Effects of phase duration and pulse rate on loudness and pitch percepts in the first auditory midbrain implant patients: Comparison to cochlear implant and auditory brainstem implant results.
The auditory midbrain implant (AMI), which is designed for stimulation of the inferior colliculus (IC), is now in clinical trials. The AMI consists of a single shank array (20 contacts) and uses a stimulation strategy originally designed for cochlear implants since it is already approved for human use and we do not yet know how to optimally activate the auditory midbrain. The goal of this study was to investigate the effects of different pulse rates and phase durations on loudness and pitch percepts because these parameters are required to implement the AMI stimulation strategy. Although each patient was implanted into a different region (i.e. lateral lemniscus, central nucleus of IC, dorsal cortex of IC), they generally exhibited similar threshold versus phase duration, threshold versus pulse rate, and pitch versus pulse rate curves. In particular, stimulation with 100 mus/phase, 250 pulse per second (pps) pulse trains achieved an optimal balance among safety, energy, and current threshold requirements while avoiding rate pitch effects. However, we observed large differences across patients in loudness adaptation to continuous pulse stimulation over long time scales. One patient (implanted in dorsal cortex of IC) even experienced complete loudness decay and elevation of thresholds with daily stimulation. Comparing these results with those of cochlear implant and auditory brainstem implant patients, it appears that stimulation of higher order neurons exhibits less and even no loudness summation for higher rate stimuli and greater current leakage for longer phase durations than that of cochlear neurons. The fact that all midbrain regions we stimulated, which includes three distinctly different nuclei, exhibited similar loudness summation effects (i.e. none for pulse rates above 250 pps) suggests a possible shift in some coding properties that is affected more by which stage along the auditory pathway rather than the types of neurons are being stimulated. However, loudness adaptation occurs at multiple stages from the cochlea up to the midbrain.


A descriptive review and discussion of litigation claims against ambulance services.
Litigation claims against the NHS are increasing. Society is less tolerant of mistakes or inadequate service and litigation claims are now becoming increasingly accepted. All claims registered with the NHS litigation authority, both closed and still open, were collated from all the ambulance trusts across England in the past 10 years. All incidents notified between 19 December 1995 and 19 April 2005 were included. The data were then analysed according to time, description of the incident, cause of the incident and type of damage incurred. Cases were also described according to the total claim. Potential actions and further work are discussed. Between 19 December 1995 and 19 April 2005 there were 272 cases of litigation conducted through the NHS litigation authority against ambulance services across the United Kingdom. The greatest proportion of claims was as a result of lack of assistance or care, which was alleged in 75 cases. Another significant proportion of cases related to a "failure/delay in treatment" or "diagnosis" accounting for 36 and 34 cases, respectively. The most common type of injury was a fatality in 69 cases and unnecessary pain in a further 56 claims. 17 claims were for sums of over pound 1 million; however, most of these cases were still ongoing. These cases are described in more detail; the type of outcome tended to be brain damage or significant spinal injury rather than a fatality, reflecting the higher cost of continuing long-term care of a chronically injured person. This study suggests that the key clinical areas that need to be addressed are obstetric care, spinal injury recognition and the decision not to convey a person to hospital. The first two of these have been addressed in the recent release of the Joint Royal Colleges Ambulance Liaison Committee guidelines. The major areas of organisation relate to reducing delays and providing the safe transfer of patients.


The impact of stroke aphasia on health and well-being and appropriate nursing interventions: an exploration using the Theory of Human Scale Development.
This paper considers the impact of aphasia on health and well-being and provides suggestions for appropriate nursing interventions. Background. Effective communication is essential to holistic care and positive outcomes for individuals affected by aphasia. When verbal communication is absent, nurses fail to adequately use alternative strategies so that the standard of nurse/patient communication is frequently poor. This is a discursive paper which reviews relevant literature and uses the Theory of Human Scale Development as a framework for discussion. The Theory of Human Scale Development is introduced. This theory emphasises that quality of life depends as much upon self-actualisation and relation building as on physical health. The theory is used within the discussion to highlight the significance of communication to quality of life and how its loss has profound psychological and social consequences. Aphasia results in 'loss of self'. The situation is exacerbated by inadequate healthcare communication strategies. Suggestions are offered regarding more appropriate strategies. Efficacy of family input is considered; nursing competence regarding language practice therapies is discussed, and the 'quest approach' is explored. Aphasia has a negative impact on relationships by denying access to support networks, which results in isolation. The individual's predicament is worsened by negative nursing responses. Positive nursing strategies, which alleviate effects of aphasia on individuals' social health, are investigated. Concept analysis and self-awareness exercises as methods of enhancing compassion skills are explored. The social model of disability is discussed to highlight the benefits to individuals of environmental adaptations. The social benefits of aphasia-group affiliation are discussed. The paper concludes by emphasising that fundamental human needs involve social and psychological as well as physical aspects. Nursing interventions must address all needs to provide holistic care in its fullest sense.


Bistability by multiple phosphorylation of regulatory proteins.
The activity of a protein can be reversibly modulated by post-translational, covalent modifications, such as phosphorylation and dephosphorylation. In many cases, the modulated protein may be phosphorylated by the same kinase on many different amino acid residues. Such multisite phosphorylations may occur progressively (during a single binding event of kinase to substrate) or distributively (the kinase dissociates from its substrate after each phosphorylation reaction). If a protein is phosphorylated by a distributive multisite mechanism, then the net activity of a population of these protein molecules can be a highly nonlinear function of the ratio of activities of the kinase and phosphatase enzymes. If the multiply phosphorylated protein is embedded in a positive feedback loop with its kinase and/or phosphatase, then the network may exhibit robust bistable behavior. Using numerical simulations and bifurcation theory, we study the properties of a particular bistable reaction network motivated by the antagonistic relationship between cyclin-dependent kinase and its multiply phosphorylated target, Cdh1, which is involved in the degradation of cyclin molecules. We characterize the bistable switch in terms of (i) the mechanism of distributive phosphorylation (ordered or disordered), (ii) the number of phosphorylation sites on the target protein, (iii) the effect of phosphorylation on the target protein (abrupt or progressive inactivation), and (iv) the effects of stochastic fluctuations in small cells with limited numbers of kinase, phosphatase and target proteins.


Smoking is associated with impaired long-term glucose metabolism in patients with type 1 diabetes mellitus.
Smoking is known to negatively influence glucose metabolism both in healthy subjects and in patients with diabetes. The aim of this study was to compare glycemic control in patients with type 1 diabetes mellitus who were smokers with those who did not smoke during a prospective long-term follow-up. In a single center, 763 patients with type 1 diabetes mellitus were included, 160 (21.0%) of them were smokers. Patients were treated with intensive insulin therapy according to existing guidelines. Glucose control was monitored quarterly, diabetes related complications and cardiovascular risk factors were assessed at least once a year. Glucose control in smokers was significantly worse than in non-smokers at baseline and during follow-up (mean HbA1c during 5047 patient-years of follow-up 7.9 ± 1.3% in smokers and 7.3 ± 1.1% in non-smokers, p < 0.001) despite a higher insulin dosage in smokers (0.71 ± 0.30 U/kg vs. 0.65 ± 0.31 U/kg in non-smokers, p = 0.046). HDL cholesterol was lower in smokers at baseline (1.53 ± 0.45 vs. 1.68 ± 0.51 in non-smokers, p = 0.048). Diabetes related complications tended to occur with a higher frequency in smokers, with a significant difference in macroalbuminuria (9.8% vs. 4.8% in non-smokers, p = 0.047). Smoking is associated with worse glucose control in patients with type 1 diabetes mellitus despite the same treatment strategies as in non-smokers. Hyperglycemia, therefore, may contribute to an earlier incidence of diabetes related complications in these patients, in addition to direct toxic effects of smoking.


Noradrenaline might enhance assertive human social behaviours: an investigation in a flatmate relationship.
The aim of the present study was to explore the role of noradrenaline on the social behaviour of healthy volunteers when they were interacting with a familiar person, their flatmate. Interaction with the flatmate was explored in a cooperative game situation. Ten pairs of same-sex healthy volunteer flatmates aged 18-25 years were recruited for the experiment. All volunteers gave written informed consent and the study was approved by the institutional ethical committee. A randomised, double blind, placebo-controlled crossover trial of reboxetine versus placebo was conducted. In each of the 10 pairs of volunteers, one (subject) volunteered to take the tablets and the other (flatmate) received no treatment. Reboxetine (4 mg/bd) and placebo were administered orally as identical capsules for 2 weeks. The subjects were randomly assigned to receive either reboxetine or placebo first and there was a two-week washout period following the first treatment. At baseline and the end of each treatment, they filled in the Beck Depression Inventory (BDI), Social Adapation Self-Evaluation Scale (SASS), and Aggression Questionnaire (AQ). Then, they were instructed to play the Tangrams game. This task elicits face-valid social behaviours such as cooperation, giving commands and unilateral grasps. Analysis of covariance showed that there was a statistical trend for reboxetine treatment to increase commands (p=0.055). This study presents preliminary evidence that two weeks' enhancement of noradrenaline transmission induced by reboxetine makes healthy volunteers more self-confident and assertive.


P2Y receptors and kidney function.
Cellular release of nucleotides is of physiological importance to regulate and maintain cell function and integrity. Also in the tubular and collecting duct system of the kidney, nucleotides are released in response to changes in cell volume or luminal flow rate and act in a paracrine and autocrine way on basolateral and luminal P2Y receptors. Recent studies using gene knockout mice assigned a prominent role to G protein-coupled P2Y(2) receptors, which are activated by both ATP and UTP. The antidiuretic hormone, arginine-vasopressin (AVP), and possibly an increase in collecting duct cell volume induce ATP release. The subsequent activation of P2Y(2) receptors inhibits AVP-induced cAMP formation and water reabsorption, which stabilizes cell volume and facilitates water excretion. An increase in NaCl intake enhances luminal release of ATP and UTP in the aldosterone-sensitive distal nephron which by activating apical P2Y(2) receptors and phospholipase C lowers the open probability of the epithelial sodium channel ENaC, thereby facilitating sodium excretion. Thus, the renal ATP/UTP/P2Y(2) receptor system not only serves to preserve cell volume and integrity but is also regulated by stimuli that derive from body NaCl homeostasis. The system also inhibits ENaC activity during aldosterone escape, i.e. when sodium reabsorption via ENaC is inappropriately high. The P2Y(2) receptor tone inhibits the expression and activity of the Na-K-2Cl cotransporter NKCC2 in the thick ascending limb and mediates vasodilation. While the role of other P2Y receptors in the kidney is less clear, the ATP/UTP/P2Y(2) receptor system regulates NaCl and water homeostasis and blood pressure.


Theoretical and experimental evaluation of detached endcaps for 3 T birdcage coils.
The use of detached endcaps for 3 T birdcage coils was investigated both theoretically and experimentally. Finite difference time domain analysis, along with workbench and MRI techniques, were used to map the radiofrequency (RF) B(1) distribution along the coil axis with and without an endcap. Without an endcap the measured B(1) value at the service end of the birdcage was only 45% of the value at the coil's center. This was improved to 85% with a detached endcap of maximum achievable diameter (375 mm), positioned 4 mm from the RF shield. The B(1) field distribution on the patient side of the coil was unaffected by the presence of the endcap. The dependence of the B(1) distribution as a function of endcap diameter was also investigated. Surprisingly, simulations and experiments show that there is an optimum ratio of endcap-to-birdcage coil diameter (approximately 1.08) that gives the best B(1) homogeneity. In the human head the optimized endcap, positioned 16 mm from the RF shield, improves the MRI signal amplitude from 55% to 85% of maximum toward the service end. This novel endcap design is easy to implement with existing birdcage coils, and could prove useful when flexibility in access to the RF coil is required.


Gene expression analyses of Arabidopsis chromosome 2 using a genomic DNA amplicon microarray.
The gene predictions and accompanying functional assignments resulting from the sequencing and annotation of a genome represent hypotheses that can be tested and used to develop a more complete understanding of the organism and its biology. In the model plant Arabidopsis thaliana, we developed a novel approach to constructing whole-genome microarrays based on PCR amplification of the 3' ends of each predicted gene from genomic DNA, and constructed an array representing more than 94% of the predicted genes and pseudogenes on chromosome 2. With this array, we examined various tissues and physiological conditions, providing expression-based validation for 84% of the gene predictions and providing clues as to the functions of many predicted genes. Further, by examining the distribution of expression along the physical chromosome, we were able to identify a region of repressed transcription that may represent a previously undescribed heterochromatic region.


The efficacy and safety of memantine for the treatment of Alzheimer's disease.
Currently, five pharmacotherapeutic options are available to treat Alzheimer's disease: memantine; the three cholinesterase inhibitors donepezil, galantamine, and rivastigmine; and combination treatments with memantine and one cholinesterase inhibitor. Selection of the best course of treatment is based upon the evidence gathered by systematic reviews and meta-analyses of randomized controlled trials. Areas covered: This article provides a risk-benefit analysis of these treatments using evidence from meta-analyses on their safety and their efficacy. Expert opinion: Memantine improves cognitive functions and behavioral disturbances more efficiently than the placebo, both as monotherapy and in combination with donepezil. Although memantine monotherapy and combination therapy are associated with a few individual adverse events such as somnolence, it is well-tolerated and its safety (all-cause discontinuation) is comparable or superior to that of the placebo (agitation). Pooled cholinesterase inhibitors are superior to the placebo in the improvement of cognitive functions, but not behavioral disturbances and they are not well-tolerated, as evaluated by the high discontinuation rate. Donepezil (10 mg/day) and oral rivastigmine and galantamine monotherapies carry the risk for some adverse events including gastrointestinal symptoms. Therefore, we consider that combined treatment with memantine and donepezil is the most useful treatment for Alzheimer's disease.


Tlx3 promotes glutamatergic neuronal subtype specification through direct interactions with the chromatin modifier CBP.
Nervous system development relies on the generation of precise numbers of excitatory and inhibitory neurons. The homeodomain transcription factor, T-cell leukemia 3 (Tlx3), functions as the master neuronal fate regulator by instructively promoting the specification of glutamatergic excitatory neurons and suppressing the specification of gamma-aminobutyric acid (GABAergic) neurons. However, how Tlx3 promotes glutamatergic neuronal subtype specification is poorly understood. In this study, we found that Tlx3 directly interacts with the epigenetic co-activator cyclic adenosine monophosphate (cAMP)-response element-binding protein (CREB)-binding protein (CBP) and that the Tlx3 homeodomain is essential for this interaction. The interaction between Tlx3 and CBP was enhanced by the three amino acid loop extension (TALE)-class homeodomain transcription factor, pre-B-cell leukemia transcription factor 3 (Pbx3). Using mouse embryonic stem (ES) cells stably expressing Tlx3, we found that the interaction between Tlx3 and CBP became detectable only after these Tlx3-expressing ES cells were committed to a neural lineage, which coincided with increased Pbx3 expression during neural differentiation from ES cells. Forced expression of mutated Tlx3 lacking the homeodomain in ES cells undergoing neural differentiation resulted in significantly reduced expression of glutamatergic neuronal subtype markers, but had little effect on the expression on pan neural markers. Collectively, our results strongly suggest that functional interplay between Tlx3 and CBP plays a critical role in neuronal subtype specification, providing novel insights into the epigenetic regulatory mechanism that modulates the transcriptional efficacy of a selective set of neuronal subtype-specific genes during differentiation.


Which patients with microscopic disease and rhabdomyosarcoma experience relapse after therapy? A report from the soft tissue sarcoma committee of the children's oncology group.
To identify which patients with rhabdomyosarcoma and microscopic residual disease (group II) are likely to not respond to therapy. Six hundred ninety-five patients with group II tumors received chemotherapy and 90% received radiation therapy on Intergroup Rhabdomyosarcoma Study (IRS)-I to IRS-IV (1972 to 1997). Tumors were subgrouped depending on the presence of microscopic residual disease only (subgroup IIa), resected positive regional lymph nodes, (subgroup IIb), or microscopic residual disease and resected positive regional lymph nodes (subgroup IIc). Overall, the 5-year failure-free survival rate (FFSR) was 73%, and patients with embryonal rhabdomyosarcoma treated on IRS-IV fared especially well (5-year FFSR, 93%; n = 90). Five-year FFSRs differed significantly by subgroup (IIa, 75% and n = 506; IIb, 74% and n = 101; IIc, 58% and n = 88; P = .0037) and treatment (IRS-I, 68%; IRS-II, 67%; IRS-III, 75%; IRS-IV, 87%; P < .001). Multivariate analysis revealed positive associations between primary site (favorable), histology (embryonal), subgroup IIa or IIb, treatment (IRS-III/IV), and better FFSRs. Patterns of treatment failure revealed local failure to be 8%, regional failure, 4%, and distant failure, 14%. The relapse pattern noted over the course of IRS-I to IRS-IV shows a decrease in the systemic relapse rates, particularly for patients with embryonal histology, suggesting that improvement in FFSRs is primarily a result of improved chemotherapy. Group II rhabdomyosarcoma has an excellent prognosis with contemporary therapy as used in IRS-III/IV, and those less likely to respond can be identified using prognostic factors: histology, subgroup, and primary site. Patients with embryonal rhabdomyosarcoma are generally cured, although patients with alveolar rhabdomyosarcoma or undifferentiated sarcoma, particularly subgroup IIc at unfavorable sites, continue to need better therapy.


Prevalence of Helicobacter pylori in patients with primary hyperparathyroidism.
Dyspeptic symptoms are common in patients with primary hyperparathyroidism (PHPT) and have been attributed to hypercalcemia; however, they may also become permanent after parathyroid surgery. We aimed to evaluate the prevalence of Helicobacter pylori in patients with PHPT and to see whether there is a relationship between dyspeptic complaints and H. pylori infection. Of 21 patients with PHPT, 18 patients had dyspeptic complaints. These 18 female patients with PHPT and dyspeptic symptoms were the study population, and 20 female volunteers with dyspeptic symptoms were the controls. An endoscopic examination was performed in all controls and in patients before parathyroid surgery. H. pylori was assessed by serological and histological evaluation. H. pylori was identified upon histological evaluation in 17 patients (94.4%) and serologically in 17 patients (94.4%). Active macroscopic and microscopic gastritis were found in 15 (83.3%) and in 17 (94.4%) of the patients, respectively. In the control group, H. pylori was identified histologically in 13 subjects (65%) and serologically in 17 subjects (85%). The prevalence of H. pylori assessed by histological examination was significantly (P < 0.05) different between patients and controls. There was a significant association between H. pylori infection identified by histology and/or serology and the presence of microscopic (r = 1; P < 0.001), as well as macroscopic (r = 0.54; P < 0.05), gastritis. In conclusion, this study showed that H. pylori infection was found frequently (85.7%) in patients with PHPT. In the management of PHPT with or without surgery, patients, especially those with dyspeptic symptoms, should be evaluated for H. pylori infection, which can be effectively eradicated by appropriate therapy.


Next-Generation Sequencing of Pulmonary Sarcomatoid Carcinoma Reveals High Frequency of Actionable MET Gene Mutations.
To further understand the molecular pathogenesis of pulmonary sarcomatoid carcinoma (PSC) and develop new therapeutic strategies in this treatment-refractory disease. Whole-exome sequencing in a discovery set (n = 10) as well as targeted MET mutation screening in an independent validation set (n = 26) of PSC were performed. Reverse transcriptase polymerase chain reaction and Western blotting were performed to validate MET exon 14 skipping. Functional studies for validation of the oncogenic roles of MET exon 14 skipping were conducted in lung adenosquamous cell line H596 (MET exon 14 skipped and PIK3CA mutated) and gastric adenocarcinoma cell line Hs746T (MET exon 14 skipped). Response to MET inhibitor therapy with crizotinib in a patient with advanced PSC and MET exon 14 skipping was evaluated to assess clinical translatability. In addition to confirming mutations in known cancer-associated genes (TP53, KRAS, PIK3CA, MET, NOTCH, STK11, and RB1), several novel mutations in additional genes, including RASA1, CDH4, CDH7, LAMB4, SCAF1, and LMTK2, were identified and validated. MET mutations leading to exon 14 skipping were identified in eight (22%) of 36 patient cases; one of these tumors also harbored a concurrent PIK3CA mutation. Short interfering RNA silencing of MET and MET inhibition with crizotinib showed marked effects on cell viability and decrease in downstream AKT and mitogen-activated protein kinase activation in Hs746T and H596 cells. Concurrent PIK3CA mutation required addition of a second agent for successful pathway suppression and cell viability effect. Dramatic response to crizotinib was noted in a patient with advanced chemotherapy-refractory PSC carrying a MET exon 14 skipping mutation. Mutational events of MET leading to exon 14 skipping are frequent and potentially targetable events in PSC.


The Impact of Peer Educators or Community Health Workers on the Progress of the UNAIDS 90-90-90 Targets in Africa: A Systematic Review and Meta-Analysis Protocol.
Africa is far behind from achieving the Joint United Nations Program on HIV and AIDS (UNAIDS) 90-90-90 targets. Evidence shows that the participation of HIV patients as peer educators and other community health workers is substantially improving the entire HIV care continuum and subsequently the UNAIDS targets. This review aims to provide the best available evidence on the impact of peer educators and/or community health workers for the three targets in Africa. We will include cohort and experimental studies published in English between 2003 and 2020. Studies which reported interventions for HIV diagnosis, initiation of ART, or virological suppression will be included for review. Three steps searching will be conducted: (i) initial search across Google Scholar, (ii) full search strategy across five databases: MEDLINE, PubMed, CINAHL, SCOPUS and Web of Science, and (iii) screening titles and abstracts. Data will be extracted using standardized instruments from the Joanna Briggs Institute Meta-Analysis of Statistics Assessment and Review Instrument (JBI-MAStARI) and analyzed through narrative synthesis, and meta-analyses and regression. Heterogeneity among quantitative studies will be assessed using Cochran Q test and Higgins I2. Ethics: A formal ethical approval will not be required as primary data will not be collected.


Cell-cycle checkpoints that ensure coordination between nuclear and cytoplasmic events in Saccharomyces cerevisiae.
Cytoskeletal organization is crucial for several aspects of cell-cycle progression but cytoskeletal elements are quite sensitive to environmental perturbations. Two novel checkpoint controls monitor the function of the actin and microtubule systems in budding yeast and operate to delay cell-cycle progression in response to cytoskeletal perturbations. In cells whose actin cytoskeleton has been perturbed, bud formation is frequently delayed and the morphogenesis checkpoint introduces a compensatory delay of nuclear division until a bud has been formed. In cells whose microtubule cytoskeleton has been perturbed, anaphase spindle elongation often occurs entirely within the mother cell, and the post-anaphase nuclear migration checkpoint introduces a compensatory delay of cytokinesis until one pole of the anaphase nucleus enters the bud. Recent studies indicate that regulators of entry into mitosis are localized to the daughter side of the mother-bud neck whereas regulators of exit from mitosis are localized to the spindle pole bodies. Thus, specific cell-cycle regulators are well-placed to monitor whether a cell has formed a bud and whether a daughter nucleus has been delivered accurately to the bud following mitosis.


[Anisakiasis in fresh fish sold in the north of Córdoba].
Anisakiasis is a parasitic zoonosis caused by live larvae of the Anisakidae Family found located in the body cavities and in the muscular systems of osseous fish and cephalopod mollusks. Humons inadvertently ingest these larvae when eating raw or undercooked infested fish. Symptoms are characterized by gastrointestinal disorders. The purpose of this study is that of ascertaining the frequency of anisakid larvae parasite infestation in fresh fish marketed in northern section of the province of Cordoba. Over a nine-month period, samples were taken of the species of sen fish sold to the greatest degree at all of the establishments in this sector. The parasite analysis was conducted at the Peñarroya Public Health Laboratory by the dissection method. A total of 1,261 samples of 18 different species were analyzed. The total frequency of parasite infestation was 15.8%. The species in which the most parasites were found was the blue whiting (Micromesistius poutassou) showing a 42% parasite infestation rate, and Anisakidos larvae were also found in: hake (Merlucius merlucius) (27.5%), whiting (Merlucius sp.) (26%), mackerel (Scomber scombrus), greater forkbeard (Phycis blennoides) (6.2%), anchovy (Engraulis encrasicolus) (5.6%) and pouting (Trisopterus luscus) (5.5%) of the samples in which parasites were found. The monthly spread of the results reveals an increase in parasite infestation during the spring months, declining progressively up to the last months of the year. There is a significant degree of Anisakidos infestation in the species marketed in the northern section of the province of Cordoba. Nevertheless, the difficulty of detecting this parasite, the vague assessment of the degree of parasite infestation tolerable or unacceptable as set forth under regulations, the fact that some traditional dishes made from raw fish require fresh or refrigerated products and, lastly, the lack or complete lack of health education on the part of the population make it advisable for this emerging problem to be approached with greater rigor.


CONFIGURE: A pipeline for identifying context specific regulatory modules from gene expression data and its application to breast cancer.
Gene expression data is widely used for identifying subtypes of diseases such as cancer. Differentially expressed gene analysis and gene set enrichment analysis are widely used for identifying biological mechanisms at the gene level and gene set level, respectively. However, the results of differentially expressed gene analysis are difficult to interpret and gene set enrichment analysis does not consider the interactions among genes in a gene set. We present CONFIGURE, a pipeline that identifies context specific regulatory modules from gene expression data. First, CONFIGURE takes gene expression data and context label information as inputs and constructs regulatory modules. Then, CONFIGURE makes a regulatory module enrichment score (RMES) matrix of enrichment scores of the regulatory modules on samples using the single-sample GSEA method. CONFIGURE calculates the importance scores of the regulatory modules on each context to rank the regulatory modules. We evaluated CONFIGURE on the Cancer Genome Atlas (TCGA) breast cancer RNA-seq dataset to determine whether it can produce biologically meaningful regulatory modules for breast cancer subtypes. We first evaluated whether RMESs are useful for differentiating breast cancer subtypes using a multi-class classifier and one-vs-rest binary SVM classifiers. The multi-class and one-vs-rest binary classifiers were trained using the RMESs as features and outperformed baseline classifiers. Furthermore, we conducted literature surveys on the basal-like type specific regulatory modules obtained by CONFIGURE and showed that highly ranked modules were associated with the phenotypes of basal-like type breast cancers. We showed that enrichment scores of regulatory modules are useful for differentiating breast cancer subtypes and validated the basal-like type specific regulatory modules by literature surveys. In doing so, we found regulatory module candidates that have not been reported in previous literature. This demonstrates that CONFIGURE can be used to predict novel regulatory markers which can be validated by downstream wet lab experiments. We validated CONFIGURE on the breast cancer RNA-seq dataset in this work but CONFIGURE can be applied to any gene expression dataset containing context information.


Generation of mouse induced pluripotent stem cells without viral vectors.
Induced pluripotent stem (iPS) cells have been generated from mouse and human somatic cells by introducing Oct3/4 and Sox2 with either Klf4 and c-Myc or Nanog and Lin28 using retroviruses or lentiviruses. Patient-specific iPS cells could be useful in drug discovery and regenerative medicine. However, viral integration into the host genome increases the risk of tumorigenicity. Here, we report the generation of mouse iPS cells without viral vectors. Repeated transfection of two expression plasmids, one containing the complementary DNAs (cDNAs) of Oct3/4, Sox2, and Klf4 and the other containing the c-Myc cDNA, into mouse embryonic fibroblasts resulted in iPS cells without evidence of plasmid integration, which produced teratomas when transplanted into mice and contributed to adult chimeras. The production of virus-free iPS cells, albeit from embryonic fibroblasts, addresses a critical safety concern for potential use of iPS cells in regenerative medicine.


The Sustainability Cycle and Loop: models for a more unified understanding of sustainability.
In spite of the considerable research on sustainability, reports suggest that we are barely any closer to a more sustainable society. As such, there is an urgent need to improve the effectiveness of human efforts towards sustainability. A clearer and more unified understanding of sustainability among different people and sectors could help to facilitate this. This paper presents the results of an inductive literature investigation, aiming to develop models to explain the nature of sustainability in the Earth system, and how humans can effectively strive for it. The major contributions are two general and complementary models, that may be applied in any context to provide a common basis for understanding sustainability: the Sustainability Cycle (S-Cycle), and the Sustainability Loop (S-Loop). Literature spanning multiple sectors is examined from the perspective of three concepts, emerging as significant in relation to our aim. Systems are shown to provide the context for human action towards sustainability, and the nature of the Earth system and its sub-systems is explored. Activities are outlined as a fundamental target that humans need to sustain, since they produce the entities both needed and desired by society. The basic behaviour of activities operating in the Earth system is outlined. Finally, knowledge is positioned as the driver of human action towards sustainability, and the key components of knowledge involved are examined. The S-Cycle and S-Loop models are developed via a process of induction from the reviewed literature. The S-Cycle describes the operation of activities in a system from the perspective of sustainability. The sustainability of activities in a system depends upon the availability of resources, and the availability of resources depends upon the rate that activities consume and produce them. Humans may intervene in these dynamics via an iterative process of interpretation and action, described in the S-Loop model. The models are briefly applied to a system described in the literature. It is shown that the S-Loop may be used to guide efforts towards sustainability in a particular system of interest, by prescribing the basic activities involved. The S-Cycle may be applied complementary to the S-Loop, to support the interpretation of activity behaviour described in the latter. Given their general nature, the models provide the basis for a more unified understanding of sustainability. It is hoped that their use may go some way towards improving the effectiveness of human action towards sustainability.


Complementary and alternative medicine for the treatment of major depressive disorder.
To review the clinical evidence supporting complementary and alternative medicine interventions for treating major depressive disorder. PubMed was searched from January 1966 to February 2010 using the term depressive disorder in combination with St John's wort, S-adenosylmethionine (SAM-e), exercise, acupuncture, omega-3 fatty acids, and folate. Only relevant human trials were selected. In a large meta-analysis, St John's wort was found to be equivalent to antidepressant drugs with fewer side effects. Exercise reduced depressive scores in 3 meta-analyses. Omega-3 fatty acids reduced depressive scores in a meta-analysis of 16 trials, but publication bias was identified. Oral SAM-e monotherapy reduced depressive scores in 4 of 5 small randomized controlled trials. Folate deficiency is associated with more severe and refractory depression, and supplementation reduced depressive scores in 2 of 3 randomized controlled trials. Acupuncture demonstrated limited efficacy in 1 meta-analysis and 5 other trials. St John's wort and regular exercise appear effective in the treatment of depression. Acupuncture appears ineffective for depression, but it might offer other health benefits. Other promising therapies include SAM-e, omega-3 fatty acid, and folic acid supplementation in selected patients; further study is warranted.


ScrFI restriction-modification system of Lactococcus lactis subsp. cremoris UC503: cloning and characterization of two ScrFI methylase genes.
Two genes from the total genomic DNA of dairy starter culture Lactococcus lactis subsp. cremoris UC503, encoding ScrFI modification enzymes, have been cloned and expressed in Escherichia coli. No homology between the two methylase genes was detected, and inverse polymerase chain reaction of flanking chromosomal DNA indicated that both were linked on the Lactococcus genome. Neither clone encoded the cognate endonuclease. The DNA sequence of one of the methylase genes (encoded by pCI931M) was determined and consisted of an open reading frame 1,170 bp long, which could encode a protein of 389 amino acids (M(r), 44.5). The amino acid sequence contained the highly characteristic motifs of an m5C methylase. Extensive regions of homology were observed with the methylases of NlaX, EcoRII, and Dcm.


The knowledge-learning-instruction framework: bridging the science-practice chasm to enhance robust student learning.
Despite the accumulation of substantial cognitive science research relevant to education, there remains confusion and controversy in the application of research to educational practice. In support of a more systematic approach, we describe the Knowledge-Learning-Instruction (KLI) framework. KLI promotes the emergence of instructional principles of high potential for generality, while explicitly identifying constraints of and opportunities for detailed analysis of the knowledge students may acquire in courses. Drawing on research across domains of science, math, and language learning, we illustrate the analyses of knowledge, learning, and instructional events that the KLI framework affords. We present a set of three coordinated taxonomies of knowledge, learning, and instruction. For example, we identify three broad classes of learning events (LEs): (a) memory and fluency processes, (b) induction and refinement processes, and (c) understanding and sense-making processes, and we show how these can lead to different knowledge changes and constraints on optimal instructional choices.


Involvement of Rb family proteins, focal adhesion proteins and protein synthesis in senescent morphogenesis induced by hydrogen peroxide.
Early passage human diploid fibroblasts develop senescent morphology prematurely within a week after a 2-hour pulse treatment with low or mild dose H(2)O(2). We test here the role of cell cycle checkpoints, cytoskeletal proteins and de novo protein synthesis in senescent morphogenesis following H(2)O(2) treatment. H(2)O(2) treatment causes transient elevation of p53 protein and prolonged inhibition of Rb hyperphosphorylation. Expression of human papillomaviral E6 gene prevented elevation of p53 but did not affect senescent morphogenesis. Expression of human papillomaviral E7 gene reduced the level of Rb protein and prevented induction of senescent morphology by H(2)O(2). The mutants of the E7 gene, in which the Rb family protein binding site was destroyed, could not reduce Rb protein or prevent H(2)O(2) from inducing senescent morphology. Senescent-like cells showed enhanced actin stress fibers. In untreated cells, vinculin and paxillin preferentially distributed along the edge of the cells. In contrast, vinculin and paxillin distributed randomly and sporadically throughout senescent-like cells. E7 expression prevented enhancement of actin filament formation and redistribution of vinculin or paxillin. Neither wild-type nor E7 cells showed changes in the protein level of actin, vinculin or paxillin measured by western blot after H(2)O(2) treatment. Finally, depletion of methionine in the culture medium after H(2)O(2) treatment prevented senescent morphogenesis without affecting dephosphorylation of Rb protein. Our results suggest that senescent morphology likely develops by a program involving activated Rb family proteins, enhancement of actin stress fibers, redistribution of focal adhesion proteins and de novo protein synthesis.


The prognostic significance of IDH1 mutations in younger adult patients with acute myeloid leukemia is dependent on FLT3/ITD status.
Mutations in the isocitrate dehydrogenase gene (IDH1) were recently described in patients with acute myeloid leukemia (AML). To investigate their prognostic significance we determined IDH1 status in 1333 young adult patients, excluding acute promyelocytic leukemia, treated in the United Kingdom MRC AML10 and 12 trials. A mutation was detected in 107 patients (8%). Most IDH1(+) patients (91%) had intermediate-risk cytogenetics. Mutations correlated significantly with an NPM1 mutation (P < .0001) but not a FLT3/ITD (P = .9). No difference in outcome between IDH1(+) and IDH1(-) patients was found in univariate or multivariate analysis, or if the results were stratified by NPM1 mutation status. However, when stratified by FLT3/ITD status, an IDH1 mutation was an independent adverse factor for relapse in FLT3/ITD(-) patients (P = .008) and a favorable factor in FLT3/ITD(+) patients (P = .02). These results suggest that metabolic changes induced by an IDH1 mutation may influence chemoresistance in a manner that is context-dependent.


Radio-frequency exposure of the yellow fever mosquito (A. aegypti) from 2 to 240 GHz.
Fifth generation networks (5G) will be associated with a partial shift to higher carrier frequencies, including wavelengths comparable in size to insects. This may lead to higher absorption of radio frequency (RF) electromagnetic fields (EMF) by insects and could cause dielectric heating. The yellow fever mosquito (Aedes aegypti), a vector for diseases such as yellow and dengue fever, favors warm climates. Being exposed to higher frequency RF EMFs causing possible dielectric heating, could have an influence on behavior, physiology and morphology, and could be a possible factor for introduction of the species in regions where the yellow fever mosquito normally does not appear. In this study, the influence of far field RF exposure on A. aegypti was examined between 2 and 240 GHz. Using Finite Difference Time Domain (FDTD) simulations, the distribution of the electric field in and around the insect and the absorbed RF power were found for six different mosquito models (three male, three female). The 3D models were created from micro-CT scans of real mosquitoes. The dielectric properties used in the simulation were measured from a mixture of homogenized A. aegypti. For a given incident RF power, the absorption increases with increasing frequency between 2 and 90 GHz with a maximum between 90 and 240 GHz. The absorption was maximal in the region where the wavelength matches the size of the mosquito. For a same incident field strength, the power absorption by the mosquito is 16 times higher at 60 GHz than at 6 GHz. The higher absorption of RF power by future technologies can result in dielectric heating and potentially influence the biology of this mosquito.


Characteristics of septic arthritis in human immunodeficiency virus-infected haemophiliacs versus other risk groups.
The cases are presented of four haemophiliacs infected with human immunodeficiency virus (HIV) and with septic arthritis among the 340 patients followed at our centre. The data of these cases and 39 additional HIV-infected haemophiliacs with septic arthritis, identified in a literature search, are reviewed. The spectrum of bacterial pathogens is limited and somewhat different from that in other risk groups. The localization is exclusively to joints affected by haemophilic arthropathy. The laboratory picture is characterized by the absence of peripheral leucocytosis, varying CD4-helper cell counts, a high erythrocyte sedimentation rate and fever. The clinical picture mimics that of haemarthrosis, often causing a delay in diagnosis. Treatment with systemic antibiotics is often sufficient, obviating the need for arthrotomy and open drainage. Prognosis related to the joint function is relatively good, but poor when related to the medium- to long-term survival of the patient.


Use of middle cerebral velocity and blood pressure for the analysis of cerebral autoregulation at various frequencies: the coherence index.
A common component in many protocols for the evaluation of cerebral autoregulation is the comparison of transcranial Doppler ultrasound (TCD) velocities with blood pressure recordings, in which correlations between these two signals correspond to impaired autoregulation. With long data sets and complicated paradigms, however, visual inspection alone cannot adequately distinguish random coincidence from consistent correlation in a statistically valid fashion. We suggest and illustrate the use of the coherence index for this purpose. To illustrate this technique, long-term recordings of TCD velocity and blood pressure were obtained from 6 normal subjects and using 23 data segments from 8 patients following subarachnoid hemorrhage. Each signal was first normalized to its mean, and coherence calculated by dividing the data into overlapping subintervals and computing an average. Coherence was specifically examined over time periods of 30 sec. Coherence calculations identified correlations between signals for which interpretation by visual inspection was unclear, and obvious correlations could be quantified. In 4 of the 6 normal subjects, the coherence was less than 0.60 but slightly greater than 0. Five of the 8 patients showed segments with coherence of greater than 0.60. The coherence index provides a quantitative tool for the evaluation of comparisons between two complex signals. As this task becomes more common in the evaluation of cerebral autoregulation, algorithms of this sort will become increasingly necessary.


Direct bonding and beyond.
We present a number of recent evaluations of direct bonding, a glueless bonding technology, performed under ambient conditions. If combined with bond-strengthening, this geometry-conserving technology is well suited for an application in far ultraviolet immersion lithography. Our term beyond direct bonding refers to taking at least one additional technological step beyond direct bonding, involving chemical interface engineering, advanced silicon-on-insulator (SOI) technology, whereby the unwanted influence of dilatation mismatch is obviated. The combination of successive direct bonding, nanopillar lattice structures and silicon-technological engineering makes it possible for us to arrange quantum dots, wires, and planes in a transversal cascade. We also address the interrelationship between direct bonding and elasticity, as well as plasticity; the latter is in relation to direct bonded glass wafers that are thermally treated to create the geometric shape, e.g., required for specific lab-on-a-chip components with a three-dimensional overall configuration.


Status of care for end stage kidney disease in countries and regions worldwide: international cross sectional survey.
To determine the global capacity (availability, accessibility, quality, and affordability) to deliver kidney replacement therapy (dialysis and transplantation) and conservative kidney management. International cross sectional survey. International Society of Nephrology (ISN) survey of 182 countries from July to September 2018. Key stakeholders identified by ISN's national and regional leaders. Markers of national capacity to deliver core components of kidney replacement therapy and conservative kidney management. Responses were received from 160 (87.9%) of 182 countries, comprising 97.8% (7338.5 million of 7501.3 million) of the world's population. A wide variation was found in capacity and structures for kidney replacement therapy and conservative kidney management-namely, funding mechanisms, health workforce, service delivery, and available technologies. Information on the prevalence of treated end stage kidney disease was available in 91 (42%) of 218 countries worldwide. Estimates varied more than 800-fold from 4 to 3392 per million population. Rwanda was the only low income country to report data on the prevalence of treated disease; 5 (<10%) of 53 African countries reported these data. Of 159 countries, 102 (64%) provided public funding for kidney replacement therapy. Sixty eight (43%) of 159 countries charged no fees at the point of care delivery and 34 (21%) made some charge. Haemodialysis was reported as available in 156 (100%) of 156 countries, peritoneal dialysis in 119 (76%) of 156 countries, and kidney transplantation in 114 (74%) of 155 countries. Dialysis and kidney transplantation were available to more than 50% of patients in only 108 (70%) and 45 (29%) of 154 countries that offered these services, respectively. Conservative kidney management was available in 124 (81%) of 154 countries. Worldwide, the median number of nephrologists was 9.96 per million population, which varied with income level. These comprehensive data show the capacity of countries (including low income countries) to provide optimal care for patients with end stage kidney disease. They demonstrate substantial variability in the burden of such disease and capacity for kidney replacement therapy and conservative kidney management, which have implications for policy.


High density molecular linkage maps of the tomato and potato genomes.
High density molecular linkage maps, comprised of more than 1000 markers with an average spacing between markers of approximately 1.2 cM (ca. 900 kb), have been constructed for the tomato and potato genomes. As the two maps are based on a common set of probes, it was possible to determine, with a high degree of precision, the breakpoints corresponding to 5 chromosomal inversions that differentiate the tomato and potato genomes. All of the inversions appear to have resulted from single breakpoints at or near the centromeres of the affected chromosomes, the result being the inversion of entire chromosome arms. While the crossing over rate among chromosomes appears to be uniformly distributed with respect to chromosome size, there is tremendous heterogeneity of crossing over within chromosomes. Regions of the map corresponding to centromeres and centromeric heterochromatin, and in some instances telomeres, experience up to 10-fold less recombination than other areas of the genome. Overall, 28% of the mapped loci reside in areas of putatively suppressed recombination. This includes loci corresponding to both random, single copy genomic clones and transcribed genes (detected with cDNA probes). The extreme heterogeneity of crossing over within chromosomes has both practical and evolutionary implications. Currently tomato and potato are among the most thoroughly mapped eukaryotic species and the availability of high density molecular linkage maps should facilitate chromosome walking, quantitative trait mapping, marker-assisted breeding and evolutionary studies in these two important and well studied crop species.


Laboratory confirmed polymethyl-methacrylate (Palacos)-hypersensitivity after cranioplasty.
Polymethyl-methacrylate (PMMA) as part of bone cement is a widely used material in the context of orthopaedic implants and also in cranioplasty. Although PMMA is characterised by excellent biocompatibility with low intrinsic toxicity and inflammatory activation, a minor portion of patients develop allergic reactions. We present the case of a 39-year-old woman with an increasing headache and a corresponding erythema over the parieto-occipital cranioplasty, which was performed 42 days prior using a PMMA compound. A patch test specific for bone cement components confirmed the diagnosis of a PMMA delayed-type hypersensitivity reaction. The prevalence of allergic reactions to bone cement components are known to vary from between 0.6% and 1.6%, however no adequate, pre-interventional diagnostic tool is currently available. Therefore, physicians are required to consider this differential diagnosis even after an extremely delayed onset of symptoms. This case describes the first ever-reported case in the literature of hypersensitivity to bone cement cranioplasty.


Plasma Saturated and Monounsaturated Fatty Acids in Behçet's Disease.
Fatty Acid (FA) composition of serum has been associated with many markers of inflammation. In this study, we tried to examine plasma Saturated Fatty Acid (SFA) and Monounsaturated Fatty Acid (MUFA) composition in Behçet's Disease (BD) patients. The associations between the circulating FA levels and some markers of inflammation have also been investigated. This study is a cross-sectional one. In fact, a total of 101 BD patients and healthy controls group of 99 subjects are enrolled. Gas Chromatograph equipped with a Capillary Split/Splitless Injector and flame ionization detector was used to analyze the plasma SFA and MUFA compositions. The high sensitivity C-Reactive Protein (hsCRP) and fibrinogen levels were measured using standard techniques. BD patients had significantly higher proportions of Mystiric Acid (MA), Palmitic Acid (PAM), Palmitoleic Acid (POA) and Stearoyl-CoA Desaturase (SCD)-16, compared to controls.The results revealed that patients with severe involvements had high levels of POA and total MUFA associated with higher SCD-16 activity compared to those with minor ones. The receiver operator characteristic curve analysis revealed that POA could well discriminate BD patients with severe clinical manifestations. In the bivariate analysis, hsCRP was found to be positively correlated with total SAFA and POA elongase activity index but negatively correlated with SCD-18 activity index. The STA, POA, elongase and SCD-16 activity index are correlated with fibrinogen. On the other hand, the multivariate analysis showed that POA remained associated with higher levels of hsCRP. Unfavourable plasma SFA and MUFA profile were reported in BD patients. POA, which is associated with higher plasma hsCRP level, may play a role in the pathogenesis of BD.


[Comparison of ertapenem-EMB Agar with traditional methods for screening carbapenem-resistant Klebsiella pneumoniae from rectal swabs].
Detection of rectal colonization with carbapenem-resistant Klebsiella pneumoniae (CRKP) is the most important step in the infection control protocols in order to prevent infections caused by CRKP which has an increasing incidence all over the world. In this study, it was aimed to compare the detection rate of 2 mg/L ertapenem EMB agar medium with the other methods recommended by various international guidelines. These methods include direct plate method using ertapenem disc, enrichment method in tryptic soy broth containing 2 mg/L ertapenem and the investigation of the predominant betalactamases in the colonized patients. The lowest inoculum detected by different methods was determined by using simulative challenge test prepared for this purpose. The ability to detect CRKP from rectal swabs was evaluated by using the clinical specimens of 801 patients. For all bacteria isolated, carbapenem susceptibility was evaluated by using E-test method, the presence of beta-lactamases was determined by using modified Hodge test (MHT), and the carbapenemase genes were investigated by using multiplex polymerase chain reaction (PCR). The lowest inoculum detected by ertapenem-EMB agar was 50 CFU/mL whereas the lowest inocula were 1 x 105 and 1 x 103, respectively by tryptic soy broth with ertapenem and direct plate method. No resistance gene were identified by PCR in 13 (39.4%) of 33 isolates, whereas blaOXA-48 was detected in 19 (95%) and blaIMP in 1 (5%) of 20 positive isolates. All of the positive strains were resistant to imipenem and ertapenem, while 2 (10%) strains were found to be susceptible to doripenem and meropenem. While MHT was negative in all strains which were negative for resistance genes, all resistance gene positive strains except one blaOXA-48 strain that was also sensitive to doripenem and meropenem, were found to be positive with MHT. According to the results of PCR, the sensitivities of the three methods were found to be 80%. The specificities, positive and negative predictive values were found to be 15.4%, 59% and 33.3% for ertapenem-EMB agar, 23%, 61.5% and 42.9% for broth with ertapenem and 61.5%, 76% and 66.6% for direct plate method, respectively. Average labor time of the methods (isolation + identification + sensitivity + MHT) was determined as 48 hours for ertapenem-EMB agar, whereas it was 96 hours for the other methods. In conclusion, since ertapenem- EMB agar method is a sensitive and rapid method, it can be used safely for the preliminary detection of CRKP without increasing the workload of the laboratory.


Salmonella enterica serovar Typhi impairs CD4 T cell responses by reducing antigen availability.
Salmonella enterica serovar Typhi is associated with a disseminated febrile illness in humans, termed typhoid fever, while Salmonella enterica serovar Typhimurium causes localized gastroenteritis in immunocompetent individuals. One of the genetic differences between both pathogens is the presence in S. Typhi of TviA, a regulatory protein that shuts down flagellin (FliC) expression when bacteria transit from the intestinal lumen into the intestinal mucosa. Here we investigated the consequences of TviA-mediated flagellum gene regulation on flagellin-specific CD4 T cell responses in a mouse model of S. Typhimurium infection. Introduction of the S. Typhi tviA gene into S. Typhimurium suppressed antigen presentation of dendritic cells to flagellin-specific CD4 T cells in vitro. Furthermore, TviA-mediated repression of flagellin expression impaired the activation and proliferation of naive flagellin-specific CD4 T cells in Peyer's patches and mesenteric lymph nodes, which was accompanied by increased bacterial dissemination to the spleen. We conclude that TviA-mediated repression of flagellin expression reduces antigen availability, thereby weakening flagellin-specific CD4 T cell responses.


Genetic interaction between transcription elongation factor TFIIS and RNA polymerase II.
Little is known about the regions of RNA polymerase II (RNAPII) that are involved in the process of transcript elongation and interaction with elongation factors. One elongation factor, TFIIS, stimulates transcript elongation by binding to RNAPII and facilitating its passage through intrinsic pausing sites in vitro. In Saccharomyces cerevisiae, TFIIS is encoded by the PPR2 gene. Deletion of PPR2 from the yeast genome is not lethal but renders cells sensitive to the uracil analog 6-azauracil (6AU). Here, we show that mutations conferring 6AU sensitivity can also be isolated in the gene encoding the largest subunit of S. cerevisiae RNAPII (RPO21). A screen for mutations in RPO21 that confer 6AU sensitivity identified seven mutations that had been generated by either linker-insertion or random chemical mutagenesis. All seven mutational alterations are clustered within one region of the largest subunit that is conserved among eukaryotic RNAPII. The finding that six of the seven rpo21 mutants failed to grow at elevated temperature underscores the importance of this region for the functional and/or structural integrity of RNAPII. We found that the 6AU sensitivity of the rpo21 mutants can be suppressed by increasing the dosage of the wild-type PPR2 gene, presumably as a result of overexpression of TFIIS. These results are consistent with the proposal that in the rpo21 mutants, the formation of the RNAPII-TFIIS complex is rate limiting for the passage of the mutant enzyme through pausing sites. In addition to implicating a region of the largest subunit of RNAPII in the process of transcript elongation, our observations provide in vivo evidence that TFIIS is involved in transcription by RNAPII.


Phenotypic Profiling Reveals that Candida albicans Opaque Cells Represent a Metabolically Specialized Cell State Compared to Default White Cells.
The white-opaque switch is a bistable, epigenetic transition affecting multiple traits in Candida albicans including mating, immunogenicity, and niche specificity. To compare how the two cell states respond to external cues, we examined the fitness, phenotypic switching, and filamentation properties of white cells and opaque cells under 1,440 different conditions at 25°C and 37°C. We demonstrate that white and opaque cells display striking differences in their integration of metabolic and thermal cues, so that the two states exhibit optimal fitness under distinct conditions. White cells were fitter than opaque cells under a wide range of environmental conditions, including growth at various pHs and in the presence of chemical stresses or antifungal drugs. This difference was exacerbated at 37°C, consistent with white cells being the default state of C. albicans in the mammalian host. In contrast, opaque cells showed greater fitness than white cells under select nutritional conditions, including growth on diverse peptides at 25°C. We further demonstrate that filamentation is significantly rewired between the two states, with white and opaque cells undergoing filamentous growth in response to distinct external cues. Genetic analysis was used to identify signaling pathways impacting the white-opaque transition both in vitro and in a murine model of commensal colonization, and three sugar sensing pathways are revealed as regulators of the switch. Together, these findings establish that white and opaque cells are programmed for differential integration of metabolic and thermal cues and that opaque cells represent a more metabolically specialized cell state than the default white state. Epigenetic transitions are an important mechanism by which microbes adapt to external stimuli. For Candida albicans, such transitions are crucial for adaptation to complex, fluctuating environments, and therefore contribute to its success as a human pathogen. The white-opaque switch modulates multiple C. albicans attributes, from sexual competency to niche specificity. Here, we demonstrate that metabolic circuits are extensively rewired between white and opaque states, so that the two cell types exhibit optimal fitness under different nutritional conditions and at different temperatures. We thereby establish that epigenetic events can profoundly alter the metabolism of fungal cells. We also demonstrate that epigenetic switching regulates filamentation and biofilm formation, two phenotypes closely associated with pathogenesis. These experiments reveal that white cells, considered the most clinically relevant form of C. albicans, are a "general-purpose" state suited to many environments, whereas opaque cells appear to represent a more metabolically specialized form of the species.


A new mapping method employing a meiotic rec-mutant of yeast.
A rapid new mapping method has been developed for localizing a dominant or recessive mutation to a particular chromosome of yeast. The procedure utilizes the ability of strains homozygous for the spo11-1 mutation to undergo chromosome segregation without appreciable recombination during sporulation. The level of sporulation in spo11-1/spo11-1 diploids is reduced and asci are often immature or abnormal in appearance; spore viability is less than 1%. The first step of the mapping procedure is the construction of a haploid spo11-1 strain carrying a recessive drug-resistance marker and the unmapped mutation(s). This strain is crossed to a set of three spo11-1 mapping tester strains containing, among them, a recessive marker on each chromosome. The resulting spo11-1/spo11-1 diploids are sporulated and plated on drug-containing medium. Viable meiotic products that express the drug-resistance marker due to chromosome haploidization are selectively recovered. These meiotic products are haploid for most, but generally not all, chromosomes. The level of disomy for individual chromosomes averages 19%. Each of the recessive chromosomal markers is expressed in approximately a third of the drug-resistant segregants. Ninety-eight percent of these segregants show no evidence of intergenic recombination. Thus, two markers located on the same chromosome, but on different homologs, are virtually never expressed in the same drug-resistant clone. The utility of this mapping procedure is demonstrated by confirming the chromosomal location of seven known markers, as well as by the assignment of a previously unmapped mutation, spo12-1, to chromosome VIII. In addition, the analysis of the products of spo11-1 meiosis indicates that several markers previously assigned to either chromosome XIV or chromosome XVII are actually on the same chromosome.


Identification of peptide inhibitors of transforming growth factor beta 1 using a phage-displayed peptide library.
Pathologies such as liver fibrosis and scleroderma are characterized by harmful levels of transforming growth factor beta 1 (TGFbeta1). These levels could be neutralized if inhibitors of this cytokine were available. With this aim we searched for peptides with binding affinity for TGFbeta1 using a phage-displayed random 15-mer peptide library. Some peptides thus identified blocked activity of TGFbeta1 in vitro, as measured by their capacity to restore growth of Mv-1-Lu cells in presence of added TGFbeta1. Also, they inhibited TGFbeta1-dependent expression of collagen type I mRNA in liver of mice orally insulted with CCl(4). Intraperitoneal administration of 50 microg of peptide P17 (the most active 15-mer peptide, also referred to as P17(1-15)) inhibited expression of collagen type I mRNA by almost 100%. Interestingly, titration experiments showed that P17(1-12) (a peptide encompassing the first 12 amino acids of P17) was approximately four times more active than P17. These results suggest that both peptides, as well as others reported here, may be of therapeutic interest in processes requiring control of undesired high levels of TGFbeta1.


Multiscale impact of researcher mobility.
International mobility facilitates the exchange of scientific, institutional and cultural knowledge. Yet whether globalization and advances in virtual communication technologies have altered the impact of researcher mobility is a relevant and open question that we address by analysing a broad international set of 26 170 physicists from 1980 to 2009, focusing on the 10-year period centred around each mobility event to assess the impact of mobility on research outcomes. We account for secular globalization trends by splitting the analysis into three periods, measuring for each period the effect of mobility on researchers' citation impact, research topic diversity, collaboration networks and geographical coordination. In order to identify causal effects we leverage statistical matching methods that pair mobile researchers with non-mobile researchers that are similar in research profile attributes prior the mobility event. We find that mobile researchers gain up to a 17% increase in citations relative to their non-mobile counterparts, which can be explained by the simultaneous increase in their diversity of co-authors, topics and geographical coordination in the period immediately following migration. Nevertheless, we also observe that researcher's completely curtail prior collaborations with their source country in 11% of the cross-border mobility events. As such, these individual-level perturbations fuel multiscale churning in scientific networks, e.g. rewiring the connectivity of individuals and ideas and affecting international integration. Together these results provide additional clarity on the complex relationship between human capital mobility and the dynamics of social capital investment, with implications for immigration and national innovation system policy.


Decrease in the numbers of dendritic cells and CD4+ T cells in cerebral perivascular spaces due to natalizumab.
To extend our studies on the prolonged and differential effect of natalizumab on T lymphocyte numbers in the cerebrospinal fluid, we investigated the number and phenotypes of leukocytes and the expression of major histocompatibility complex (MHC) classes I and II in cerebral perivascular spaces (CPVS). We hypothesized that natalizumab reduces the number of antigen presenting cells in CPVS. A case-control study in which inflammatory cell numbers in the CPVS of cerebral tissue were assessed by immunohistochemical staining. A patient with multiple sclerosis (MS) who developed progressive multifocal leukoencephalopathy (PML) during natalizumab therapy. Controls included location-matched cerebral autopsy material of patients without disease of the central nervous system, patients with MS not treated with natalizumab, and patients with PML not associated with natalizumab therapy. The absolute number of CPVS in the patient with MS treated with natalizumab was significantly lower than in the control groups owing to extensive destruction of the tissue architecture. The expression of MHC class II molecules and the number of CD209+ dendritic cells were significantly decreased in the CPVS of the patient with MS treated with natalizumab. No CD4+ T cells were detectable. Our observations may explain the differential and prolonged effects of natalizumab therapy on leukocyte numbers in the cerebrospinal fluid.


[Low dose oral contraceptives: 30 microg are still used?].
The choice between oral contraceptives (OC) containing 30 or 20 microg of ethinylestradiol (EE) is founded on clinical sign and medical history of the women. Not always a lower dose of EE cause less side effects than an higher dose. Often 20-microg-EE OC induces menstrual cycle alterations and sexual dysfunctions, inducing the women to stop the treatment. Low estrogens concentration have a negative effect on external genital tract, with a consequent vaginal dryness and dispareunia. It is known that OC with 20-microg of EE determine a lower increase of sex hormone binding globulin compared to 30 mg EE and the consequence can be a reduction in antiandrogen effect of OC. OC containing 30 microg of EE have a positive effect on peak in young women, particularly in lean subjects. Moreover, 30 microg of EE induce a better ovarian suppression associated with a lower steroidal production during the week of interruption. Besides, 30-microg-EE OC works well in blocking ovarian cysts formation in women with endocrine dysfunctions like polycystic ovary syndrome or with previous luteal cysts. In conclusion, an OC with 30 microg of EE and an antiandrogen progestin is better than another with 20 microg of EE with the same progestin, because 30 microg of EE have a more powerful antiandrogenic action and guarantee very good cosmetics and endocrine results.


Formation of modulated phases and domain rigidification in fatty acid-containing lipid membranes.
We investigated the phase behavior of lipid membranes containing fatty acids (FAs) by microscopy and differential scanning calorimetry. We used palmitic acid (saturated FA), oleic acid (cis-isomer of unsaturated FA), elaidic acid (trans-isomer of unsaturated FA), and phytanic acid (branched FA) and examined the effects of FAs on phase-separated structures in lipid bilayer membranes consisting of dioleolylphosphocholine (DOPC)/dipalmitoylphosphocholine (DPPC)/cholesterol (Chol). Palmitic acid and elaidic acid exclude Chol from the DPPC-rich phase. As a result, the liquid-ordered phase formed by DPPC and Chol transforms into a solid-ordered phase. Oleic acid and phytanic acid significantly reduce the line tension at the liquid domain boundary. This decrease in line tension leads to the formation of modulated phases, such as striped, hexagonal, and polygonal domains. We measured the line tension and the interdomain interaction in these specific domains by an image analysis. The result showed that oleic acid and phytanic acid-containing vesicles as well as palmitic acid-containing vesicles are not spherical, and this domain-induced deformation is explained theoretically.


N-terminal domain of Pyrococcus furiosus l-asparaginase functions as a non-specific, stable, molecular chaperone.
The enzyme l-asparaginase of Pyrococcus furiosus (PfA) functions as a dimer with each monomer consisting of distinct N- and C-terminal domains (NPfA and CPfA, respectively), connected by a linker. Here we present data to show that NPfA functions as a non-specific molecular chaperone. Independently expressed NPfA refolded spontaneously whereas CPfA formed insoluble aggregates. However, when mixed and refolded together, NPfA augmented CPfA to fold with ~90% recovery. NPfA also protected a variety of substrate proteins from thermal and refolding-mediated aggregation as monitored by a reduction in light scattering. The co-appearance of substrate protein with NPfA in antibody pull-down assays as well as in eluted gel filtration peaks indicated direct protein-protein interaction. These interactions were hydrophobic in nature as determined by 8-anilino-1-naphthalene sulfonic acid fluorescence. NPfA inhibited polyglutamine-mediated amyloid formation and also facilitated disintegration of preformed amyloid fibrils of amyloid-β (1-42) as determined by reverse-phase HPLC-based sedimentation assay and thioflavin T binding assays, respectively. Dynamic light scattering experiments suggested that NPfA readily assembled into polydispersed oligomeric species. With no sequence similarity to α-crystallin or any known molecular chaperone, we present here NPfA as a novel molecular chaperone.


Alignment behaviors of short peptides provide a roadmap for functional profiling of metagenomic data.
Functional assignments for short-read metagenomic data pose a significant computational challenge due to perceived unpredictability of alignment behavior and the inability to infer useful functional information from translated protein-fragments/peptides. To address this problem, we have examined the predictability of short peptide alignments by systematically studying alignment behavior of large sets of short peptides generated from well-characterized proteins as well as hypothetical proteins in the KEGG database. Using test sets of peptides modeling the length and phylogenetic distributions of short-read metagenomic data, we observed that peptides from well-characterized proteins had indistinguishable alignments to proteins from the same orthologous family and proteins from different families. Nonetheless, the patterns contained remarkable phylogenetic and structural signals, with alignments of even very short peptides naturally restricted to their orthologous family and/or proteins having similar structural folds. In stark contrast, peptides from "hypothetical proteins" had only sparse hit patterns with low frequencies and much lower identities. By weighting the structure-driven alignments and filtering peptides with behaviors similar to those derived from "hypothetical proteins", we demonstrate that the accuracy of abundance predictions of protein families is dramatically improved. Evolutionary processes have dispersed protein folds across multiple protein families, precluding accurate functional assignment to short peptides, whose alignment behavior is non-random and driven by structure. Algorithms that filter sparse peptides and weight hit patterns of peptides from "known space" dramatically improve quantification of functions from diverse mixtures of peptides and should substantially improve applications of metagenomic analyses requiring accurate quantitative measures of functional families.


Crystallization of a soluble form of the rat T-cell surface glycoprotein CD4 complexed with Fab from the W3/25 monoclonal antibody.
The structure of the T-lymphocyte cell surface glycoprotein CD4 is of considerable biological and medical interest. Recombinant rat CD4 expressed in soluble form in mammalian cells and complexed with W3/25 monoclonal Fab fragments formed crystals that diffract to 3.5 A and have the orthorhombic space group P2(1)2(1)2 or P2(1)2(1)2(1). The unit cell has dimensions a = 317 A, b = 161 A and c = 41.8 A and the asymmetric unit consists of two CD4:Fab complexes. These crystals are of suitable quality for X-ray diffraction analysis.


Muscle protein catabolism after severe burn: effects of IGF-1/IGFBP-3 treatment.
To determine the effects of recombinant human insulin-like growth factor-1 (IGF-1) complexed with its principal binding protein, IGFBP-3, on skeletal muscle metabolism in severely burned children. Severe burns are associated with a persistent hypermetabolic response characterized by hyperdynamic circulation and severe muscle catabolism and wasting. Previous studies showed that nutritional support and pharmacologic intervention with anabolic agents such as growth hormone and insulin abrogated muscle wasting and improved net protein synthesis in the severely burned. The use of these agents, however, has several adverse side effects. A new combination of IGF-1 and IGFBP-3 is now available for clinical study. Twenty-nine severely burned children were prospectively studied before and after treatment with 0.5, 1, 2, or 4 mg/kg/day IGF-1/IGFBP-3 to determine net balance of protein across the leg, muscle protein fractional synthetic rates, and glucose metabolism. Another group was studied in a similar fashion without IGF-1/IGFBP-3 treatment as time controls. Seventeen of 29 children were catabolic before starting treatment. The infusion of 1.0 mg/kg/day IGF-1/IGFBP-3 increased serum IGF-1, which did not further increase with 2.0 and 4.0 mg/kg/day. IGF-1/IGFBP-3 treatment at 1 to 4 mg/ kg/day improved net protein balance and increased muscle protein fractional synthetic rates. This effect was more pronounced in catabolic children. IGF-1/IGFBP-3 did not affect glucose uptake across the leg or change substrate utilization. IGF-1/IGFBP-3 at doses of 1 to 4 mg/kg/day attenuates catabolism in catabolic burned children with negligible clinical side effects.


How many species of flowering plants are there?
We estimate the probable number of flowering plants. First, we apply a model that explicitly incorporates taxonomic effort over time to estimate the number of as-yet-unknown species. Second, we ask taxonomic experts their opinions on how many species are likely to be missing, on a family-by-family basis. The results are broadly comparable. We show that the current number of species should grow by between 10 and 20 per cent. There are, however, interesting discrepancies between expert and model estimates for some families, suggesting that our model does not always completely capture patterns of taxonomic activity. The as-yet-unknown species are probably similar to those taxonomists have described recently-overwhelmingly rare and local, and disproportionately in biodiversity hotspots, where there are high levels of habitat destruction.


Photoinduced dimerization of a photosensory DNA-binding protein EL222 and its LOV domain.
EL222 is a blue light sensor protein consisting of a light-oxygen-voltage (LOV) domain (EL-LOV domain) at the N-terminus and a helix-turn-helix DNA-binding domain at the C-terminus. EL222 acts as a light dependent transcriptional factor. The photochemical reactions of EL222 and the light sensing properties of the LOV domain were investigated. Concentration dependent experiments revealed that the EL-LOV domain is in equilibrium between the dimer and the monomer in the dark state, and the main photoreaction is the dimerization reaction between a monomer in the ground state and that in the excited state. The equilibrium constant and the intrinsic rate constants of dimerization were determined. EL222 was found to also exhibit photoinduced dimerization even in the absence of target DNA, although the yield of the reaction was low (∼0.08 compared with that of the EL-LOV domain). This observation suggests that there are inhomogeneous conformations, open and closed types, of EL222 in solution.


MRI, Clinical Examination, and Mammography for Preoperative Assessment of Residual Disease and Pathologic Complete Response After Neoadjuvant Chemotherapy for Breast Cancer: ACRIN 6657 Trial.
The objective of our study was to determine the accuracy of preoperative measurements for detecting pathologic complete response (CR) and assessing residual disease after neoadjuvant chemotherapy (NACT) in patients with locally advanced breast cancer. The American College of Radiology Imaging Network 6657 Trial prospectively enrolled women with ≥ 3 cm invasive breast cancer receiving NACT. Preoperative measurements of residual disease included longest diameter by mammography, MRI, and clinical examination and functional volume on MRI. The accuracy of preoperative measurements for detecting pathologic CR and the association with final pathology size were assessed for all lesions, separately for single masses and nonmass enhancements (NMEs), multiple masses, and lesions without ductal carcinoma in situ (DCIS). In the 138 women with all four preoperative measures, longest diameter by MRI showed the highest accuracy for detecting pathologic CR for all lesions and NME (AUC = 0.76 and 0.84, respectively). There was little difference across preoperative measurements in the accuracy of detecting pathologic CR for single masses (AUC = 0.69-0.72). Longest diameter by MRI and longest diameter by clinical examination showed moderate ability for detecting pathologic CR for multiple masses (AUC = 0.78 and 0.74), and longest diameter by MRI and longest diameter by mammography showed moderate ability for detecting pathologic CR for tumors without DCIS (AUC = 0.74 and 0.71). In subjects with residual disease, longest diameter by MRI exhibited the strongest association with pathology size for all lesions and single masses (r = 0.33 and 0.47). Associations between preoperative measures and pathology results were not significantly influenced by tumor subtype or mammographic density. Our results indicate that measurement of longest diameter by MRI is more accurate than by mammography and clinical examination for preoperative assessment of tumor residua after NACT and may improve surgical planning.


A novel member of the interferon receptor family complements functionality of the murine interferon gamma receptor in human cells.
Expression of the human interferon gamma receptor (IFN-gamma R) in mouse cells is not sufficient to confer biological responsiveness to human IFN-gamma and vice versa. An additional species-specific component is required for signal transduction. We identified this cofactor by expression cloning in simian COS cells stably transfected with the nonfunctional murine IFN-gamma R and a IFN-gamma-inducible reporter construct encoding the human Tac antigen (interleukin-2 receptor alpha chain, CD25). A cDNA clone was obtained that, upon stable transfection, rendered human HEp-2 cells expressing the murine IFN-gamma R fully responsive to murine IFN-gamma. This cDNA encodes a novel 332 amino acid type I transmembrane protein that belongs to the IFN receptor family and that we designate IFN-gamma R beta chain.


Use of multiplex allele-specific polymerase chain reaction (MAS-PCR) to detect multidrug-resistant tuberculosis in Panama.
The frequency of individual genetic mutations conferring drug resistance (DR) to Mycobacterium tuberculosis has not been studied previously in Central America, the place of origin of many immigrants to the United States. The current gold standard for detecting multidrug-resistant tuberculosis (MDR-TB) is phenotypic drug susceptibility testing (DST), which is resource-intensive and slow, leading to increased MDR-TB transmission in the community. We evaluated multiplex allele-specific polymerase chain reaction (MAS-PCR) as a rapid molecular tool to detect MDR-TB in Panama. Based on DST, 67 MDR-TB and 31 drug-sensitive clinical isolates were identified and cultured from an archived collection. Primers were designed to target five mutation hotspots that confer resistance to the first-line drugs isoniazid and rifampin, and MAS-PCR was performed. Whole-genome sequencing confirmed DR mutations identified by MAS-PCR, and provided frequencies of genetic mutations. DNA sequencing revealed 70.1% of MDR strains to have point mutations at codon 315 of the katG gene, 19.4% within mabA-inhA promoter, and 98.5% at three hotspots within rpoB. MAS-PCR detected each of these mutations, yielding 82.8% sensitivity and 100% specificity for isoniazid resistance, and 98.4% sensitivity and 100% specificity for rifampin resistance relative to DST. The frequency of individual DR mutations among MDR strains in Panama parallels that of other TB-endemic countries. The performance of MAS-PCR suggests that it may be a relatively inexpensive and technically feasible method for rapid detection of MDR-TB in developing countries.


Quasiregularity and its discontents: the legacy of the past tense debate.
Rumelhart and McClelland's chapter about learning the past tense created a degree of controversy extraordinary even in the adversarial culture of modern science. It also stimulated a vast amount of research that advanced the understanding of the past tense, inflectional morphology in English and other languages, the nature of linguistic representations, relations between language and other phenomena such as reading and object recognition, the properties of artificial neural networks, and other topics. We examine the impact of the Rumelhart and McClelland model with the benefit of 25 years of hindsight. It is not clear who "won" the debate. It is clear, however, that the core ideas that the model instantiated have been assimilated into many areas in the study of language, changing the focus of research from abstract characterizations of linguistic competence to an emphasis on the role of the statistical structure of language in acquisition and processing.


[Physiological function mediated by histamine synthesis].
Histamine is involved in a variety of physiologic responses, such as inflammation, type I allergy, gastric acid secretion, and neurotransmission. Previous studies have focused on specific receptors for histamine and histamine release through degranulation, and the regulation of histamine synthesis and its physiologic roles remain to be clarified. We have studied histidine decarboxylase (HDC), the rate-limiting enzyme for mammalian histamine synthesis. Immunocytochemical approaches with an anti-HDC antibody revealed that histamine synthesis occurs in two distinct compartments of mast cells, cytosol and granules, and is regulated by the posttranslational processing of HDC. We also found that histamine synthesis in mast cells is markedly induced by IgE even in the absence of antigens, which may be relevant to enhanced responses of mast cells under allergic conditions. We then developed HDC-deficient mice by gene targeting to investigate the physiologic roles of histamine. We not only confirmed that histamine is essential for type I allergy and stimulates gastric acid secretion, but also found that histamine may regulate the proliferation and differentiation of mast cells. Furthermore, in HDC-deficient mice histamine produced by infiltrated neutrophils can suppress the production of antitumoral cytokines, such as interferon-gamma and tumor necrosis factor-alpha through H2 receptors in the tumor tissues. In this review, we describe recent topics in histamine research, including our results focusing on histamine synthesis and its physiologic roles.


Switchable synchronisation of pirouetting motions in a redox-active [3]rotaxane.
In this study, the crown/ammonium [3]rotaxane R2 is reported which allows a switchable synchronisation of wheel pirouetting motions. The rotaxane is composed of a dumbbell-shaped axle molecule with two mechanically interlocked macrocycles which are decorated with a redox-active tetrathiafulvalene (TTF) unit. Electrochemical, spectroscopic, and electron paramagnetic resonance experiments reveal that rotaxane R2 can be reversibly switched between four stable oxidation states (R2, R2˙+, R22(˙+), and R24+). The oxidations enable non-covalent, cofacial interactions between the TTF units in each state-including a stabilised mixed-valence (TTF2)˙+ and a radical-cation (TTF˙+)2 dimer interaction-which dictate a syn (R2, R2˙+, and R22(˙+)) or anti (R24+) ground state co-conformation of the wheels in the rotaxane. Furthermore, the strength of these wheel-wheel interactions varies with the oxidation state, and thus electrochemical switching allows a controllable synchronisation of the wheels' pirouetting motions. DFT calculations explore the potential energy surface of the counter-rotation of the two interacting wheels in all oxidation states. The controlled coupling of pirouetting motions in rotaxanes can lead to novel molecular gearing systems which transmit rotational motion by switchable non-covalent interactions.


Ukrain - a new cancer cure? A systematic review of randomised clinical trials.
Ukrain is an anticancer drug based on the extract of the plant Chelidonium majus L. Numerous pre-clinical and clinical investigations seem to suggest that Ukrain is pharmacologically active and clinically effective. We wanted therefore to critically evaluate the clinical trial data in the form of a systematic review. Seven electronic databases were searched for all relevant randomised clinical trials. Data were extracted and validated by both authors, tabulated and summarised narratively. The methodological quality was assessed with the Jadad score. Seven trials met our inclusion criteria. Without exception, their findings suggest that Ukrain has curative effects on a range of cancers. However, the methodological quality of most studies was poor. In addition, the interpretation of several trials was impeded by other problems. The data from randomised clinical trials suggest Ukrain to have potential as an anticancer drug. However, numerous caveats prevent a positive conclusion, and independent rigorous studies are urgently needed.


Brain activity during biofeedback relaxation: a functional neuroimaging investigation.
The mechanisms by which cognitive processes influence states of bodily arousal are important for understanding the pathogenesis and maintenance of stress-related morbidity. We used PET to investigate cerebral activity relating to the cognitively driven modulation of sympathetic activity. Subjects were trained to perform a biofeedback relaxation exercise that reflected electrodermal activity and were subsequently scanned performing repetitions of four tasks: biofeedback relaxation, relaxation without biofeedback and two corresponding control conditions in which the subjects were instructed not to relax. Relaxation was associated with significant increases in left anterior cingulate and globus pallidus activity, whereas no significant increases in activity were associated with biofeedback compared with random feedback. The interaction between biofeedback and relaxation, highlighting activity unique to biofeedback relaxation, was associated with enhanced anterior cingulate and cerebellar vermal activity. These data implicate the anterior cingulate cortex in the intentional modulation of bodily arousal and suggest a functional neuroanatomy of how cognitive states are integrated with bodily responses. The findings have potential implications for a mechanistic account of how therapeutic interventions, such as relaxation training in stress-related disorders, mediate their effects.


Phosphorylation of AKT: a mutational analysis.
Akt (cellular homolog of murine thymoma virus akt8 oncogene) is an essential component of the PI3K (phosphatidylinositol 3-kinase) pathway. Its activity is stimulated by receptor tyrosine kinases and G-protein coupled receptors and plays a critical role in the regulation of cell proliferation, differentiation and apoptosis. A gain of function in Akt can lead to uncontrolled cell proliferation and resistance to apoptosis, both hallmarks of oncogenic transformation. In this communication, we have investigated the phosphorylation at the Akt residues T308, S473 and T450 and their roles in oncogenic transformation and signaling. We find that T450 phosphorylation has only a minimal part in these activities. In contrast, the phosphorylation of T308 and of S473 fulfills essential, distinct, and non-overlapping functions that we define with inactivating and with phosphomimetic mutations of these sites.


Appropriate use criteria for stress single-photon emission computed tomography sestamibi studies: a quality improvement project.
We previously reported the application of the 2005 American College of Cardiology Foundation appropriate use criteria for stress single-photon emission computed tomography (SPECT) imaging to patients at Mayo Clinic (Rochester, MN) in 2005 and 2006. A subsequent internal quality improvement project focused on physician education in an attempt to reduce the rate of inappropriate SPECT studies. Our 2008 physician education effort, focused on 4 specific indications that accounted for 88% of the inappropriate SPECT studies, included a presentation at medical grand rounds, a publication in the staff newsletter, meetings with physician administrators, and focused presentations to departments/divisions with many ordering physicians. We then remeasured the appropriateness of SPECT studies using previously published methods. The general categories of study indications, eg, after revascularization, were similar in 273 SPECT patients in 2008 and in our 2005 (n=284) and 2006 (n=284) cohorts. There was a trend suggesting a change in the overall classification of appropriateness over time (P=0.08) and a significant change in the rate of inappropriate studies over time (P=0.018). Inappropriate studies decreased from 14.4% in 2005 to 7.0% in 2006 before initiation of the quality improvement project. After completion of the quality improvement project, inappropriate studies increased to 11.7% (P=0.06). The 95% confidence limits for the 4.7% increase in inappropriate studies after the quality improvement project included a decrease of 0.2% and an increase of 9.6%. This quality improvement project, focused on feedback, physician education, and remeasurement, did not reduce the rate of inappropriate stress SPECT studies in a single academic medical center. Similar limited interventions focused on physician education alone may have limited benefit. More extensive intervention may be necessary to improve the quality of care with appropriateness criteria.


The catechol-O-methyltransferase gene: its regulation and polymorphisms.
The catechol-O-methyltransferase (COMT) gene is of significant interest to neuroscience, due to its role in modulating dopamine function. COMT is dynamically regulated; its expression is altered during normal brain development and in response to environmental stimuli. In many cases the underlying molecular basis for these effects is unknown; however, in some cases (e.g., estrogenic regulation in the case of sex differences) regulatory mechanisms have been identified. COMT contains several functional polymorphisms and haplotypes, including the well-studied Val158Met polymorphism. Here I review the regulation of COMT and the functional polymorphisms within its sequence with respect to brain function.


Quadratic cost functional for wave-front reconstruction.
A quadratic cost functional for reconstruction of a high-resolution wave front from a coarse wave front is presented. The functional uses as data the position and the direction of the coarse wave front that had previously been computed with a ray-tracing method. This functional uses an optical relationship between the ray information and the wave front's shape to reconstruct a high-density wave front. The performance of the proposed functional is illustrated by reconstruction of complicated wave fronts for which this functional has an accuracy that is superior to that of conventional interpolation methods.


Clinical Utility of HLA-B*58:01 Genotyping to Prevent Allopurinol-Induced SJS/TEN.
Purpose: A 28-year-old male reported to our hospital with Stevens-Johnson syndrome/toxic epidermal necrolysis (SJS/TEN) overlap syndrome that developed as an adverse drug reaction (ADR) to allopurinol. HLA-B*58:01 allele is associated with an increased risk of developing allopurinol-induced SJS/TEN. Methods: Genomic DNA was extracted from peripheral blood leukocytes. DNA sequencing was done using SANGER sequencing method. Results: Pharmacogenetic testing results revealed positive for HLA-B*58:01 allele. Symptoms of the patient receded after allopurinol withdrawal. Conclusion: The thrust of personalized therapy is from decoding the individual specific genetic variations astutely for better therapeutic outcomes such as reducing the ADRs. Pharmacogenetic testing is emerging as a safe, fast, and economic screening tool for personalized therapy by preventing ADRs. Pharmacogenetic HLA-B*58:01 allele testing before allopurinol administration could significantly reduce the incidence of SJS/TEN and associated mortalities/morbidities and thereby represent a potential cost-effective intervention.