Miracle-dz/UniFAR-FTUs huggingface dataset:
Plasmodium falciparum Merozoite Surface Protein 8 Is a Ring-Stage Membrane Protein That Localizes to the Parasitophorous Vacuole of Infected Erythrocytes

ABSTRACT To date, the following seven glycosylphosphatidylinositol (GPI)-anchored merozoite antigens have been described in Plasmodium falciparum: merozoite-associated surface protein 1 (MSP-1), MSP-2, MSP-4, MSP-5, MSP-8, MSP-10, and the rhoptry-associated membrane antigen. Of these, MSP-1, MSP-8, and MSP-10 possess a double epidermal growth factor (EGF)-like domain at the C terminus, and these modules are considered potential targets of protective immunity. In this study, we found that surprisingly, P. falciparum MSP-8 is transcribed and translated in the ring stage and is absent from the surface of merozoites. MSP-8 is the only GPI-anchored protein known to be expressed at this time. It is synthesized as a mature 80-kDa protein which is rapidly processed to a C-terminal 17-kDa species that contains the double EGF module. As determined by a combination of immunofluorescence and membrane purification approaches, it appears likely that MSP-8 initially localizes to the parasite plasma membrane in the ring stage. Although the C-terminal 17-kDa fragment is present in more mature stages, at these times it is found in the food vacuole. We successfully disrupted the MSP-8 gene in P. falciparum, a process that validated the specificity of the antibodies used in this study and also demonstrated that MSP-8 does not play a role essential to maintenance of the erythrocyte cycle. This finding, together with the observation that MSP-8 is exclusively intracellular, casts doubt over the viability of this antigen as a vaccine. However, it is still possible that MSP-8 is involved in an early parasitophorous vacuole function that is significant for pathogenesis in the human host.
Southern European glacial refugia: A tale of tales

Interpretations of current diversity patterns based on the contraction/expansion model forced by climatic oscillations during the last two million years are commonplace in phylogeographic literature. Of the wealth of scientific studies accumulated during the past two decades in Europe, the ones we understand best are those mostly from higher latitudes, probably because patterns were simplified to a great extent by major losses of diversity during glacial periods. In Southern European regions (or in general, in those places where ice effects were less severe) the situation is quite different and to some extent opposite. These regions are referred to as refugia because they are known to contain more genetic diversity than elsewhere. This is not only due to preservation of genotypes that went extinct in other places, however, but also to the intensity and accumulation of a number of processes in a patchy landscape across a varied topography. A lack of general phylogeographic patterns in these regions is one consequence. Speaking of a single refugium to refer to each of the peninsulas, however, is an oversimplification. Even speaking of multiple unconnected refugia does not adequately reflect the complexity of the processes that shaped the current genetic and specific diversity.
Gene expression Markers improve clustering of CGH data

Motivation: We consider the problem of clustering a population of Comparative Genomic Hybridization (CGH) data samples using similarity based clustering methods. A key requirement for clustering is to avoid using the noisy aberrations in the CGH samples. Results: We develop a dynamic programming algorithm to identify a small set of important genomic intervals calledmarkers. Theadvantage of using these markers is that the potentially noisy genomic intervals are excluded during the clustering process. We also develop two clustering strategies using these markers. The first one, prototype-based approach, maximizes the support for the markers. The second one, similarity-based approach, develops a new similarity measure called RSimand refinesclusterswith theaimofmaximizing theRSimmeasure between the samples in the same cluster. Our results demonstrate that the markers we found represent the aberration patterns of cancer types well and they improve the quality of clustering significantly. Availability: All software developed in this paper and all the datasets used are available from the authors upon request. Contact: juliu@cise.ufl. edu
Vaccinia virus strain NYVAC induces substantially lower and qualitatively different human antibody responses compared with strains Lister and Dryvax

The antibody responses elicited by immunization of humans with vaccinia virus (VACV) strains Lister, Dryvax and NYVAC have been determined and compared. Neutralizing antibodies against intracellular mature virus (IMV) and extracellular enveloped virus (EEV), and binding antibody titres (ELISA) against the EEV protein B5, the IMV proteins A27 and H3, and VACV-infected cell lysate were measured. Lister and Dryvax induced broadly similar antibody titres, consistent with the fact that these vaccines each protected against smallpox. In contrast, antibody titres induced by NYVAC were significantly lower than those induced by both Lister and Dryvax. Moreover, there were qualitative differences with NYVAC-immunized subjects failing to induce A27-specific antibodies. These observations suggest that although NYVAC is a safer VACV strain, it does not induce an optimal VACV-specific antibody response. However, NYVAC strains engineered to express antigens from other pathogens remain promising candidate vaccines for immunization against other diseases.
Safety and Health at Work

Background: Previous research has shown that paramedics are exposed to risks in the form of injuries to the musculoskeletal system. In addition, there are studies showing that they are also at increased risk of cardiovascular disease, cancer, and psychiatric diseases, which can partly be explained by their constant exposure to stress. The aim of this study is to evaluate whether the use of shoulder straps decreases physical effort in the form of decreased heart rate and cortisol concentration. Methods: A stretcher with a dummy was carried by 20 participants for 400 m on two occasions, one with and one without the shoulder straps. Heart rate was monitored continuously and cortisol samples were taken at intervals of 0 minutes, 15 minutes, 30 minutes, 45 minutes, and 60 minutes. Each participant was her or his own control. Results: A significant decrease in heart rate and cortisol concentration was seen when shoulder straps were used. The median values for men (with shoulder straps) at 0 minutes was 78 bpm/21.1 nmol/L (heart rate/cortisol concentration), at 15 minutes was 85 bpm/16.9 nmol/L, and at 60 minutes was 76 bpm/15.7 nmol/L; for men without shoulder straps, these values were 78 bpm/21.9 nmol/L, 93 bpm/ 21.9 nmol/L, and 73 bpm/20.5 nmol/L. For women, the values were 85 bpm/23.3 nmol/L, 92 bpm/ 20.8 nmol/L, and 70 bpm/18.4 nmol/L and 84 bpm/32.4 nmol/L, 100 bpm/32.5 nmol/L, and 75 bpm/ 25.2 nmol/L, respectively. Conclusion: The use of shoulder straps decreases measurable physical stress and should therefore be implemented when heavy equipment or a stretcher needs to be carried. An easy way to ensure that staff use these or similar lifting aids is to provide them with personalized, well-adapted shoulder straps. Another better option would be to routinely sewn these straps into the staff’s personal alarm jackets so they are always in place and ready to be used. Copyright 2015, Occupational Safety and Health Research Institute. Published by Elsevier. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
Cytotoxic T Lymphocyte-associated Antigen 4 Polymorphisms Correlated with Graves’ Disease in Patients of Han Ethnicity in Yunnan, China

Objective: To investigate the correlations between polymorphisms at position 49 in exon 1 and position 318 in the promoter of the cytotoxic T lymphocyte-associated antigen 4 (CTLA-4) gene and autoimmune thyroid diseases in a Han Chinese population. Methods: Polymerase chain reaction-restriction fragment length polymorphism was utilized. The MseI and BbvI restriction endonucleases were used to detect and analyse position 49 in exon 1 and position 318 in the promoter as well as the T/C alleles of the CTLA-4 gene in peripheral blood samples from 112 patients with Graves’ disease (GD), 101 with Hashimoto’s thyroiditis (HT) and 100 healthy individuals. Results: At position 49 of exon 1, the frequencies of the GG genotype and the G allele in the GD group (χ2 = 12.147; p = 0.002) were statistically significantly higher than those in the control group (χ2 = 9.925; p = 0.002), while no statistically significant differences were found between the frequencies of the GG genotype and the G allele in the HT group (χ2 = 1.195; p = 0.550) and those in the control group (χ2 = 0.984; p = 0.321). No statistically significant differences in the promoter (-318) or the T/C alleles were observed among the three groups. Position 49 in the 17th codon of exon 1 of the CTLA-4 gene may be a candidate susceptibility marker in patients of Han ethnicity with GD. Conclusion: This finding helps us to better understand the genetic risks for GD and provides a direction for targeted gene therapy.
Bayesian Approach: An Alternative to Periodogram and Time Axes Estimation for Known and Unknown White Noise

This study describes the Bayesian approach as an alternative approach for estimating time axes parameters and the periodogram (power spectrum) associated with sinusoidal model when the white noise (sigma) is known or unknown. The conventional method of estimating the time axes parameters and the periodogram has been via the Schuster method that relies solely on Maximum Likelihood Estimation (MLE). The Bayesian alternative approach proposed in this work, on the other hand, adopted the Maximum a Posteriori (MAP) via the Markov Chain Monte Carlo (MCMC) in order to checkmate the problem of re-parameterization and overparameterization associated with MLE in the conventional practice. The rates of heartbeat variability at exactly an hour and two hours after birth of one thousand eight hundred (1800) newly born babies in a state hospital were recorded and subjected to both the Bayesian approach and Schuster approach for inferences. The periodogram estimates, exactly an hour and two hours of after birth, were estimated to be 0.7395 and 0.7549, respectively and it was deduced that rates of heartbeat (frequency) variability moderated and stabilized the pulse among the babies after two hours of birth. In addition, MAP mean estimates of the parameters approximately equals to the true mean of estimates when round up to curb the problem of re-parameterization and overparameterization that do affect Schuster method via MLE.
Summary of alluvial channel data from flume experiments, 1956-61

The invention pertains to a front or back panel for motorbuses, having an arcuate framework, the vertical edges of which are constituted each by a shaped bar designed for imparting great strength to said panel, said bar serving as an upright of the body of the motorbus during the assembly of the latter.
Growing old in a changing climate: meeting the challenges of an ageing population and climate change

Climate change and an ageing population in the United Kingdom bring together two key policy challenges which need to be addressed to ensure a safe, secure, equitable and sustainable future. Vulnerability of people in old age arises from the interactions between advantages and disadvantages accumulated during the course of one's life and the experience of threats in later life. Whether this interaction creates a better or worse outcome depends on the individual's coping resources. Climate vulnerability in old age requires an understanding of exposure factors and their distribution over time and the way individuals manage or fail to mobilise social, material and public resources to protect themselves from bad outcomes. Section 4.4 of this report covers the possible effects of climate change on transport.
Nitrogen cycling during the Cretaceous, Cenomanian‐Turonian Oceanic Anoxic Event II

Low δ15N values, ranging from +1.2‰ to −3.9‰, and atomic carbon/nitrogen (C/N) ratios of 25–50 are characteristic of “black shales” deposited during the Cenomanian‐Turonian boundary interval and Oceanic Anoxic Event II (OAE II). An observed antithetic relationship between C/N ratios and δ15N could suggest a predominance of terrestrially derived organic matter or a diagenetic control on δ15N variability shifting bulk δ15N values lower. However, Hydrogen Indices (HI) generally >450, and a positive correlation of HI with C/N mitigates against a significant terrestrial organic matter fraction. High C/N values are likely the result preferential degradation of labile, N‐rich compounds during early diagenesis and loss of N as ammonium from sediments through time. A hypothetical model that considers the degradation of a 15N‐enriched labile protein fraction yields only small, 1–2‰ negative shifts in δ15N. However, 15N depletion during diagenesis is contrary to normal isotope kinetics which should result in 15N enrichment of bulk organic matter. Therefore we conclude that the bulk δ15N values in this study reflect primary changes in the nitrogen cycle. The δ15N data support the hypothesis of expanded nitrogen fixation driven by upwelling of nutrient‐nitrogen poor, phosphorus replete waters during OAE II and from the mid‐Cenomanian to Santonian at Demerara Rise. The low δ15N values, which are significantly lower than bulk δ15N values in modern regions where nitrogen fixation is known to be important, probably result from a more significant fraction of dissolved inorganic nitrogen being produced by nitrogen fixation. During the peak of OAE II a marked shift to lower δ15N values is observed. This shift possibly reflects greater utilization of 15N‐depleted ammonium during a chemocline upward excursion (CUE). Dominance of low δ15N values from other periods of more widespread marine anoxia is likely the result of similar processes.
Functional and Biochemical Characterization of Human Eukaryotic Translation Initiation Factor 3 in Living Cells

ABSTRACT The main role of the translation initiation factor 3 (eIF3) is to orchestrate formation of 43S-48S preinitiation complexes (PICs). Until now, most of our knowledge on eIF3 functional contribution to regulation of gene expression comes from yeast studies. Hence, here we developed several novel in vivo assays to monitor the integrity of the 13-subunit human eIF3 complex, defects in assembly of 43S PICs, efficiency of mRNA recruitment, and postassembly events such as AUG recognition. We knocked down expression of the PCI domain-containing eIF3c and eIF3a subunits and of eIF3j in human HeLa and HEK293 cells and analyzed the functional consequences. Whereas eIF3j downregulation had barely any effect and eIF3a knockdown disintegrated the entire eIF3 complex, eIF3c knockdown produced a separate assembly of the a, b, g, and i subunits (closely resembling the yeast evolutionary conserved eIF3 core), which preserved relatively high 40S binding affinity and an ability to promote mRNA recruitment to 40S subunits and displayed defects in AUG recognition. Both eIF3c and eIF3a knockdowns also severely reduced protein but not mRNA levels of many other eIF3 subunits and indeed shut off translation. We propose that eIF3a and eIF3c control abundance and assembly of the entire eIF3 and thus represent its crucial scaffolding elements critically required for formation of PICs.
Terrestrial Ecosystems at Toolik Lake, Alaska

The broad aim of terrestrial research of the Arctic LTER is to develop a predictive understanding of the distribution of tundra ecosystems in the landscape; of the controls over their structure, functioning, and biogeochemical cycles; and of their interactions with each other and with the local and regional environment. Ultimately this leads to predictions of how they will respond to anthropogenic, development-related disturbances and to global environmental change. To meet this aim the research includes a combination of (1) comparative analyses of contrasting ecosystem types, (2) long-term monitoring of key system properties and processes in relation to local weather variation and secular climate change, and (3) long-term experimental manipulations of environmental factors related to global change. The conceptual framework for this research emphasizes interactions among multiple limiting factors in regulating biodiversity and overall carbon and other element budgets, with a particular emphasis on temperature, light, and soil nutrient availability as dominant controls. Effects of varying species composition on ecosystem OUP UNCORRECTED PROOF – REVISES, Wed Nov 2
Improving the Upper‐Ocean Temperature in an Ocean Climate Model (FESOM 1.4): Shortwave Penetration Versus Mixing Induced by Nonbreaking Surface Waves

As the first mature global ocean general circulation model based on unstructured‐mesh methods, the multiresolution Finite Element Sea ice‐Ocean Model (FESOM) has shown great capability in reconstructing the ocean and sea ice in both standalone and coupled simulations at a relatively low computational cost. Parameterizations of some important processes, including the vertical mixing induced by surface waves, however, are still missing, contributing to temperature biases in the upper ocean. In this work we incorporate the vertical mixing induced by nonbreaking surface waves derived from a wave model into FESOM and compare its effect with that of shortwave penetration, another key process to vertically redistribute the heat in the upper ocean. Numerical experiments with and without the shortwave penetration scheme and the nonbreaking surface wave mixing reveal that both processes ameliorate the simulation of upper‐ocean temperature in middle and low latitudes mainly on the summer hemisphere. The role of nonbreaking surface waves is more pronounced in decreasing the mean cold biases at 50 m (by 1.0 °C, in comparison to 0.5 °C achieved by applying shortwave penetration). We conclude that the incorporation of mixing induced by nonbreaking surface waves into FESOM is practically very helpful and suggest that it needs to be considered in other ocean climate models as well.
Ergebnisse seismischer Messungen auf dem Aletschgletscher

Seismic measurements on the Aletsch Glacier in the region or the "Konkordiaplatz" have permitted the calculation of Pand S-wave velocities and their increase with depth. The max. P-wave velocity of 3.732 ± 0,013 km/sec and the max. S-wave velocity or 1.70. ± 0.005km/sec were reached at a depth of approximately 45 m. After applying a eorreetion for temperature arid water content to the empirical formula for P-wave veloeity and density given by Robin (1958), the density and the elastic eonstants of the iee as weil as their increase with depth h ave been computed. Using the maximum of the P-wave velocity the water eontent has been estimated to be 0.2 0;. for depth greater than 45 m. Since measurements have been made along profiles, an approximate threedimensional interpretation of the refieetions was possible only at intersections of different profiles. In general all interpretation has to be made under the assumption of the normal to the refiector lymg in the plane of the profile and the vertical. Under this limitation a depth map of the "Konkordiaplatz" can be drawn up. The maximum ice thickness oceurring in this region is 890 m. Sowohl in seiner Lange wie auch in seiner Flache ist der Aletschgletscher der groste Gletscher der Alpen. Seismische Messungen seiner Machtigkeit liegen nur vereinzelt vor, so einige Messungen von Mothes (1929) und von Sus trunk (1947). Mit einer Machtigkeit von ca. 800 m, wie sie Mothes am Konkordiaplatz gemessen hat, ist der Aletschgletscher insbesondere im Gebiet des Konkordiaplatzes der machtigste Gletscher der Alpen. 1958 konnten in Vorbereitung der Internationalen Glaziologischen Gronland-Expedition seismische Arbeiten im Gebiet des Konkordiaplatzes durchgefuhrt werden. Mit dem Abschlus der Gronland-Expedition 1967/68 war es moglich, dieses Material zu bearbeiten und zuganglich zu machen. Die Abbildung 1 gibt die Lage der Profile wieder, auf denen diese seismischen Messungen durchgefuhrt werden konnten. Der Abbildung liegt ein Ausschnitt der 1: 10000-Karte, Stand September 1957, der Eidgenossischen Landestopographie von 1964 zugrunde. Die Untersuchungen wurden mit einer 24spurigen seismischen Apparatur und Geophonen mit 16 Hz Eigenfrequenz auf den angegebenen Profilen bei einer grosten Auslage von 1409 m mit Ladungen zwischen 50 und 1000 g durchgefuhrt. Die Registrierung erfolgte mit einem Filmvorschub von 30 cm/'sec. Gute Registrierungen liesen bei der vorherrschenden Frequenz von ca. 80 Hz der Longitudinalwellen eine Ablesegenauigkeit von ± 1 msec zu. Etwa 50 Filme standen fur die Bearbeitung zur Verfugung. *) Dr. F. Thyssen, Institut fur Geophysik der Universitat Munster, 44 Munster (Westf.), Steinfurter Strase 107 Dipl. -Geophys. M. Ahmad, 112-J/2, P.E. C.H. S. , Karachi 29, W. Pakistan
Recombinant Hepatitis B surface antigen production in Aspergillus niger

75 INTRODUCTION . 76 MATERIALS AND METHODS . 80 RESULTS . 85 DISCUSSION . 95 MANUSCRIPT 2. 110 Improved Hepatitis B surface antigen production in Aspergillus niger through the evaluation of genetic selection using gene fusion and a starched based selection pressure . 110 ABSTRACT . 11
Predictors of Youth Violence

Identifying and addressing the predictors of youth violence at appropriate points in youth development is important for prevention. Unfortunately, there have been few high-quality longitudinal studies of the predictors of youth violence. The Office of Juvenile Justice and Delinquency Prevention’s (OJJDP’s) Study Group on Serious and Violent Juvenile Offenders (Study Group) brought 22 researchers together for 2 years to analyze current research on risk and protective factors and the development of serious and violent juvenile offending careers.
Chlorinated aliphatic and aromatic hydrocarbons biodegradation: bioaugmentation tests in slurry microcosmos and study of the catabolic potential of microbial community in the interface between groundwater and surface water

In this work we studied the long-term growth process of two microbial consortia effective in the aerobic cometabolic biodegradation of a mixture of 6 chlorinated aliphatic hydrocarbons (CAHs), and the effectiveness of these consortia as inocula for the bioaugmentation of different types of microcosms. The main goals of the study were to verify the maintenance of the consortia’s capacity to degrade a CAH mixture during a prolonged growth process in the absence of the CAHs, and to verify the consortia’s effectiveness in CAH biodegradation upon inoculation in slurry microcosms set up with different types of aquifer materials. The propaneutilizing consortium generally proved the most effective one, being able to biodegrade vinyl chloride, cisand trans-1,2-dichloroethylene, trichloroethylene, 1,1,2-trichloroethane and 1,1,2,2-tetrachloroethane at all the CAH concentrations tested. Both consortia maintained unaltered CAH degradation capacities during a 300-day growth period in the absence of the CAHs and were effective in inducing the rapid onset of CAH depletion upon inoculation in slurry microcosms set up with 5 types of aquifer materials. A consortium developed in microcosms supplied with both methane and propane combined the best degradation capacities of the two single-substrate consortia. The degree of conversion of the organic Cl to chloride ion was equal as an average to 90%. Growth of CAH-degrading Consortia in Methaneand Propane-fed Bioreactors