Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of a gene causing human cytochrome c oxidase deficiency by integrative genomics

Identifying the genes responsible for human diseases requires combining information about gene position with clues about biological function. The recent availability of whole-genome data sets of RNA and protein expression provides powerful new sources of functional insight. Here we illustrate how such data sets can expedite disease-gene discovery, by using them to identify the gene causing Leigh syndrome, French-Canadian type (LSFC, Online Mendelian Inheritance in Man no. 220111), a human cytochrome c oxidase deficiency that maps to chromosome 2p16-21. Using four public RNA expression data sets, we assigned to all human genes a “score” reflecting their similarity in RNA-expression profiles to known mitochondrial genes. Using a large survey of organellar proteomics, we similarly classified human genes according to the likelihood of their protein product being associated with the mitochondrion. By intersecting this information with the relevant genomic region, we identified a single clear candidate gene, LRPPRC. Resequencing identified two mutations on two independent haplotypes, providing definitive genetic proof that LRPPRC indeed causes LSFC. LRPPRC encodes an mRNA-binding protein likely involved with mtDNA transcript processing, suggesting an additional mechanism of mitochondrial pathophysiology. Similar strategies to integrate diverse genomic information can be applied likewise to other disease pathways and will become increasingly powerful with the growing wealth of diverse, functional genomics data.
Logical approaches to Machine Learning---an overview

The ability to learn from observations and experience seems to be crucial for any intelligent being. Likewise, Machine Learning plays a central role in Artificial Intelligence research. Learning is no different from many other cognitive phenomena in that it resists a general definition. A first try could be: learning is the ability to improve on a certain task. For instance, the task may be face recognition, weather prediction, or taking the derivative of functions. This definition has a behavioral flavour, taking the performer of the task as a black box and judging its performance only from the outside. We will make the additional assumption that the performer consists of a procedural engine and a declarative knowledge base, and that its performance is improved by improving the knowledge base rather than the engine. For instance, the knowledge needed for recognising faces might be expressed in terms of classification rules, listing the characteristic features of specific faces; the ability to recognise faces can be improved by improving the classification rules. From this viewpoint, learning is the ability to acquire new or better knowledge. This declarative view of learning does not cover systems which improve their behaviour by improving their procedural engine, such as neural nets. This is not to say that such systems don’t learn, but it is a fundamentally different kind of learning, which falls beyond the scope of this paper.
Automatic Annotation of Digital Images using Colour Structure and Edge Direction

The focus of this paper is on automatic annotation for semantic image retrieval. This work is aimed at identifying visual descriptors that are most relevant, effective and suitable for semantic annotation tasks. We propose an image annotation system based on support vector machines and a combination of descriptors that includes a gradient direction histogram and several MPEG-7 visual descriptors. The system is tested on a large database of 7200 cityscape and landscape images. The results indicate that when descriptors are used individually, the proposed gradient direction histogram performs best. However, when descriptors are combined, the accuracy is improved. The presented results confirm that combining the gradient direction histogram and colour structure produces the best results.
Congestion and Awareness Control in Cooperative Vehicular Systems

Cooperative vehicular systems have been identified as a promising solution to overcome the current and future needs for increasing traffic safety and efficiency, while providing infotainment and added-value services on the move. To achieve their objectives, cooperative vehicular systems will be based on wireless communications between vehicles and with other infrastructure nodes, and will have to deal with highly dynamic nodes, challenging propagation conditions, and stringent application requirements. By looking at cooperative applications and their data traffic, as well as the current and foreseen spectrum allocations for cooperative vehicular systems, there is a risk that the corresponding radio channels could easily be saturated if no control algorithms are used. The saturation of the radio channels would result in unstable vehicular communications, and thus in an inefficient operation of cooperative systems. As a prime example of upcoming ubiquitous networks contributing to the vision of “a thousand radios per person,” cooperative vehicular systems need to be designed to scale to high densities of radios without centralized coordination, while at the same time guaranteeing the requirements of the implemented applications and services, for example the stringent needs of active traffic safety applications. In this paper, we survey and classify various decentralized methods to control the load on the radio channels and to ensure each vehicle's capacity to detect and communicate with the relevant neighboring vehicles, with a particular focus on approaches based on transmit power and rate control. Finally, we discuss the open research challenges that are imposed by different application requirements and potential existing contradictions.
Runtime Code Generation for Huffman Decoders

Runtime code generation is not a new concept [1] and has been widely used for improving the performance of programs at runtime. Typical examples include Just-In-Time (JIT) compilation [2], [3] and dynamic optimization systems [4], [5]. A class of programs that can benefit from runtime code generation are programs with an execution path that is determined by runtime data, which remain unchanged during execution and their size is constant with regard to the total size of the input data. An example of such a program is a huffman decoder.
SOAR–OSIRIS observations of the Sh 2-307 H ii region: triggered star formation beyond the Solar Circle

This work aims to study the Sh 2-307 H II region and related stellar population. Near-infrared imaging and spectroscopic observations in the direction of Sh 2-307 were performed using the Ohio State InfraRed Imager/Spectrometer (OSIRIS) at the Southern Observatory for Astrophysical Research (SOAR) Telescope. The photometric data were analysed from colour-colour and colour-magnitude diagrams, while the spectroscopic results were interpreted from the comparison of the science spectra with those obtained from known OB stars. From J-, Hand K-band spectra of the brightest source in the cluster, we conclude that it has a near-infrared spectrum compatible with those of 09V-09.5V stars. Using the derived spectral type and the respective J-, H- and K-band photometry, we compute a heliocentric distance of 3.2 ± 0.5 kpc, which, for R 0 = 8 kpc, puts this cluster at more than 10 kpc from the Galactic Centre. From the Brγ, H 2 and continuum narrow-band images we were able to detect both the near-infrared (NIR) counterpart of the associated H II region and the interface between the ionized and cool molecular gas. Using the 5-GHz continuum flux density taken from the Parkes-MIT-NRAO (PMN) catalogue and the Brγ narrow-band image, we estimate that the H II region has a mean diameter of 0.94 ± 0.15 pc, mean electron density of 550 cm -3 and a dynamical age of 1.6 x 10 6 yr. The large fraction of sources presenting excess emission at 2 μm suggests that the stellar population is very young, with many sources still in the pre-main-sequence accreting phase. By the use of theoretical pre-main-sequence tracks we derived a cluster mean age of about 2.5 Myr, and from the analyses of the fraction of excess emission sources as a function of their spatial distribution we found evidence for an age spread for the embedded pre-main-sequence stellar population. Finally, from the study of the spatial distribution of the low-mass sources relative to the main cluster source and associated photodissociation zones, we conclude that the O-type star has probably been triggering the star formation process in the region.
Aromatase inhibition 2013: clinical state of the art and questions that remain to be solved

Following their successful implementation for the treatment of metastatic breast cancer, the ‘third-generation’ aromatase inhibitors (anastrozole, letrozole, and exemestane) have now become standard adjuvant endocrine treatment for postmenopausal estrogen receptor-positive breast cancers. These drugs are characterized by potent aromatase inhibition, causing >98% inhibition of estrogen synthesis in vivo. A recent meta-analysis found no difference in anti-tumor efficacy between these three compounds. As of today, aromatase inhibitor monotherapy and sequential treatment using tamoxifen followed by an aromatase inhibitor for a total of 5 years are considered equipotent treatment options. However, current trials are addressing the potential benefit of extending treatment duration beyond 5 years. Regarding side effects, aromatase inhibitors are not found associated with enhanced risk of cardiovascular disease, and enhanced bone loss is prevented by adding bisphosphonates in concert for those at danger of developing osteoporosis. However, arthralgia and carpal tunnel syndrome preclude drug administration among a few patients. While recent findings have questioned the use of aromatase inhibitors among overweight and, in particular, obese patients, this problem seems to focus on premenopausal patients treated with an aromatase inhibitor and an LH-RH analog in concert, questioning the efficacy of LH-RH analogs rather than aromatase inhibitors among overweight patients. Finally, recent findings revealing a benefit from adding the mTOR inhibitor everolimus to endocrine treatment indicate targeted therapy against defined growth factor pathways to be a way forward, by reversing acquired resistance to endocrine therapy.
Quantifying organ donation rates by donation service area

Previous measures of OPO performance based on population counts have been deemed inadequate, and the need for new methods has been widely accepted. This article explains recent developments in OPO performance evaluation methodology, including those developed by the SRTR. As a replacement for the previously established measure of OPO performance – donors per million population – using eligible deaths as a national metric has yielded promising results for understanding variations in donation rates among the donation service areas assigned to each OPO. A major improvement uses "notifiable deaths" as a denominator describing a standardized maximal pool of potential donors. Notifiable deaths are defined as in‐hospital deaths among ages 70 years and under, excluding certain diagnosis codes related to infections, cancers, etc. A most proximal denominator for determining donation rates is "eligible deaths," which includes only those deaths meeting the criteria for organ donation upon initial assessment. Neither measure is based on the population of a geographic unit, but on restricted upper limits of deaths that could be potential donors in any one locale (e.g., hospital or OPO). The inherent strengths and weaknesses of metrics such as donors per eligible deaths, donors per notifiable deaths, and number of organs per donor are discussed in detail.
A Catalog of Morphologically Classified Galaxies from the Sloan Digital Sky Survey: North Equatorial Region

We present a catalog of morphologically classified bright galaxies in the north equatorial stripe (230 deg2) derived from the Third Data Release of the Sloan Digital Sky Survey (SDSS). Morphological classification is performed by visual inspection of images in the g band. The catalog contains 2253 galaxies complete to a magnitude limit of r = 16 after Galactic extinction correction, selected from 2658 objects that are judged to be extended in the photometric catalog in the same magnitude limit. A total of 1866 galaxies in our catalog have spectroscopic information. A brief statistical analysis is presented for the frequency of morphological types and mean colors in the catalog. A visual inspection of the images reveals that the rate of interacting galaxies in the local universe is approximately 1.5% in the r ≤ 16 sample. A verification is made for the photometric catalog generated by the SDSS, especially as to its bright-end completeness.
Association patterns and social dynamics of killer whales (Orcinus orca) in Greater Puget Sound

Killer whales were observed in the inland marine waters of Washington and British Columbia from March to November 1982 and January to November 1983. The majority of the research occurred in Haro Strait in the San Juan Islands. All whales were individually identifiable from naturally occurring marks and scars on the dorsal fin and back. Many whales were identified visually in the field with the aid of a photographic guide to individuals (Biggs et al. 1987). Seventy-two whales comprised the study population. Data collection concentrated on group composition and spacing, identification and associations of all whales present, and the recording of the dominant behavior occurring at that time. Behaviors were categorized from combinations of quantifiable parameters of group composition, spacing of individuals, speed and direction of travel, and the occurrence of specific behaviors such as leaps, tail slaps, penile erections, etc. (Osborne 1986). Behaviors were pooled into four major groups: feeding, travel, rest and social/sexual behaviors. The results suggest the following hypothesis about the social organization of the killer whales resident to Greater Puget Sound. As a whale ages, it moves from an integrated position within the community, based on its relationship with its mother to a less integrated period during adolescence in which social ties remain primarily through the older female generation. With full adulthood, dependency upon these “allo-mothers” (N.J. Haenel 1986) declines and direct affiliation with the mothers are re-established. Adult whales remain with the maternal sub-group. Close associations between adult whales appear to be based on relationship between direct kin. Fission from the main material sub-group and the establishment of separate subgroups may be the result of several factors including the age of the older female and the number, ages, and sex of her offspring, including adult sons. When older females die out, siblings or cousins may separate more permanently, forming new lineages or pods.
Understanding peer distribution in the global internet

The fast-growing traffic of peer-to-peer applications, most notably BitTorrent, is putting unprecedented pressure to Internet service providers. Understanding the peer distribution over the global Internet thus becomes critical toward building new generation of ISP-friendly peer-to-peer systems. There are unfortunately significant scalability and representability challenges in measuring and understanding realworld peer distribution. In this article we demonstrate a novel hybrid measurement methodology that uses the PlanetLab as a distributed probing platform to interact with BitTorrent trackers and peers in the global Internet. Our design achieves fast real-time scanning of genuine online peers; yet we carefully avoid the potential copyright infringement and traffic overhead for PlanetLab. From three months¿ data of over 9 million peers, we identify fundamental issues in conventional traffic locality designs, and also shed new light on re-engineering trackers and reusing historically downloaded data to make BitTorrent a better storage system.
Institutional report - Thoracic non-oncologic Surgical management of pneumothorax: significance of effective admission or communication strategies between the district general hospitals and specialized unit

A preoperative delay in emergency surgery for spontaneous pneumothorax is associated with a poor outcome after surgery and a prolonged hospital stay. To reduce preoperative delays, all tertiary referrals from district general hospitals to our thoracic surgery unit were processed through a ‘clinical decisions unit’ (CDU). Prior to the establishment of the CDU, these patients were added to a waiting list for a surgical bed. This study has reviewed the effect of this change in admission policy on the efficiency of treatment for non-elective spontaneous pneumotho rax. An intergroup comparison (pre-CDU group vs. post-CDU group) was made of the following parameters: referral to transfer time, transfer to surgery time and length of inpatient stay in the referring and tertiary hospitals. There were no significant differences in gender, diagnosis, treatment in the referring hospitals, postoperative clinical outcome, or indications for or type of surgery. The total length of inpatient stay in the referring and tertiary hospitals was significantly reduced for the post-CDU group (12 vs. 15 days; P<0.001), which was attributed to the earlier transfer of patients (18 vs. 78 hours; P<0.001) hours. Allowing surgical access to a traditional medical admission unit is therefore, cost-effective and significantly improves the efficiency of non-elective pneumothorax surgery .  2011 Published by European Association for Cardio-Thoracic Surgery. All rights reserved.
HA Triggers the Switch from MEK1 SUMOylation to Phosphorylation of the ERK Pathway in Influenza A Virus-Infected Cells and Facilitates Its Infection

Several post-translational modifications in host cells are hijacked by pathogens to facilitate their propagation. A number of components of the influenza virus have been reported to be modified by small ubiquitin-like modifier (SUMO) proteins during infection. We hypothesized that the MAPK/ERK pathway could be modified by SUMO1 because the SUMOylation of MEK1 was quickly eliminated after influenza A virus infection. We identified host cell MEK1 as a target of SUMO1 through LC/MS/MS, and enhanced MEK1 SUMOylation inhibited the infection of the virus, while inhibition of host cell MEK1 SUMOylation facilitated virus propagation. Further investigation demonstrated that the MAPK/ERK pathway is downregulated by MEK1 SUMOylation, which is inhibited by influenza virus infection. Furthermore, membrane accumulation of hemagglutinin promoted MEK1 phosphorylation and gradually abrogated the MEK1 SUMOylation. Taken together, we report a possible mechanism in which HA may trigger the ERK pathway in influenza A virus-infected cells as the switch from MEK1 SUMOylation to phosphorylation, facilitating virus infection.
Remote Sens

The upcoming satellite mission EnMAP offers the opportunity to retrieve information on the seasonal development of vegetation parameters on a regional scale based on hyperspectral data. This study aims to investigate whether an analysis method for the retrieval of leaf area index (LAI), developed and validated on the 4 m resolution scale of six airborne datasets covering the 2012 growing period, is transferable to the spaceborne 30 m resolution scale of the future EnMAP mission. The widely used PROSAIL model is applied to generate look-up-table (LUT) libraries, by which the model is inverted to derive LAI information. With the goal of defining the impact of different selection criteria in the inversion process, different techniques for the LUT based inversion are tested, such as several cost functions, type and amount of artificial noise, number of considered solutions and type of averaging method. The optimal inversion procedure (Laplace, median, 4% inverse multiplicative noise, 350 out of 100,000 averages) is identified by validating the results against corresponding in-situ measurements (n = 330) of LAI. Finally, the best performing LUT inversion (R = 0.65, RMSE = 0.64) is adapted to simulated EnMAP data, generated from the airborne acquisitions. The comparison of the retrieval results to upscaled maps of LAI, previously validated on the 4 m scale, shows that the optimized retrieval method can successfully be transferred to spaceborne EnMAP data. OPEN ACCESS Remote Sens. 2015, 7 10322
Gain-Enhancement Techniques for CMOS Folded Cascode LNAs at Low-Voltage Operations

In this paper, gain-enhancement techniques suitable for folded cascode low-noise amplifiers (LNAs) at low-voltage operations are presented. By employing a forward bias and a capacitive divider at the body of the MOSFETs, the LNA circuit can operate at a reduced supply voltage while maintaining an enhanced gain due to suppression of the negative impact of the body transconductance. In addition, Gm-boosting stage is introduced to further increase the LNA gain at the cost of circuit linearity. Using a standard 0.18-mum CMOS process, two folded cascode LNAs are demonstrated at the 5-GHz band based on the proposed topologies. Consuming a dc power of 1.08 mW from a 0.6-V supply voltage, the LNA with the forward-body-bias technique demonstrates a gain of 10.0 dB and a noise figure of 3.37 dB. The measured Pin - 1dB and IIP3 are -18 and -8.6 dBm, respectively. For the LNA with Gm -boosting feedback, a remarkable gain of 14.1 dB gain is achieved with a dc power of 1.68 mW.
Quadrupedal bounding with spring-damper body joint

Stable locomotion indicates a stable limit cycle generated in the dynamic system. Although quadrupedal bound gait models have been investigated, there is no research which shows the generation of limit cycle and its dynamic properties. In the present study, we analyze a quadrupedal bound gait model which goes down slope and has back and front bodies with spring-damper joint between the bodies. We found the periodic bound gait which achieves a stable limit cycle and convergence property against perturbations.
Optimal Data Collection for Improved Rankings Expose Well-Connected Graphs

Given a graph where vertices represent alternatives and arcs represent pairwise comparison data, the statistical ranking problem is to find a potential function, defined on the vertices, such that the gradient of the potential function agrees with the pairwise comparisons. Our goal in this paper is to develop a method for collecting data for which the least squares estimator for the ranking problem has maximal information. Our approach, based on experimental design, is to view data collection as a bi-level optimization problem where the inner problem is the ranking problem and the outer problem is to identify data which maximizes the informativeness of the ranking. Under certain assumptions, the data collection problem decouples, reducing to a problem of finding graphs with large algebraic connectivity. This reduction of the data collection problem to graph-theoretic questions is one of the primary contributions of this work. As an application, we study the 2011-12 NCAA football schedule and propose schedules with the same number of games which are significantly more informative. Using spectral clustering methods to identify highly-connected communities within the division, we argue that the NCAA could improve its notoriously poor rankings by simply scheduling more out-of-conference games.