Miracle-dz/UniFAR-FTUs huggingface dataset:
Kit‐like immunoreactivity in the zebrafish gastrointestinal tract reveals putative ICC

Gastrointestinal (GI) motility results from the coordinated actions of enteric neurons, interstitial cells of Cajal (ICC), and smooth muscle cells. The GI tract of the zebrafish has a cellular anatomy that is essentially similar to humans. Although enteric nerves and smooth muscle cells have been described, it is unknown if ICC are present in the zebrafish. Immunohistochemistry and PCR were used determine expression for the zebrafish Kit orthologue in the zebrafish gastrointestinal tract. Cells displaying Kit‐like immunoreactivity were identified in the muscular layers of the adult zebrafish gastrointestinal tract. Two layers of Kit‐positive cells were identified, one with multipolar cells located between the longitudinal and circular smooth muscle layers and one with simple bipolar cells located deep in the circular muscle layer. Primers specifically designed to amplify mRNA coding for two zebrafish kit genes, kita and kitb, and two kit ligands, kitla and kitlb, amplified the expected transcript from total RNA isolated from zebrafish GI tissues. The Sparse mutant, a kita null mutant, showed reduced contraction frequency and increased size of the GI tract indicating a functional role for kita. These data establish the presence of a cellular network with Kit‐like immunoreactivity in the myenteric plexus region of the zebrafish GI tract, adjacent to enteric neurons. Expression of kita and kitb, and the ligands kitla and kitlb, were verified in the adult GI tract. The anatomical arrangement of the Kit‐positive cells strongly suggests that they are ICC. Developmental Dynamics 236:903–911, 2007. © 2007 Wiley‐Liss, Inc.
Two Nuclear Dot‐Associated Proteins, PML and SplOO, are Often Co‐Autoimmunogenic in Patients with Primary Biliary Cirrhosis

The nucleoproteins Sp100 and PML, the first an autoantigen predominant in patients with primary biliary cirrhosis (PBC) and the second a transformation and cell growth suppressing protein aberrantly expressed in promyelocytic leukaemia ceils, were recently shown to colocalize in dot‐like nuclear domains. Here we analysed whether PML, like Sp100, is also an autoantigen in patients with PBC and other autoimmune diseases, and whether both proteins interact directly. Testing sera from autoimmune patients using an immunoprecipitation assay with radiolabelled PML and an immunofluorescence assay based on a cell hne overexpressing PML, autoantibodies (Aabs) against PML were found in the majority of anti‐Sp100 Aab positive patients. Only very few patients with PBC or other autoimmune diseases contained anti‐PML or anti‐Sp100 Aabs exclusively. In contrast to Sp100, immunoreactivity of recombinant PML in immunoblots was only weak and was directed to one region. This suggests that anti‐PML Aabs recognize fewer and preferentially conformation‐dependent epitopes. In an immuno precipitation assay using in vitro synthesized Sp 100 and PML proteins and Abs to recombinant proteins, no direct interaction was observed. Taken together, these data indicate that Aabs against PML are as highly prevalent and specific for patients with PBC as those against Sp100. The colocalization of these autoantigens and the frequent co‐occurence of the corresponding Aabs might reflect an association of both proteins mediated by one or several other proteins.
Application of Isotonic Regression in Predicting Business Risk Scores

an isotonic regression model fits an isotonic function of the explanatory variables to estimate the expectation of the response variable. In other words, as the function increases, the estimated expectation of the response must be non-decreasing. With this characteristic, isotonic regression could be a suitable option to analyze and predict business risk scores. A current challenge of isotonic regression is the decrease of performance when the model is fitted in a large data set e.g. more than four or five dimensions. This paper attempts to apply isotonic regression models into prediction of business risk scores using a large data set – approximately 50 numeric variables and 24 million observations. Evaluations are based on comparing the new models with a traditional logistic regression model built for the same data set. The primary finding is that isotonic regression using distance aggregate functions does not outperform logistic regression. The performance gap is narrow however, suggesting that isotonic regression may still be used if necessary since isotonic regression may achieve better convergence speed in massive data sets. Keywords—component; isotonic regression; logistic regression; business risk score; PAVA; additive isotonic model.
Usability of Methodology from the USA for Measuring Effect of Corporate Tax on Organizational Form in the Czech Republic

The goal of this paper is to examine the methodology, used by authors Mackie-Mason and Gordon for measuring effects of corporate tax on business organization form, which is connected to issue of double taxation, in the United States and find out, if the same approach can be applied on business environment in the Czech Republic. Eventually recommend changes for this methodology to be more suitable for this environment taking into account its specific factors.
Identification of three feline immunodeficiency virus (FIV) env gene subtypes and comparison of the FIV and human immunodeficiency virus type 1 evolutionary patterns

Feline immunodeficiency virus (FIV) is a lentivirus associated with AIDS-like illnesses in cats. As such, FIV appears to be a feline analog of human immunodeficiency virus (HIV). A hallmark of HIV infection is the large degree of viral genetic diversity that can develop within an infected individual and the even greater and continually increasing level of diversity among virus isolates from different individuals. Our goal in this study was to determine patterns of FIV genetic diversity by focusing on a 684-nucleotide region encompassing variable regions V3, V4, and V5 of the FIV env gene in order to establish parallels and distinctions between FIV and HIV type 1 (HIV-1). Our data demonstrate that, like HIV-1, FIV can be separated into distinct envelope sequence subtypes (three are described here). Similar to that found for HIV-1, the pairwise sequence divergence within an FIV subtype ranged from 2.5 to 15.0%, whereas that between subtypes ranged from 17.8 to 26.2%. However, the high number of synonymous nucleotide changes among FIV V3 to V5 env sequences may also include a significant number of back mutations and suggests that the evolutionary distances among FIV subtypes are underestimated. Although only a few subtype B viruses were available for examination, the pattern of diversity between the FIV A and B subtypes was found to be significantly distinct; subtype B sequences had proportionally fewer mutations that changed amino acids, compared with silent changes, suggesting a more advanced state of adaptation to the host. No similar distinction was evident for HIV-1 subtypes. The diversity of FIV genomes within individual infected cats was found to be as high as 3.7% yet twofold lower than that within HIV-1-infected people over a comparable region of the env gene. Despite these differences, significant parallels between patterns of FIV evolution and HIV-1 evolution exist, indicating that a wide array of potentially divergent virus challenges need to be considered in FIV vaccine and pathogenesis studies.
Neuropsychological effects of carbamazepine and phenytoin

We previously reported that carbamazepine had fewer adverse neuropsychological effects than phenytoin, but it is now clear that our patients had much higher phenytoin than carbamazepine serum levels. When persons with high initial phenytoin levels were excluded, the statistical significance of all neuropsychological differences between the drugs disappeared.
Involvement of serotonin transporter extracellular loop 1 in serotonin binding and transport

Residues Tyr-110 through Gly-115 of serotonin transporter were replaced, one at a time, with cysteine. Of these mutants, only G113C retained full activity for transport, Q111C and N112C retained partial activity, but Y110C, G114C and G115C were inactive. Poor surface expression was at least partly responsible for the lack of transport by G114C and G115C. In membrane preparations, Y110C through G113C all bound a high affinity cocaine analog similarly to the wild type. Treatment with methanethiosulfonate reagents increased the transport activity of Q111C and N112C to essentially wild-type levels but had no measurable effect on the other mutants. The decreased activity of Q111C and N112C resulted from an increase in the KM for serotonin that was not accompanied by a decrease in serotonin binding affinity. Superfusion experiments indicated a defect in 5-HT exchange. Modification of the inserted cysteine residues reversed the increase in KM and the poor exchange, also with no effect on serotonin affinity. The results suggest that Gln-111 and Asn-112 are not required for substrate binding but participate in subsequent steps in the transport cycle.
Coactivator requirements for p53‐dependent transcription in the yeast Saccharomyces cerevisiae

p53 is a sequence‐specific DNA‐binding transcription factor and key regulator of cell cycle arrest and apoptosis. p53 is mutated in most human cancers and these mutations generally impair its ability to activate transcription. When expressed in Saccharomyces cerevisiae, p53 acts as a strong transcriptional activator allowing yeast to be used as a model system to study the effects of p53 mutations on activity. However, little is known about the exact mechanisms by which p53 functions in yeast. Using 76 mutant yeast strains, we have evaluated the effect of deleting components of the ADA, COMPASS, INO80, ISW1, Mediator, RSC, SAGA, SAS, SLIK, SWI/SNF, and SWR1 transcriptional regulatory complexes on p53‐dependent transcription. In addition, we examined the role of histone H2B ubiquitylation by Rad6/Bre1 on p53 activation. Overall, our analysis indicates that there are several remarkable similarities between p53‐dependent transcription in yeast and mammalian cells, suggesting that yeast can serve as a valid model system for at least some aspects of p53 function. © 2007 Wiley‐Liss, Inc.
Prognostic Value of Dynamic Susceptibility Contrast-Enhanced and Diffusion-Weighted MR Imaging in Patients with Glioblastomas

BACKGROUND AND PURPOSE: Prediction of survival in patients with glioblastomas is important for individualized treatment planning. This study aimed to assess the prognostic utility of presurgical dynamic susceptibility contrast and diffusion-weighted imaging for overall survival in patients with glioblastoma. MATERIALS AND METHODS: MR imaging data from pathologically proved glioblastomas between June 2006 to December 2013 in 58 patients (mean age, 62.7 years; age range, 22–89 years) were included in this retrospective study. Patients were divided into long survival (≥15 months) and short survival (<15 months) groups, depending on overall survival time. Patients underwent dynamic susceptibility contrast perfusion and DWI before surgery and were treated with chemotherapy and radiation therapy. The maximum relative cerebral blood volume and minimum mean diffusivity values were measured from the enhancing part of the tumor. RESULTS: Maximum relative cerebral blood volume values in patients with short survival were significantly higher compared with those who demonstrated long survival (P < .05). No significant difference was observed in the minimum mean diffusivity between short and long survivors. Receiver operator curve analysis demonstrated that a maximum relative cerebral blood volume cutoff value of 5.79 differentiated patients with low and high survival with an area under the curve of 0.93, sensitivity of 0.89, and specificity of 0.90 (P < .001), while a minimum mean diffusivity cutoff value of 8.35 × 10−4mm2/s had an area under the curve of 0.55, sensitivity of 0.71, and specificity of 0.47 (P > .05) in separating the 2 groups. CONCLUSIONS: Maximum relative cerebral blood volume may be used as a prognostic marker of overall survival in patients with glioblastomas.
A low-jitter clock and data recovery for GDDR5 interface trainings

In this paper, a clock and data recovery (CDR) based on digital phase interpolators using proportional-integral controller, PI2 CDR, is proposed for GDDR5 interface trainings, i.e. read training and write training. The proposed CDR is composed of a deserializer, a phase detector, a programmable accumulator, a proportional-integral (PI) controller and four digital phase interpolators instead of two for the purpose of glitch free. Issues such as glitches during the phase switching and phase variation caused by different loads are discussed. Simulation results show that the proposed PI2 CDR provides trade-off between low CDR jitter and low power consumption compared to modified and adaptive CDRs.
Masking Period Patterns and Forward Masking for Speech-Shaped Noise: Age-Related Effects

Objective: The purpose of this study was to assess age-related changes in temporal resolution in listeners with relatively normal audiograms. The hypothesis was that increased susceptibility to nonsimultaneous masking contributes to the hearing difficulties experienced by older listeners in complex fluctuating backgrounds. Design: Participants included younger (n = 11), middle-age (n = 12), and older (n = 11) listeners with relatively normal audiograms. The first phase of the study measured masking period patterns for speech-shaped noise maskers and signals. From these data, temporal window shapes were derived. The second phase measured forward-masking functions and assessed how well the temporal window fits accounted for these data. Results: The masking period patterns demonstrated increased susceptibility to backward masking in the older listeners, compatible with a more symmetric temporal window in this group. The forward-masking functions exhibited an age-related decline in recovery to baseline thresholds, and there was also an increase in the variability of the temporal window fits to these data. Conclusions: This study demonstrated an age-related increase in susceptibility to nonsimultaneous masking, supporting the hypothesis that exacerbated nonsimultaneous masking contributes to age-related difficulties understanding speech in fluctuating noise. Further support for this hypothesis comes from limited speech-in-noise data, suggesting an association between susceptibility to forward masking and speech understanding in modulated noise.
Relation of Complementary‐Alternative Medicine use with glomerular filtration rate and depression in patients with chronic kidney disease at predialysis stage

Complementary and alternative medicine is a broad field of health including all health care practices and methods, and their accompanying theories and beliefs. In the present study, we aimed to examine the frequency of complementary‐alternative medicine use, and its relation with glomerular filtration rate and depression in patients with chronic kidney disease at predialysis stage.
Shared Decision Making for Psychiatric Rehabilitation Services Before Discharge from Psychiatric Hospitals

ABSTRACT Shared decision making (SDM) is an effective health communication model designed to facilitate patient engagement in treatment decision making. In mental health, SDM has been applied and evaluated for medications decision making but less for its contribution to personal recovery and rehabilitation in psychiatric settings. The purpose of this pilot study was to assess the effect of SDM in choosing community psychiatric rehabilitation services before discharge from psychiatric hospitalization. A pre-post non-randomized design with two consecutive inpatient cohorts, SDM intervention (N = 51) and standard care (N = 50), was applied in two psychiatric hospitals in Israel. Participants in the intervention cohort reported greater engagement and knowledge after choosing rehabilitation services and greater services use at 6-to-12-month follow-up than those receiving standard care. No difference was found for rehospitalization rate. Two significant interaction effects indicated greater improvement in personal recovery over time for the SDM cohort. SDM can be applied to psychiatric rehabilitation decision making and can help promote personal recovery as part of the discharge process.
Beyond the “C” in MCI: Noncognitive Symptoms in Amnestic and Non-amnestic Mild Cognitive Impairment

ABSTRACT Introduction: How frequent and how clinically important are mood and behavioral symptoms among older adults with mild cognitive impairment (MCI)? Although these noncognitive behavioral symptoms (NCBS) are not represented in the diagnostic criteria for MCI, their clinical significance is increasingly recognized. Methods: To address this question, the authors identified a cohort of consecutively evaluated patients from a psychiatric hospital's outpatient memory clinic. These patients' records contained both a clinical assessment and a standardized set of evaluations including the Mini-Mental State Exam, the Neuropsychiatric Inventory (NPI), and the Geriatric Depression Scale. Using a standardized chart-review approach, the presence of any NPI-screened symptom was identified and the frequencies of specific NPI-screened symptoms were calculated for the Memory Clinic MCI cohort and for amnestic and non-amnestic MCI subgroups. Results: A total of 116 patient records were reviewed. Thirty-eight patients with MCI were identified. Twenty-two of these met criteria for amnestic MCI by Mayo Clinic criteria while 16 met criteria for non-amnestic MCI. At least one NPI-screened mood or behavioral symptom was present in 86.8% of these MCI patients. Depression/dysphoria (63.3%), apathy (60.5%), anxiety (47.4%), irritability (44.7%), and nighttime behaviors (42.1%) were the most frequent. While depression/dysphoria was distributed similarly between amnestic and non-amnestic subgroups, apathy was significantly more frequently associated with the amnestic subtype of MCI, and nighttime behaviors were more frequently associated with the non-amnestic subtype. Conclusion: Although the presence of NCBS is not required for a diagnosis of MCI, these symptoms are frequently present and constitute an important source of morbidity. Apathy and depression may be difficult to differentiate, but targeted treatment of depression may fail to address apathy. Recognizing the limitations of this preliminary study, the authors suggest that apathy may be more characteristic of amnestic MCI while nighttime behaviors may be more characteristic of non-amnestic MCI.
Application of multivariate statistical techniques for differentiation of ripe banana flour based on the composition of elements

Major (sodium, potassium, calcium, magnesium) and minor elements (iron, copper, zinc, manganese) and one heavy metal (lead) of Cavendish banana flour and Dream banana flour were determined, and data were analyzed using multivariate statistical techniques of factor analysis and discriminant analysis. Factor analysis yielded four factors explaining more than 81% of the total variance: the first factor explained 28.73%, comprising magnesium, sodium, and iron; the second factor explained 21.47%, comprising only manganese and copper; the third factor explained 15.66%, comprising zinc and lead; while the fourth factor explained 15.50%, comprising potassium. Discriminant analysis showed that magnesium and sodium exhibited a strong contribution in discriminating the two types of banana flour, affording 100% correct assignation. This study presents the usefulness of multivariate statistical techniques for analysis and interpretation of complex mineral content data from banana flour of different varieties.
Semi-Supervised Learning Techniques in Artificial Olfaction: A Novel Approach to Classification Problems and Drift Counteraction

Semi-supervised learning is a promising research area aiming to develop pattern recognition tools capable to exploit simultaneously the benefits from supervised and unsupervised learning techniques. These can lead to a very efficient usage of the limited number of supervised samples achievable in many artificial olfaction problems like distributed air quality monitoring. We believe it can also be beneficial in addressing another source of limited knowledge we have to face when dealing with real world problems: concept and sensor drifts. In this paper we describe the results of two artificial olfaction investigations that show semi-supervised learning techniques capabilities to boost performance of state-of-the art classifiers and regressors. The use of semi-supervised learning approach resulted in the effective reduction of drift-induced performance degradation in long-term on-field continuous operation of chemical multisensory devices.
The influence of landscape on gene flow in the eastern massasauga rattlesnake (Sistrurus c. catenatus): insight from computer simulations

Understanding how gene flow shapes contemporary population structure requires the explicit consideration of landscape composition and configuration. New landscape genetic approaches allow us to link such heterogeneity to gene flow within and among populations. However, the attribution of cause is difficult when landscape features are spatially correlated, or when genetic patterns reflect past events. We use spatial Bayesian clustering and landscape resistance analysis to identify the landscape features that influence gene flow across two regional populations of the eastern massasauga rattlesnake, Sistrurus c. catenatus. Based on spatially explicit simulations, we inferred how habitat distribution modulates gene flow and attempted to disentangle the effects of spatially confounded landscape features. We found genetic clustering across one regional landscape but not the other, and also local differences in the effect of landscape on gene flow. Beyond the effects of isolation‐by‐distance, water bodies appear to underlie genetic differentiation among individuals in one regional population. Significant effects of roads were additionally detected locally, but these effects are possibly confounded with the signal of water bodies. In contrast, we found no signal of isolation‐by‐distance or landscape effects on genetic structure in the other regional population. Our simulations imply that these local differences have arisen as a result of differences in population density or tendencies for juvenile rather than adult dispersal. Importantly, our simulations also demonstrate that the ability to detect the consequences of contemporary anthropogenic landscape features (e.g. roads) on gene flow may be compromised when long‐standing natural features (e.g. water bodies) co‐exist on the landscape.