and communicates periodically to the central monitoring server by using WiFi or GSM/GPRS connection. A graphical user interface running on the central monitoring server for displaying the measurements was developed. Power consumption by the used devices was also minimized.
Automated generation of representations in vision

Presents a general strategy for automated generation of efficient representations in vision. The approach is highly task oriented and what constitutes the relevant information is defined by a set of examples. The examples are pairs of situations that are dependent through the chosen feature but are otherwise independent. Particularly important concepts in the work are mutual information and canonical correlation. How visual operators and representation can be generated from examples are presented for a number of features, e.g. local orientation, disparity and motion. Interesting similarities to biological vision functions are observed. The results clearly demonstrates the potential of combining advanced filtering techniques and learning strategies based on canonical correlation analysis.
Island tameness: living on islands reduces flight initiation distance

One of Darwin's most widely known conjectures is that prey are tame on remote islands, where mammalian predators are absent. Many species appear to permit close approach on such islands, but no comparative studies have demonstrated reduced wariness quantified as flight initiation distance (FID; i.e. predator–prey distance when the prey begins to flee) in comparison with mainland relatives. We used the phylogenetic comparative method to assess influence of distance from the mainland and island area on FID of 66 lizard species. Because body size and predator approach speed affect predation risk, we included these as independent variables. Multiple regression showed that FID decreases as distance from mainland increases and is shorter in island than mainland populations. Although FID increased as area increased in some models, collinearity made it difficult to separate effects of area from distance and island occupancy. FID increases as SVL increases and approach speed increases; these effects are statistically independent of effects of distance to mainland and island occupancy. Ordinary least-squares models fit the data better than phylogenetic regressions, indicating little or no phylogenetic signal in residual FID after accounting for the independent variables. Our results demonstrate that island tameness is a real phenomenon in lizards.
Localised primary amyloidosis of the urinary bladder: case series of two patients

Isolated amyloidosis of the lower urinary tract is rare. This report presents localised primary amyloidosis of the urinary bladder as a rare cause of macroscopic haematuria. Treatment of bladder amyloidosis mainly consists of controlling the haematuria. For small localised lesions, the favoured approach is transurethral resection (TUR) of the lesion.
Notice of Violation of IEEE Publication PrinciplesMultipole Nonlinear Response of Metamaterials

On the nonlinear optical response of meta-materials evoked by first and second order multipoles. The analytical ground on which the approach bases permits for new insights into the functionality of meta-materials. For the sake of clarity we focus here on the split-ring resonator, although the introduced formalism can be applied to arbitrary structures. We derive the equations that describe linear and nonlinear light propagation where special emphasis is put on second harmonic generation. This contribution basically aims at stretching versatile and exist-ing concepts to describe light propagation in nonlinear media towards the realm of meta-materials.
Information Integration and Disaster Data Management ( DisDM ) ∗ †

Recent disasters such as the 2003 SARS outbreak, the 2004 Asian tsunami, the 2005 Kashmir/Pakistan earthquake and 2005 hurricanes Katrina and Rita clearly identified the shortcomings of IT solutions for disaster rescue and recovery. Of particular note was the accompanying disaster of the lack of viable or deployed data management solutions, specifically information integration and information sharing solutions. In this position paper, we identify some specific challenges to information integration and sharing that is driven by the requirements of disaster data management (DisDM). We then identify a brief summary of needed technologies and methods for DisDM.
An internal region of the peroxisomal membrane protein PMP47 is essential for sorting to peroxisomes

Targeting sequences on peroxisomal membrane proteins have not yet been identified. We have attempted to find such a sequence within PMP47, a protein of the methylotrophic yeast, Candida boidinii. This protein of 423 amino acids shows sequence similarity with proteins in the family of mitochondrial carrier proteins. As such, it is predicted to have six membrane-spanning domains. Protease susceptibility experiments are consistent with a six-membrane-spanning model for PMP47, although the topology for the peroxisomal protein is inverted compared with the mitochondrial carrier proteins. PMP47 contains two potential peroxisomal targeting sequences (PTS1), an internal SKL (residues 320- 322) and a carboxy terminal AKE (residues 421-423). Using a heterologous in vivo sorting system, we show that efficient sorting occurs in the absence of both sequences. Analysis of PMP47- dihydrofolate reductase (DHFR) fusion proteins revealed that amino acids 1-199 of PMP47, which contain the first three putative membrane spans, do not contain the necessary targeting information, whereas a fusion with amino acids 1-267, which contains five spans, is fully competent for sorting to peroxisomes. Similarly, a DHFR fusion construct containing residues 268-423 did not target to peroxisomes while residues 203-420 appeared to sort to that organelle, albeit at lower efficiency than the 1-267 construct. However, DHFR constructs containing only amino acids 185-267 or 203-267 of PMP47 were not found to be associated with peroxisomes. We conclude that amino acids 199-267 are necessary for peroxisomal targeting, although additional sequences may be required for efficient sorting to, or retention by, the organelles.
The D2 Dopamine Receptor Gene as a Determinant of Reward Deficiency Syndrome

The dopaminergic system, and in particular the dopamine D2 receptor, has been profoundly implicated in reward mechanisms in the brain. Dysfunction of the D2 dopamine receptors leads to aberrant substance seeking behaviour (alcohol, drug, tobacco, and food) and other related behaviours (pathological gambling, Tourette's syndrome, and attention deficit hyperactivity disorder). We propose that variants of the D2 dopamine receptor gene are important common genetic determinants of the ‘reward deficiency syndrome’.
Editorial: When (and How) Is Theory of Mind Useful? Evidence from Life-Span Research

The Theory of Mind (ToM) paradigm was born almost 40 years ago with the study “Does the chimpanzee have a theory of mind? ” by Premack and Woodruff (1978). Several papers (meta-analyses, reviews) have tried to describe the state-of-art, both in general and with respect to specific constructs. From a historical perspective it is possible to identify some relevant turning points in this field of research. ToM, which initially began as a cognitive theory, has subsequently been hybridized to include socio-cultural and/or psychoanalytic perspectives. Within the socio-cultural framework ToM is considered as an outcome of internalization processes in the Vygotskian Zone of Proximal Development; within the psychoanalytic perspective the mentalization process, as ToM is often named, is viewed as a result of the successful relationships with caregivers equipped with a sufficient reflective function. In both cases, intersubjectivity acts as the core concept and the link between ToM and affective relationships have become a new object of investigation. Moreover, there has been increased interest in life-span research from the early stages of life up to the elderly. ToM neural correlates have also been investigated. It has been hypothesized that ToM continues to evolve in a manner that involves both behavioral skills and neural plasticity. Furthermore, the search for novel and more ecological methods aimed to enrich a stronger external relevance. In this regard it has been recognized that “have ToM” and “use ToM” are two deeply different concepts. Furthermore, the use of ToM is linked to the global sphere of social competencies: many studies have tried to understand the predictive role of ToM or at least its connections with other social skills. The present Research Topic (RT) deals with theoretical and empirical contexts with the scope to understand “when” and “how” ToM emerges as a relevant component of social competencies devoted to promoting adaptation and well-being. First, the temporal element, “when,” is referred not only to the chronological dimension of developmental, but also to the subjective relational, circumstances of life, i.e., type of affective relationships, typical vs. non-typical or clinical development and so on. Second, “how” is referred to as the phenomenology of this process, namely the behavioral mode or the neural patterns as well as the connections between them. The RT investigates classic ToM constructs, from the initial concept of “false belief” to pretense and storytelling. Moreover, there are several contributions which aim to use the power of the understanding of subjectivity, in which ToM consists, for educational and therapeutic purposes. The relevance of ToM for the clinical view is supported by the DSM V which includes social competencies in the nosographic framework of developmental impairments (i.e., autism spectrum disorders and social/pragmatic communication disorder) and neurocognitive disorders.
Edinburgh Research Explorer SmartSociety – A Platform for Collaborative People-Machine Computation SmartSociety – A Platform for Collaborative People-Machine Computation

—Society is moving towards a socio-technical ecosys- tem in which physical and virtual dimensions of life are inter-twined and where people interactions ever more take place with or are mediated by machines. Hybrid Diversity-aware Collective Adaptive Systems (HDA-CAS) is a new generation of socio- technical systems where humans and machines synergetically complement each other and operate collectively to achieve their goals. HDA-CAS introduce the fundamental properties of hybridity and collectiveness, hiding from the users the complexities associated with managing the collaboration and coordination of machine and human computing elements. In this paper we present an HDA-CAS system called SmartSociety, supporting computations with hybrid human/machine collectives. We de- scribe the platform’s architecture and functionality, validate it on two real-world scenarios involving human and machine elements and present a performance evaluation.