Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome Sequence Comparisons: Hurdles in the Fast Lane to Functional Genomics

An important computational technique for extracting the wealth of information hidden in human genomic sequence data is to compare the sequence with that from the corresponding region of the mouse genome, looking for segments that are conserved over evolutionary time. Moreover, the approach generalises to comparison of sequences from any two related species. The underlying rationale (which is abundantly confirmed by observation) is that a random mutation in a functional region is usually deleterious to the organism, and hence unlikely to become fixed in the population, whereas mutations in a non-functional region are free to accumulate over time. The potential value of this approach is so attractive that the public and private projects to sequence the human genome are now turning to sequencing the mouse, and you will soon be able to compare the human and mouse sequences of your favourite genomic region. We are currently witnessing an explosion of computer tools for comparative analysis of two genomic sequences. Here the capabilities of two new network servers for comparing genomic sequences from any pair of closely related species are sketched. The Syntenic Gene Prediction Program SGP-I utilises sequence comparisons to enhance the ability to locate protein coding segments in genomic data. PipMaker attempts to determine all conserved genomic regions, regardless of their function.
Influence of Motor Cortex Stimulation During Motor Training on Neuroplasticity as a Potential Therapeutic Intervention

ABSTRACT Rehabilitation options to promote neuroplasticity may be enhanced when patients are engaged in motor practice during repetitive transcranial magnetic stimulation (rTMS). Twelve participants completed 3 separate sessions: motor practice, motor practice with rTMS, and rTMS only: motor practice consisted of 30 isometric contractions and subthreshold rTMS was 30, 3-s trains at 10 Hz. Assessments included the Box and Block Test (BBT), force steadiness (10% of the maximum voluntary contraction), and TMS (cortical excitability, intracortical inhibition, and intracortical facilitation). Participants significantly increased BBT scores following the combined condition. Force steadiness improved after all 3 conditions (p < .05). TMS outcomes depended on intervention condition with significant increases in facilitation following the motor practice plus rTMS condition. All interventions influenced motor control, yet are likely modulated differently when combining motor practice plus rTMS. These results help guide the clinical utility of rTMS as an intervention to influence motor control.
Are Cuckoos Maximizing Egg Mimicry by Selecting Host Individuals with Better Matching Egg Phenotypes?

Background Avian brood parasites and their hosts are involved in complex offence-defense coevolutionary arms races. The most common pair of reciprocal adaptations in these systems is egg discrimination by hosts and egg mimicry by parasites. As mimicry improves, more advanced host adaptations evolve such as decreased intra- and increased interclutch variation in egg appearance to facilitate detection of parasitic eggs. As interclutch variation increases, parasites able to choose hosts matching best their own egg phenotype should be selected, but this requires that parasites know their own egg phenotype and select host nests correspondingly. Methodology/Principal Findings We compared egg mimicry of common cuckoo Cuculus canorus eggs in naturally parasitized marsh warbler Acrocephalus palustris nests and their nearest unparasitized conspecific neighbors having similar laying dates and nest-site characteristics. Modeling of avian vision and image analyses revealed no evidence that cuckoos parasitize nests where their eggs better match the host eggs. Cuckoo eggs were as good mimics, in terms of background and spot color, background luminance, spotting pattern and egg size, of host eggs in the nests actually exploited as those in the neighboring unparasitized nests. Conclusions/Significance We reviewed the evidence for brood parasites selecting better-matching host egg phenotypes from several relevant studies and argue that such selection probably cannot exist in host-parasite systems where host interclutch variation is continuous and overall low or moderate. To date there is also no evidence that parasites prefer certain egg phenotypes in systems where it should be most advantageous, i.e., when both hosts and parasites lay polymorphic eggs. Hence, the existence of an ability to select host nests to maximize mimicry by brood parasites appears unlikely, but this possibility should be further explored in cuckoo-host systems where the host has evolved discrete egg phenotypes.
Teaching with Rewards and Punishments: Reinforcement or Communication?

Teaching with evaluative feedback involves expectations about how a learner will interpret rewards and punishments. We formalize two hypotheses of how a teacher implicitly expects a learner to interpret feedback – a reward-maximizing model based on standard reinforcement learning and an action-feedback model based on research on communicative intent – and describe a virtual animal-training task that distinguishes the two. The results of two experiments in which people gave learners feedback for isolated actions (Exp. 1) or while learning over time (Exp. 2) support the action-feedback model over the reward-maximizing model.
Designing reasonable accommodation of the workplace: a new methodology based on risk assessment

If working tasks are carried out in inadequate conditions, workers with functional limitations may, over time, risk developing further disabilities. While several validated risk assessment methods exist for able-bodied workers, few studies have been carried out for workers with disabilities. This article, which reports the findings of a Study funded by the Italian Ministry of Labour, proposes a general methodology for the technical and organisational re-design of a worksite, based on risk assessment and irrespective of any worker disability. To this end, a sample of 16 disabled workers, composed of people with either mild or severe motor disabilities, was recruited. Their jobs include business administration (5), computer programmer (1), housewife (1), mechanical worker (2), textile worker (1), bus driver (1), nurse (2), electrical worker (1), teacher (1), warehouseman (1). By using a mix of risk assessment methods and the International Classification of Functioning (ICF) taxonomy, their worksites were re-designed in view of a reasonable accommodation, and prospective evaluation was carried out to check whether the new design would eliminate the risks. In one case – a man with congenital malformations who works as a help-desk operator for technical assistance in the Information and Communication Technology (ICT) department of a big organisation – the accommodation was actually carried out within the time span of the study, thus making it possible to confirm the hypotheses raised in the prospective assessment.
Simultaneous bilateral cataract surgery in general anesthesia patients.

BACKGROUND The aim of this study was to evaluate the indications, safety, benefits, disadvantages and advantages, and the visual outcomes for simultaneous bilateral cataract surgery (SBCS) under general anesthesia. METHODS This retrospective case review pertained to a period spanning from June 1998 through June 2005 inclusively, and comprised of 27 consecutive patients (54 eyes) that underwent simultaneous bilateral cataract surgery under general anesthesia at the Kaohsiung Chang Gung Memorial Hospital, Taiwan. Surgery modalities included phacoemulsification, extracapsular cataract extraction, lens aspiration and intraocular lens implantation. Outcome measures included postoperative best correct visual acuity (BCVA) as well as intraoperative and postoperative complication rates. Due to the bipolas distribution of the age, we arbitrarily divided our cases into younger group (Group Y, younger than 20 years old) and older group (Group O, equal to or older than 20 years old). RESULTS Thirty-eight of the 54 eyes (60% in the younger group and 76.5% in the older group), featuring measured preoperative and postoperative BSCVA, achieved improved visual acuity following SBCS. Two eyes (5.9% in the older group) demonstrated poorer visual acuity postoperatively than preoperatively. Seven patients (40% in the younger group and 17.6% in the older group) were not able to express VA due to their particular medical conditions such as mental disease and young age. Intraoperative and postoperative complication rates were similar to those cited in previous reports of analogous but unilateral extracapsular surgery and simultaneous bilateral cataract surgery. Endophthalmitis did not arise in any of the eyes operated upon and reported on herein, and no examples of bilateral complications that resulted in visual loss occurred in our patients. CONCLUSION SBCS could be a good choice when cataract surgery needs to be performed under general anesthesia. The relative benefits of SBCS under general anesthesia could eclipse the associated enhanced risks of this surgery.
Joint Source-Channel Coding Using Real BCH Codes for Robust Image Transmission

In this paper, a new still image coding scheme is presented. In contrast with standard tandem coding schemes, where the redundancy is introduced after source coding, it is introduced before source coding using real BCH codes. A joint channel model is first presented. The model corresponds to a memoryless mixture of Gaussian and Bernoulli-Gaussian noise. It may represent the source coder, the channel coder, the physical channel, and their corresponding decoder. Decoding algorithms are derived from this channel model and compared to a state-of-art real BCH decoding scheme. A further comparison with two reference tandem coding schemes and the proposed joint coding scheme for the robust transmission of still images has been presented. When the tandem scheme is not accurately tuned, the joint coding scheme outperforms the tandem scheme in all situations. Compared to a tandem scheme well tuned for a given channel situation, the joint coding scheme shows an increased robustness as the channel conditions worsen. The soft performance degradation observed when the channel worsens gives an additional advantage to the joint source-channel coding scheme for fading channels, since a reconstruction with moderate quality may be still possible, even if the channel is in a deep fade
Soliciting and Providing Social Support Over the Internet: An Investigation of Online Eating Disorder Support Groups

Using a longitudinal, systematic random sample of 490 postings, this study analyzed the type of social support provided, the strategies used to solicit social support, and the themes on the top 5 Yahoo! eating disorder discussion boards. Optimal match theory was used as the theoretical framework for the study. Results suggest that messages providing informational support were more prevalent than those providing instrumental support. Also, the findings revealed that the most frequent strategy for soliciting support was sharing experiences and the most frequent theme was positive affect. The results of the study highlight the significance of prosocial communication exchanges on these discussion boards.
MPCD: a new interactive on-line crystallization data bank for screening strategies.

The Marseille Protein Crystallization Database (MPCD) is a new crystallization database, freely accessible via http://www.crmcn. univ-mrs.fr/mpcd/, populated with information found in the BMCD and CYCLOP. This new online database includes details about macromolecules (such as name, pI, molecular weight, number of subunits), crystallization conditions, methods and additives used in an easy-to-compare table form. It allows users to choose their own crystallization parameters, to create tables for further analysis and also to enter new proteins and crystallization conditions in order to supplement this database. As an essential tool in structural biology, this crystallization database will be highly relevant to crystal growers, when connected to the Protein Data Bank, for the crystallogenesis of a variety of structurally distinct molecules and assemblies, and to macromolecular and biomaterial researchers designing structures.
Association of Alcohol Consumption with the Risk of Ocular Trauma

This study was conducted to evaluate the influence of alcohol consumption on the risk of ocular trauma. We retrospectively reviewed the medical records of 1,024 patients who visited emergency department and received ophthalmologic examination from January 1 to December 31, 2009. The patients were divided into 2 groups: those with ocular trauma (n = 494) and those without (n = 530); the influence of alcohol consumption was compared between these 2 groups. In the ocular trauma group, the association of the causes and types of ocular trauma with alcohol consumption was evaluated. One of 530 patients of no trauma group and 117 (23.7%) of 494 patients of trauma group were related with alcohol intake, and the difference was statistically significant (P < 0.001). Concerning the causes, physical assault was significantly more common in alcohol-associated injury (P < 0.001). Regarding the types of injury, orbital wall fracture and hyphema showed a significant association with alcohol consumption (P < 0.001). Older age and nighttime injury were significantly related to the increased risk of alcohol-associated ocular trauma (P = 0.018 and < 0.001, respectively). In conclusion, alcohol consumption significantly increases the risk of ocular trauma.
Generative Prior Knowledge for Discriminative Classification

We present a novel framework for integrating prior knowledge into discriminative classifiers. Our framework allows discriminative classifiers such as Support Vector Machines (SVMs) to utilize prior knowledge specified in the generative setting. The dual objective of fitting the data and respecting prior knowledge is formulated as a bilevel program, which is solved (approximately) via iterative application of second-order cone programming. To test our approach, we consider the problem of using WordNet (a semantic database of English language) to improve low-sample classification accuracy of newsgroup categorization. WordNet is viewed as an approximate, but readily available source of background knowledge, and our framework is capable of utilizing it in a flexible way.
COSMOLOGY WITH PHOTOMETRIC SURVEYS OF TYPE Ia SUPERNOVAE

We discuss the extent to which photometric measurements alone can be used to identify Type Ia supernovae (SNIa) and to determine the redshift and other parameters of interest for cosmological studies. We fit the light curve data of the type expected from a survey such as the one planned with the Large Synoptic Survey Telescope (LSST) and also remove the contamination from the core-collapse SNe to SNIa samples. We generate 1000 SNIa mock flux data for each of the LSST filters based on existing design parameters, then use a Markov Chain Monte Carlo analysis to fit the redshift, apparent magnitude, stretch factor, and the phase of the SNIa. We find that the model fitting works adequately well when the true SNe redshift is below 0.5, while at z < 0.2 the accuracy of the photometric data is almost comparable with spectroscopic measurements of the same sample. We discuss the contamination of Type Ib/c (SNIb/c) and Type II supernova (SNII) on the SNIa data set. We find that it is easy to distinguish the SNII through the large χ2 mismatch when fitting to photometric data with Ia light curves. This is not the case for SNIb/c. We implement a statistical method based on the Bayesian estimation in order to statistically reduce the contamination from SNIb/c for cosmological parameter measurements from the whole SNe sample. The proposed statistical method also evaluates the fraction of the SNIa in the total SNe data set, which provides a valuable guide to establish the degree of contamination.
Potential enterotoxicity and antimicrobial resistance pattern of Aeromonas species isolated from pet turtles and their environment

To investigate the potential enterotoxicity and antimicrobial resistance of aeromonads from pet turtles as a risk for human infection, one hundred and two Aeromonas spp. were isolated from the feces, skin and rearing environments of pet turtles and identified by biochemical and gyrB sequence analyses. Aeromonas enteropelogenes was the predominant species among the isolates (52.9%) followed by A. hydrophila (32.4%), A. dharkensis (5.9%), A. veronii (4.9%) and A. caviae (3.9%). Their potential enterotoxicities were evaluated by PCR assays for detecting genes encoding cytotoxic enterotoxin (act) and two cytotonic enterotoxins (alt and ast). 75.8% of A. hydrophila isolates exhibited the act+/alt+/ast+ genotype, whereas 94.4% of A. enteropelogenes isolates were determined to be act−/alt−/ast−. In an antimicrobial susceptibility test, most isolates were susceptible to all tested antibiotics except amoxicillin, ampicillin, cephalothin, chloramphenicol and tetracycline. Non-susceptible isolates to penicillins (ampicillin and amoxicillin) and fluoroquinolones (ciprofloxacin and norfloxacin) were frequently observed among the A. enteropelogenes isolates. Few isolates were resistant to imipenem, amikacin, ceftriaxone and cefotaxime. Collectively, these results suggest that pet turtles may pose a public health risk of infection by enterotoxigenic and antimicrobial resistant Aeromonas strains.
Community Analysis of Ammonia and Nitrite Oxidizers during Start-Up of Nitritation Reactors

ABSTRACT Partial nitrification of ammonium to nitrite under oxic conditions (nitritation) is a critical process for the effective use of alternative nitrogen removal technologies from wastewater. Here we investigated the conditions which promote establishment of a suitable microbial community for performing nitritation when starting from regular sewage sludge. Reactors were operated in duplicate under different conditions (pH, temperature, and dilution rate) and were fed with 50 mM ammonium either as synthetic medium or as sludge digester supernatant. In all cases, stable nitritation could be achieved within 10 to 20 days after inoculation. Quantitative in situ hybridization analysis with group-specific fluorescent rRNA-targeted oligonucleotides (FISH) in the different reactors showed that nitrite-oxidizing bacteria of the genus Nitrospira were only active directly after inoculation with sewage sludge (up to 4 days and detectable up to 10 days). As demonstrated by quantitative FISH and restriction fragment length polymorphism (RFLP) analyses of the amoA gene (encoding the active-site subunit of the ammonium monooxygenase), the community of ammonia-oxidizing bacteria changed within the first 15 to 20 days from a more diverse set of populations consisting of members of the Nitrosomonas communis and Nitrosomonas oligotropha sublineages and the Nitrosomonas europaea-Nitrosomonas eutropha subgroup in the inoculated sludge to a smaller subset in the reactors. Reactors operated at 30°C and pH 7.5 contained reproducibly homogeneous communities dominated by one amoA RFLP type from the N. europaea-N. eutropha group. Duplicate reactors at pH 7.0 developed into diverse communities and showed transient population changes even within the ammonia oxidizer community. Reactors at pH 7.5 and 25°C formed communities that were indistinguishable by the applied FISH probes but differing in amoA RFLP types. Communities in reactors fed with sludge digester supernatant exhibited a higher diversity and were constantly reinoculated with ammonium oxidizers from the supernatant. Therefore, such systems could be maintained at a higher dilution rate (0.75 day−1 compared to 0.2 day−1 for the synthetic wastewater reactors). Despite similar reactor performance with respect to chemical parameters, the underlying community structures were different, which may have an influence on stability during perturbations.
TRAF4 acts as a silencer in TLR‐mediated signaling through the association with TRAF6 and TRIF

Toll‐like receptors (TLR) and nicotinamide adenine dinucleotide phosphate (NADPH) oxidase play an essential role in intracellular eradication of engulfed pathogens. Here, we demonstrate the physical and functional association between components of the cytosolic NADPH oxidase and TLR‐mediated signaling molecules. Cytosolic components of NADPH oxidase suppressed TLR‐mediated NF‐κB activation as well as IFN‐β promoter activation. We demonstrate that TNF‐associated factor (TRAF) 4 associates with p47phox, a component of cytosolic NADPH oxidase, and physically interacts and functionally counteracts with TRAF6 and Toll‐IL‐1 receptor (TIR) domain‐containing adaptor‐inducing IFN‐β (TRIF) molecules that critically regulate TLR‐mediated signaling. TRAF4 mRNA expression was elicited in RPMI 8226 cells following LPS or CpG DNA treatment. These results suggest that TRAF4 participates in the molecular mechanism underlying silencing of TLR‐mediated signaling through the interaction with molecules harboring phagosome/endosome membrane.
Plantar Fascia: Imaging Diagnosis and Guided Treatment

Plantar fasciopathy is a common cause of heel pain. This article covers the imaging anatomy of the hindfoot, the imaging findings on ultrasound and magnetic resonance imaging (MRI) of plantar fasciopathy, plantar fibromas, trauma, Achilles tendonopathy, neural compression, stress fractures of the os calcis and other heel pad lesions. Thickening of the plantar fascia insertion more than 5 mm either on ultrasound or MRI is suggestive of plantar fasciopathy. Ultrasound is superior to MRI for diagnosis of plantar fibroma as small low signal lesions on MRI are similar to the normal plantar fascia signal. Ultrasound demonstrates low echogenicity compared with the echogenic plantar fascia. Penetrating injuries can appear bizarre due to associated foreign body impaction and infection. Achilles tendonopathy can cause heel pain and should be considered as a possible diagnosis. Treatment options include physical therapy, ECSWT, corticosteroid injection, and dry needling. Percutaneous US guided treatment methods will be described.
ANALYSIS OF THE FOLKSONOMY OF FREESOUND

User generated content shared in online communities is often described using collaborative tagging systems where users assign labels to content resources. As a result, a folksonomy emerges that relates a number of tags with the resources they label and the users that have used them. In this paper we analyze the folksonomy of Freesound, an online audio clip sharing site which contains more than two million users and 150,000 user-contributed sound samples covering a wide variety of sounds. By following methodologies taken from similar studies, we compute some metrics that characterize the folksonomy both at the global level and at the tag level. In this manner, we are able to better understand the behavior of the folksonomy as a whole, and also obtain some indicators that can be used as metadata for describing tags themselves. We expect that such a methodology for characterizing folksonomies can be useful to support processes such as tag recommendation or automatic annotation of online resources.