Miracle-dz/UniFAR-FTUs huggingface dataset:
A supervised learning approach to the ensemble clustering of genes

High-throughput techniques have become a primary approach to gathering biological data. These data can be used to explore relationships between genes and guide development of drugs and other research. However, the deluge of data contains an overwhelming amount of unknown information about the organism under study. Therefore, clustering is a common first step in the exploratory analysis of high-throughput biological data. We present a supervised learning approach to clustering that utilises known gene-gene interaction data to improve results for already commonly used clustering techniques. The approach creates an ensemble similarity measure that can be used as input to any clustering technique and provides results with increased biological significance while not altering the clustering method.
Neural Processing of Counting in Evolved Spiking and McCulloch-Pitts Agents

This article investigates the evolution of autonomous agents that perform a memory-dependent counting task. Two types of neurocontrollers are evolved: networks of McCulloch-Pitts neurons, and spiking integrate-and-fire networks. The results demonstrate the superiority of the spiky model in evolutionary success and network simplicity. The combination of spiking dynamics with incremental evolution leads to the successful evolution of agents counting over very long periods. Analysis of the evolved networks unravels the counting mechanism and demonstrates how the spiking dynamics are utilized. Using new measures of spikiness we find that even in agents with spiking dynamics, these are usually truly utilized only when they are really needed, that is, in the evolved subnetwork responsible for counting.
A metric-based approach to enhance design quality through meta-pattern transformations

During the evolution of object-oriented legacy systems, improving the design quality is. most often a highly demanded objective. For such systems which have a large number of classes and are subject to frequent modifications, detection and correction of design defects is a complex task. The use of automatic detection and correction tools can be helpful for this task. Various research approaches have proposed transformations that improve the quality of an object-oriented systems while preserving its behavior This paper proposes a framework where a catalogue of object-oriented metrics can be used-as indicators for automatically detecting situations where a particular transformation can be applied to improve the quality of an object-oriented legacy system. The correction process is based on analyzing the impact of various meta-pattern transformations on these object-oriented metrics.
The Limits of intellectual property rights: Lessons from the spread of illegal transgenic seeds in India

Genetically modified seeds have to be approved by biosafety regulators before they can be commercialized. Illegal seeds are, however, common in many developing countries including Brazil, China and India. They potentially pose dangers to biosafety and also undermine the intellectual property rights of firms that own the genetically modifed traits. Their unchecked spread has been attributed to the near impossibility of enforcement when potential violators involve millions of small farmers. Based on a survey of cotton growers in Gujarat, India in 2004, and an examination of the structure of cotton seed production this paper finds that the government, in fact, possesed the information and means to enforce the law. A contingent valuation exercise reveals high relative valuations for illegal seeds correlated with the perceived costs of pesticide application. We discuss how that matters to the political cost of enforcement and to socially optimal policies
Understanding undergraduates’ problems from determinants of Facebook continuance intention

ABSTRACT As social networks’ popularity has increased, so have the attendant problems. The purpose of this study is to identify the important problems by exploring the determinants of Facebook continuance intention from a negative perspective. A questionnaire survey and interview method is used to provide a deep understanding of both the problems and their causes. The research hypotheses are empirically evaluated using the responses from a field survey of 555 undergraduates. The results indicate that previous usage behaviour is the most important determinate of continuance intention. There is a positive causal relationship between perceived privacy self-protection and usage behaviour. In addition to a common privacy issue, this study discovers some problems such as underestimating the potential risks, having misconceptions and lacking legal and information security knowledge. Moreover, this study presents a diagnostic system that administrators can use to detect students’ key problems and understand the reasons behind students’ behaviour.
Transcriptional Network of Multiple Capsule and Melanin Genes Governed by the Cryptococcus neoformans Cyclic AMP Cascade

ABSTRACT Cryptococcus neoformans is an opportunistic human fungal pathogen that elaborates several virulence attributes, including a polysaccharide capsule and melanin pigments. A conserved Gα protein/cyclic AMP (cAMP) pathway controls melanin and capsule production. To identify targets of this pathway, we used an expression profiling approach to define genes that are transcriptionally regulated by the Gα protein Gpa1. This approach revealed that Gpa1 transcriptionally regulates multiple genes involved in capsule assembly and identified two additional genes with a marked dependence on Gpa1 for transcription. The first is the LAC1 gene, encoding the laccase enzyme that catalyzes a rate-limiting step in diphenol oxidation and melanin production. The second gene identified (LAC2) is adjacent to the LAC1 gene and encodes a second laccase that shares 75% nucleotide identity with LAC1. Similar to the LAC1 gene, LAC2 is induced in response to glucose deprivation. However, LAC2 basal transcript levels are much lower than those for LAC1. Accordingly, a lac2 mutation results in only a modest delay in melanin formation. LAC2 overexpression suppresses the melanin defects of gpa1 and lac1 mutants and partially restores virulence of these strains. These studies provide mechanistic insights into the regulation of capsule and melanin production by the C. neoformans cAMP pathway and demonstrate that multiple laccases contribute to C. neoformans melanin production and pathogenesis.
Security enhancement in ad hoc network with ID-based cryptosystem

As ad hoc network has advanced, the importance of security increases more and more. But it suffers from the restriction that ad hoc network does not have the established infrastructure. In this paper we propose a security-enhanced model with ID-based cryptosystem, which removes the necessity for any infrastructure and provides sound authentication and a more secure and concrete routing protocol with aggregate signature. ID-based aggregate signature scheme, which is also proposed in this paper, removes the necessity for certificate transmission and verification. And it reduces communication cost significantly because our aggregate scheme compresses many signatures into only one signature keeping the same security level as existing signature schemes
Long-term high resolution wear studies of high current density electrical brushes

With renewed interest in sliding electrical contacts for application in doubly-fed asynchronous induction wind turbine generators, focus on optimizing the wear life of high current density electrical brushes has re-emerged. This is due to the service and maintenance costs associated with some wind turbine sites, especially offshore. An automated test apparatus has been built and tests conducted to study the long-term wear behavior of silver-graphite brushes running on tin-bronze slip rings with high time- and spatial resolution. The results of the tests have shown that the tribo-film deposited on the slip ring adapts rapidly to changing operating conditions such as current load. The tests have also indicated that the long-term brush wear behavior is surprisingly dynamic and that the wear process may be subject to tribo-film instabilities which account for short periods of rapid wear separated by longer periods of mild wear.
Robot social presence and gender: Do females view robots differently than males?

Social-psychological processes in humans will play an important role in long-term human-robot interactions. This study investigates people's perceptions of social presence in robots during (relatively) short interactions. Findings indicate that males tend to think of the robot as more human-like and accordingly show some evidence of “social facilitation” on an arithmetic task as well as more socially desirable responding on a survey administered by a robot. In contrast, females saw the robot as more machine-like, exhibited less socially desirable responding to the robot's survey, and were not socially facilitated by the robot while engaged in the arithmetic tasks. Various alternative accounts of these findings are explored and the implications of these results for future work are discussed.
Association between Serum Uric Acid Level and Metabolic Syndrome and Its Sex Difference in a Chinese Community Elderly Population

Objective. This study aimed to evaluate the association between serum uric acid (SUA) levels within a normal to high range and the risk of metabolic syndrome (MetS) among community elderly and explore the sex difference. Design and Methods. A cross-sectional study was conducted in a representative urban area of Beijing between 2009 and 2010. A two-stage stratified clustering sampling method was used and 2102 elderly participants were included. Results. The prevalence of hyperuricemia and MetS was 16.7% and 59.1%, respectively. There was a strong association between hyperuricemia and four components of MetS in women and three components in men. Multiple logistic regression analysis showed ORs of hyperuricemia for MetS were 1.67 (95% CI: 1.11–2.50) in men and 2.73 (95% CI: 1.81–4.11) in women. Even in the normal range, the ORs for MetS increased gradually according to SUA levels. MetS component number also showed an increasing trend across SUA quartile in both sexes (P for trend < 0.01). Conclusion. This study suggests that higher SUA levels, even in the normal range, are positively associated with MetS among Chinese community elderly, and the association is stronger in women than men. Physicians should recognize MetS as a frequent comorbidity of hyperuricemia and take early action to prevent subsequent disease burden.
Internal speech functioning and speechreading in deafened and normal hearing adults.

The present study compared internal speech functioning in two groups of subjects: deafened and normal hearing adults. Internal speech functioning was assessed by means of either direct testing (i.e. rhyme-judgement tasks) or indirect testing (lexical access tests). No differences between the groups across tasks was obtained for speed. Neither was there any difference in accuracy level assessed by indirect tests. For direct testing the deafened group performed at a significantly lower level of accuracy. Accuracy was also correlated with the number of years that they had been deaf. It was concluded that one of the primary consequences of an acquired deafness is that the representational aspects of internal speech deteriorate over time, whereas the mechanical aspects remain relatively intact. Intercorrelations between accuracy level in direct testing and speechreading performance also suggest that speechreading ability declines. Clinical implications of the results are discussed.
WATER QUALITY IN MANAGEMENT INTENSIVE GRAZING AND CONFINED FEEDING DAIRY FARM WATERSHEDS

Title of Dissertation: WATER QUALITY IN MANAGEMENT INTENSIVE GRAZING AND CONFINED FEEDING DAIRY FARM WATERSHEDS Rachel Esther Gilker, Ph.D., 2005 Dissertation Directed By: Professor Ray R. Weil, Natural Resource Sciences and Landscape Architecture Dairy farm size has increased in the United States, while the profit margin has decreased. An alternative to confined feeding dairy farming is management intensive grazing (MIG), a grass-based system relying on rotational grazing for most of the herd’s dietary requirements. Previous research has measured high levels of nitrate leaching under MIG, citing the liquid nature and high nitrogen (N) content of urine. However, this research included heavy N fertilizer applications or was conducted on monolith lysimeters with artificial leaching processes and did not accurately represent mid-Atlantic MIG dairy farms. Phosphorus (P) losses have typically been attributed to runoff and erosion but are now being ascribed to leaching as well. To measure the magnitude of N and P losses to groundwater, we sampled shallow groundwater and pore water on one confined feeding and two MIG-based Maryland dairy farms between 2001 and 2004. Transects of nested piezometers and ceramic-tipped suction lysimeters were installed in two watersheds on each farm. Two streams running through two of the grazed watersheds were also sampled to measure the effects of grazing on surface water. For three years, groundwater and surface water samples were collected biweekly and pore water was collected when conditions made it possible. Samples were analyzed for inorganic N and dissolved reactive P and were digested for determination of dissolved organic N and P, pools previously not considered major sources of nutrient loss. Seasonal mean nitrate concentrations under the grazed watersheds remained below the EPA maximum contaminant load of 10 mg L with only two exception s on the grazed watersheds. Mean nitrate concentrations in the four grazed watersheds ranged from 3 to 7.44 mg L. Nitrogen losses were closely correlated to farm N surpluses. Groundwater P concentrations exceeded the EPA surface water critical levels in all six watersheds. Geologic factors, rather than dairy farm management, played a large role in P losses. In all watersheds, substantial pools of dissolved organic N and P were measured in groundwater. Low nitrate losses under MIG as well as the environmental advantages inherent in a grass-based system make grazing a viable Best Management Practice. WATER QUALITY IN MANAGEMENT INTENSIVE GRAZING AND CONFINED FEEDING DAIRY FARM WATERSHEDS
Humans recognize emotional arousal in vocalizations across all classes of terrestrial vertebrates: evidence for acoustic universals

Writing over a century ago, Darwin hypothesized that vocal expression of emotion dates back to our earliest terrestrial ancestors. If this hypothesis is true, we should expect to find cross-species acoustic universals in emotional vocalizations. Studies suggest that acoustic attributes of aroused vocalizations are shared across many mammalian species, and that humans can use these attributes to infer emotional content. But do these acoustic attributes extend to non-mammalian vertebrates? In this study, we asked human participants to judge the emotional content of vocalizations of nine vertebrate species representing three different biological classes—Amphibia, Reptilia (non-aves and aves) and Mammalia. We found that humans are able to identify higher levels of arousal in vocalizations across all species. This result was consistent across different language groups (English, German and Mandarin native speakers), suggesting that this ability is biologically rooted in humans. Our findings indicate that humans use multiple acoustic parameters to infer relative arousal in vocalizations for each species, but mainly rely on fundamental frequency and spectral centre of gravity to identify higher arousal vocalizations across species. These results suggest that fundamental mechanisms of vocal emotional expression are shared among vertebrates and could represent a homologous signalling system.
Manganese‐enhanced MRI of the mouse auditory pathway

Functional mapping of the lateral lemniscus and the superior olivary complex as part of the auditory pathway was accomplished for the first time in mice in vivo using manganese‐enhanced MRI (2.35T, 3D FLASH, 117 μm isotropic resolution). These and other auditory centers in the brainstem presented with pronounced signal enhancements after systemic administration of manganese chloride when animals were exposed to acoustic stimuli for 48 hr, but not when kept in a quiet environment. The results indicate an activation‐dependent accumulation of manganese in the neural circuit composed of the cochlear nucleus, the superior olivary complex, the lateral lemniscus, and the inferior colliculus. The marked enhancement of the lateral lemniscus suggests that the stimulus‐related accumulation of manganese reflects not only a regional uptake from extracellular fluid but also a concurrent delivery by axonal transport within the auditory system. Magn Reson Med 60:210–212, 2008. © 2008 Wiley‐Liss, Inc.
Comparative analysis of the response of various land covers to an exceptional rainfall event in the central Spanish Pyrenees, October 2012

The hydrological and geomorphological effects of an exceptional rainstorm event that occurred in the central Spanish Pyrenees during 19–21 October 2012 were studied in five experimental catchments under various land covers: (i) subhumid badlands; (ii) dense forest; (iii) an abandoned farmland area recolonized by shrubs and forest patches; and (iv) subalpine grasslands. Hydrographs and sedigraphs demonstrated that vegetation cover is a major factor affecting the control of floods even during exceptional rainstorms, at least at the spatial scale at which the phenomenon was studied (catchment sizes: 0.3–2.8 km2) and under dry catchment conditions. The combined precipitation over the two days (c. 250 mm) was the greatest for any two‐day event recorded since 1950 in the central‐western Pyrenees for all but one of the stations in the study. Five pulses of most intense rainfall were recorded. The forested catchment did not react to the two most intense rainfall pulses, because of the very low antecedent level of the water table. The main peak flow occurred only when at least a part of the catchment was saturated. The abandoned farmland catchment had two small peak discharges at the beginning of the event, which were produced by infiltration excess overland flow from eroded areas close to the main stream. During the third most intense rainfall period a large part of this catchment contributed to runoff and a relatively high peak discharge was produced. The badland catchment reacted immediately from the beginning of the rainstorm, yielding very high discharges accompanied by high suspended sediment concentrations. The subalpine catchment showed a hydrograph mirroring the hyetograph, with brief but intense hydrological responses to increased precipitation, because of the marked gradients and the presence of bare rock in the headwaters. A high volume of bedload was carried during the peak discharge. Copyright © 2013 John Wiley & Sons, Ltd.
Post-surgical inflammatory neuropathy.

UNLABELLED Post-surgical neuropathies are usually attributed to mechanical factors, such as compression, stretch, contusion or transection. The role of inflammatory mechanisms in neuropathies occurring after surgeries is poorly appreciated and not well characterized, and may provide a rationale for immunotherapy. A total of 23 selected patients with post-surgical neuropathies received nerve biopsies, of which 21 demonstrated increased inflammation. Here we report the clinical features in these 21 cases of biopsy-confirmed and 12 cases of clinically suspected post-surgical inflammatory neuropathies, in whom no trauma to the nerves was documented. All neuropathies developed within 30 days of a surgical procedure. Of 33 patients, 20 were male and the median age was 65 years (range 24-83). Surgical procedures were orthopaedic (n=14), abdominal/pelvic (n=12), thoracic (n=5) and dental (n=2). Patients developed focal (n=12), multifocal (n=14) or diffuse (n=7) neuropathies. Focal and multifocal neuropathies typically presented with acute pain and weakness, and focal neuropathies often mimicked mechanical aetiologies. Detailed analyses, including clinical characteristics, electrophysiology, imaging and peripheral nerve pathology, were performed. Electrophysiology showed axonal damage. Magnetic resonance imaging of roots, plexuses and peripheral nerves was performed in 22 patients, and all patients had abnormally increased T(2) nerve signal, with 20 exhibiting mild (n=7), moderate (n=12) or severe (n=1) enlargement. A total of 21 patients had abnormal nerve biopsies that showed increased epineurial perivascular lymphocytic inflammation (nine small, five moderate and seven large), with 15 diagnostic or suggestive of microvasculitis. Evidence of ischaemic nerve injury was seen in 19 biopsies. Seventeen biopsies had increased axonal degeneration suggesting active neuropathy. Seventeen biopsied patients were treated with immunotherapy. In 13 cases with longitudinal follow-up (median 9 months, range 3-71 months), the median neuropathy impairment score improved from 30 to 24 at the time of last evaluation (P=0.001). IN CONCLUSION (i) not all post-surgical neuropathies are mechanical, and inflammatory mechanisms can be causative, presenting as pain and weakness in a focal, multifocal or diffuse pattern; (ii) these inflammatory neuropathies may be recognized by their spatio-temporal separation from the site and time of surgery and by the characteristic magnetic resonance imaging features; (iii) occasionally post-surgical inflammatory and mechanical neuropathies are difficult to distinguish and nerve biopsy may be required to demonstrate an inflammatory mechanism, which in our cohort often, but not exclusively, exhibited pathological features of microvasculitis and ischaemia; and (iv) recognizing the role of inflammation in these patients' neuropathy led to rational immunotherapy, which may have resulted in the subsequent improvement of neurological symptoms and impairments.
Uterine rupture and perinatal outcome

Background. In view of the increasing number of caesarean sections (CS), we wanted to investigate the clinical aspects of uterine rupture including perinatal outcome. Methods. A retrospective investigation of 24,181 deliveries at Stockholm South General Hospital between 1999 and 2004. Patient notes from cases with ICD‐codes 0710 and 0711 were studied together with charts from previous deliveries and neonatal data from the Paediatric Department. Results. Some 22 cases of uterine rupture were found, giving an incidence of 0.9 per 1,000 deliveries. In all cases, the diagnosis was confirmed at laparotomy. In 19/22 cases, the rupture occurred in patients with a previous uterine scar, 18 of whom were delivered at term and one at 16 gestational weeks. One case of intrauterine fetal death was noted. Of the remaining 20 newborns, 9 had a 5‐min Apgar ≤7, one died after 3 days, and one had neurological sequele at follow‐up. The remaining 18 newborns were healthy at discharge and up to 1 year of age. Conclusions. A previous uterine scar was the single most obvious risk factor. A positive finding was the relatively low risk of long‐term post‐asphyctic sequele in the newborns.
Operating Room: Relational Spaces and Microinstitutional Change in Surgery1

One of the great paradoxes of institutional change is that even when top managers in organizations provide support for change in response to new regulation, the employees whom new programs are designed to benefit often do not use them. This 15‐month ethnographic study of two hospitals responding to new regulation demonstrates that using these programs may require subordinate employees to challenge middle managers with opposing interests. The article argues that relational spaces—areas of isolation, interaction, and inclusion that allow middle‐manager reformers and subordinate employees to develop a cross‐position collective for change—are critical to the change process. These findings have implications for research on institutional change and social movements.