Miracle-dz/UniFAR-FTUs huggingface dataset:
The effects of poor sleep quality on cognitive function of patients with cirrhosis.

OBJECTIVES This study was conducted to assess the ill-defined relationship between sleep quality and multiple, specific domains of cognitive function in patients with cirrhosis. METHODS A comprehensive battery of neuropsychological tests (divided into six neurocognitive domains) and a standardized, validated measure of sleep quality (Pittsburgh Sleep Quality Index [PSQI]) were administered to patients with cirrhosis and without evidence of overt hepatic encephalopathy, recruited from liver transplant and advanced liver disease clinics (n = 34). An inflammatory bowel disease (IBD) control group (n = 23) was similarly recruited and evaluated to control for the secondary effect of a chronic illness on cognition. PSQI global and component scores were used to predict cognitive function in each neurocognitive domain, using linear regression. RESULTS Global PSQI scores were significantly higher (indicating poorer sleep quality) in the cirrhosis group (median [range] = 10 [1-19]) than in IBD controls = 5 (1-14); p = 0.002). After controlling for age and education, short duration of sleep was associated with impaired memory for patients with cirrhosis; the use of soporific agents was associated with poor visual-perceptual function in patients with IBD. CONCLUSIONS Poor sleep was associated with worsening of the already impaired cognitive function of patients with cirrhosis.
Merosin‐integrin promotion of skeletal myofiber cell survival: Differentiation state‐distinct involvement of p60Fyn tyrosine kinase and p38α stress‐activated MAP kinase

Myofiber survival and suppression of anoikis depend in large part on the merosin (laminin‐2/‐4)‐integrin α7β1D cell adhesion system; however, the question remains as to the nature of the signaling molecules/pathways involved. In the present study, we investigated this question using the C2C12 cell model of myogenic differentiation and its merosin‐ and laminin‐deficient derivatives. Herein, we report that: 1) of four members of the Src family of tyrosine kinases studied (p60Src, p53/56Lyn, p59Yes, or p60Fyn), the expression and activity of p60Fyn are found in myotubes exclusively; 2) a severe decrease of p60Fyn activity correlates with myotube apoptosis/anoikis induced by pharmocological compounds (herbimycin A or PP2) which inhibit tyrosine kinases of the Src family, by merosin deficiency and by β1 integrin inhibition; 3) myoblast survival depends on Fak and the MEK/Erk pathway, in contrast to myotubes; 4) the PI3‐K pathway is not involved in either myoblast or myotube survival; and 5) p38α SAPK stimulation and activity (but not that of p38β) are required in the progression of myotube apoptosis/anoikis induced by p60Fyn inhibition, merosin deficiency or β1 integrin‐inhibition; however, p38 is not involved in myoblast apoptosis. Taken together, these results suggest that the promotion of myotube survival by the merosin‐α7β1D adhesion system involves p60Fyn, and that disruptions in this cell adhesion system induce myotube apoptosis/anoikis through a p38α SAPK‐dependent pathway. J. Cell. Physiol. 191: 69–81, 2002. © 2002 Wiley‐Liss, Inc.
Surrogate-based cross-correlation for particle image velocimetry

This paper presents a novel surrogate-based cross-correlation (SBCC) framework to improve the correlation performance between two image signals. The basic idea behind the SBCC is that an optimized surrogate filter/image, supplanting one original image, will produce a more robust and more accurate correlation signal. The cross-correlation estimation of the SBCC is formularized with an objective function composed of surrogate loss and correlation consistency loss. The closed-form solution provides an efficient estimation. To our surprise, the SBCC framework could provide an alternative view to explain a set of generalized cross-correlation (GCC) methods and comprehend the meaning of parameters. With the help of our SBCC framework, we further propose four new specific cross-correlation methods, and provide some suggestions for improving existing GCC methods. A noticeable fact is that the SBCC could enhance the correlation robustness by incorporating other negative context images. Considering the sub-pixel accuracy and robustness requirement of particle image velocimetry (PIV), the contribution of each term in the objective function is investigated with particles' images. Compared with the state-of-the-art baseline methods, the SBCC methods exhibit improved performance (accuracy and robustness) on the synthetic dataset and several challenging real experimental PIV cases.
Progression in Atherosclerosis: Histological Features and Pathophysiology of Atherosclerotic Lesions

In this article, we present an illustrated and brief review of the literature concerning the histological and pathophysiological features of human atherosclerosis. Although the basic descriptive terms remain unchanged, the classification systems have evolved, and a uniform terminology is essential in clinical and laboratory researches. We discuss the major difficulties in classifying atherosclerotic lesions and give an overview of the most important histological classification systems as provided by the American Heart Association and Virmani et al (Arterioscler Thromb Vasc Biol. 2000;20:1262). Furthermore, we present the most recent literature concerning plaque progression, including enlargement of the lipid core and neovascularization.
[Self-esteem of boys with attention deficit hyperactivity disorder - pilot study].

AIM To compare the self concept of boys with ADHD and health subjects; to determine which symptoms ofADHD, oppositional defiant disorder (ODD) or conduct disorder (CD) have the greatest impact on self-concept. METHOD Polish version of The Harter Self-Esteem Questionnaire (HSEQ) was filled by boys with ADHD and control group. In addition, a diagnosis of ODD and CD was made in ADHD group. RESULTS A significant difference was observed between boys with ADHD and control group on the following scales of HSEQ: Global Self-Esteem Subscale, Social Acceptance Subscale and Scholastic Performance Subscale. No significant influence of the quantity and intensity of ADHD and ODD symptoms on self-esteem was found. A significant correlation was indicated between all scales of HSEQ and quantity and intensity of symptoms ofADHD. CONCLUSIONS Boys with ADHD have lower self-esteem than their healthy peers and their global self-esteem, social acceptance and school skills are most affected. The presence of conduct disorder (CD) had the greatest impact on the decrease of self esteem in ADHD group.
Structural destabilization of the recombinant thermophilic TthL11 ribosomal protein by a single amino acid substitution

Abstract Thermus thermophilus L11 protein has previously been reported to be resistant against tryptic and chymotryptic proteolysis under native conditions. With a single amino acid substitution, namely Trp101Arg, conformational changes were induced that resulted in the exhibition of specific amino acids that served as targets for tryptic and chymotryptic action and rendered the protein highly unstable even during purification. This unexpected process was evidenced by the isolation with size exclusion gel chromatography of the wellstructured chymotryptic N-terminal domain in a high amount and its characterization both by Edman degradation and QTOF-EMS spectroscopy. On the other hand, the substitution of Val38Cys, which did not contribute to structural changes, indicates a very possible implication of this amino acid in the protein methylation process. The data reported in this work illustrate the distinctive amino acid dynamics in a thermophilic protein, which, while serving the function common to its counterparts from mesophilic organisms, has had to adapt to the extreme environmental conditions typical of thermophilic organisms.
Spatiotemporal dictionary learning for undersampled dynamic MRI reconstruction via joint frame-based and dictionary-based sparsity

Image reconstruction using compressed sensing relies on sparse representations of signals in some dictionary. Current state-of-the-art dictionary-learning methods are designed for spatial images and fail to systematically generalize to dynamic imaging scenarios where the spatiotemporal data, and thereby the spatiotemporal dictionary atoms, exhibit joint coherence in space and time leading to low rank. This paper proposes a novel method for learning low-rank spatiotemporal dictionaries. While leading compressed-sensing reconstruction methods employ either l1 analysis or synthesis approaches using mathematical frames (e.g. overcomplete wavelets), approaches using dictionary learning (very recent) ignore the frame-based l1-sparsity constraints. This paper proposes a novel method combining frame-based l1 analysis with spatiotemporal-dictionary based sparsity (related to l1 synthesis). The results demonstrate improved reconstructions, on simulated and clinical highly-undersampled dynamic images, using the combined approach.
Secretion of thymidine kinase to increase the effectivity of suicide gene therapy results in the loss of enzymatic activity

Low efficiency of gene transfer is one of the major limitations of gene therapy. A solution to this problem may be transmission; by modification of the transgene, the gene product can be secreted and internalized by the surrounding cells. Cancer gene therapy using the herpes simplex thymidine kinase (HSV-TK) suicide gene is a promising treatment, and TK has been used in clinical trials with some success. However, this kind of therapy has limited efficacy due to the low level of gene transfer reached. A modified TK protein, capable of migrating from the producing cell to neighboring cells, would result in a greater proportion of cells affected by the treatment. As a first step towards transmission, we constructed a secretory form of HSV-TK by including the Igκ leader peptide in the gene. An endoplasmatic reticulum export signal was added to the construct to further improve its secretion. Secretion and protein production in cancer cells, the enzymatic activity of the modified proteins and the ability of the modified TK to sensitize cancer cells to ganciclovir were tested. Addition of the Igκ leader resulted in high levels of secretion of HSV-TK, with up to 70% of the total amount of protein secreted. Inclusion of an ER export signal did not further improve secretion. The enzyme activity of the secreted TK however, was decreased when compared to native TK. This study is the first to report on secretion of TK, and provides a first step in a novel strategy to improve the efficiency of cancer gene therapy. The loss of function in secreted TK however, may present a major hurdle in the development of a transmitted form of TK.
Hydroxymethylation of microRNA-365-3p Regulates Nociceptive Behaviors via Kcnh2

DNA 5-hydroxylmethylcytosine (5hmC) catalyzed by ten-eleven translocation methylcytosine dioxygenase (TET) occurs abundantly in neurons of mammals. However, the in vivo causal link between TET dysregulation and nociceptive modulation has not been established. Here, we found that spinal TET1 and TET3 were significantly increased in the model of formalin-induced acute inflammatory pain, which was accompanied with the augment of genome-wide 5hmC content in spinal cord. Knockdown of spinal TET1 or TET3 alleviated the formalin-induced nociceptive behavior and overexpression of spinal TET1 or TET3 in naive mice produced pain-like behavior as evidenced by decreased thermal pain threshold. Furthermore, we found that TET1 or TET3 regulated the nociceptive behavior by targeting microRNA-365-3p (miR-365-3p). Formalin increased 5hmC in the miR-365-3p promoter, which was inhibited by knockdown of TET1 or TET3 and mimicked by overexpression of TET1 or TET3 in naive mice. Nociceptive behavior induced by formalin or overexpression of spinal TET1 or TET3 could be prevented by downregulation of miR-365-3p, and mimicked by overexpression of spinal miR-365-3p. Finally, we demonstrated that a potassium channel, voltage-gated eag-related subfamily H member 2 (Kcnh2), validated as a target of miR-365-3p, played a critical role in nociceptive modulation by spinal TET or miR-365-3p. Together, we concluded that TET-mediated hydroxymethylation of miR-365-3p regulates nociceptive behavior via Kcnh2. SIGNIFICANCE STATEMENT Mounting evidence indicates that epigenetic modifications in the nociceptive pathway contribute to pain processes and analgesia response. Here, we found that the increase of 5hmC content mediated by TET1 or TET3 in miR-365-3p promoter in the spinal cord is involved in nociceptive modulation through targeting a potassium channel, Kcnh2. Our study reveals a new epigenetic mechanism underlying nociceptive information processing, which may be a novel target for development of antinociceptive drugs.
Use of a Genus- and Species-Specific Multiplex PCR for Identification of Enterococci

ABSTRACT The 16S rRNA gene has previously been used to develop genus-specific PCR primers for identification of enterococci. In addition, the superoxide dismutase gene (sodA) has been identified as a potential target for species differentiation of enterococci. In this study, Enterococcus genus-specific primers developed by Deasy et al. (E1/E2) were incorporated with species-specific primers based upon the superoxide dismutase (sodA) gene for development of a multiplex PCR. This assay provides simultaneous genus and species identification of 23 species of enterococci using seven different reaction mixtures. Accuracy of identification of the multiplex PCR was determined by comparisons to standard biochemical testing, the BBL Crystal kit, VITEK, and API Rapid ID 32 Strep. Isolates from swine feces, poultry carcasses, environmental sources, and retail food were evaluated and, overall, results for 90% of the isolates tested by PCR agreed with results obtained using standard biochemical testing and VITEK. Eighty-five percent and 82% of PCR results agreed with results from the API Rapid ID 32 Strep and BBL Crystal tests, respectively. With the exception of concurrence between identification using standard biochemical testing and VITEK (85%) and between BBL Crystal and VITEK (83%), the percent agreement for PCR was higher than or equal to any other pairwise comparison. Multiplex PCR for genus and species determination of enterococci provides an improved, rapid method for identification of this group of bacteria.
Influences on the drinking of heavier drinkers: Interactional realities in seeking to 'change drinking cultures'.

INTRODUCTION AND AIMS 'Changing drinking culture' is a prominent goal in the Australian state of Victoria's current alcohol strategy-seeking a shift so that 'excessive drinking isn't seen as the norm'. As a social activity, there is a strong collective aspect to drinking and associated behaviour: customs within the drinking group and at the level of social worlds of drinking operate both to increase and to control drinking patterns and associated behaviours. The paper considers how risky drinkers and those in social worlds of heavy drinking experience others' expectations about drinking. DESIGN AND METHODS Using Victorian population survey responses (n = 2092 adults who had consumed alcohol in previous year) to identify those in a social world of group drinking, and a subcategory who are also risky drinkers, the paper explores pressures on those in these categories both to drink more and to drink less, whether from family members, from work colleagues, or from friends. RESULTS Those who are both risky and social drinkers are much more likely than other drinkers to report pressures to drink more from friends and workmates, and even from family members, although they more often report pressures from family members to drink less than to drink more. DISCUSSION AND CONCLUSIONS Efforts to change a drinking culture, it is argued, must take account of the collective nature of drinking and of the interplay of influences at interpersonal and subcultural levels if they are to be effective in reducing rates of heavy drinking and alcohol problems. [Room R, Callinan S, Dietze P. Influences on the drinking of heavier drinkers: Interactional realities in seeking to 'change drinking cultures'. Drug Alcohol Rev 2015].
Measurement of “True” Glucose Production Rates in Infancy and Childhood with 6,6-Dideuteroglucose

“New” glucose production has been measured in 54 infants and children for the first time by continuous three-to-four-hour infusion of the safe, nonradioactive tracer 6,6-dideuterogiucose. The use of combined gas chromatography-mass spectrometry with monitoring of selected ions allowed deuterium enrichment in blood glucose to be measured on microliter samples with an error of less than 2 per cent. In the young child, glucose production increased in a slightly curvilinear manner from 1 kg. to 25 kg. body weight, when it reached 140 mg. per minute, almost the adult value of 173 mg. per minute (2.28 ± 0.23 mg./kg. ·min., mean ± S.E.). Normalized for weight, glucose production in premature infants was 5.46 ± 0.31 mg. /kg. ·min., in term neonates averaged 6.07 ± 0.46 mg. /kg. · min., in children below the age of six years was 7.1 ± 0.27 mg. /kg. · min., and in late childhood averaged 5.4 ± 0.28 mg. / kg. · min. Relative to estimated brain weight, however, glucose production was essentially linear from the 1-kg. premature infant to the 80-kg. adult. These data, the first measurements of “new” glucose production in childhood, suggest that brain size may be a principal determinant of those factors that regulate hepatic glucose output throughout life.
The Use of Virtual Reality in the Production of Cue-Specific Craving for Cigarettes: A Meta-Analysis.

INTRODUCTION The cue-reactivity procedure has demonstrated that smokers respond with increases in subjective craving in the presence of smoking-related cues. Virtual reality is an emerging mode of cue presentation for cue-reactivity research. Despite the successful implementation of virtual reality during the last decade, no systematic review has investigated the magnitude of effects across studies. METHODS This research systematically reviewed findings from studies using virtual reality in cigarette craving assessment. Eligible studies assessed subjective craving for cigarettes in smokers exposed to smoking-related and neutral environments. Cohen's d was used to assess differences in craving between smoking-related and nonsmoking-related virtual environments. A random effects approach was used to combine effect sizes. RESULTS A total of 18 studies involving 541 smokers was included in the final analyses. Environments with smoking-related cues produced significant increases in craving relative to environments without smoking-related cues. The mean overall effect size (Cohen's d) was 1.041 (SE = 0.12, 95% CI = 0.81 to 1.28, Z = 8.68, P < .001). CONCLUSIONS The meta-analysis suggested that presentations of smoking cues through virtual reality can produce strong increases in craving among cigarette smokers. This strong cue-reactivity effect, which was comparable in magnitude to the craving effect sizes found with more conventional modes of cue presentation, supports the use of virtual reality for the generation of robust cue-specific craving in cue-reactivity research.
Subarray-Based Coordinated Beamforming Training for mmWave and Sub-THz Communications

Millimeter-wave (mmWave) and sub-Terahertz (THz) communications are compelling as an enabler for next-generation wireless networks. In this paper, we study mmWave and sub-THz systems with array-of-subarray architecture. To accommodate the ultrabroad bandwidth in the mmWave and sub-THz bands, time-delay phase shifters are introduced in system design. Our goal is to investigate beamforming training with hybrid processing to extract the dominant channel information, which would fully exploit channel characteristics while respecting the nature of circuit hardware. In particular, codebooks based on time-delay phase shifters are defined and structured. Then, two multi-resolution time-delay codebooks are designed through subarray coordination. One is built on adaptation of physical beam directions, and the other relies on dynamic approximation of beam patterns. Also, a low-complexity system implementation with modifications on the time-delay codebooks is studied. Furthermore, based on the proposed codebooks, a hierarchical beamforming training strategy with reduced overhead is developed to enable simultaneous training for multiple users. Simulation results show that the proposed multi-resolution time-delay codebooks could provide sufficient beam gains and are robust over large bandwidth. Also, the effectiveness of the hierarchical beamforming training is verified.
Characterization of a secretory proteinase of Candida parapsilosis and evidence for the absence of the enzyme during infection in vitro

The opportunistic yeastlike fungi of the genus Candida comprise three species which are proteolytic in vitro. Among them, C. albicans and C. tropicalis are of foremost medical importance. However, a strict correlation between extracellular proteolytic activity and virulence is opposed by the low virulence of the third proteolytic species, C. parapsilosis. We purified the secretory acid proteinase of C. parapsilosis (clinical isolate 265). The enzyme is a carboxyl proteinase (EC 3.4.23) like all other secretory Candida proteinases handled so far. Proteinase 265 is distinguished by a lower molecular weight (approximately 33,000); it has increased hydrophobicity, which accounts for inhibition of the enzyme by hemin, and required the presence of nonionic detergent in the initial steps of purification. The enzyme already undergoes alkaline denaturation at neutrality. Its activity is thus confined to the acid microenvironment of the fungal cell wall. Within this range, the enzyme may degrade immunoglobulins like immunoglobulin A1 (IgA1), IgA2, and secretory IgA. No indication was found for glycosylation of proteinase 265 and the related enzyme of C. albicans CBS 2730. However, the comparable proteinase of C. tropicalis 293 was identified as a manno protein. Antiserum against proteinase 265 cross-reacted strongly with corresponding enzymes from other Candida species. Antisera against proteinases of C. albicans and C. tropicalis reacted only weakly with proteinase 265. Thus, secretory Candida proteinases are likely to possess common and species-specific antigenic sites. In contrast to C. albicans, infection of phagocytes by C. parapsilosis 265 was not accompanied by secretion of fungal proteinase. This lack of induction of the enzyme under conditions of infection may account for the low virulence of most isolates of C. parapsilosis.
Computation of the Posterior Probability of Linkage Using ‘High Effect’ Genetic Model Priors

Objectives: The posterior probability of linkage, or PPL, directly measures the probability that a disease gene is linked to a marker. By placing a Bayesian prior on the elements of the genetic model, it allows for an unknown genetic model without the inflationary effects of maximization. The standard technique uses essentially uniform priors over the elements of the penetrance vector. However, much of the parameter space corresponds to models that seem unlikely to yield substantial evidence for linkage: for example, models with very high phenocopy rates. Methods: A new class of priors on the elements of the genetic model is examined both theoretically and in simulations. These priors place 0% probability over models with low sibling relative risk, λs. Results: Focusing the prior probability on high λs models does tend to increase the mean PPL for linked markers, and to decrease the mean PPL for unlinked markers. However, the power to detect linkage remains virtually unchanged. Moreover, under these priors, the PPL occasionally yields unacceptably high values under no linkage. Conclusions: It appears important to retain prior probability over apparently ‘uninformative’ genetic models to accurately characterize the amount of evidence for linkage represented by the data.