Miracle-dz/UniFAR-FTUs huggingface dataset:
CYSTOID MACULAR DEGENERATION IN CHRONIC CENTRAL SEROUS CHORIORETINOPATHY

Purpose To describe the optical coherence tomography (OCT) and fluorescein angiography findings in the macula of eyes with chronic central serous chorioretinopathy (CSC) and reduced central vision. Methods Using OCT, clinical examination, and fluorescein and indocyanine green (ICG) angiography, the authors examined eight eyes of seven patients with CSC, an attached macula, and reduced central vision of 20/200 or worse. All had a history of chronic CSC with resolution of the subretinal fluid in the macular area and poor vision. Results Patient ages ranged from 55 to 82 years (mean, 66 years). All eight eyes had some parafoveal, patchy RPE atrophy with corresponding transmission hyperfluorescence (window defect) on fluorescein angiography. Five eyes also had a window defect in the foveal area. With OCT, the foveal area revealed variable areas of cystoid change and atrophy in seven of the eight eyes. In four of these eyes, the cystoid changes were not seen on clinical examination or fluorescein angiography. The seven eyes with cystoid changes imaged with OCT had no intraretinal leakage of fluorescein in the foveal region. The authors categorized these eyes as having cystoid macular degeneration (CMD). One other eye had foveal thinning or atrophy without cystoid changes. Conclusions Intraretinal cystoid spaces without intraretinal leakage, or CMD, was a common finding in eyes with chronic CSC and reduced central vision after resolution of subretinal fluid. OCT was useful to establish the presence of CMD and foveal atrophy, even when these changes were not clearly evident on clinical examination or fluorescein angiography. Chronic foveal detachment and antecedent intraretinal leakage were proposed to be the mechanisms for the development of the changes. CMD in conjunction with foveal atrophy was an important clinical finding to account for the poor visual outcome in patients with CSC.
A General Framework for Mixed Graphical Models

\Mixed Data" comprising a large number of heterogeneous variables (e.g. count, binary, continuous, skewed continuous, among other data types) are prevalent in varied areas such as genomics and proteomics, imaging genetics, national security, social networking, and Internet advertising. There have been limited eorts at statistically modeling such mixed data jointly, in part because of the lack of computationally amenable multivariate distributions that can capture direct dependencies between such mixed variables of dierent types. In this paper, we address this by introducing a novel class of Block Directed Markov Random Fields (BDMRFs). Using the basic building block of node-conditional univariate exponential families from Yang et al. (2012), we introduce a class of mixed conditional random eld distributions, that are then chained according to a block-directed acyclic graph to form our class of Block Directed Markov Random Fields (BDMRFs). The Markov independence graph structure underlying a BDMRF thus has both directed and undirected edges. We introduce conditions under which these distributions exist and are normalizable, study several instances of our models, and propose scalable penalized conditional likelihood estimators with statistical guarantees for recovering the underlying network structure. Simulations as well as an application to learning mixed genomic networks from next generation sequencing expression data and mutation data demonstrate the versatility of our methods.
Cerebral ventricle dimensions as risk factors for schizophrenia and affective psychosis: an epidemiological approach to analysis

Synopsis A case–control study was undertaken of volumetric computerized tomographic scan measures in 216 consecutive admissions for functional psychosis and 67 healthy community controls. Odds ratio analysis demonstrated significant linear trends in the association between increasing lateral and third ventricle volumes, and both RDC schizophrenia (N = 121) and schizoaffective disorder (N = 41); cases were consistently associated with larger volumes than controls. There was an association between larger third, but not lateral, ventricle size in affective psychoses (N = 54). These associations were statistically independent of intracranial volume, sex, social class and ethnicity, factors which were significantly associated with ventricular measures in the controls. There was no evidence of a threshold corresponding to the notion of normal versus enlarged ventricles. Within the schizophrenia group, there were no large or significant associations between ventricle dimensions and age at onset, duration of illness or pre-morbid social functioning. Neither obstetric complications nor a family history of schizophrenia or other psychiatric illness was associated with large ventricles in these cases.
How Cells Activate ATR

ATR is a critical upstream regulator of checkpoint responses to incompletely replicated and damaged DNA. However, it had not been understood how the kinase activity of ATR is switched on during checkpoint responses. TopBP1 and its homologs are necessary for both DNA replication and checkpoint control. A recent report from this laboratory demonstrated that TopBP1 functions as an activator of ATR. It had been known that TopBP1 accumulates at sites of replicative stress and DNA damage. Thus, interaction of ATR with a critical protein at stalled replication forks and sites of DNA damage triggers its activation. This finding helps to explain how aberrant DNA structures in the genome induce ATR-dependent signaling processes.
Risk-Based Allocation of Principal Portfolios

Risk-based asset allocation strategies are mainly used to diversify nominal asset weights. In this paper, we discuss the diversification of risk factors. The analysis is based on the idea of Partovi and Caputo (2004), who use principal component analysis to transform a portfolio into a set of uncorrelated principal portfolios. Risk-based asset allocation strategies can be applied to these uncorrelated sources of risk. A similar route has been taken by Meucci (2009) with his idea of a maximum entropy portfolio. We discuss the relation of this approach with the concept of principal risk parity. Both strategies are backtested against nominal diversification strategies in a multi-asset portfolio. We find no evidence that risk diversification does outperform nominal diversification and discuss possible reasons for this.
Versioning: Go Vertical in a Horizontal Market?

Abstract The issue of versioning of information goods has resurfaced, in part as a result of the recent popularity of downloadable contents (DLC) among video game manufacturers. The central idea behind the DLC strategy, zero-day DLCs in particular, is that consumers who find the base version of a game to be sufficiently close to their tastes would want more of its capabilities and would pay a premium to upgrade by purchasing a DLC. To better understand the implications of such a product-line strategy, in this work, we combine the literature on versioning with that on consumer learning. In doing so, we uncover an interesting economic phenomenon that, for an experience good, a manufacturer’s desire to vertically differentiate could actually stem from its inability to otherwise elicit unobserved heterogeneity in consumers’ perceived fit. In other words, we generalize versioning to accommodate both vertical and horizontal heterogeneity.
Viscoelastic properties of chondrocytes from normal and osteoarthritic human cartilage

The deformation behavior and mechanical properties of articular chondrocytes are believed to play an important role in their response to mechanical loading of the extracellular matrix. This study utilized the micropipette aspiration test to measure the viscoelastic properties of chondrocytes isolated from macroscopically normal or end‐stage osteoarthritic cartilage. A three‐parameter standard linear solid was used to model the viscoelastic behavior of the cells. Significant differences were found between the mechanical properties of chondrocytes isolated from normal and osteoarthritic cartilage. Specifically, osteoarthritic chondrocytes exhibited a significantly higher equilibrium modulus (0.33 ± 0.23 compared with 0.24 ± 0.11 kPa), instantaneous modulus (0.63 ± 0.51 compared with 0.41 ± 0.17 kPa), and apparent viscosity (5.8 ± 6.5 compared with 3.0 ± 1.8 kPa‐s) compared with chondrocytes isolated from macroscopically normal, nonosteoarthritic cartilage. The elastic moduli and relaxation time constant determined experimentally in this study were used to estimate the apparent biphasic properties of the chondrocyte on the basis of the equation for the gel relaxation time of a biphasic material. The differences in viscoelastic properties may reflect alterations in the structure and composition of the chondrocyte cytoskeleton that have previously been associated with osteoarthritic cartilage. Coupled with earlier theoretical models of cell‐matrix interactions in articular cartilage, the increased elastic and viscous properties suggest that the mechanical environment of the chondrocyte may be altered in osteoarthritic cartilage.
A novel multiwavelet-based interpolation algorithm of images

Based on the theory of multiwavelet analysis and fractal dimensions, a novel adaptive image interpolation algorithm is proposed. By one level multiwavelet decomposition, the image is transformed into four low frequency bands and twelve high frequency bands. Using the fractal dimensions of high frequency bands, every band of two level multiwavelet transform for high-resolution image is obtained adaptively. Through two level inverse multiwavelet transform, more distinct interpolated image can be obtained. The experimental results shows that the new algorithm has overcome shortcomings of the blur effects that interpolating with the scalar wavelet transform and has better results comparing with the traditional image interpolation methods such as bilinear or bicubic ones.
Interpretation of NOTCH3 mutations in the diagnosis of CADASIL

CADASIL is an autosomal dominant inherited disease, characterized by mid-adult onset of cerebrovascular disease and dementia. CADASIL is caused by mutations in the NOTCH3 gene, which encodes the NOTCH3 protein. Pathogenic mutations in CADASIL are highly distinctive in the sense that they lead to the loss or gain of a cysteine residue in 1 of the 34 EGFr domains of the NOTCH3 protein. The majority are missense mutations, but small deletions, insertions and splice-site mutations have been reported, which typically also lead to a numerical cysteine alteration. Whether numerical cysteine-altering mutations are a rule in CADASIL remains subject of debate, as there are reports suggesting pathogenicity of other types of mutations. However, for most of these the association with CADASIL was later revoked or is questionable. Here, we discuss and provide recommendations for the interpretation of NOTCH3 mutations in the diagnosis of CADASIL.
Adaptive Ensemble Method Based on Spatial Characteristics for Classifying Imbalanced Data

The class imbalance problems often reduce the classification performance of the majority of standard classifiers. Many methods have been developed to solve these problems, such as cost-sensitive learning methods, synthetic minority oversampling technique (SMOTE), and random oversampling (ROS). However, the existing methods still have some problems due to the possible performance loss of useful information and overfitting. To solve the problems, we propose an adaptive ensemble method by using the most advanced feature of self-adaption by considering an average Euclidean distance between test data and training data, where the average distance is calculated by -nearest neighbors (KNN) algorithm. Simulation results are provided to confirm that the proposed method has a better performance than existing ensemble methods.
Are survival rates for Tyrol published in the Eurocare studies biased?

Objective. To investigate whether survival rates published in the EUROCARE studies for Tyrol are distorted, we evaluated data quality in the Cancer Registry of Tyrol. Material and methods. Potential errors in completeness of Tyrolean incidence data were assessed by applying semi-quantitative and quantitative methods, in part by comparing indices for Tyrol with those of neighboring countries published in Cancer Incidence in Five Continents. Validity of patient survival status was checked for all cancer patients diagnosed in 1997 (n = 2 556). For all 1 026 of these patients still alive at end of 2007, we re-assessed survival status. Finally, we re-abstracted date of diagnosis for a subset of 295 patients. Results. Quality indices on completeness showed no greater bias with the exception of borderline ovarian cancer, which was in part miscoded in the early nineties. Some differences for bladder cancer and prostate cancer between Tyrol and neighboring countries are due to PSA testing and pathology diagnosis. Concerning patient survival status, four cases were erroneously assessed as alive, five cases died outside Austria, three cases were proven not to belong to the population of Tyrol at time of diagnosis and 21 cases emigrated. Absolute errors in survival rates were less than 0.5 for up to five-year survival rates and less than 1.0 for ten year survival rates. Conclusions. Evaluation of data quality in the Cancer Registry of Tyrol demonstrated that the survival rates published for Tyrol are only minimally biased by registration or analysis procedures. However, access to data on emigration, which until now is not possible because of data protection restrictions, would reduce the bias in patient survival status, bearing in mind that the extent of emigration of cancer patients is expected to increase in Austria over the coming years.
Clinical and radiographic changes at implants supporting single-unit crowns (SCs) and fixed dental prostheses (FDPs) with one cantilever extension. A retrospective study.

OBJECTIVES To evaluate the clinical and radiographic changes at implants in posterior maxillary and mandibular areas supporting single-unit crowns (SCs) and fixed dental prostheses (FDPs) with one mesial or distal cantilever extension after an observation period of at least 3 years. MATERIAL AND METHODS Seventeen subjects with 19 implant-supported SCs and 21 subjects with 21 implant-supported FDPs fulfilled the inclusion criteria. All FDPs were supported by two implants and had a span of 3-4 units. All reconstructions were incorporated in the posterior maxilla or mandible. The mesial and distal radiographic marginal bone loss from baseline (i.e. delivery of the reconstruction) to the follow-up examination was averaged and compared between SCs supporting one cantilever extension with that of implants supporting FDPs adjacent to or distant from the cantilever extension. Changes in mean pocket probing depth (PPD) were calculated and compared between the three groups. RESULTS The mean observation period was 78.2 ± 34.5 months for SCs supported by one implant and 67.8 ± 29.8 months for FDPs supported by two implants. No implant loss occurred, yielding a 100% survival rate. At baseline, the mean radiographic bone levels ± SD were 2.6 ± 0.3 mm for implants supporting SCs, 2.6 ± 0.3 mm for implants of FDPs adjacent to the cantilever extension, and 2.4 ± 0.5 mm for implants of FDPs distant from the cantilever extension. At follow-up, the corresponding mean bone levels ± SD were 2.7 ± 0.4, 2.7 ± 0.5, and 2.8 ± 0.5 mm, respectively. No statistically significant differences (P > 0.05) were observed comparing the mean marginal bone loss between the three groups. Moreover, mean changes in PPD between baseline and follow-up were not statistically significantly different (P > 0.05) between the three groups. CONCLUSION The presence of one mesial or distal cantilever extension in the posterior maxilla or mandible does not jeopardize the marginal bone levels of implants supporting SCs or short-span FDPs after a mean observation period of at least 5 years.
Stress Response and Adaptation of Listeria monocytogenes 08-5923 Exposed to a Sublethal Dose of Carnocyclin A

ABSTRACT Carnocyclin A (CCLA) is an antimicrobial peptide produced by Carnobacterium maltaromaticum ATCC PTA-5313, which can be used to control the growth of Listeria monocytogenes in ready-to-eat meat products. The aim of this research was to elucidate the cellular responses of L. monocytogenes 08-5923 exposed to a sublethal dose of CCLA. Microarray, quantitative reverse transcription-PCR, tandem mass spectrometry, and electron microscopy were used to investigate the alteration in gene expression, protein production, and morphological changes in cells of Listeria following treatment with CCLA. The genes involved in metabolism (baiE, trn, and pykA), cell wall synthesis (murZ and dacB2), and cell division (clpE and divIVA) were upregulated following a 15-min exposure to CCLA as a result of stress responses. Genes involved in cell division, cell wall synthesis, flagellar synthesis, and metabolism were downregulated after 4 h as a result of adaptation. Analysis of total soluble proteins confirmed the downregulation of pykA and gnd after 4 h of exposure to CCLA. The absence of flagella was observed in L. monocytogenes following 30 h of exposure to CCLA. A sublethal dose of CCLA induced adaptation in L. monocytogenes 08-5923 by inhibition of expression of genes and proteins critical for synthesis of cell wall structures and maintaining metabolic functions. Both the mannose- and cellobiose-specific phosphotransferase systems could be targets for CCLA.
Cross‐linking FtsZ polymers into coherent Z rings

A key event in bacterial cytokinesis is the formation of the Z ring, which serves as a mechanical scaffold that recruits other cytokinetic proteins to establish functional divisomes. This scaffolding function of Z rings is essential throughout cytokinesis, but the underlying molecular interactions are poorly understood. Here we report that a widely conserved FtsZ binding protein, ZapA, has cytological, biochemical and biophysical properties that argue for the importance of cross‐linking interactions between FtsZ polymers in the coherence of Z rings. Escherichia coli zapA null mutant cells have Z rings that are structurally looser and many helical precursors of Z rings fail to coalesce into coherent rings. Biophysical behaviour of FtsZ in the presence of ZapA reveals that ZapA not only bundles, but also cross‐links FtsZ polymers, which makes it the first cross‐linking protein of the bacterial cytoskeleton. Cross‐linking in vitro occurs at the stoichiometry of FtsZ–ZapA interaction at the Z rings in vivo, where nearly all intracellular ZapA is dynamically associated. ZapA also stabilizes longitudinal bonds between FtsZ monomers since it promotes the polymerization of FtsZ mutants with lesions at the polymerization interface and since it reverses the inhibitory effects of SulA, a known antagonist of FtsZ longitudinal interactions.
Yurii Rogozhin's Contributions to the Field of Small Universal Turing Machines

In the field of small universal Turing machines, Yurii Rogozhin holds a special prize: he was first to close off an infinite number of open questions by drawing a closed curve that separates the infinite set of Turing machines that are universal from a finite set of small machines for which we don't yet know. Rogozhin did this by finding the smallest known universal Turing machines at the time, both in terms of number of states and number of symbols. This brief note summarises this and a few of Yurii's other contributions to the field, including his work with Manfred Kudlek on small circular Post machines.
HIV testing in men who have sex with men: are we ready to take the next HIV testing test?

Increases in new HIV infections among men who have sex with men (MSM) are now reported from nearly every industrialised country context,1 and the news from resource-poor settings is worse still—extremely high background prevalence, increases in new infections and only very limited access to care and prevention.2 3 With the weakening commitment of MSM to consistent condom use (at the population level),4 5 and with the growing popularity of different behavioural risk-reduction strategies (negotiated agreements, serosorting and strategic positioning),6 7 8 and the increasing uptake and enactment of pharmacoprophylaxis by MSM (pre and postexposure prophylaxis),9 10 it is little wonder public health and prevention practitioners are highly sensitive to changes in the HIV testing practice and patterns of MSM. From a public health perspective HIV testing rates are a factor in estimating the scale of the problem in this population group. For MSM as individuals knowing their HIV status is something quite different. It is no longer important just because it permits them to maximise the benefits of early HIV treatment interventions (if it ever was? ). Regular and repeated HIV testing are becoming increasingly understood as gateway behaviours that open a range of potentially effective HIV prevention options, which may not include condoms, but for which knowledge of HIV status is the essential starting point. Whether as public health and prevention practitioners this was our intention, whether we choose to acknowledge and support it, and whether we are willing to step up and work to support MSM who enact these practices to do so as effectively as possible is the point …
Dissociation of NS5 from cell fractions containing West Nile virus-specific polymerase activity

West Nile virus replication complexes were partially purified from cytoplasmic extracts of virus-infected cells by centrifugation through a 20% glycerol cushion. Numerous cell proteins, as well as the largest nonstructural protein, NS5, were separated from the replication complexes without significant loss of in vitro West Nile virus polymerase activity.
When do open-loop strategies for combustion control work?

This paper addresses open-loop control strategies that involve a low-frequency modulation of the fuel injection for suppression of pressure oscillations in combustion systems. Such a strategy has been employed in a number of recent investigations. Using a physically based model, analytical explanations for the effectiveness of such a low pulsing strategy are provided in this paper. Conditions are derived on the frequency and the duty cycle used in the control strategy that lead to stabilization in the combustor, underideal and nonideal switching strategies, and in the presence of hysteresis.
Mutations in the E1 Hydrophobic Domain of Rubella Virus Impair Virus Infectivity but Not Virus Assembly

ABSTRACT Rubella virus (RV) virions contain three structural proteins, a capsid protein that interacts with viral genomic RNA to form a nucleocapsid and two membrane glycoproteins, E2 and E1. We found that substitution of either an aspartic acid residue at Gly93 (G93D) or a glycine residue at Pro104 (P104G) in the internal hydrophobic domain of E1 affected virus infectivity but not virus assembly. Viruses carrying G93D and P104G mutations had impaired infectivity, reduced 1,000-fold and 10-fold, respectively. A revertant was isolated from the G93D mutant. Sequencing analysis showed that the substituted aspartic acid residue in G93D mutant had reverted to the original glycine residue, suggesting the involvement of Gly93 in membrane fusion during viral entry.