Miracle-dz/UniFAR-FTUs huggingface dataset:
Repressive Chromatin Affects Factor Binding at Yeast HO (Homothallic Switching) Promoter*

Background: Expression of the yeast HO gene is tightly regulated, with a large complex promoter. Results: The Rpd3(L) histone deacetylase is recruited twice by distinct factors to different promoter regions. Conclusion: Chromatin represses the HO promoter, making multiple coactivators required for gene expression. Significance: Multiple factors contribute to the establishment of a tightly repressed, cell cycle-regulated promoter. The yeast HO gene is tightly regulated, with multiple activators and coactivators needed to overcome repressive chromatin structures that form over this promoter. Coactivator binding is strongly interdependent, as loss of one factor sharply reduces recruitment of other factors. The Rpd3(L) histone deacetylase is recruited to HO at two distinct times during the cell cycle, first by Ash1 to the URS1 region of the promoter and then by SBF/Whi5/Stb1 to URS2. SBF itself is localized to only a subset of its potential binding sites in URS2, and this localization takes longer and is less robust than at other SBF target genes, suggesting that binding to the HO promoter is limited by chromatin structures that dynamically change as the cell cycle progresses. Ash1 only binds at the URS1 region of the promoter, but an ash1 mutation results in markedly increased binding of SBF and Rpd3(L) at URS2, some 450 bp distant from the site of Ash1 binding, suggesting these two regions of the promoter interact. An ash1 mutation also results in increased coactivator recruitment, Swi/Snf and Mediator localization in the absence of the normally required Gcn5 histone acetyltransferase, and HO expression even in the presence of a taf1 mutation affecting TFIID activity that otherwise blocks HO transcription. Ash1 therefore appears to play a central role in generating the strongly repressive environment at the HO promoter, which limits the binding of several coactivators at URS2 and TATA region.
Long aboral projections of Dogiel type II, AH neurons within the myenteric plexus of the guinea pig small intestine

Enteric AH neurons, with multipolar Dogiel type II morphology, project around the circumference of the intestine to myenteric ganglia, the submucosa and mucosa. Using retrograde labeling in vitro, intracellular recording, dye filling and immunohistochemistry, the projections of these neurons along the intestine were studied. When the retrograde tracer, Dil, was applied to the myenteric plexus, labeled nerve cell bodies were located up to 111 mm orally but only 13 mm aborally, demonstrating a marked difference in the lengths of projections up and down the small intestine. Of labeled nerve cell bodies located 2–110 mm orally, 43% had Dogiel type II morphology and of these, 70% were immunoreactive for calbindin, a calcium binding protein exclusive to Dogiel type II neurons. Intracellular filling with neurobiotin revealed several long circumferentially directed nerve fibers and short, filamentous dendrites; thus these were “dendritic” Dogiel type II neurons. This class accounts for approximately 3–4% of all myenteric neurons, and about 10% of all Dogiel type II neurons. Intracellular recordings revealed AH cell characteristics, with long afterhyperpolarizations following their action potentials, pronounced slow excitatory synaptic inputs and a lack of fast excitatory synaptic inputs. Antidromic action potentials could be evoked from the Dil application site in some cells, confirming their aboral projection. This is the first account of a major aboral projection of AH/Dogiel type II neurons and suggests an important role in aborally directed reflexes in the intestine.
A note on group colorings

We study a concept of group coloring introduced by Jaeger et al. We show that the group chromatic number of a graph with minimum degree δ is greater than δ/(2, ln δ) and we answer several open questions on the group chromatic number of planar graphs: a construction of a bipartite planar graph with group chromatic number four and a 3‐colorable planar graph with group chromatic number five are presented. We also observe that several upper bounds on the choice number for various subclasses of planar graphs also translate to the concept of group colorings. © 2005 Wiley Periodicals, Inc. J Graph Theory
Self‐management plans in the primary care of patients with chronic obstructive pulmonary disease

Objective and background: The role of COPD self‐management plans in improving health outcomes remains unclear. The objective of this study was to assess whether self‐management plans administered in primary care have beneficial effects on quality of life, self‐care behaviour and health outcomes in the long term for patients with COPD.
Safety of electroconvulsive therapy in patients receiving long-term warfarin therapy.

OBJECTIVE To investigate the safety of electroconvulsive therapy (ECT) in patients receiving long-term warfarin therapy. PATIENTS AND METHODS Retrospective data were reviewed for 35 consecutively hospitalized patients who received long-term warfarin therapy and ECT at the Mayo Clinic in Rochester, Minn, between January 1, 1994, and December 31, 2001. RESULTS A total of 300 ECT treatments were administered to the 35 patients. Of 284 ECT treatments for which data were available, no ECT-related complications due to anticoagulation occurred despite increases in blood pressure and pulse rate. One patient experienced ventricular tachycardia, resulting in transfer to a cardiology service for temporary monitoring. No other serious ECT-related adverse effects were noted. The rate of intertreatment delirium was similar to that reported in other studies. CONCLUSIONS Electroconvulsive therapy in patients receiving long-term warfarin therapy appears to be safe. Although no major adverse effects were identified in our case series, additional prospective evaluation is warranted.
Use of Dronabinol Improves Appetite and Reverses Weight Loss in HIV/AIDS-Infected Patients

Objective: To determine whether dronabinol affects appetite and weight status in patients living with HIV/AIDS. Methods: A retrospective chart review was conducted to analyze weight and appetite changes and nausea status in patients with HIV/AIDS who received dronabinol for 3 to 12 months from January 11, 1993, to March 17, 2003. Results: Of the 117 patients who lost weight before baseline, 63% maintained or gained weight. In patients receiving dronabinol for 1 year, the mean weight gain (± SD) was 3.7 ± 10.6 lb. The percentage of patients experiencing loss of appetite decreased significantly from 71% at baseline to 26% at 1 month (P < .001) and continued to decline throughout the trial. The percentage of patients experiencing nausea at baseline (38%) decreased consistently from week 2 on; this change from baseline was significant at month 6 (P = .031). Conclusion: When taken for 3 months to 1 year, dronabinol significantly improves appetite and reverses weight loss in patients living with HIV/AIDS.
Heroin Overdose Deaths and Heroin Purity Between 1990 and 2000 in Istanbul, Turkey *

Abstract: Turkey has continuously experienced problems with abuse of, and addiction to, opium derivatives. In this study, we analyzed the relationship between heroin overdose deaths and the characteristics of seized opium derivatives. Data were gathered from the Council of Forensic Medicine of the Ministry of Justice in Istanbul from 1990 to 2000. There were 636 heroin‐related deaths during this period, 595 of which were classified as heroin overdose deaths. Mean crude and weighted heroin purities remained relatively constant and were calculated to be 46% (57–34%) and 51% (39–59%), respectively. The weight of heroin and the number of heroin seizures, but not the heroin purity, were significantly associated with the number of heroin‐related deaths. Prevention strategies are needed to reduce the number of deaths caused by overdoses in countries situated on drug trafficking routes. These strategies should focus on drug trafficking, by providing increased levels of, and support for, law enforcement, stopping the supply of precursor chemicals, and combating corruption among border officials.
Hardware authentication based on PUFs and SHA-3 2nd round candidates

Security features are getting a growing interest in microelectronics. Not only entities have to authenticate in the context of a high secure communication but also the hardware employed has to be trusted. Silicon Physical Unclonable Functions (PUFs) or Physical Random Functions, which exploits manufacturing process variations in integrated circuits, have been used to authenticate the hardware in which they are included and, based on them, several cryptographic protocols have been reported. This paper describes the hardware implementation of a symmetric-key authentication protocol in which a PUF is one of the relevant blocks. The second relevant block is a SHA-3 2nd round candidate, a Secure Hash Algorithm (in particular Keccak), which has been proposed to replace the SHA-2 functions that have been broken no long time ago. Implementation details are discussed in the case of Xilinx FPGAs.
Role of the CM2 Protein in the Influenza C Virus Replication Cycle

ABSTRACT CM2 is the second membrane protein of influenza C virus. Although its biochemical characteristics, coding strategy, and properties as an ion channel have been extensively studied, the role(s) of CM2 in the virus replication cycle remains to be clarified. In order to elucidate this role, in the present study we generated CM2-deficient influenza C virus-like particles (VLPs) and examined the VLP-producing 293T cells, VLPs, and VLP-infected HMV-II cells. Quantification of viral RNA (vRNA) in the VLPs by real-time PCR revealed that the CM2-deficient VLPs contain approximately one-third of the vRNA found in wild-type VLPs although no significant differences were detected in the expression levels of viral components in VLP-producing cells or in the number and morphology of the generated VLPs. This finding suggests that CM2 is involved in the genome packaging process into VLPs. Furthermore, HMV-II cells infected with CM2-deficient VLPs exhibited significantly reduced reporter gene expression. Although CM2-deficient VLPs could be internalized into HMV-II cells as efficiently as wild-type VLPs, a smaller amount of vRNA was detected in the nuclear fraction of CM2-deficient VLP-infected cells than in that of wild-type VLP-infected cells, suggesting that the uncoating process of the CM2-deficient VLPs in the infected cells did not proceed in an appropriate manner. Taken together, the data obtained in the present study indicate that CM2 has a potential role in the genome packaging and uncoating processes of the virus replication cycle.
Evaluation of Two Approaches for Assessing the Genetic Similarity of Virioplankton Populations as Defined by Genome Size

ABSTRACT Viral production estimates show that virioplankton communities turn over rapidly in aquatic ecosystems. Thus, it is likely that the genetic identity of viral populations comprising the virioplankton also change over temporal and spatial scales, reflecting shifts in viral-host interactions. However, there are few approaches that can provide data on the genotypic identity of viral populations at low cost and with the sample throughput necessary to assess dynamic changes in the virioplankton. This study examined two of these approaches—T4-like major capsid protein (g23) gene polymorphism and randomly amplified polymorphic DNA-PCR (RAPD-PCR) fingerprinting—to ask how well each technique could track differences in virioplankton populations over time and geographic location. Seasonal changes in overall virioplankton composition were apparent from pulsed-field gel electrophoresis (PFGE) analysis. T4-like phages containing similar g23 proteins were found within both small- and large-genome populations, including populations from different geographic locations and times. The surprising occurrence of T4-like g23 within small genomic groups (23 to 64 kb) indicated that the genome size range of T4-like phages may be broader than previously believed. In contrast, RAPD-PCR fingerprinting detected high genotypic similarity within PFGE bands from the same location, time, and genome size class without the requirement for DNA sequencing. Unlike g23 polymorphism, RAPD-PCR fingerprints showed a greater temporal than geographic variation. Thus, while polymorphism in a viral signature gene, such as g23, can be a powerful tool for inferring evolutionary relationships, the degree to which this approach can capture fine-scale variability within virioplankton populations is less clear.
Effect of ependymal and pial surfaces on convection-enhanced delivery.

OBJECT Convection-enhanced delivery (CED) is increasingly used to investigate new treatments for central nervous system disorders. Although the properties of CED are well established in normal gray and white matter central nervous system structures, the effects on drug distribution imposed by ependymal and pial surfaces are not precisely defined. To determine the effect of these anatomical boundaries on CED, the authors infused low MW and high MW tracers for MR imaging near ependymal (periventricular) and pial (pericisternal) surfaces. METHODS Five primates underwent CED of Gd-diethylenetriamine pentaacetic acid (Gd-DTPA; MW 590 D) or Gd-bound albumin (Gd-albumin; MW 72,000 D) during serial real-time MR imaging (FLAIR and T1-weighted sequences). Periventricular (caudate) infusions were performed unilaterally in 1 animal (volume of infusion [Vi] 57 microl) and bilaterally in 1 animal with Gd-DTPA (Vi = 40 mul on each side), and bilaterally in 1 animal with Gd-albumin (Vi = 80 microl on each side). Pericisternal infusions were performed in 2 animals with Gd-DTPA (Vi = 190 microl) or with Gd-albumin (Vi = 185 microl) (1 animal each). Clinical effects, MR imaging, and histology were analyzed. RESULTS Large regions of the brain and brainstem were perfused with both tracers. Intraparenchymal distribution was successfully tracked in real time by using T1-weighted MR imaging. During infusion, the volume of distribution (Vd) increased linearly (R2 = 0.98) with periventricular (mean Vd/Vi ratio +/- standard deviation; 4.5 +/- 0.5) and pericisternal (5.2 +/- 0.3) Vi, but did so only until the leading edge of distribution reached the ependymal or pial surfaces, respectively. After the infusate reached either surface, the Vd/Vi decreased significantly (ependyma 2.9 +/- 0.8, pia mater 3.6 +/- 1.0; p < 0.05) and infusate entry into the ventricular or cisternal cerebrospinal fluid (CSF) was identified on FLAIR but not on T1-weighted MR images. CONCLUSIONS Ependymal and pial boundaries are permeable to small and large molecules delivered interstitially by convection. Once infusate reaches these surfaces, a portion enters the adjacent ventricular or cisternal CSF and the tissue Vd/Vi ratio decreases. Although T1-weighted MR imaging is best for tracking intraparenchymal infusate distribution, FLAIR MR imaging is the most sensitive and accurate for detecting entry of Gd-labeled imaging compounds into CSF during CED.
Factors associated with success of telaprevir- and boceprevir-based triple therapy for hepatitis C virus infection

AIM To evaluate new therapies for hepatitis C virus (HCV), data about real-world outcomes are needed. METHODS Outcomes of 223 patients with genotype 1 HCV who started telaprevir- or boceprevir-based triple therapy (May 2011-March 2012) at the Mount Sinai Medical Center were analyzed. Human immunodeficiency virus-positive patients and patients who received a liver transplant were excluded. Factors associated with sustained virological response (SVR24) and relapse were analyzed by univariable and multivariable logistic regression as well as classification and regression trees. Fast virological response (FVR) was defined as undetectable HCV RNA at week-4 (telaprevir) or week-8 (boceprevir). RESULTS The median age was 57 years, 18% were black, 44% had advanced fibrosis/cirrhosis (FIB-4 ≥ 3.25). Only 42% (94/223) of patients achieved SVR24 on an intention-to-treat basis. In a model that included platelets, SVR24 was associated with white race [odds ratio (OR) = 5.92, 95% confidence interval (CI): 2.34-14.96], HCV sub-genotype 1b (OR = 2.81, 95%CI: 1.45-5.44), platelet count (OR = 1.10, per x 104 cells/μL, 95%CI: 1.05-1.16), and IL28B CC genotype (OR = 3.54, 95%CI: 1.19-10.53). Platelet counts > 135 x 103/μL were the strongest predictor of SVR by classification and regression tree. Relapse occurred in 25% (27/104) of patients with an end-of-treatment response and was associated with non-FVR (OR = 4.77, 95%CI: 1.68-13.56), HCV sub-genotype 1a (OR = 5.20; 95%CI: 1.40-18.97), and FIB-4 ≥ 3.25 (OR = 2.77; 95%CI: 1.07-7.22). CONCLUSION The SVR rate was 42% with telaprevir- or boceprevir-based triple therapy in real-world practice. Low platelets and advanced fibrosis were associated with treatment failure and relapse.
Serum IgE levels in liver cirrhosis.

Abstract. Hypergammaglobulinemia is a well‐known feature of liver cirrhosis, but studies on serum IgE in this setting are limited. The present study evaluates serum IgE concentration in a group of cirrhotic patients and examines their relationship with aetiological, clinical and analytical parameters (including liver function tests and hepatic phagocytic activity). The presence of specific IgE against common dietary antigens was also investigated. Total serum IgE was determined by enzyme immunoassay (EIA) in 52 cirrhotics (27 alcoholic and 25 non‐alcoholic, including eight virus B and seven virus C‐related cirrhosis, three primary biliary cirrhosis, three cryptogenic, three haemochromatosis and one Wilson's disease) and 34 healthy subjects (used as controls). Serum IgE (1U/ml) in contols was not significantly different from that of cirrhotic patients (median 42, range 2–726 vs median 86, range 2‐> 1000, respectively) (P=NS). However, serum IgE among alcoholics (median 199, range 19‐ < 1000) was higher than that of controls (P < 0‐001), virus B‐related cirrhotics (median 25, range 3‐< 1000) (P < 0‐05), virus C‐related cirrhotics (median 47, range 2‐170) (P < 0‐05), or nonalcoholic cirrhotics as a whole (median 23, range 2‐< 1000) (P < 0.01). High IgE levels (≥ 170 1U/ml) were detected in 55.5% of alcoholics compared with only 12% of nonalcoholic cirrhotics (P < 0.01). Moreover, IgE levels were very high (> 1000 1U/ml) in six patients of the alcoholic group (22.2%) compared with only one non‐alcoholic patient (4%). Increased serum IgE levels did not seem to be related to either parameters of liver function (serum bilirubin, albumin, prothrombin or Child‐Pugh score), hepatic phagocytic function or other immunoglobulins. Skin‐prick tests failed to demonstrate increased sensitization to eight common dietary antigens in the patients studied. On multivariate analysis, only the alcoholic aetiology of the disease correlated with high serum IgE levels. These data suggest that increased serum IgE might be a common and rather specific feature of chronic alcoholic liver disease.
Relevance of Liver Enzyme Elevations With Four Different Neuroleptics: A Retrospective Review of 7,263 Treatment Courses

Data on liver enzyme elevations were collected in a retrospective study of 7,263 treatment courses with haloperidol, clozapine, perphenazine, and perazine. Charts of 233 patients hospitalized between 1980 and 1992 at Tübingen University Psychiatric Clinic were selected because clinically relevant increases of liver enzymes had been detected during monotherapy with one of the four examined neuroleptics. At least one hepatic enzyme (mostly alanine aminotransferase [ALAT]) exceeded the established reference range of 3-fold elevations of ALAT, aspartate aminotransferase, γ-glutamyl transpeptidase, and glutamate dehydrogenase and 2-fold elevations of alkaline phosphatase (AP) during monotherapy with clozapine in 15%, perazine in 7.6%, perphenazine in 4%, and haloperidol in 2.4% of the cases. If all liver enzyme abnormalities with any elevation greater than the conventional upper limits are considered, incidences were as follows: clozapine, 78%; perphenazine, 62%; perazine, 59%; and haloperidol, 50%. Testing for overall differences within the four neuroleptics resulted in significantly different incidences of liver enzyme elevations (χ2 test, p < 0.0001). Threefold increases of AP (>540 U/L) were seen in three patients receiving haloperidol (0.3%) only. Twofold increases of AP (>360 U/L) were distributed as follows: clozapine, 1%; haloperidol, 0.8%; perazine, 0.3%; and perphenazine, 0.1%. Only in the group with 1-fold elevations of AP (>180 U/L) were the differences within the drug regimens significant (clozapine, 40.3%; haloperidol, 33.2%; perphenazine, 23.4%; and perazine, 23.1%; χ2 test, p < 0.0001). In the period under study, no instance of icterus occurred.
Major cysteine peptidases of Entamoeba histolytica are required for aggregation and digestion of erythrocytes but are dispensable for phagocytosis and cytopathogenicity

Cysteine peptidases of Entamoeba histolytica (EhCPs) are considered to be important pathogenicity factors. It has been described that under standard axenic culture conditions, only three (ehcp‐a1, ehcp‐a2 and ehcp‐a5) out of approximately 50 cysteine peptidase genes present in the E. histolytica genome are substantially expressed, thus representing the set of major EhCPs. In this study, transcriptional silencing of the major peptidase genes was used to characterize their physiological role in more detail. Analysing the transfectants a fourth major cysteine peptidase activity belonging to EhCP‐A7 could be characterized. Neither cytopathic activity nor phagocytosis of erythrocytes was altered in CP‐inactivated amoebae. However, a significant difference in haemolytic activity was observed. EhCP‐A1 and EhCP‐A7 apparently had no influence on haemolytic activity, whereas transfectants silenced for ehcp‐a5 as well as those silenced for all major peptidases showed a significant reduction in their haemolytic activity. Furthermore, cells silenced for ehcp‐a1 and ehcp‐a7 and more effectively cells silenced in all major ehcps were impaired in digesting of phagocytosed erythrocytes. Moreover, amoebae silenced for all major peptidase genes lost the ability to form aggregates of erythrocytes prior to phagocytosis.
Factorial Invariance of the 13-item Sense of Coherence Scale across Gender

This study examined the gender invariance of the 13-item Sense of Coherence (SOC) scale. Confirmatory factor analyses indicated that a single factor model with one pair of correlated errors fit the data well. Invariance testing indicated that the scale is both congeneric and tau equivalent, meaning that a single latent SOC construct holds equally well for males and females, and that both genders demonstrate an equivalent pattern of factor loadings. There was little evidence in support of latent factor mean equivalence across gender. Explanations for the lack of factor mean equivalence were discussed and recommendations for future research were suggested.