Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficiency in Complexity: Composition and Dynamic Nature of Mimivirus Replication Factories

ABSTRACT The recent discovery of multiple giant double-stranded DNA (dsDNA) viruses blurred the consensual distinction between viruses and cells due to their size, as well as to their structural and genetic complexity. A dramatic feature revealed by these viruses as well as by many positive-strand RNA viruses is their ability to rapidly form elaborate intracellular organelles, termed “viral factories,” where viral progeny are continuously generated. Here we report the first isolation of viral factories at progressive postinfection time points. The isolated factories were subjected to mass spectrometry-based proteomics, bioinformatics, and imaging analyses. These analyses revealed that numerous viral proteins are present in the factories but not in mature virions, thus implying that multiple and diverse proteins are required to promote the efficiency of viral factories as “production lines” of viral progeny. Moreover, our results highlight the dynamic and highly complex nature of viral factories, provide new and general insights into viral infection, and substantiate the intriguing notion that viral factories may represent the living state of viruses. IMPORTANCE Large dsDNA viruses such as vaccinia virus and the giant mimivirus, as well as many positive-strand RNA viruses, generate elaborate cytoplasmic organelles in which the multiple and diverse transactions required for viral replication and assembly occur. These organelles, which were termed “viral factories,” are attracting much interest due to the increasing realization that the rapid and continuous production of viral progeny is a direct outcome of the elaborate structure and composition of the factories, which act as efficient production lines. To get new insights into the nature and function of viral factories, we devised a method that allows, for the first time, the isolation of these organelles. Analyses of the isolated factories generated at different times postinfection by mass spectrometry-based proteomics provide new perceptions of their role and reveal the highly dynamic nature of these organelles.
Tumor marker pyruvate kinase type tumor M2 in patients suffering from diabetic nephropathy.

INTRODUCTION Compared to normal tissues all tumors investigated so far and especially those with a metastatic potential overexpress an isoenzyme of the pyruvate kinase, the pyruvate kinase type tumor M2 (TU M2-PK). Because of its monomeric structure, the TU M2-PK has no function at all. PATIENTS AND METHODS Using an enzyme-linked immuno sorbent assay (ELISA) developed by ScheBooTech (Wettenberg, Germany) we measured the concentration of TU M2-PK in EDTA-plasma of 12 probands with insulin-dependent diabetes mellitus and 91 patients suffering from non-insulin-dependent diabetes mellitus, both with diabetic nephropathy. Moreover we focused on the way it compares to other metabolic markers such as HbA1c, glucose and proteins. RESULTS Among the 12 patients afflicted by insulin-dependent diabetes mellitus 17%, and the 91 probands with non-insulin-dependent diabetes mellitus as many as 19% of the samples were raised over the cut-off of 25 U/ml EDTA-plasma. A correlation with the other investigated parameters could not be found. CONCLUSION This study shows that the TU M2-PK in EDTA-plasma of patients with diabetic nephropathy presents 38.8% "false-positive" data and thus must be questioned as a tumor marker.
Information Systems Management

One of the perennial top issues in surveys of IT management concerns is IT alignment. It always seems to be in the top-ten, but cyclically rises to number-one at times of economic decline. When the economy turns down, information services departments are called upon to redouble their vigilance on spending and to focus their attention on projects and initiatives that are in line with the near-term objectives of the overall business. The enterprises that have developed collaborative management processes between the business and information services organizations do this best and with the least amount of disruption. In fact, it seems that there has been tremendous progress in the past ten or fifteen years in terms of leadership and management practices on the part of both business and information services organizations that have contributed to a dramatic improvement in the handling of downward economic adjustments. Upward economic change, on the other hand, poses more perplexing challenges.
The Geography of Foreign R&D Within a Host Country

Abstract Recent research on multinational firms emphasizes the learning and knowledge-creating aspects of foreign direct investment. According to this view, multinationals may be pulled abroad in order to “harness the new sources of knowledge and ideas embedded in regionally based centers of innovation” (Florida and Kenney 1994). This paper develops and tests a set of hypotheses linking the technological characteristics of regions within a host country to levels of R&D investment in those regions by foreign multinationals. We argue that the economic geography offoreign R&D investment can be understood through an evolutionary lens in which the tacit and embodied characteristics of knowledge give rise to its locational boundedness—and hence an incentivefor firms to be proximate to these resources. We further argue that the existing “site-selection” literature is misplaced in focusing solely on the geography of new facilities and investments by multinational firms. When viewed through an evolutionary lens, the economic geography of foreign R&D can be understood as a cumulative process of expansion, contraction, and adaptation by firms of existingfacilities in host-country locations. Firms, in essence, make an ongoing series of joint location-technology choices that largely determine the observable pattern of FDI in R&D. To test our hypotheses, we utilize a comprehensive database of patenting activity by US. -based subsidiaries between 1977 and 1990. Results show broad-level support for our claims.
Nasal complaints and signs of disease in farmers – a methodological study

Conclusion. The methods used in this study are suitable for field studies that involve examinations of groups of workers. For individual examinations, there is no gold standard method that can discriminate work-related discomfort from other causes of rhinitis. Objectives. Studies of the effects of occupation on farmers’ health have mainly focused on lower airways; few studies have examined effects on upper airways. This study investigated nasal functions in three groups of farmers (swine, milk and grain producers) and a control group using different methods, suitable for field studies. Subjects and methods. Health-related complaints were examined and several functional tests, such as expirogram, olfactory threshold test, acoustic rhinometry, nasal lavage with biomarkers of inflammation (eosinophilic cationic proteins (ECP), myeloperoxidase (MPO), tryptase, albumin) and allergy tests were performed. The different tests were correlated to nasal complaints and to each other. Results. Nasal blockage complaints were more common among farmers; overall, nasal polyps were more frequent in grain producers. Objective parameters showed more pronounced mucosal swelling in farmers and higher concentrations of ECP in nasal lavage compared with controls. Lung function, olfactory threshold, atopy frequency and allergen-specific IgE to the storage mite Lepidoglyphus destructor did not differ between farmers and controls. Mucosal swelling measured with acoustic rhinometry was more pronounced in subjects with nasal complaints, hypersensitivity, nasal polyps and symptoms from lower airways. There was a correlation between biomarkers in nasal lavage (MPO, albumin and ECP).
Taxonomies for automated question triage in digital reference

We identify (1) several taxonomies of questions at different levels of linguistic analysis, according to which questions received by digital reference services are classified, and (2) a simple categorization of triage recipients. The utility of these taxonomies and categorizations of triage recipients is discussed as the basis for systems for automating triage and other steps in the digital reference process.
Herpes simplex virus type 2 and human papillomavirus type 16 in cervicitis, dysplasia and invasive cervical carcinoma

Sera and biopsies of cervical lesions from 55 women with benign or malignant disease were analyzed for evidence of infection with herpes simplex virus type 2 (HSV‐2) or human papillomavirus (HPV). In addition, information regarding known risk factors for cervical cancer was obtained by interview. The sera were tested for HSV‐2 antibodies and the biopsies were tested for HPV or HSV DNA sequences by Southern blot hybridization. HSV‐2 sequences were detected in 2/13 (15%) invasive neoplasms and in 1/12 (7%) benign lesions. Under non‐stringent conditions of hybridization, reactions with HPV DNA were detected in biopsies of 2/17 (12%) inflammatory lesions, 6/12 (50%) intraepithelial neoplasms and 13/20 (65%) invasive neoplasms. All but one of the positive biopsies of invasive cancer, but only 4/11 biopsies of non‐invasive lesions, contained HPV‐16 DNA as determined by stringent hybridization conditions. Women with cervical cancer possessed the risk factors associated with the disease. Cigarette smoking and the presence of HPV‐16 DNA were the most prominent risk factors. No evidence of an interaction between HSV‐2 and HPV‐16 was found among the cases of invasive cervical cancer.
Developmental Arrest and Mouse Antral Not-Surrounded Nucleolus Oocytes1

ABSTRACT The antral compartment in the ovary consists of two populations of oocytes that differ by their ability to resume meiosis and to develop to the blastocyst stage. For reasons still not entirely clear, antral oocytes termed surrounded nucleolus (SN; 70% of the population of antral oocytes) develop to the blastocyst stage, whereas those called not-surrounded nucleolus (NSN) arrest at two cells. We profiled transcriptomic, proteomic, and morphological characteristics of antral oocytes and observed that NSN oocyte arrest is associated with lack of cytoplasmic lattices coincident with reduced expression of MATER and ribosomal proteins. Cytoplasmic lattices have been shown to store maternally derived mRNA and ribosomes in mammalian oocytes and embryos, and MATER has been shown to be required for cytoplasmic lattice formation. Thus, we isolated antral oocytes from a Matertm/tm mouse and we observed that 84% of oocytes are of the NSN type. Our results provide the first molecular evidence to account for inability of NSN-derived embryos to progress beyond the two-cell stage; these results may be relevant to naturally occurring preimplantation embryo demise in mammals.
Fencing the bear? Explaining US foreign policy towards Russian interventions

ABSTRACT Despite the burgeoning literature on Russia’s renewed power politics, little attention has been paid to the fact that US reactions towards Russia’s military interventions were all but coherent. The USA has chosen weak measures in Georgia in 2008 (shaming) compared to its assertive response in Ukraine in 2014 (sanctions, hard deterrence). This article assesses the explanatory power of neorealist, liberal and constructivist theories for the variation in US reactions towards Russian interventions in Georgia and Ukraine. Our argument is that the constructivist perspective explains the cases best as it highlights the power and communality of normative assessments. The Ukraine crisis was perceived by the USA as a violation of core international norms, especially the non-use of force and the principle of territorial integrity. Relevant international norm carriers shared this assessment of the conflict. In contrast, the perception of the Georgian war centred on the issue of democracy promotion. While democracy is an important aim of US foreign policy, it does not summon the same normative importance as general principles of international law. Furthermore, the perception of the Georgian war remained contested among Western allies, which decreased the communality of the normative assessment.
Salt sensitivity of the morphometry of Artemia franciscana during development: a demonstration of 3D critical windows

ABSTRACT A 3D conceptual framework of ‘critical windows’ was used to examine whether the morphometry of Artemia franciscana is altered by salinity exposure during certain key periods of development. Artemia franciscana were hatched at 20 ppt (designated control salinity) and were then exposed to 10, 30, 40 or 50 ppt either chronically (days 1–15) or only on days 1–6, 7–9, 10–12 or 13–15. On day 15, maturity was assessed and morphometric characteristics, including mass, total body length, tail length and width, length of the third swimming appendage and eye diameter, were measured. Maturation and morphometry on day 15 were influenced by the exposure window and salinity dose. Artemia franciscana were generally larger following exposure to 10 and 40 ppt during days 1–6 and 7–9 when compared with days 10–12 and 13–15, in part due to a higher percentage of mature individuals. Exposure to different salinities on days 1–6 produced the greatest differences in morphometry, and thus this appears to be a period in development when A. franciscana is particularly sensitive to salinity. Viewing the developmental window as three-dimensional allowed more effective visualization of the complex interactions between exposure window, stressor dose and the magnitude of morphometric changes in A. franciscana. Summary: A novel 3D critical window construct reveals how morphometry of Artemia is influenced by salinity level and the time of salinity exposure during development.
Biogeographic patterns of soil diazotrophic communities across six forests in the North America

Soil diazotrophs play important roles in ecosystem functioning by converting atmospheric N2 into biologically available ammonium. However, the diversity and distribution of soil diazotrophic communities in different forests and whether they follow biogeographic patterns similar to macroorganisms still remain unclear. By sequencing nifH gene amplicons, we surveyed the diversity, structure and biogeographic patterns of soil diazotrophic communities across six North American forests (126 nested samples). Our results showed that each forest harboured markedly different soil diazotrophic communities and that these communities followed traditional biogeographic patterns similar to plant and animal communities, including the taxa–area relationship (TAR) and latitudinal diversity gradient. Significantly higher community diversity and lower microbial spatial turnover rates (i.e. z‐values) were found for rainforests (~0.06) than temperate forests (~0.1). The gradient pattern of TARs and community diversity was strongly correlated (r2 > 0.5) with latitude, annual mean temperature, plant species richness and precipitation, and weakly correlated (r2 < 0.25) with pH and soil moisture. This study suggests that even microbial subcommunities (e.g. soil diazotrophs) follow general biogeographic patterns (e.g. TAR, latitudinal diversity gradient), and indicates that the metabolic theory of ecology and habitat heterogeneity may be the major underlying ecological mechanisms shaping the biogeographic patterns of soil diazotrophic communities.
Management and outcomes of patients with reduced ejection fraction after acute myocardial infarction in cardiac rehabilitation centers

Abstract Background: We aimed to describe the contemporary management of patients with systolic chronic heart failure (CHF) during a cardiac rehabilitation (CR) stay and present outcomes with focus on lipids, blood pressure, exercise capacity, and clinical events. Methods: Comparison of 3199 patients with moderately or severely impaired left ventricular ejection fraction (low EF, 13.3%) and 20,913 patients with slightly reduced or normal LVEF (normal EF, 86.7%) who underwent an inpatient CR period of about 3 weeks in 2009–2010. Results: Patients with low EF compared to those with normal EF were somewhat older (65.1 vs. 63.0 years, p < 0.0001), and more often had risk factors such as diabetes mellitus (39.7% vs. 32.0%, p < 0.0001) or other comorbidities. The overall rate of patients with regular physical activity of at least 90 minutes per week prior to CR was low overall (54.4%), and reduced in patients with low EF compared to those with normal EF (47.7% vs. 55.5%, p < 0.0001). The rate of patients that achieved lower LDL cholesterol (<100 mg/dl), total cholesterol (<200 mg/dl) and triglyceride (<150 mg/dl) values at discharge increased compared to baseline. Mean blood pressure was substantially lower in the low EF group compared to the normal EF group both at baseline (124/75 vs. 130/78 mmHg, p < 0.0001) and at discharge (119/72 vs. 124/74 mmHg, p < 0.0001). Maximum exercise improved substantially in both groups (at baseline 71 vs. 91 Watts, p < 0.0001; at discharge 85 vs. 105 Watts, p < 0.0001). Event rates during CR were low, and only 0.3% in the low EF group died. As limitations to this study, information on brain natriuretic peptide (BNP), N-terminal pro-brain natriuretic peptide (NT-pro BNP) and/or cardiac troponin were not documented, and no long-term information was collected beyond the 3-week CR stay. Conclusions: Patients with CHF account for a considerable proportion of patients in CR. Also patients with moderate/severe EF benefited from participation in CR, as their lipid profile and physical fitness improved.
Foreign Direct Investment in Nigeria: Reassessing the Role of Market Size

This paper examines the influence of market size on foreign direct investment to Nigeria for the period 1970 – 2011. It answers the question: do multinational enterprises consider market size in the allocation of their foreign direct investment (FDI) to Nigeria? Unlike similar previous studies on Nigeria, this paper examines market size in terms of economy size and population size. Autoregressive Distributed Lag (ARDL) model and Granger Causality Tests were estimated. The results show that economy size and population size has positive and significant effect on foreign direct investment to Nigeria. Market size also Granger causes FDI to Nigeria. This paper, therefore, concludes that multinational enterprises consider Nigerian market size in the allocation of their foreign direct investment (FDI) to the country.
Decreased jejunal uptake of labeled folic acid ( 3 H-PGA) in alcoholic patients: roles of alcohol and nutrition.

Abstract The jejunal uptake of labeled folic acid (3H-PGA) was measured in chronic alcoholic patients without definite liver disease. The intestine was perfused through a triple lumen tube with a solution containing 3H-PGA in a concentration of 25 ng per milliliter. Uptake was low in eight patients who gave a history of poor diet during the alcoholic binge that preceded admission (20.4 per cent ± 4.16 S.D.). A significantly greater value was obtained in nine abstinent subjects fed a hospital diet for two weeks (36.5 per cent ± 5.75). The subsequent administration of ethanol for two weeks to seven patients did not change the mean uptake of 3H-PGA (34.8 per cent ± 9.87). This study confirms that the absorption of folic acid is decreased in malnourished, actively drinking alcoholics. The data suggest that the functional defect is caused by poor nutrition rather than a toxic effect of ethanol on the jejunum.
Do Patients With Chronic Low Back Pain Have a Lower Level of Aerobic Fitness Than Healthy Controls?: Are Pain, Disability, Fear of Injury, Working Status, or Level of Leisure Time Activity Associated With the Difference in Aerobic Fitness Level?

Study Design. Prospective case series with historical controls (normative data). Objectives. To compare the aerobic fitness level of patients with chronic low back pain (CLBP) with healthy controls matched for gender, age, and level of sport activity and to evaluate the association of the difference in aerobic fitness level with pain intensity, duration and degree of disability, fear of injury, and level of activity during work, including household and leisure time. Summary and Background Data. Controversy exists whether patients with CLBP have a lower level of aerobic fitness and whether this level may partly depend on the patients’ activity level. Methods. A total of 108 CLBP patients completed questionnaires regarding pain, disability, fear of injury, and activity level and performed a modified Åstrand submaximal cycling test. The maximum oxygen consumption (VO2max) was calculated and compared with normative data. Multiple linear regression analysis was performed with the difference of the level of aerobic fitness as dependent variable. Results. VO2max could be calculated in 78% of the patients. Both men and women with CLBP had significant lower VO2max than the healthy referents (10 mL/kg LBM • min−1 and 5.6 mL/kg LBM • min−1 respectively, P < 0.001), and this difference was significantly greater in men (P = 0.03). Multiple regression analysis showed that the level of aerobic fitness was not associated with the presumed variables. The patients who stopped the test prematurely were older (P = 0.02) and more disabled (P = 0.01). Conclusion. CLBP patients, especially men, seem to have a reduced aerobic fitness level compared with the normative population. No explanatory factor for that loss could be identified.
Rapid T cell receptor‐mediated SHP‐1 S591 phosphorylation regulates SHP‐1 cellular localization and phosphatase activity

Since the tyrosine phosphatase SHP‐1 plays a major role in regulting T cell signaling, we investigated regulation thereof by Ser/Thr phosphorylation. We found that T cell receptor (TCR) stimulation induced fast (≤1 min) and transient phosphorylation of SHP‐1 S591 in both Jurkat and human peripheral blood T‐cells (PBT). Phosphorylation of S591 in T‐cells could be mediated artificially by a constitutive active PKC‐theta construct, but the dose dependence of inhibition by PKC inhibitors indicated that PKCs were not the relevant basophilic kinase in the physiological response. S591 phosphorylation inhibited phosphatase function since a S591D mutant had lower activity than the S591A mutant. Additional evidence that S591 phosphorylation alters SHP‐1 function was provided by studies of Jurkat cells stably expressing SHP‐1 wild type or mutants. In those cells, S591D mutation reduced the capacity of transfected SHP‐1 to inhibit TCR‐induced phosphorylation of PLC‐γ1. Interestingly, SHP‐1 Y536 phosphorylation (previously shown to augment phosphatase activity) was also induced in PBT by TCR signal but at a much later time compared with S591 (∼30 min). S591 phosphorylation also altered cellular distribution of SHP‐1 because: 1) SHP‐1 in lipid rafts and a sheared membrane fraction was hypophosphorylated; 2) In stably transfected Jurkat cell lines, S591D mutant protein had reduced presence in both lipid raft and the sheared membrane fraction; 3) S591 phosphorylation prevented nuclear localization of a C‐terminal GFP tagged SHP‐1 construct. Our studies also shed light on an additional mechanism regulating SHP‐1 nuclear localization, namely conformational autoinhibition. These findings highlight elegant regulation of SHP‐1 by sequential phosphorylation of serine then tyrosine.