Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Monomorphic and Divergent Haplotypes in the 2006-2007 Norovirus GII/4 Epidemic Population by Genomewide Tracing of Evolutionary History

ABSTRACT Our norovirus (NoV) surveillance group reported a >4-fold increase in NoV infection in Japan during the winter of 2006-2007 compared to the previous winter. Because the increase was not linked to changes in the surveillance system, we suspected the emergence of new NoV GII/4 epidemic variants. To obtain information on viral changes, we conducted full-length genomic analysis. Stool specimens from 55 acute gastroenteritis patients of various ages were collected at 11 sites in Japan between May 2006 and January 2007. Direct sequencing of long PCR products revealed 37 GII/4 genome sequences. Phylogenetic study of viral genome and partial sequences showed that the two new GII/4 variants in Europe, termed 2006a and 2006b, initially coexisted as minorities in early 2006 in Japan and that 2006b alone had dominated over the resident GII/4 variants during 2006. A combination of phylogenetic and entropy analyses revealed for the first time the unique amino acid substitutions in all eight proteins of the new epidemic strains. These data and computer-assisted structural study of the NoV capsid protein are compatible with a model of antigenic drift with tuning of the structure and functions of multiple proteins for the global outgrowth of new GII/4 variants. The availability of comprehensive information on genome sequences and unique protein changes of the recent global epidemic variants will allow studies of diagnostic assays, molecular epidemiology, molecular biology, and adaptive changes of NoV in nature.
The Political Economy of the Tunisian revolution

The Tunisian revolution has economic and social causes. It was carried out against exclusion and crony capitalism. We thus show that it can be apprehended by a political economy approach, which alone can explain the collapse of authoritarianism. The latter was able to remain in place thanks to compromises that linked the State to the poor classes, to labour and to capital. Nevertheless, the insertion of the Tunisian economy into globalization “from the bottom”, its inability to absorb graduates and the unjustified enrichment of the clans, upset the equilibrium of the system, and especially the social contract based on ascendant social mobility and the ideal of meritocracy. These ruptures helped social groups to unite in calling for the departure of Ben Ali and his family.
Plasmid-mediated transfer of the bla(NDM-1) gene in Gram-negative rods.

The latest threat of multidrug-resistant Gram-negative bacteria corresponds to the emergence of carbapenemase NDM-1 (New Delhi metallo-β-lactamase) producers, mostly in Enterobacteriacae. Five bla(NDM) (-1) -positive plasmids of different incompatibility groups (IncL/M, FII, A/C and two untypeable plasmids) from clinical Enterobacteriaceae were evaluated for conjugation properties and host specificity. Successful conjugative transfers were obtained using all tested enterobacterial species as recipients (Escherichia coli, Klebsiella pneumoniae, Salmonella typhimurium and Proteus mirabilis) and all plasmid types. Conjugation frequencies varied from 1 × 10(-4) to 6 × 10(-8) transconjugants per donor. Higher conjugation rates were obtained for two plasmids at 30 °C compared with that observed at 25 and 37 °C. Carbapenems used as selector did not lead to higher conjugation frequencies. None of the five plasmids was transferable to Acinetobacter baumannii or Pseudomonas aeruginosa by conjugation. This work underlines how efficient the spread of the carbapenemase bla(NDM) (-1) gene could be among Enterobacteriaceae.
Human adult T-cell leukemia virus: complete nucleotide sequence of the provirus genome integrated in leukemia cell DNA.

Human retrovirus adult T-cell leukemia virus (ATLV) has been shown to be closely associated with human adult T-cell leukemia (ATL) [Yoshida, M. , Miyoshi, I. & Hinuma, Y. (1982) Proc. Natl. Acad. Sci. USA 79, 2031-2035]. The provirus of ATLV integrated in DNA of leukemia T cells from a patient with ATL was molecularly cloned and the complete nucleotide sequence of 9,032 bases of the proviral genome was determined. The provirus DNA contains two long terminal repeats (LTRs) consisting of 755 bases, one at each end, which are flanked by a 6-base direct repeat of the cellular DNA sequence. The nucleotides in the LTR could be arranged into a unique secondary structure, which could explain transcriptional termination within the 3' LTR but not in the 5' LTR. The nucleotide sequence of the provirus contains three large open reading frames, which are capable of coding for proteins of 48,000, 99,000, and 54,000 daltons. The three open frames are in this order from the 5' end of the viral genome and the predicted 48,000-dalton polypeptide is a precursor of gag proteins, because it has an identical amino acid sequence to that of the NH2 terminus of human T-cell leukemia virus (HTLV) p24. The open frames coding for 99,000- and 54,000-dalton polypeptides are thought to be the pol and env genes, respectively. On the 3' side of these three open frames, the ATLV sequence has four smaller open frames in various phases; these frames may code for 10,000-, 11,000-, 12,000-, and 27,000-dalton polypeptides. Although one or some of these open frames could be the transforming gene of this virus, in preliminary analysis, DNA of this region has no homology with the normal human genome.
Feature Dependencies as Change Propagators : An Exploratory Study on Perfective Maintenance of Software Product Lines

Context: A Software Product Line (SPL) is a set of software systems (products) that share common functionalities, so-called features. When different features are related, we consider this as feature dependencies. As the SPL evolves, dealing with feature dependencies in the source code in a costand effort-effective way is challenging. During the code maintenance of SPLs, features must eventually be updated when changes in other features affect them. In other words, any change in the code associated with a feature might imply changes to one or more dependent features. Thus, a main concern in product-line maintenance is to preserve consistency between related features by propagating changes (i.e., change propagation). Objective: The objective of the study presented in this paper therefore is to examine the relation between feature dependency and change propagation. It is important to find whether there is a relation between feature dependency and change propagation. If so, it is also important to understand this relation in order to minimise the maintenance effort. Method: We investigate change propagations through feature dependencies in perfective maintenance on five evolving mediumsized SPLs which encompass twenty-one representations of the SPL’s evolution scenarios. Results: The results have empirically confirmed for the first the close relation between feature dependency and change propagation. We also identified code parts that are more likely to cause change propagation when changed. The results also revealed that the extent of change propagation in SPL features might be higher than the one found in studies in modules of stand-alone programs (i.e., non-SPL). Finally, we also found a concentration of change propagation in a few feature dependencies. Conclusion: In general, the results show that there is a relation between feature dependencies and change propagation, however such relation is not alike for all dependencies. This counter-intuitive conclusion indicates that (i) a general feature dependency minimisation might not ameliorate the change propagation, and (ii) characterising feature dependency properties must be analysed beforehand to drive maintenance effort to important dependencies.
Managing multidimensional knowledge assets: HR configurations in professional service firms

The purpose of this article is to illustrate empirically how HR practices are configured to manage multidimensional knowledge assets. It contributes directly to the configurational approaches to HRM by identifying HRM systems that are used to manage various types of knowledge assets. First, we develop a framework from theory to categorise knowledge assets into human (industry and firm specific), social (entrepreneurial and co-operative) and organisational capital (mechanistic and organic). Within this framework, we draw on data gathered in the 12 professional services firms to understand how HR practices enable the management of each knowledge asset. We identify two configurations of HR practices (organisationally and professionally focused). These configurations do not exist in isolation but are used simultaneously by organisations via either a targeted (different practices in different parts of the organisation) or a temporally segregated way (different practices for the same group of employees over time).
Professionalism vs Commercialism: The Association between Non-Audit Services (NAS) and Audit Independence

The implications of the provision of NAS to audit clients on audit independence have attracted considerable regulatory and research attention. This study contributes to this topical issue by investigating the association between NAS and audit independence using actual fee data and a more appropriate context that enables a proper "ex post" assessment of the correctness of the auditor's opinion decision. The results are consistent with the notion that auditors exhibit low propensity to issue a going-concern qualification to clients generating higher proportions of NAS fees to total fees and raise independence implications regarding the joint provision of audit and NAS. Copyright Blackwell Publishers Ltd 2001.
A new goatfish of the genus Upeneus (Mullidae) from Lombok, Indonesia and first verified record of U. asymmetricus for the Indian Ocean.

Upeneus lombok n. sp. is described from two specimens collected off Lombok, Indonesia, at depths of 54-76 m, and one subadult specimen from the local fish market at Tanjung Luar, Lombok. Four specimens of U. asymmetricus were collected at the same fish market representing the first record of the species since its description from two Philippine Islands in 1954. These two species are compared in detail and with five congeneric species that all share a 7-spined dorsal fin and a high gill-raker count. Upeneus lombok n. sp. differs from all other congeners in having a short snout (snout length 9.0-9.6% SL) combined with a low anal fin (anal-fin height 12-13% SL in adults, 15% in single subadult). The newly recorded U. asymmetricus specimens differ from their types only slightly and all eight specimens together differ from all congeneric species in the combination of 7 dorsal spines, 12-14 pectoral fin rays, 26-28 total gill rakers, short pectoral fins (pectoral-fin length 18-21% SL) and short jaws (upper jaw length 8.7-11% SL). In both species the caudal-fin colour patterns of fresh fish are of diagnostic significance, the only exception being a close similarity between Upeneus lombok n.sp. , U. saiab, and U. seychellensis. Additional comparisons with 14 Upeneus species which overlap in distribution or occur in nearby areas are also made. Needs for further taxonomic exploration of the Indonesian-Philippine region and for enhanced attention to the economic and ecological importance of Upeneus species are discussed.
Electroencephalographic Approximate Entropy Changes in Healthy Volunteers during Remifentanil Infusion

Background:The aim of this study was to investigate the independent effect of remifentanil on the approximate entropy (ApEn) in frontoparietal montages. The authors investigated which montages were relevant to assess the remifentanil effect on the electroencephalogram. Spectral edge frequency and the canonical univariate parameter were used as comparators. Methods:Twenty-eight healthy volunteers were enrolled. With recording of the electroencephalogram at the F3, F4, Cz, P3, and P4 montages, remifentanil was infused at the rate of 1–8 &mgr;g · kg−1 · min−1 for 15–20 min. The relation between remifentanil concentration and the electroencephalographic parameters were tested by Spearman correlation. Signal-to-noise ratio, artifact robustness, coefficient of variation of the median baseline and maximal electroencephalographic effects, and ratio of average maximal electroencephalographic effect to interindividual baseline variability were measured. The performance of ApEn as an index of remifentanil effect site concentrations was tested by prediction probability. Results:Approximate entropy showed significant correlation (R = −0.6465, P < 0.0001) with remifentanil concentration. It provided comparable signal-to-noise ratio, artifact robustness, and ratio of average maximal electroencephalographic effect to interindividual baseline variability to 95% spectral edge frequency. The coefficients of variation of the median baseline and maximal electroencephalo graphic effects were smallest in ApEn. Parietal montages showed higher ratios of average maximal electroencephalographic effect to interindividual baseline variability for all electroencephalographic parameters and lower coefficients of variation of the baseline values for ApEn and 95% spectral edge frequency than frontal montages. The prediction probability of ApEn was 0.7730. Conclusions:Approximate entropy derived from a parietal montage is appropriate for the assessment of the remifentanil effect on the electroencephalogram.
A Convex Formulation for Mixed Regression: Near Optimal Rates in the Face of Noise

Mixture models represent the superposition of statistical processes, and are natural in machine learning and statistics. Despite the prevalence and importance of mixture models, little is known in the realm of efficient algorithms with strong statistical guarantees. The Expectation-Minimization (EM) approach is perhaps the most popular, yet save for the Gaussian mixture clustering problem, few guarantees exist. For mixed regression in the noiseless setting, in particular, only recently has an EM-like algorithm been able to provide near-tight guarantees. In the noisy setting, tensor approaches have recently succeeded in providing a tractable and statistically consistent approach, but require a sample complexity much higher than the information-theoretic limits. We consider the mixed regression problem with two components, under adversarial and stochastic noise. Using a lifting to a higher dimensional space, we give a convex optimization formulation that provably recovers the true solution, with near-optimal sample complexity and error bounds. In the noiseless setting, our results remove the extra log factor from recent (and best-to-date) work, thus achieving exact recovery with order-wise as many samples as the degrees of freedom. In the general setting with noise, our results represent the first (and currently only known) tractable algorithm guaranteeing successful recovery with tight bounds on sample complexity and recovery errors.
Labour force sequences, unemployment spells and their effect on subjective well-being set points

Drawingupon recent psychological literature, we examine the effect of employment statuses pre- and post-unemployment on levels of subjective well-being (SWB),and the return to pre-unemployment levels, i.e. set points. Data came from the British Household Panel Survey. SWB was measured using the GHQ-12 and a question on life satisfaction; Employment status was self-reported. Multilevel, jointed, piecewise, growth curve regression models were used to explore associations by gender, specifically whether different labour force sequences produced different growth curves and rates of adaptation. Overall, there was a tendency for men and women to return to well-being set points for both outcomes. However, findings showed differences by labour force sequence and SWB measure. Women who experienced unemployment between spells of employment returned to their SWB setpoint at a faster rate of return for GHQ than for life satisfaction, while for men, the rates of return were similar to each other. Women who were employed prior to unemployment and then became economically inactive showed a return to their GHQ set point, but there was no return to their life satisfaction setpoint. Economically inactive participants pre-unemployment, who then gained employment, also showed a return to their well-being set point. After economic inactivity and then unemployment, only men experienced a significant increase in life satisfaction upon return to economic inactivity. The findings showed that following unemployment, return to subjective well-being setpoint was quicker for people who became employed than for people who became economically inactive. There were also differences in the return to SWB setpoint by type of economic inactivity upon exiting unemployment.
The role of early follow-up computed tomography imaging in the management of traumatic brain injury patients with intracranial hemorrhage.

BACKGROUND The purpose of this study was to investigate whether routine follow-up computed tomography (CT) for patients with head injury, in the absence of clinical indications, alters patient management. METHODS Nonpenetrating head injury patients admitted to San Francisco General Hospital during an 18-month period were reviewed. Patients not surgically treated at presentation and with a routine follow-up head CT within 24 hours were included. Surgical and nonsurgical interventions after repeat CT were assessed. Clinical and imaging parameters were correlated with progressive hemorrhagic injury (PHI) and with delayed development of surgical lesions. RESULTS PHI was identified in 49 (42%) of 116 patients. None of these patients required a nonoperative intervention in response to the PHI. Six of these patients developed a neurologic change concurrent with routine follow-up imaging and required operative intervention. Thus, no patient underwent an intervention in response to a worsening head CT in the absence of clinical findings. Of the six patients who developed a surgical lesion, two had increased intracranial pressure, one had a change in pupillary examination, three had worsening mental status, and one had change in the motor examination. Univariate risk factors for development of a delayed surgical lesion included 5 to 10 mm of midline shift (p = 0.001), basal cistern effacement (p = 0.01), and higher Marshall score (p = 0.01) on initial CT imaging. CONCLUSIONS Although PHI is common with head injury, delayed interventions in the absence of clinical indicators are uncommon. Our data suggest that early follow-up CT imaging in the setting of head trauma is not routinely indicated. We suggest that assessment, based on the severity of findings on initial brain imaging and serial clinical examinations, should guide the need for follow-up imaging in the setting of head trauma.
Old and new paradigms for cirrhosis associated coagulation abnormalities

In liver disease one of the liver's functions related to blood coagulation, hemostasis, is disturbed. This mani- fests as hypercoagulability in some patients and as excessive bleeding in others. Objective: The objective of this study was to review current evidence about blood coagulation disorders in cirrhotic patients. Methods: We conducted a search using the following "MESH" terms: blood coagulation disorders, cirrhosis, hemostasis, hypercoagulability, bleeding and blood coagulation tests. From the results articles whose titles and abstracts best fit with the aim of this review were chosen. Results: From 146 articles obtained, 76 were selected and used to construct this article. Conclusion: Despite the diverse blood coagulation disorders present in cirrhotic patients, the hemostatic system accomplishes a new balance that currently used blood coagulation tests fail to show. This is the why these cannot be considered useful tools for predicting the risk of bleeding or thrombotic complications.
Consulting the oracle: ten lessons from using the Delphi technique in nursing research.

AIM The aim of this paper was to provide insight into the Delphi technique by outlining our personal experiences during its use over a 10-year period in a variety of applications. BACKGROUND As a means of achieving consensus on an issue, the Delphi research method has become widely used in healthcare research generally and nursing research in particular. The literature on this technique is expanding, mainly addressing what it is and how it should be used. However, there is still much confusion and uncertainty surrounding it, particularly about issues such as modifications, consensus, anonymity, definition of experts, how 'experts' are selected and how non-respondents are pursued. DISCUSSION This issues that arise when planning and carrying out a Delphi study include the definition of consensus; the issue of anonymity vs. quasi-anonymity for participants; how to estimate the time needed to collect the data, analyse each 'round', feed back results to participants, and gain their responses to this feedback; how to define and select the 'experts' who will be asked to participate; how to enhance response rates; and how many 'rounds' to conduct. CONCLUSION Many challenges and questions are raised when using the Delphi technique, but there is no doubt that it is an important method for achieving consensus on issues where none previously existed. Researchers need to adapt the method to suit their particular study.
Regulation and cell-type-specific activity of a promoter located upstream of the latency-associated transcript of herpes simplex virus type 1

To identify promoter regions which control expression of the latency-associated transcript (LAT) of herpes simplex virus type 1 (HSV-1), we constructed a series of recombinant vectors in which various sequences upstream of LAT were linked to the chloramphenicol acetyltransferase gene and tested for expression efficiency by transfection into tissue culture cells. In HeLa cells no activity was observed from the region (-250 to +201) immediately surrounding the nominal 5' end of LAT, but high levels of activity were observed by using different fragments within the region -1267 to -594. This promoter activity was largely contained within the 140-base-pair region from -797 to -658 and was 20- to 50-fold stronger than typical HSV delayed-early promoters and at least as strong as the activity from the simian virus 40 (SV40) enhancer-promoter region or the HSV immediate-early 110,000-Mr (IE110K) promoter region. In human neuroblastoma cells (IMR-32), there was a dramatic switch in relative activities in favor of the LAT promoter, so that it was 45- and 200-fold stronger than the IE110K and SV40 constructs, respectively. Furthermore, optimal activity in the neuroblastoma cells required sequences within the region -1267 to -797. This region had little effect on activity in HeLa cells. We also show that the LAT promoter activity was very efficiently repressed by the IE175K protein. From internal deletion analysis, the site of repression was located within a 55-base-pair region just downstream of a potential TATA box. This region exhibited a high degree of homology with the IE175K cap site and may be a binding site for the IE175K protein.