Miracle-dz/UniFAR-FTUs huggingface dataset:
Dissecting the Unique Nucleotide Specificity of Mimivirus Nucleoside Diphosphate Kinase

ABSTRACT The analysis of the Acanthamoeba polyphaga mimivirus genome revealed the first virus-encoded nucleoside diphosphate kinase (NDK), an enzyme that is central to the synthesis of RNA and DNA, ubiquitous in cellular organisms, and well conserved among the three domains of life. In contrast with the broad specificity of cellular NDKs for all types of ribo- and deoxyribonucleotides, the mimivirus enzyme exhibits a strongly preferential affinity for deoxypyrimidines. In order to elucidate the molecular basis of this unique substrate specificity, we determined the three-dimensional (3D) structure of the Acanthamoeba polyphaga mimivirus NDK alone and in complex with various nucleotides. As predicted from a sequence comparison with cellular NDKs, the 3D structure of the mimivirus enzyme exhibits a shorter Kpn loop, previously recognized as a main feature of the NDK active site. The structure of the viral enzyme in complex with various nucleotides also pinpointed two residue changes, both located near the active site and specific to the viral NDK, which could explain its stronger affinity for deoxynucleotides and pyrimidine nucleotides. The role of these residues was explored by building a set of viral NDK variants, assaying their enzymatic activities, and determining their 3D structures in complex with various nucleotides. A total of 26 crystallographic structures were determined at resolutions ranging from 2.8 Å to 1.5 Å. Our results suggest that the mimivirus enzyme progressively evolved from an ancestral NDK under the constraints of optimizing its efficiency for the replication of an AT-rich (73%) viral genome in a thymidine-limited host environment.
Classification of Listeria monocytogenes Persistence in Retail Delicatessen Environments Using Expert Elicitation and Machine Learning

Increasing evidence suggests that persistence of Listeria monocytogenes in food processing plants has been the underlying cause of a number of human listeriosis outbreaks. This study extracts criteria used by food safety experts in determining bacterial persistence in the environment, using retail delicatessen operations as a model. Using the Delphi method, we conducted an expert elicitation with 10 food safety experts from academia, industry, and government to classify L. monocytogenes persistence based on environmental sampling results collected over six months for 30 retail delicatessen stores. The results were modeled using variations of random forest, support vector machine, logistic regression, and linear regression; variable importance values of random forest and support vector machine models were consolidated to rank important variables in the experts’ classifications. The duration of subtype isolation ranked most important across all expert categories. Sampling site category also ranked high in importance and validation errors doubled when this covariate was removed. Support vector machine and random forest models successfully classified the data with average validation errors of 3.1% and 2.2% (n = 144), respectively. Our findings indicate that (i) the frequency of isolations over time and sampling site information are critical factors for experts determining subtype persistence, (ii) food safety experts from different sectors may not use the same criteria in determining persistence, and (iii) machine learning models have potential for future use in environmental surveillance and risk management programs. Future work is necessary to validate the accuracy of expert and machine classification against biological measurement of L. monocytogenes persistence.
Effects of Encoding Style, Expectation of Retrieval Mode, and Retrieval Style on Memory for Action Phrases

The purpose of this study was to examine the effects of encoding style, expectation of retrieval mode, and retrieval style on memory for action phrases using the recall test and the source-monitoring test. In Exp. 1, the subjects were asked to memorize action phrases with a variety of encoding styles (verbal, performance, imaging), expectation of retrieval mode to-be-remembered, to-be-performed, to-be-forgotten), and retrieval style (verbal, enacted). Analysis showed that memory for action phrases was affected by processes of encoding, i.e., type of encoding and expectation of retrieval at encoding, rather than retrieval. Also, action phrases, which were either acted out, or in which performance was imaged, or where enacting was expected later at the encoding phase, were recalled better. These results were replicated in Exp. 2, in which subjects were asked to identify the source of memories at the time of the recall test. However, results of the source-monitoring test in Exp. 1 which required, following the recall test, that participants recall as many of the test-expectation condition of action phrases as possible, showed that source memory for phrases enacted at encoding was weaker than for those in which performance was imaged or expected later but not enacted at encoding. Since, in Exp. 2, source memory for enacted items at encoding was maintained at a relatively high level, it is suggested that source memory for enacted action phrases at encoding might decay rapidly. In addition, a robust directed forgetting effect was observed in verbal and imaging encoding hut not in performance encoding.
Association between the 21-gene recurrence score assay and risk of locoregional recurrence in node-negative, estrogen receptor-positive breast cancer: results from NSABP B-14 and NSABP B-20.

PURPOSE The 21-gene OncotypeDX recurrence score (RS) assay quantifies the risk of distant recurrence in tamoxifen-treated patients with node-negative, estrogen receptor (ER)-positive breast cancer. We investigated the association between RS and risk for locoregional recurrence (LRR) in patients with node-negative, ER-positive breast cancer from two National Surgical Adjuvant Breast and Bowel Project (NSABP) trials (NSABP B-14 and B-20). PATIENTS AND METHODS RS was available for 895 tamoxifen-treated patients (from both trials), 355 placebo-treated patients (from B-14), and 424 chemotherapy plus tamoxifen-treated patients (from B-20). The primary end point was time to first LRR. Distant metastases, second primary cancers, and deaths before LRR were censored. RESULTS In tamoxifen-treated patients, LRR was significantly associated with RS risk groups (P < .001). The 10-year Kaplan-Meier estimate of LRR was 4. % (95% CI, 2.3% to 6.3%) for patients with a low RS (< 18), 7.2% (95% CI, 3.4% to 11.0%) for those with intermediate RS (18-30), and 15.8% (95% CI, 10.4% to 21.2%) for those with a high RS (> 30). There were also significant associations between RS and LRR in placebo-treated patients from B-14 (P = .022) and in chemotherapy plus tamoxifen-treated patients from B-20 (P = .028). In multivariate analysis, RS was an independent significant predictor of LRR along with age and type of initial treatment. CONCLUSION Similar to the association between RS and risk for distant recurrence, a significant association exists between RS and risk for LRR. This information has biologic consequences and potential clinical implications relative to locoregional therapy decisions for patients with node-negative and ER-positive breast cancer.
IS1414, an Escherichia coliInsertion Sequence with a Heat-Stable Enterotoxin Gene Embedded in a Transposase-Like Gene

ABSTRACT Enteroaggregative Escherichia coli (EAEC) heat-stable enterotoxin 1 (EAST1) was originally discovered in EAEC but has also been associated with enterotoxigenic E. coli (ETEC). Multiple genomic restriction fragments from each of three ETEC strains of human origin showed homology with an EAST1 gene probe. A single hybridizing fragment was detected on the plasmid of ETEC strain 27D that also encodes heat-stable enterotoxin Ib and colonization factor antigen I. We isolated and characterized this fragment, showing that it (i) carries an allele of astA nearly identical to that originally reported from EAEC 17-2 and (ii) expressed enterotoxic activity. Sequence analysis of the toxin coding region revealed thatastA is completely embedded within a 1,209-bp open reading frame (ORF1), whose coding sequence is on the same strand but in the −1 reading frame in reference to the toxin gene. In vitro expression of the predicted Mr-∼46,000 protein product of ORF1 was demonstrated. ORF1 is highly similar to transposase genes of IS285 from Yersinia pestis, IS1356 from Burkholderia cepacia, and ISRm3 from Rhizobium meliloti. It is bounded by 30-bp imperfect inverted repeat sequences and flanked by 8-bp direct repeats. Based on these structural features, pathognomonic of a regular insertion sequence, this element was designated IS1414. Preliminary experiments to show IS1414 translocation were unsuccessful. Overlapping genes of the type suggested by the IS1414 core region have heretofore not been described in bacteria. It seems to offer a most efficient mechanism for intragenomic and horizontal dissemination of EAST1.
A direct proof of the coding theorem for discrete sources with memory

In this paper we provide an alternate method of proving the existence theorem for the coding of discrete stationary ergodic sources subject to a fidelity constraint. This method differs from previously published proofs for sources with memory in that a random coding argument is obtained directly for the coding of source n -tuples. The main advantage of the technique employed in this paper is that it can easily be extended to yield the basis for the proof of the coding theorem for more general sources (e.g., nonergodic) and for sources with unknown parameters.
An overview of membrane transport proteins in Saccharomyces cerevisiae

All eukaryotic cells contain a wide variety of proteins embedded in the plasma and internal membranes, which ensure transmembrane solute transport. It is now established that a large proportion of these transport proteins can be grouped into families apparently conserved throughout organisms. This article presents the data of an in silicio analysis aimed at establishing a preliminary classification of membrane transport proteins in Saccharomyces cerevisiae. This analysis was conducted at a time when about 65% of all yeast genes were available in public databases. In addition to ∼60 transport proteins whose function was at least partially known, ∼100 deduced protein sequences of unknown function display significant sequence similarity to membrane transport proteins characterized in yeast and/or other organisms. While some protein families have been well characterized by classical genetic experimental approaches, others have largely if not totally escaped characterization. The proteins revealed by this in silicio analysis also include a putative K+ channel, proteins similar to aquaporins of plant and animal origin, proteins similar to Na+‐solute symporters, a protein very similar to electroneural cation‐chloride co‐transporters, and a putative Na+‐H+ antiporter. A new research area is anticipated: the functional analysis of many transport proteins whose existence was revealed by genome sequencing.
How much are people willing to pay for efficient waste management schemes? A benefit transfer application

To socially justify the need for better municipal solid waste management services, especially in the light of the limited availability of public funds, it is important to quantify the monetary value of the potential social and environmental benefits offered by them. This article aims at estimating society’s willingness to pay improved municipal solid waste management and establishing suitable reference values using the ‘benefit transfer’ method. To this direction, relevant studies from the global scientific and grey literature in the field of municipal solid waste management valuation are analysed and two different transfer approaches are implemented. According to the analysis, the mean annual willingness to pay per household is 88.4 USD2014 (5%-trimmed mean: 78.7 USD2014; 95% confidence interval lower bound: 64.8 USD2014 and upper bound: 112.0 USD2014). The analysis yields estimates with a high standard deviation and notably broad confidence intervals, owing to design issues of the primary studies, the different socioeconomic profiles of the populations surveyed and the existing level of municipal solid waste management services. Thus, a meta-regression model is estimated to explore the sources of heterogeneity and facilitate more accurate transfer values. Nevertheless, the limited number of observations and some methodological issues in the design and conduct of the original surveys set certain challenges and increase the level of uncertainty of the transfer values.
A Survey of Pharmacy Education in Thailand

Objective. To explore the current status of pharmacy education in Thailand. Methods. The International Pharmaceutical Federation of the World Health Organization’s (FIP-WHO) Global Survey of Pharmacy Schools was used for this study. The survey instrument was distributed to the deans of the 19 faculties (colleges) of pharmacy in Thailand. Results. More than half the colleges have been in existence less than 20 years, and the government owns 80% of them. There were 2 paths of admission to study pharmacy: direct admission and central admission system. The doctor of pharmacy (PharmD) programs can be divided into 4 types. Approximately 60% of all teaching staff holds a doctoral degree. Regarding the work balance among teaching staff, around 60% focus on teaching activities, 20% focus on research, and less than 20% focus on patient care services concurrent with real practice teaching. The proportion of student time dedicated to theory, practice, and research in PharmD programs is 51.5%, 46.7%, and 1.8%, respectively. Sites owned by the colleges or by others were used for student training. Colleges followed the Office of the National Education Standards’ Internal Quality Assurance (IQA) and External Quality Assurance (EQA), and the Pharmacy Council’s Quality Assessment (ONESQA) . Conclusion. This study provides a picture of the current status of curriculum, teaching staff, and students in pharmacy education in Thailand. The curriculum was adapted from the US PharmD program with the aim of meeting the country’s needs and includes industrial pharmacy and public health tracks as well as clinical tracks. However, this transition in pharmacy education in Thailand needs to be monitored and evaluated.
Smooth-muscle progenitor cells isolated from patients with moyamoya disease: novel experimental cell model.

OBJECT Moyamoya disease (MMD) is a cerebrovascular occlusive disease affecting bilateral internal carotid termini. Smooth-muscle cells are one of the major cell types involved in this disease process. The characteristics of circulating smooth-muscle progenitor cells (SPCs) in MMD are poorly understood. The authors purified SPCs from the peripheral blood of patients with MMD and sought to identify differentially expressed genes (DEGs) in SPCs from these patients. METHODS The authors cultured and isolated SPCs from the peripheral blood of patients with MMD (n = 25) and healthy control volunteers (n = 22). After confirmation of the cellular phenotype, RNA was extracted from the cells and DEGs were identified using a commercially available gene chip. Real-time quantitative reverse transcription polymerase chain reaction was performed to confirm the putative pathogenetic DEGs. RESULTS The SPC-type outgrowth cells in patients with MMD invariably showed a hill-and-valley appearance under microscopic examination, and demonstrated high α-smooth muscle actin, myosin heavy chain, and calponin expression (96.5% ± 2.1%, 42.8% ± 18.6%, and 87.1% ± 8.2%, respectively), and minimal CD31 expression (less than 1%) on fluorescence-activated cell sorter analysis. The SPCs in the MMD group tended to make more irregularly arranged and thickened tubules on the tube formation assay. In the SPCs from patients with MMD, 286 genes (124 upregulated and 162 downregulated) were differentially expressed; they were related to cell adhesion, cell migration, immune response, and vascular development. CONCLUSIONS With adequate culture conditions, SPCs could be established from the peripheral blood of patients with MMD. These cells showed specific DEGs compared with healthy control volunteers. This study provides a novel experimental cell model for further research of MMD.
Evolving role of endovascular treatment for MCA bifurcation aneurysms: case series of 184 aneurysms and review of the literature

Abstract Objective: This study evaluates the role of endovascular therapy for middle cerebral artery (MCA) aneurysms and its evolution over time. We are reporting a large case series of 184 MCA aneurysms and comparative analysis of the literature. Methods: This was a retrospective review of a prospectively maintained database including all patients with MCA bifurcation aneurysms embolized between 2000 and 2013. There were 184 aneurysms in 166 patients, with 71 ruptured and 113 nonruptured aneurysms. Results: Stent assistance was required in 70 cases (38·0%) and 3 cases (1·6%) required ‘Y’ stenting. The initial rate of total aneurysm occlusion was 59·8% and at delayed follow up was 90·1%. Seven embolizations resulted in thrombo-embolic complications (3·8%), with no cases of aneurysm re-bleeding, wire perforations, or other hemorrhages. Three patients with ruptured aneurysms died of causes unrelated to the embolization, and none with nonruptured aneurysms died in the follow-up period (total mortality 1·6% at 30 days post-procedure). A total of seven aneurysms (3·9%) required retreatment with an average follow up of 41 months. Prior to dedicated aneurysm stents, 68·8% of patients underwent embolization with the remainder surgically treated. Following the introduction of aneurysm stents in 2002, 92·0% of MCA aneurysms treated were embolized. Conclusions: During the past decade we have seen a treatment paradigm shift in MCA aneurysm treatment from surgical treatment to endovascular treatment. Developments in 3D angiography, more compliant balloons, dedicated aneurysm stents, complex coils, and antiplatelet therapy regimes have led to this transition for safe and effective management of these patients.
Predictors of adherence to atypical antipsychotics (risperidone or olanzapine) in older patients with schizophrenia: an open study of 3½ years duration

Although the evidence base for the use of antipsychotics in older people with schizophrenia is generally of low quality, it tends to support the use of atypical antipsychotics. Only limited information regarding longer term adherence to these apparently more effective drugs is available. The aim of this study was to determine predictors of adherence to risperidone or olanzapine in patients over 60.
Usage of cardiac simulation results in source localization of focal epicardial arrhythmias using statistical estimation

Mapping of the epicardium is possible with the usage of multielectrode venous catheters; however, most of epicardial surface is still inaccessible. To overcome this problem a method called statistical estimation was proposed, in which the relationship between catheter measurements and the remaining sites are created from previously obtained high resolution maps, called the training set. Thus, there is a need for the acquisition of high resolution epicardial maps from patients during open-chest procedures. In this study we hypothesize that epicardial maps created from computer simulations might be used in combination with maps from patients, so that the need for data acquisition during open-chest procedures would be reduced. We used high-resolution epicardial activation maps acquired from 13 dog heart experiments, 470 maps from 12 experiments (training set) and 50 maps from a separate experiment (test set). Hearts were paced from sites regularly distributed over the epicardium. The simulations of focal arrhythmias originating from epicardium were performed using a modified version of FitzHugh-Nagumo cardiac model within the ventricles of the Auckland canine heart model. We registered the experimental and simulation heart geometries using iterative closest-points algorithm and procrustes method. We started simulations from sites that corresponded to the pacing sites on the experimental geometry and created a simulated activation map database (470 maps) and compared the simulation results with the corresponding experimental maps. Finally, we performed the statistical estimation on the test set by adjusting the content of the training set in such a way that simulated maps constituted 100%, 75%, 50%, 25%, and 0% of the training set. Mean correlation coefficient (CC) between the simulated and experimental activation maps was 0.88. Mean CC and the arrhythmia source localization error worsened only from 0.93 to 0.92, and 9.65 mm to 12.14 mm when simulated activation maps constituted 50% of the training set. This study showed the feasibility of including cardiac simulation results in the training set for source localization of focal epicardial arrhythmias using statistical estimation.
The use of targeted therapies in pancreatic neuroendocrine tumours: patient assessment, treatment administration, and management of adverse events

Together with the use of novel oral targeted therapies, a multidisciplinary approach can be used to effectively treat patients with advanced pancreatic neuroendocrine tumours (pNETs). Here we review the integration of the oncology nurse to the newly developed oral treatment setting for patients with pNETs. From the outset, the nurse must be involved in various processes, including performance of baseline assessments (e.g. blood pathology, cardiac and lung function testing, patient history) and general medical observations, treatment administration, dietary guidance, evaluation of comorbidities, and review of concomitant medications. Patient education and establishment of a strong partnership in care before the start of pNET therapy ultimately increase treatment adherence and reduce potential toxicities. Regular review of general patient status and disease progression and continuous monitoring of adverse events also help enhance treatment outcomes and subsequently improve quality of life. Nurses’ knowledge of agent-specific toxicities and prompt, proactive management is a critical aspect of care. In essence, as the pNET treatment landscape evolves, the role of the healthcare professional in overall patient care must shift accordingly.
[Detection of Brucella canis by immunochromatography method in vague dogs captured in Temuco city, Chile, 2011].

BACKGROUND Brucella canis is responsible for brucellosis in dogs, causing reproductive disorders and is considered a zoonoses, as described in several countries. The epidemiological data are scarce in our country. AIM To determine the prevalence of Brucella canis in vague dogs in Temuco city and housed in the Temuco Kennel. METHODS Quantitative and cross-section study. We used 400 samples of dogs of both sexes, different ages and mainly mixed race, which were tested by immunochromatography. RESULTS Antibodies were detected in 4 samples Brucella canis which represented 1% of the population studied, 2 females (0.5%) and 2 males (0.5%). DISCUSSION We conclude that dogs are infected by B. canis in a low range but remains a risk condition to the health of the human population if not maintained adequate sanitary control of pets, like vague dogs.