Miracle-dz/UniFAR-FTUs huggingface dataset:
Remediation of memory disorders in schizophrenia

Background. Memory deficits are commonly experienced by patients with schizophrenia, often persist even after effective psychotropic treatment of psychotic symptoms and have been demonstrated to interfere with many aspects of successful psychiatric rehabilitation. Because of significant impact on functional outcome, effective remediation of cognitive deficits has been increasingly cited as an essential component of comprehensive treatment. Efforts to remediate memory deficits have met with circumscribed success, leaving uncertain whether schizophrenia patients can be taught, without experimental induction, independently to employ semantic encoding or a range of other mnemonic techniques. Method. We examined the feasibility of using memory and problem solving teaching techniques developed within educational psychology – techniques which promote intrinsic motivation and task engagement through contextualization and personalization of learning activities – to remediate memory deficits in a group of in-patients with chronic schizophrenia spectrum disorders. Results. Although our memory remediation group significantly improved on the memory remediation task, they did not make greater gains on measures of immediate paragraph recall or list learning than the control groups. Conclusions. Targeted remediation of memory appears to yield task specific improvement but the gains do not generalize to other memory tasks. Subjects receiving memory remediation failed to independently activate mnemonic encoding strategies learned and used successfully within training tasks to other general measures of verbal learning and memory.
Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC)

MOTIVATION Pathway Hunter Tool (PHT), is a fast, robust and user-friendly tool to analyse the shortest paths in metabolic pathways. The user can perform shortest path analysis for one or more organisms or can build virtual organisms (networks) using enzymes. Using PHT, the user can also calculate the average shortest path (Jungnickel, 2002 Graphs, Network and Algorithm. Springer-Verlag, Berlin), average alternate path and the top 10 hubs in the metabolic network. The comparative study of metabolic connectivity and observing the cross talk between metabolic pathways among various sequenced genomes is possible. RESULTS A new algorithm for finding the biochemically valid connectivity between metabolites in a metabolic network was developed and implemented. A predefined manual assignment of side metabolites (like ATP, ADP, water, CO(2) etc.) and main metabolites is not necessary as the new concept uses chemical structure information (global and local similarity) between metabolites for identification of the shortest path.
Analyse de la diversité génomique des populations de Cronartium ribicola, agent responsable de la rouille vésiculeuse du pin blanc

The goal of this research was to develop coding genetic markers for the white pine blister rust (WPBR) causal agent, Cronartium ribicola, without bias for populations from eastern or western North America. Eight markers were used to genotype 80 individuals, using the SSCP (Single-Strand Conformation Polymorphism) technique, allowing to study genetic variability within these populations. This study confirmed the presence of a barrier to gene flow between populations located east and west of the Prairies, populations from the Rockies having grouped with western populations. The genetic differentiation between eastern and western populations is highly significant and nucleotide diversity was three times higher in eastern populations. Furthermore, an hybrid between C. ribicola and Cronartium comandrae, causal agent of comandra blister rust, is reported for the first time.
Influence of high ovarian hormones on QT interval duration in young African women

The longer QT interval duration observed in women compared to men is usually attributed to sexual hormones. The aim of our study was to investigate, among black African women, the influence of hormonal variations during the menstrual cycle on the duration of the QT interval. Fourteen young black African women, healthy, sedentary, aged 24 ± 1.7 years, with a regular menstrual cycle (28 ± 1 days) were selected from 59 volunteers. At each phase of their menstrual cycle, menstrual 2.9 ± 0.6 days, follicular 13 ± 1.5 days, and luteal 23.1 ± 1.4 days, an electrocardiogram was performed in supine position after a resting period of 30 min, to measure QT interval duration. QT interval was corrected by Bazett's (QTcb) and Fridericia's (QTcf) formulae. Then, blood samples were obtained to measure estradiol, progesterone, and serum electrolytes (K+, Ca2+, Mg2+). There was no significant difference in uncorrected QT intervals between the three phases of the menstrual cycle. It was the same for QTcb and QTcf. Moreover, during the menstrual cycle, we did not observe any correlation between each QT, QTcb, QTcf, and estradiol levels which raised during the follicular phase (356.61 ± 160.77 pg/mL) and progesterone levels which raised during the luteal phase (16.38 ± 5.88 ng/mL). Finally, the method of Bland and Altman demonstrated that the corrections of QT by Bazett and Fridericia formulae were not interchangeable. The results of this study showed that high levels of estradiol and progesterone in young black African women did not influence the QT, QTcb and QTcf intervals duration during the menstrual cycle.
Enterohemorrhagic Escherichia coli Biofilms Are Inhibited by 7-Hydroxyindole and Stimulated by Isatin

ABSTRACT Since indole is present at up to 500 μM in the stationary phase and is an interspecies biofilm signal (J. Lee, A. Jayaraman, and T. K. Wood, BMC Microbiol. 7:42, 2007), we investigated hydroxyindoles as biofilm signals and found them also to be nontoxic interspecies biofilm signals for enterohemorrhagic Escherichia coli O157:H7 (EHEC), E. coli K-12, and Pseudomonas aeruginosa. The genetic basis of EHEC biofilm formation was also explored, and notably, virulence genes in biofilm cells were repressed compared to those in planktonic cells. In Luria-Bertani medium (LB) on polystyrene with quiescent conditions, 7-hydroxyindole decreased EHEC biofilm formation 27-fold and decreased K-12 biofilm formation 8-fold without affecting the growth of planktonic cells. 5-Hydroxyindole also decreased biofilm formation 11-fold for EHEC and 6-fold for K-12. In contrast, isatin (indole-2,3-dione) increased biofilm formation fourfold for EHEC, while it had no effect for K-12. When continuous-flow chambers were used, confocal microscopy revealed that EHEC biofilm formation was reduced 6-fold by indole and 10-fold by 7-hydroxyindole in LB. Whole-transcriptome analysis revealed that isatin represses indole synthesis by repressing tnaABC 7- to 37-fold in EHEC, and extracellular indole levels were found to be 20-fold lower. Furthermore, isatin repressed the AI-2 transporters lsrABCDFGKR, while significantly inducing the flagellar genes flgABCDEFGHIJK and fliAEFGILMNOPQ (which led to a 50% increase in motility). 7-Hydroxyindole induces the biofilm inhibitor/stress regulator ycfR and represses cysADIJPU/fliC (which led to a 50% reduction in motility) and purBCDEFHKLMNRT. Isogenic mutants showed that 7-hydroxyindole inhibits E. coli biofilm through cysteine metabolism. 7-Hydroxyindole (500 μM) also stimulates P. aeruginosa PAO1 biofilm formation twofold; therefore, hydroxyindoles are interspecies bacterial signals, and 7-hydroxyindole is a potent EHEC biofilm inhibitor.
Quantum dimensions and their non-Archimedean degenerations

We derive explicit dimension formulas for irreducible $M_F$-spherical $K_F$-representations where $K_F$ is the maximal compact subgroup of the general linear group $GL(d,F)$ over a local field $F$ and $M_F$ is a closed subgroup of $K_F$ such that $K_F/M_F$ realizes the Grassmannian of $n$-dimensional $F$-subspaces of $F^d$. We explore the fact that $(K_F,M_F)$ is a Gelfand pair whose associated zonal spherical functions identify with various degenerations of the multivariable little $q$-Jacobi polynomials. As a result, we are led to consider generalized dimensions defined in terms of evaluations and quadratic norms of multivariable little $q$-Jacobi polynomials, which interpolate between the various classical dimensions. The generalized dimensions themselves are shown to have representation theoretic interpretations as the quantum dimensions of irreducible spherical quantum representations associated to quantum complex Grassmannians.
Hyperendemic Campylobacter jejuni in guinea pigs (Cavia porcellus) raised for food in a semi-rural community of Quito, Ecuador.

Domestic animals and animal products are the source of pathogenic Campylobacter jejuni and C. coli in industrialized countries, yet little is known about the transmission of these bacteria in developing countries. Guinea pigs (Cavia porcellus) are commonly raised for food in the Andean region of South America, however, limited research has characterized this rodent as a reservoir of zoonotic enteric pathogens. In this study, we examined the prevalence of Campylobacter spp. in 203 fecal samples from domestic animals of 59 households in a semi-rural parish of Quito, Ecuador. Of the twelve animal species studied, guinea pigs showed the highest prevalence of C. jejuni (n = 39/40; 97.5%). Multilocus sequence typing (MLST) was used to characterize the genetic relationship of C. jejuni from domestic animals and 21 sequence types (STs) were identified. The majority of STs from guinea pigs appeared to form new clonal complexes that were not related to STs of C. jejuni isolated from other animal species and shared only a few alleles with other C. jejuni previously characterized. The study identifies guinea pigs as a major reservoir of C. jejuni and suggests that some C. jejuni strains are adapted to this animal species.
Effects of the transient outward potassium current on action potential upstroke velocities tested using the dynamic clamp technique

The voltage-gated transient outward potassium current (Ito1) plays a prominent role in the early repolarization phase of the cardiac action potential (AP) and thereby contributes to the refractory period and inotropic state of the myocardium. The current is largely responsible for differences in AP repolarization between species, between left and right ventricle, and transmurally, and it is affected by various pathophysiological conditions, such as heart failure. In voltage clamp experiments, Ito1 already activates during depolarization to potentials near −50 to −30 mV, suggesting that Ito1 may be active during the AP upstroke, but whether it modulates the maximal AP upstroke velocity (dV/dtmax) is unknown. In the present study, we addressed this issue using the dynamic clamp configuration of the patch-clamp technique. Experimental data were acquired from HEK-293 cells expressing the fast sodium current that is responsible for the rapid cardiac AP upstroke. The fast component of Ito1 (Ito, f) was computed in real time and injected into the HEK-293 cell during its upstroke. Ito, f density, activation rate, and voltage dependence were varied. We conclude that Ito, f may modulate dV/dtmax and AP overshoot, but only if its activation is fast and its activation threshold is near −50 to −40 mV.
Normobaric hyperoximia increases hypoxia‐induced cerebral injury: DTI study in rats

Perinatal hypoxia affects normal neurological development and can lead to motor, behavioral and cognitive deficits. A common acute treatment for perinatal hypoxia is oxygen resuscitation (hyperoximia), a controversial treatment. Magnetic resonance imaging (MRI), including diffusion tensor imaging (DTI), was performed in a P7 rat model of perinatal hypoxia to determine the effect of hyperoximia. These studies were performed on two groups of animals: 1) animals which were subjected to ischemia followed by hypoxia (HI), and 2) HI followed by hyperoximic treatment (HHI). Lesion volumes on high resolution MRI and DTI derived measures, fractional anisotropy (FA), mean diffusivity (MD), and axial and radial diffusivities (λl and λt, respectively) were measured in vivo one day, one week, and three weeks after injury. Most significant differences in the MRI and DTI measures were found at three weeks after injury. Specifically, three weeks after HHI injury resulted in significantly larger hyperintense lesion volumes (95.26 ± 50.42 mm3) compared to HI (22.25 ± 17.62 mm3). The radial diffusivity λt of the genu of corpus callosum was significantly larger in HHI (681 ± 330 × 10−6 mm2/sec) than in HI (486 ± 96 × 10−6 mm2/sec). Over all, most significant differences in all the DTI metrics (FA, MD, λt, λl) at all time points were found in the corpus callosum. Our results suggest that treatment of perinatal hypoxia with normobaric oxygen does not ameliorate, but exacerbates damage. © 2009 Wiley‐Liss, Inc.
Diagnosis of B-Cell Non-Hodgkin Lymphomas with Small-/Intermediate-Sized Cells in Cytopathology

Fine needle sampling is a fast, safe, and potentially cost-effective method of obtaining tissue for cytomorphologic assessment aimed at both initial triage and, in some cases, complete diagnosis of patients that present clinically with lymphadenopathy. The cytologic diagnosis of B-cell non-Hodgkin lymphomas composed of small-/intermediate-sized cells, however, has been seen as an area of great difficulty even for experienced observers due to the morphologic overlap between lymphoma and reactive lymphadenopathies as well as between the lymphoma entities themselves. Although ancillary testing has improved diagnostic accuracy, the results from these tests must be interpreted within the morphological and clinical context to avoid misinterpretation. Importantly, the recognition of specific cytologic features is crucial in guiding the appropriate selection of ancillary tests which will either confirm or refute a tentative diagnosis. For these reasons, we here review the cytologic characteristics particular to five common B-cell non-Hodgkin lymphomas which typically cause the most diagnostic confusion based on cytological assessment alone: marginal zone lymphoma, follicular lymphoma, mantle cell lymphoma, chronic lymphocytic leukemia/small lymphocytic lymphoma, and lymphoplasmacytic lymphoma. We summarize the most pertinent cytomorphologic features for each entity as well as for reactive lymphoid hyperplasia, contrast them with each other to facilitate their recognition, and highlight common diagnostic pitfalls.
High-Resolution Global Analysis of the Influences of Bas1 and Ino4 Transcription Factors on Meiotic DNA Break Distributions in Saccharomyces cerevisiae

Meiotic recombination initiates with DNA double-strand breaks (DSBs) made by Spo11. In Saccharomyces cerevisiae, many DSBs occur in “hotspots” coinciding with nucleosome-depleted gene promoters. Transcription factors (TFs) stimulate DSB formation in some hotspots, but TF roles are complex and variable between locations. Until now, available data for TF effects on global DSB patterns were of low spatial resolution and confined to a single TF. Here, we examine at high resolution the contributions of two TFs to genome-wide DSB distributions: Bas1, which was known to regulate DSB activity at some loci, and Ino4, for which some binding sites were known to be within strong DSB hotspots. We examined fine-scale DSB distributions in TF mutant strains by deep sequencing oligonucleotides that remain covalently bound to Spo11 as a byproduct of DSB formation, mapped Bas1 and Ino4 binding sites in meiotic cells, evaluated chromatin structure around DSB hotspots, and measured changes in global messenger RNA levels. Our findings show that binding of these TFs has essentially no predictive power for DSB hotspot activity and definitively support the hypothesis that TF control of DSB numbers is context dependent and frequently indirect. TFs often affected the fine-scale distributions of DSBs within hotspots, and when seen, these effects paralleled effects on local chromatin structure. In contrast, changes in DSB frequencies in hotspots did not correlate with quantitative measures of chromatin accessibility, histone H3 lysine 4 trimethylation, or transcript levels. We also ruled out hotspot competition as a major source of indirect TF effects on DSB distributions. Thus, counter to prevailing models, roles of these TFs on DSB hotspot strength cannot be simply explained via chromatin “openness,” histone modification, or compensatory interactions between adjacent hotspots.
‘To test or not to test’, the arguments for and against thrombophilia testing in obstetrics

Clinicians increasingly investigate women for thrombophilias due to their associations with venous thromboembolism and placenta-mediated pregnancy complication. These associations, however, are modest and based largely on retrospective data from studies with heterogeneous classifications and populations, leading to discordance between evidence and guidelines. Current evidence suggests a contributory rather than causative role for thrombophilia in placenta-mediated pregnancy complication and venous thromboembolism. With little evidence of benefit from antithrombotic therapy in placenta-mediated pregnancy complication, thrombophilia screening remains controversial. Given the low absolute risk of placenta-mediated pregnancy complication and gestational venous thromboembolism with heritable thrombophilia, universal screening is inappropriate. Selective screening for antiphospholipid syndrome is supported by robust evidence of benefit. Conversely, selective screening for heritable thrombophilia has not been shown to effectively manage placenta-mediated pregnancy complication. Therefore, at present heritable thrombophilia screening is not warranted for placenta-mediated pregnancy complication. Until we have better evidence from better stratified patient groups, caution should remain if we wish to practice evidence-based medicine.
Results of the APML3 trial incorporating all-trans-retinoic acid and idarubicin in both induction and consolidation as initial therapy for patients with acute promyelocytic leukemia

Background Initial therapy for patients with acute promyelocytic leukemia most often involves the combination of all-trans-retinoic acid with anthracycline-based chemotherapy. The role of non-anthracycline drugs in induction and consolidation is less well-established and varies widely between different cooperative group protocols. Design and Methods In an attempt to minimize relapse and maximize survival for patients with newly diagnosed acute promyelocytic leukemia, the Australasian Leukaemia and Lymphoma Group utilized all-trans-retinoic acid and idarubicin as anti-leukemic therapy for both induction and consolidation. The protocol (known as APML3) was subsequently amended to incorporate maintenance with all-trans-retinoic acid, methotrexate and 6-mercaptopurine. Results Eight (8%) of 101 patients died within 30 days, and 91 (90%) achieved complete remission. With a median estimated potential follow-up of 4.6 years, 4-year overall survival was 84%, and 71% of the patients remained in remission at 4 years. The cumulative incidence of all relapses was 28.1%, with 15 of the 25 relapses initially identified as an isolated molecular relapse. Both FLT3 mutations (internal tandem duplications and codon 835/836 kinase domain mutations) and increased white cell count at diagnosis were associated with inferior overall survival, but in multivariate analyses only FLT3 mutations remained significant (hazard ratio 6.647, P=0.005). Maintenance therapy was significantly associated with improved remission duration (hazard ratio 0.281, P<0.001) and disease-free survival (hazard ratio 0.290, P<0.001). Conclusions The combination of all-trans-retinoic acid and just two cycles of idarubicin followed by triple maintenance produced durable remissions in most patients, but patients with high-risk disease, especially those with FLT3 mutations, require additional agents or alternative treatment approaches. The significant reduction in relapse seen after the addition of maintenance to the protocol supports a role for maintenance in the context of relatively low chemotherapy exposure during consolidation. (actr.org.au identifier: ACTRN12607000410459)
An investigation of the microbial contamination of dental unit air and water lines.

AIM The objective of this study was to measure the microbial contamination released from dental unit air lines (DUAL) and dental unit water lines (DUWL). MATERIALS AND METHODS Emissions from DUAL and DUWL from five dental units supplied by a central water source (tap) and a centralised air supply were sampled three times over a five- week period. Air was forced through sterile water and then plated onto selective agar using apparatus designed to spread the sample solution evenly, and then incubated at room temperature for seven days. Colonies were then counted and the concentration of bacteria present was determined and expressed as colony forming units per millilitre (cfu/ml) per minute. The same procedure was used to evaluate five other dental units, which had attached independent water reservoir (bottle) systems (IWR). Only deionised water was added to the bottles and unit waterlines were cleaned weekly with alkaline peroxide based solution. Values were expressed as cfu/ml. RESULTS Air and water specimens obtained from dental units supplied with tap water had microbial counts significantly (t-test, p < 0.05) greater than IWR dental units. CONCLUSIONS Results indicate that IWR can reduce the numbers of micro-organisms released from DUWL. However, the effectiveness of such systems should be routinely monitored. Emissions from DUAL seems to reflect the levels of microbial contamination present in DUWL.
The Impact of Observational Learning on Physical Activity Appraisal and Exertion Following Experimental Back Injury and the Role of Pain-Related Fear

Chronic low back pain (CLBP) is one of the most prevalent and disabling health conditions in the US and worldwide. Biomedical explanations of acute injury fail to account for why some individuals experience remission of pain and restoration of physical function while others do not. Pain-related fear, accompanied by elevated appraisals of physical exertion and avoidance of physical activity, has emerged as a central psychosocial risk factor for transition from acute injury to chronic pain and disability. Research has indicated that these pain-related factors may be maintained through observational learning mechanisms. To date, no studies have experimentally examined the role of observational learning and pain-related fear in the context of actual musculoskeletal injury. Accordingly, the present study examined the impact of observational learning and pain-related fear on activity appraisals and exertion following experimentally- induced acute low back injury. Healthy participants' appraisal of standardized movement tasks along with measures of physical exertion were collected prior to and following a procedure designed to induce delayed onset muscle soreness (DOMS) to the lower back. Following induction of DOMS, participants observed a video prime depicting CLBP patients exhibiting either high or low pain behavior during similar standardized movements. In line with hypothesized effects, participants assigned to the high pain behavior prime demonstrated greater elevation in pain and harm appraisals as well as greater decrement in physical exertion. Further in line with hypotheses, significant changes in appraisal and physical performance following the high pain behavior prime were only observed among participants endorsing high pain-related fear during baseline assessment. Discussion of findings addresses potential mechanisms of action as well as study limitations and direction for future research.