Miracle-dz/UniFAR-FTUs huggingface dataset:
Purine nucleoside phosphorylase. 3. Reversal of purine base specificity by site-directed mutagenesis.

Human purine nucleoside phosphorylase (PNP) is highly specific for 6-oxopurine nucleosides with a catalytic efficiency (kcat/KM) for inosine 350000-fold greater than for adenosine. Crystallographic studies identified Asn243 and Glu201 as the residues largely responsible for the substrate specificity. Results from mutagenesis studies demonstrated that the side chains for both residues were also essential for efficient catalysis [Erion, M. D. , et al. (1997a) Biochemistry 36, 11725-11734]. Additional mechanistic studies predicted that Asn243 participated in catalysis by stabilizing the transition state structure through hydrogen bond donation to N7 of the purine base [Erion, M. D. , et al. (1997b) Biochemistry 36, 11735-11748]. In an effort to alter the substrate specificity of human PNP, mutants of Asn243 and Glu201 were designed to reverse hydrogen bond donor and acceptor interactions with the purine base. Replacement of Asn243 with Asp, but not with other amino acids, led to a 5000-fold increase in kcat for adenosine and a 4300-fold increase in overall catalytic efficiency. Furthermore, the Asn243Asp mutant showed a 2.4-fold preference for adenosine relative to inosine and a 800000-fold change in substrate specificity (kcat/KM) relative to wild-type PNP. The double mutant, Asn243Asp::Glu201Gln, exhibited a 190-fold increase in catalytic efficiency with adenosine relative to wild-type PNP, a 480-fold preference for adenosine relative to inosine, and a 1.7 x 10(8)-fold change in preference for adenosine over inosine relative to wild-type PNP. The Asn243Asp mutant was also shown to synthesize 2,6-diaminopurine riboside with a catalytic efficiency (1.4 x 10(6) M-1 s-1) on the same order of magnitude as wild-type PNP with its natural substrates hypoxanthine and guanine. The Asn243Asp mutants represent examples in which protein engineering significantly altered substrate specificity while maintaining high catalytic efficiency.
Stress echocardiography

Stress echocardiography has become an accepted noninvasive method for the diagnosis of coronary artery disease. Stress echocardiography is more sensitive than exercise electrocardiography and as sensitive and specific as radionuclide perfusion studies for detecting coronary artery disease. Pharmacologic stress echocardiography using dobutamine also has excellent diagnostic accuracy for patients who are unable to exercise. Dobutamine stress echocardiography can provide prognostic data to determine perioperative cardiac risks in patients who are undergoing vascular surgery.
Does neighbourhood count in affecting children's journeys to schools?

This study examines two factors affecting children's school journeys – independent mobility and accessible school opportunities. Two time-geography based indicators, the spatial extent of potential path area and the number of weighted school places reachable (labelled OPP), are estimated. Multi-level modelling has been developed to analyse the interplay of individual, household and neighbourhood factors. Hong Kong is used as a case study because the neighbourhood effects on school provision within compact cities have not been well studied. The results show that 30.4% of the children's school journeys were made without adult companions. Half of the children walked to schools. The multi-level analysis suggests that nearly 90% of the variance in both indicators was found at the individual level. Neighbourhood, though not a decisive factor, does have impacts on the number of accessible school choices.
Chronic sinusitis in Malta--correlation between symptoms and CT scan.

INTRODUCTION The diagnosis of chronic rhinosinusitis (CRS) is clinical as it is based on patient symptoms. Sinus CT has been used as an objective measure of CRS with varying degrees of success and correlation to patient symptoms. AIMS This study aimed to investigate the relationship between patient symptoms, nasal endoscopic findings and CT in a small Mediterranean island community. A cohort of 305 consecutive patients with symptoms of CRS, that persisted despite maximal medical therapy, was evaluated by medical history, clinical examination and nasal endoscopy followed by sinus CT. Scans scoring 2 or higher on the Lund-Mckay scoring system were classified as positive for sinusitis while those scoring 0 or 1 were classified as negative for sinusitis. SETTING The setting of this study was a busy otolaryngological practice on a small Mediterranean island using a computerised database. RESULTS In total, 172 patients (56%) had positive and 133 (44%) had negative CT scans. Males with CRS were significantly more likely to have a positive CT (chi squared test, p=0.0005). Postnasal drip/rhinorrhoea, nasal obstruction and hyposmia as primary symptoms were significantly more likely to be associated with a positive CT (chi squared test p=0.0001). Patients presenting with facial pain as the primary symptom were significantly more likely to have a negative CT (chi squared test, p=0.0001). Middle meatal pus or nasal polyps on nasal endoscopy were significantly more likely to be associated with a subsequently positive CT (chi squared test, p<0.0001). Mucosal oedema of the middle meatus was a non-specific finding. CT positive patients were more likely to be treated surgically while CT negative patients were more likely to be treated with medication (chi squared test, p=0.0001). CONCLUSION Patients were followed up for a mean of 2 years. Overall, there was a good or improved outcome in 81% of patients. Those with a positive CT did significantly well with surgical treatment.
‘we got our heads together and came up with a plan’

This study investigated young children’s perceptions of their role in curriculum development in one Canadian preschool. There is no consensus that children have a role to play in developing curriculum. However, the United Nations Convention on the Rights of the Child (1989) confirms children’s right to be listened to about all aspects of their lives. Based on interviews with 34 children and three teachers, this study demonstrates the children feel they play an active role in curriculum development and implementation, but teachers make the final decisions about curriculum content. The children expressed a desire to influence the curriculum in new ways, but their ability to do so may be constrained by structural factors within and beyond the preschool.
BMC Medical Informatics and Decision Making

Background: Over a period of 40 years, SNOMED has developed from a pathology-specific nomenclature (SNOP) into a logic-based health care terminology. In spite of its long existence and continuous evolvement, it is yet unknown to what extent SNOMED is used in clinical practice, and what benefits were achieved. The aim of this paper is to investigate this by providing an overview of published studies in which a version of SNOMED was studied or applied. Methods: This paper analyzes the use of SNOMED over time, as reflected in scientific publications, by means of Medline literature search in PubMed. The search included papers from 1966 until June 2006. For each selected paper the following characteristics were classified: version, medical domain, coding moment (during or after the care process), usage, and type of evaluation (e.g., does SNOMED work, does SNOMED help). Results: 250 papers were included in this research. The number of annual publications has increased, as has the number of domains in which SNOMED is being used. Theoretical studies mainly concern comparison of SNOMED to other terminological systems and SNOMED as an illustration of a terminological systems' theory. Few studies are available on the usage of SNOMED in clinical practice, largely involving coding information and retrieval/aggregation based on SNOMED codes. Conclusion: The clinical application of SNOMED is broadening beyond pathology. The majority of studies concern proving the value of SNOMED in theory. Fewer studies are available on the usage of SNOMED in clinical practice. Literature gives no indication of the use of SNOMED for direct care purposes such as decision support.
Identification of an NADH-Cytochrome b5Reductase Gene from an Arachidonic Acid-Producing Fungus,Mortierella alpina 1S-4, by Sequencing of the Encoding cDNA and Heterologous Expression in a Fungus,Aspergillus oryzae

ABSTRACT Based on the sequence information for bovine and yeast NADH-cytochrome b5 reductases (CbRs), a DNA fragment was cloned from Mortierella alpina 1S-4 after PCR amplification. This fragment was used as a probe to isolate a cDNA clone with an open reading frame encoding 298 amino acid residues which show marked sequence similarity to CbRs from other sources, such as yeast (Saccharomyces cerevisiae), bovine, human, and rat CbRs. These results suggested that this cDNA is a CbR gene. The results of a structural comparison of the flavin-binding β-barrel domains of CbRs from various species and that of the M. alpina enzyme suggested that the overall barrel-folding patterns are similar to each other and that a specific arrangement of three highly conserved amino acid residues (i.e., arginine, tyrosine, and serine) plays a role in binding with the flavin (another prosthetic group) through hydrogen bonds. The corresponding genomic gene, which was also cloned fromM. alpina 1S-4 by means of a hybridization method with the above probe, had four introns of different sizes. These introns had GT at the 5′ end and AG at the 3′ end, according to a general GT-AG rule. The expression of the full-length cDNA in a filamentous fungus,Aspergillus oryzae, resulted in an increase (4.7 times) in ferricyanide reduction activity involving the use of NADH as an electron donor in the microsomes. The M. alpina CbR was purified by solubilization of microsomes with cholic acid sodium salt, followed by DEAE-Sephacel, Mono-Q HR 5/5, and AMP-Sepharose 4B affinity column chromatographies; there was a 645-fold increase in the NADH-ferricyanide reductase specific activity. The purified CbR preferred NADH over NADPH as an electron donor. This is the first report of an analysis of this enzyme in filamentous fungi.
Inferring search behaviors using partially observable markov model with duration (POMD)

This paper presents Partially Observable Markov model with Duration (POMD), a statistical method that addresses the challenge of understanding sophisticated user behaviors from the search log in which some user actions, such as reading and skipping search results, cannot be observed and recorded. POMD utilizes not only the positional but also the temporal information of the clicks in the log. In this work, we treat the user engagements with a search engine as a Markov process, and model the unobservable engagements as hidden states. POMD differs from the traditional hidden Markov model (HMM) in that not all the hidden state transitions emit observable events, and that the duration of staying in each state is explicitly factored into the core statistical model. To address the training and decoding issues emerged as the results of the variations, we propose an iterative two-stage training algorithm and a greedy segmental decoding algorithm respectively. We validate the proposed algorithm with two sets of experiments. First, we show that the search behavioral patterns inferred by POMD match well with those reported in the eye tracking experiments. Secondly, through a series of A/B comparison experiments, we demonstrate that POMD can distinguish the ranking qualities of different search engine configurations much better than the patterns inferred by the model proposed in the previous work. Both of the experimental results suggest that POMD can provide a statistical and quantitative way to understand the sophisticated search behaviors by simply mining the search logs.
A Coprological Study of Parasitism in Orangutans (Pongo pygmaeus) in Indonesia

Fecal specimens from 89 orangutans (36 captive, 34 rehabilitant, and 19 wild) at different locations in Indonesia were examined. Strongyloides spp, Balantidium coli, and strongylid nematodes were the most common infestations detected. A syngamid nematode, Mammomonogamus sp, is reported for the first time in orangutans.
Using Species Distribution Models to Predict Potential Landscape Restoration Effects on Puma Conservation

A mosaic of intact native and human-modified vegetation use can provide important habitat for top predators such as the puma (Puma concolor), avoiding negative effects on other species and ecological processes due to cascade trophic interactions. This study investigates the effects of restoration scenarios on the puma’s habitat suitability in the most developed Brazilian region (São Paulo State). Species Distribution Models incorporating restoration scenarios were developed using the species’ occurrence information to (1) map habitat suitability of pumas in São Paulo State, Southeast, Brazil; (2) test the relative contribution of environmental variables ecologically relevant to the species habitat suitability and (3) project the predicted habitat suitability to future native vegetation restoration scenarios. The Maximum Entropy algorithm was used (Test AUC of 0.84 ± 0.0228) based on seven environmental non-correlated variables and non-autocorrelated presence-only records (n = 342). The percentage of native vegetation (positive influence), elevation (positive influence) and density of roads (negative influence) were considered the most important environmental variables to the model. Model projections to restoration scenarios reflected the high positive relationship between pumas and native vegetation. These projections identified new high suitability areas for pumas (probability of presence >0.5) in highly deforested regions. High suitability areas were increased from 5.3% to 8.5% of the total State extension when the landscapes were restored for ≥ the minimum native vegetation cover rule (20%) established by the Brazilian Forest Code in private lands. This study highlights the importance of a landscape planning approach to improve the conservation outlook for pumas and other species, including not only the establishment and management of protected areas, but also the habitat restoration on private lands. Importantly, the results may inform environmental policies and land use planning in São Paulo State, Brazil.
Glutathione-dependent metabolism of cis-3-(9H-purin-6-ylthio)acrylic acid to yield the chemotherapeutic drug 6-mercaptopurine: evidence for two distinct mechanisms in rats.

cis-3-(9H-Purin-6-ylthio)acrylic acid (PTA) is a structural analog of azathioprine, a prodrug of the antitumor and immunosuppressive drug 6-mercaptopurine (6-MP). In this study, we examined the in vitro and in vivo metabolism of PTA in rats. Two metabolites of PTA, 6-MP and the major metabolite, S-(9H-purin-6-yl)glutathione (PG), were formed in a time- and GSH-dependent manner in vitro. Formation of 6-MP and PG occurred nonenzymatically, but 6-MP formation was enhanced 2- and 7-fold by the addition of liver and kidney homogenates, respectively. Purified rat liver glutathione S-transferases enhanced 6-MP formation from PTA by 1.8-fold, whereas human recombinant alpha, mu, and pi isozymes enhanced 6-MP formation by 1.7-, 1.3-, and 1.3-fold, respectively. In kidney homogenate incubations, PG accumulation was only observed during the first 15 min because of further metabolism by gamma-glutamyltranspeptidase, dipeptidase, and beta-lyase to yield 6-MP, as indicated by the use of the inhibitors acivicin and aminooxyacetic acid. Based on these results and other lines of evidence, two different GSH-dependent pathways are proposed for 6-MP formation: an indirect pathway involving PG formation and further metabolism to 6-MP, and a direct pathway in which PTA acts as a Michael acceptor. HPLC analyses of urine of rats treated i.p. with PTA (100 mg/kg) showed that 6-MP was formed in vivo and excreted in urine without apparent liver or kidney toxicity. Collectively, these studies show that PTA is metabolized to 6-MP both in vitro and in vivo and may therefore be a useful prodrug of 6-MP.
Delay and knowledge mediation in human causal reasoning

Contemporary theories of causal induction have focussed largely on the question of how evidence in the form of covariations between causes and effects is used to compute measures of causal strength. A very important precursor enabling such computations is that the reasoner notices that a cause and effect have co-occurred. Standard laboratory experiments have usually bypassed this problem by presenting participants directly with covariational information. As a result, relatively little is known about how humans identify causal relations in real time. What evidence exists, however, paints a rather unflattering picture of human causal induction and converges to the conclusion that humans cannot identify causal relations if cause and effect are separated by more than a few seconds. Associative learning theory has interpreted these findings to indicate that temporal contiguity is essential to causal inference. I argue instead that contiguity is not essential, but that the influence of time in causal inference is crucially dependent on people's beliefs and expectations about the timeframe of the causal relation in question. First I demonstrate that humans are capable of dissociating temporal contiguity from causal strength; more specifically, they can learn that a given event exerts a stronger causal influence when it is temporally separated from the effect than when it is contiguous with it. Then I re-investigate a paradigm commonly used to study the effects of delay on human causal induction. My experiments employed one crucial additional manipulation regarding participants' awareness of potential delays. This manipulation was sufficient to reduce the detrimental effects of delay. Three other experiments employed a similar strategy, but relied on implicit instructions about the timeframe of the causal relation in question. Overall, results support the hypothesis that knowledge mediates the timeframe of covariation assessment in human causal induction. Implications for associative learning and causal power theories are discussed.
Serotonergic nuclei of the raphe are not affected in human ageing

Sleep disorders increase with ageing. The serotonergic system has been linked with sleep regulation. In fatal familial insomnia, a prion disease with insomnia as one major clinical feature, we recently observed a disturbance in the serotonergic system as likely substrate of typical symptoms. Using immunohistochemistry for the serotonin synthesizing enzyme, tryptophan hydroxylase, we investigated the serotonergic median raphe nuclei (dorsal raphe nucleus, superior central nucleus, and raphe obscurus nucleus) in brains of an older (n = 12; age range 62–84 years) and a younger group (n = 10; age range 5–29 years). We found no significant difference between age groups in the percentage of neurons able to synthesize serotonin. Other changes might relate to sleep disturbances in the elderly.
Automatic Semantic Activation Is No Myth

The claim that semantic activation is an automatic process was recently called a myth, on the basis of the finding that if letter search is performed on a prime word, semantic priming effects on response time are eliminated, whereas repetition effects are preserved. The absence of semantic activation, however, cannot be validly inferred from the lack of response time effects, and converging evidence is needed. To this end, we examined the event-related potential correlate of priming, the N400 amplitude modulation, in a letter-search priming paradigm. Our experiment replicated the response time effects and demonstrated that the N400 amplitude successfully differentiates cross-case repetition priming, semantic priming, and neutral conditions. The results clearly indicate that the meaning of the prime word was processed and that semantic activation indeed was present in the letter-search task. The notion that semantic activation is an automatic process should not be abandoned prematurely.
Isolation and characterization of plasma membrane-associated cortical granules from sea urchin eggs

Cortical granules, which are specialized secretory organelles found in ova of many organisms, have been isolated from the eggs of the sea urchins Arbacia punctulata and Strongylocentrtus pupuratus by a simple, rapid procedure. Electron micropscope examination of cortical granules prepared by this procedure reveals that they are tightly attached to large segments of the plasma membrane and its associated vitelline layer. Further evidence that he cortical granules were associated with these cell surface layers was obtained by (125)I-labeling techniques. The cortical granule preparations were found to be rich in proteoesterase, which was purified 32-fold over that detected in a crude homogenate. Similarly, the specific radioactivity of a (125)I-labeled, surface glycoprotein was increased 40-fold. These facts, coupled with electron microscope observations, indicate the isolation procedure yields a preparation in which both the cortical granules and the plasma membrane-vitelline layer are purified to the same extent. Gel electrophoresis of the membrane-associated cortical granule preparation reveals the presence of at least eight polypeptides. The major polypeptide, which is a glycotprotein of apparent mol wt of 100,000, contains most of the radioactivity introduced by (125)I-labeling of the intact eggs. Lysis of the cortical granules is observed under hypotonic conditions, or under isotonic conditions if Ca(2+) ion is present. When lysis is under isotonic conditions is induced by addition of Ca(2+) ion, the electron-dense contents of the granules remain insoluble. In contrast, hypotonic lysis results in release of the contents of the granule in a soluble form. However, in both cases the (125)I-labeled glycoprotein remains insoluble, presumably because it is a component of either the plasma membrane or the vitelline layer. All these findings indicate that, using this purified preparation, it should be possible to carry out in vitro studies to better define some of the initial, surface-related events observed in vivo upon fertilization.
Learning, Livelihoods, and Social Mobility: Valuing Girls' Education in Central India

This article is concerned with the relationship between education, aspiration, and social mobility in Chhattisgarh, central India. I am interested in how the ideology of education as an intrinsic “social good” squares with the everyday experiences of marginalized adivasi (tribal) girls. My aim is to understand why education is differently valued by children and adults, and the ways in which girls' education-related aspirations are altered in relation to the changing possibilities of realizing them.