Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Diagnosis of Invasive Aspergillosis and Detection of Azole Resistance by a Newly Commercialized PCR Kit

ABSTRACT Aspergillus fumigatus is the main species responsible for aspergillosis in humans. The diagnosis of aspergillosis remains difficult, and the rapid emergence of azole resistance in A. fumigatus is worrisome. The aim of this study was to validate the new MycoGENIE A. fumigatus real-time PCR kit and to evaluate its performance on clinical samples for the detection of A. fumigatus and its azole resistance. This multiplex assay detects DNA from the A. fumigatus species complex by targeting the multicopy 28S rRNA gene and specific TR34 and L98H mutations in the single-copy-number cyp51A gene of A. fumigatus. The specificity of cyp51A mutation detection was assessed by testing DNA samples from 25 wild-type or mutated clinical A. fumigatus isolates. Clinical validation was performed on 88 respiratory samples obtained from 62 patients and on 69 serum samples obtained from 16 patients with proven or probable aspergillosis and 13 patients without aspergillosis. The limit of detection was <1 copy for the Aspergillus 28S rRNA gene and 6 copies for the cyp51A gene harboring the TR34 and L98H alterations. No cross-reactivity was detected with various fungi and bacteria. All isolates harboring the TR34 and L98H mutations were accurately detected by quantitative PCR (qPCR) analysis. With respiratory samples, qPCR results showed a sensitivity and specificity of 92.9% and 90.1%, respectively, while with serum samples, the sensitivity and specificity were 100% and 84.6%, respectively. Our study demonstrated that this new real-time PCR kit enables sensitive and rapid detection of A. fumigatus DNA and azole resistance due to TR34 and L98H mutations in clinical samples.
Zero skew clock-tree optimization with buffer insertion/sizing and wire sizing

Clock distribution is crucial for timing and design convergence in high-performance very large scale integration designs. Minimum-delay/power zero skew buffer insertion/sizing and wire-sizing problems have long been considered intractable. In this paper, we present ClockTune , a simultaneous buffer insertion/sizing and wire-sizing algorithm which guarantees zero skew and minimizes delay and power in polynomial time. Extensive experimental results show that our algorithm executes very efficiently. For example, ClockTune achieves 45/spl times/ delay improvement for buffering and sizing an industrial clock tree with 3101 sink nodes on a 1.2-GHz Pentium IV PC in 16 min, compared with the initial routing. Our algorithm can also be used to achieve useful clock skew to facilitate timing convergence and to incrementally adjust the clock tree for design convergence and explore delay-power tradeoffs during design cycles. ClockTune is available on the web (http://vlsi.ece.wisc.edu/Tools.htm).
Cornichons Modify Channel Properties of Recombinant and Glial AMPA Receptors

Ionotropic glutamate receptors, which underlie a majority of excitatory synaptic transmission in the CNS, associate with transmembrane proteins that modify their intracellular trafficking and channel gating. Significant advances have been made in our understanding of AMPA-type glutamate receptor (AMPAR) regulation by transmembrane AMPAR regulatory proteins. Less is known about the functional influence of cornichons—unrelated AMPAR-interacting proteins, identified by proteomic analysis. Here we confirm that cornichon homologs 2 and 3 (CNIH-2 and CNIH-3), but not CNIH-1, slow the deactivation and desensitization of both GluA2-containing calcium-impermeable and GluA2-lacking calcium-permeable (CP) AMPARs expressed in tsA201 cells. CNIH-2 and -3 also enhanced the glutamate sensitivity, single-channel conductance, and calcium permeability of CP-AMPARs while decreasing their block by intracellular polyamines. We examined the potential effects of CNIHs on native AMPARs by recording from rat optic nerve oligodendrocyte precursor cells (OPCs), known to express a significant population of CP-AMPARs. These glial cells exhibited surface labeling with an anti-CNIH-2/3 antibody. Two features of their AMPAR-mediated currents—the relative efficacy of the partial agonist kainate (IKA/IGlu ratio 0.4) and a greater than fivefold potentiation of kainate responses by cyclothiazide—suggest AMPAR association with CNIHs. Additionally, overexpression of CNIH-3 in OPCs markedly slowed AMPAR desensitization. Together, our experiments support the view that CNIHs are capable of altering key properties of AMPARs and suggest that they may do so in glia.
LOSSLESS CONTOUR COMPRESSION USING CHAIN-CODE REPRESENTATIONS AND CONTEXT TREE CODING

In this paper we experimentally study the context tree coding of contours in two alternative chain-code representations. The contours of the image regions are intersecting, resulting in many contour segments, each contour segment being represented by its starting position and a subsequence of chain-code symbols. A single stream of symbols is obtained, under a given ordering of the segments, by concatenating their subsequences. We present efficient ways for the challenging task of ordering the contour segments. The necessary starting positions and the chain-code symbols are encoded using context tree coding. The coding is performed in a semi-adaptive way, designing at the encoder by dynamical programming the context tree, whose structure is encoded as side information. The symbols are encoded using adaptively collected distributions at each context of the encoded tree. We study for depth map images and fractal images the tree-depth of the optimal context tree and the similarity of the context trees resulted to be optimal for each image.
The Global Effects of Intellectual Property Rights : Measuring What Cannot Be Seen

Despite the obvious practical importance of the question, economists did not attempt until the 1990s to assess empirically the effects of international variations in the strength of IPRs. Without such evidence, the field lay open to strong claims on both sides of the debate—a situation that remains largely true today. Thus, for example, advocates of global harmonization of strongly protective standards made powerful assertions about the trade-distorting effects of weak and variable IPRs in order to buttress the case for their inclusion in the Uruguay Round negotiations. Their opponents argued that strengthening global IPRs would cause monopolization of trade and technology transfer, leading to widespread competitive abuses. These arguments clearly were based on strong assumptions with limited systematic evidence available to support any of them. The situation was even more stark than the earlier acute shortage of information on how patent systems affect innovation and welfare, which had prompted Priest (1986, 19) to lament, “The ratio of empirical demonstration to assumption in this literature must be very close to zero. ” In the last decade, a number of economists have made strenuous efforts to help close this information gap. Some analysts developed numerical indices to characterize the strength of patent rights across nations. These in turn were used to study the impact of patent regimes on international trade, FDI, and technology licensing. This chapter reviews the evidence compiled in such studies; it concludes that, in the main, the strength of IPRs is a significant and positive determinant of international commercial activity. Stronger global IPRs could enhance the dynamic efficiency with which resources are allocated internationally, which should help mitigate any adverse distributional consequences.
Ideology and the US Congressional Vote

A large class of theoretical models posits that voters choose candidates on the basis of issue congruence, but convincing empirical tests of this key claim remain elusive. The most persistent difficulty is obtaining comparable spatial estimates for winning and losing candidates, as well as voters. We address these issues using candidate surveys to characterize the electoral platforms for winners and losers, and large issue batteries in 2008 and 2010 to estimate voter preferences. Questions that were answered by both candidates and citizens allow us to jointly scale these estimates. We find robust evidence that vote choice in congressional elections is both strongly associated with spatial proximity and that individual-level and contextual variables commonly associated with congressional voting behavior condition the magnitude of its importance. Our results have important implications for theories of voter decision-making and electoral institutions.
Quadriceps Function and Hamstrings Co-Activation After Anterior Cruciate Ligament Reconstruction.

CONTEXT Individuals with anterior cruciate ligament reconstruction (ACLR) have quadriceps dysfunction that contributes to physical disability and posttraumatic knee osteoarthritis. Quadriceps function in the ACLR limb is commonly evaluated relative to the contralateral uninjured limb. Bilateral quadriceps dysfunction is common in individuals with ACLR, potentially biasing these evaluations. OBJECTIVE To compare quadriceps function between individuals with ACLR and uninjured control participants. DESIGN Cross-sectional study. SETTING Research laboratory. PATIENTS OR OTHER PARTICIPANTS Twenty individuals with unilateral ACLR (age = 21.1 ± 1.7 years, mass = 68.3 ± 14.9 kg, time since ACLR = 50.7 ± 21.3 months; females = 14; Tegner Score = 7.1 ± 0.3; 16 patellar tendon autografts, 3 hamstrings autografts, 1 allograft) matched to 20 control participants (age = 21.2 ± 1.2 years, mass = 67.9 ± 11.3 kg; females = 14; Tegner Score = 7.1 ± 0.4) on age, sex, body mass index, and Tegner Activity Scale. MAIN OUTCOME MEASURE(S) Maximal voluntary isometric knee extension was performed on an isokinetic dynamometer. Peak torque (PT), rate of torque development (RTD), electromyographic (EMG) amplitude, central activation ratio (CAR), and hamstrings EMG amplitude were assessed during maximal voluntary isometric knee extension and compared between groups using independent-samples t tests. Relationships between hamstrings co-activation and quadriceps function were assessed using Pearson correlations. RESULTS Participants with anterior cruciate ligament reconstruction displayed lesser quadriceps PT (1.86 ± 0.74 versus 2.56 ± 0.37 Nm/kg, P = .001), RTD (39.4 ± 18.7 versus 52.9 ± 16.4 Nm/s/kg, P = .03), EMG amplitude (0.25 ± 0.12 versus 0.37 ± 0.26 mV, P = .04), and CAR (83.3% ± 11.1% versus 93.7% ± 3.2%, P = .002) and greater hamstrings co-activation (27.2% ± 12.8% versus 14.3% ± 3.7%, P < .001) compared with control participants. Correlations were found between hamstrings co-activation and PT (r = -0.39, P = .007), RTD (r = -0.30, P = .03), and EMG amplitude (r = -0.30, P = .03). CONCLUSIONS Individuals with ACLR possessed deficits in PT, RTD, and CAR compared with control participants. Peak torque is the net result of all agonist and antagonist activity, and lesser PT in individuals with ACLR is partially attributable to greater hamstrings co-activation.
An Extended Algorithm to Enhance the Performance of the Gridbus Broker with Data Restoring Technique

There are various types of Grids have been developed to support different types of Applications. The Gridbus broker that mainly focused on Data Grid mediates access to distributed resources by discovering suitable data and computational resources, job monitoring, accessing local or remote data sources during job execution, collecting and presenting results. In this paper, we present an enhanced version of Grid Service Broker scheduling on Global Data Grids with job restoration point. In the present version of scheduling algorithm, if any job associated with an application becomes failed during its runtime then the scheduling algorithm just marked the job as failed and reset. But it does not keep any track of the percentage of the work has already been done by the job. In Contrast, our proposed enhanced algorithm utilizes a restore point to store the proportion of task completed by an executor. In case of failure, it starts the job from that restored point rather than its initial point. From the experimental result, we have found that our proposed algorithm increases the performance of the present scheduling algorithm.
Investigating the Relationship between Stable Personality Characteristics and Automatic Imitation

Automatic imitation is a cornerstone of nonverbal communication that fosters rapport between interaction partners. Recent research has suggested that stable dimensions of personality are antecedents to automatic imitation, but the empirical evidence linking imitation with personality traits is restricted to a few studies with modest sample sizes. Additionally, atypical imitation has been documented in autism spectrum disorders and schizophrenia, but the mechanisms underpinning these behavioural profiles remain unclear. Using a larger sample than prior studies (N=243), the current study tested whether performance on a computer-based automatic imitation task could be predicted by personality traits associated with social behaviour (extraversion and agreeableness) and with disorders of social cognition (autistic-like and schizotypal traits). Further personality traits (narcissism and empathy) were assessed in a subsample of participants (N=57). Multiple regression analyses showed that personality measures did not predict automatic imitation. In addition, using a similar analytical approach to prior studies, no differences in imitation performance emerged when only the highest and lowest 20 participants on each trait variable were compared. These data weaken support for the view that stable personality traits are antecedents to automatic imitation and that neural mechanisms thought to support automatic imitation, such as the mirror neuron system, are dysfunctional in autism spectrum disorders or schizophrenia. In sum, the impact that personality variables have on automatic imitation is less universal than initial reports suggest.
Duplication and Retention Biases of Essential and Non-Essential Genes Revealed by Systematic Knockdown Analyses

When a duplicate gene has no apparent loss-of-function phenotype, it is commonly considered that the phenotype has been masked as a result of functional redundancy with the remaining paralog. This is supported by indirect evidence showing that multi-copy genes show loss-of-function phenotypes less often than single-copy genes and by direct tests of phenotype masking using select gene sets. Here we take a systematic genome-wide RNA interference approach to assess phenotype masking in paralog pairs in the Caenorhabditis elegans genome. Remarkably, in contrast to expectations, we find that phenotype masking makes only a minor contribution to the low knockdown phenotype rate for duplicate genes. Instead, we find that non-essential genes are highly over-represented among duplicates, leading to a low observed loss-of-function phenotype rate. We further find that duplicate pairs derived from essential and non-essential genes have contrasting evolutionary dynamics: whereas non-essential genes are both more often successfully duplicated (fixed) and lost, essential genes are less often duplicated but upon successful duplication are maintained over longer periods. We expect the fundamental evolutionary duplication dynamics presented here to be broadly applicable.
Superconvergence and a posteriori error estimation in triangular mixed finite elements

Summary. In this paper,we prove superconvergence results for the vector variable when lowest order triangular mixed ﬁnite elements of Raviart-Thomas type [17] on uniform triangulations are used, i.e., that the H (div; Ω )-distance between the approximate solution and a suitable projection of the real solution is of higher order than the H (div; Ω )-error. We prove results for both Dirichlet and Neumann boundary conditions. Recently, Duran [9] proved similar results for rectangular mixed ﬁnite elements, and superconvergence along the Gauss-lines for rectangular mixed ﬁnite elements was considered by Douglas, Ewing, Lazarov and Wang in [11], [8] and [18]. The triangular case however needs some extra effort. Using the superconvergence results, a simple postprocessing of the approximate solution will give an asymptotically exact a posteriori error estimator for the L 2 ( Ω )-error in the approximation of the vector variable.
On the molecular phylogeny of sponges (Porifera)

In the past decade molecular genetic markers have been introduced for research on the evolution and systematics of sponges. Historically, sponges have been difficult to classify due to lack of complex characters with the result that hypothesised phylogenetic relationships for various sponge taxa have changed rapidly over the past few years. Here, we summarize the current status of systematic and phylogenetic hypotheses proposed for sponges. We discuss the relationships among the three classes, Calcarea (calcareous sponges), Hexactinellida (glass sponges) and Demospongiae, as well as those among the members within each class. While molecular phylogenies of hexactinellids corroborate previous morphological hypotheses, phylogenetic hypotheses based on rDNA sequence analyses in Calcarea largely conflict with the previous, typological classifications. Many demosponge taxa have only recently been shown to be para– or polyphyletic and thus their new clades and other phylogenetic relationships have only now begun to be tested using current molecular approaches.
Gaussian mixture models for classification of neonatal seizures using EEG

A real-time neonatal seizure detection system is proposed based on a Gaussian mixture model classifier. The system includes feature transformation techniques and classifier output postprocessing. The detector was evaluated on a database of 20 patients with 330 h of recordings. A detailed analysis of the choice of parameters for the detector is provided. A mean good detection rate of 79% was obtained with only 0.5 false detections per hour. A thorough review of all misclassified events was performed, from which a number of patterns causing false detections were identified.
Pairwise Analysis Can Account for Network Structures Arising from Spike-Timing Dependent Plasticity

Spike timing-dependent plasticity (STDP) modifies synaptic strengths based on timing information available locally at each synapse. Despite this, it induces global structures within a recurrently connected network. We study such structures both through simulations and by analyzing the effects of STDP on pair-wise interactions of neurons. We show how conventional STDP acts as a loop-eliminating mechanism and organizes neurons into in- and out-hubs. Loop-elimination increases when depression dominates and turns into loop-generation when potentiation dominates. STDP with a shifted temporal window such that coincident spikes cause depression enhances recurrent connections and functions as a strict buffering mechanism that maintains a roughly constant average firing rate. STDP with the opposite temporal shift functions as a loop eliminator at low rates and as a potent loop generator at higher rates. In general, studying pairwise interactions of neurons provides important insights about the structures that STDP can produce in large networks.
On the convexity in Kronecker structured covariance estimation

A classical model for the covariance of a random matrix is the Kronecker product of two smaller covariance matrices associated with the rows and columns. Maximum likelihood estimation in such structures involves a non-convex optimization problem and is traditionally handled via an alternating maximization Flip-Flop technique. We prove that the problem is actually geodesically convex on the manifold of positive definite matrices. This allows for better analysis, efficient numerical solutions, and simple extensions through the use of additional geodesically convex regularizations. As an example, we propose to shrink the solution towards the identity when the number of samples is insufficient. We demonstrate the advantages of this approach using computer simulations.
Functional Disability in Elderly Nigerians: Results from the Ibadan Study of Aging

Functional disability is a common reason for loss of independence and need for informal care by elderly persons. There is little information on the profile of disability and the level of unmet need for care in elderly persons living in sub‐Saharan Africa. Using a multistage clustered sampling of households conducted in the Yoruba‐speaking area of Nigeria (representing 22% of the national population), persons aged 65 and older (N=2,152) were assessed for disability in activities of daily living and instrumental activities of daily living. Respondents were assessed for self‐reports of physical health, for major depressive disorder, and for availability of informal care. The prevalence of any functional disability (defined as inability to independently perform any function) was 9.2% (standard error 0.6). In logistic regression analysis, high risks of disability were associated with female sex, older age, and urban dwelling. Risks were also high for persons with chronic pain, those with poor self‐reported overall health, and those with evidence of undernutrition. Disabled persons had poorer quality of life and were more likely to suffer from major depressive disorder; 19.8% of disabled elderly persons lacked any informal care, and this unmet need for care increased the likelihood of having depression. The findings suggest a high burden of unmet need for care in a large section of disabled elderly persons in this African community undergoing demographic and social changes. Social factors relating to urbanization and poverty may be associated with the occurrence of disability and inability to access informal care.
The State of Transportation for People With Intellectual and Developmental Disabilities in Medicaid Home and Community-Based Services 1915(c) Waivers

Transportation is the most frequently reported problem for people with disabilities. While some people with disabilities have difficulty with limited or no public transportation systems, others have trouble with inaccessible infrastructures and systems. In addition, people with intellectual and developmental disabilities (IDD) often have trouble with many of the skills that navigating transportation requires. Although accessible transportation is crucial for independent living, Medicaid only requires states cover nonemergency medical transportation and does not require transportation related to other aspects necessary for community living such as accessing work, errands, or recreational activities. The purpose of this article is to examine Medicaid Home and Community-Based Services (HCBS) 1915(c) waivers, the largest provider of long-term services and supports for people with IDD, to see how transportation is provided for people with IDD. Our examination of 99 waivers for FY 2013 revealed 58 waivers provided transportation-specific services and 71 waivers provided transportation within another service. The majority of waivers provided transportation for people with IDD through these two means; however, this transportation was often limited to very specific purposes. From our findings, it appears transportation services for people with IDD in waivers need to be expanded to support community access and integration.