E×B Flux Driven Detachment Bifurcation in the DIII-D Tokamak.

A bifurcative step transition from low-density, high-temperature, attached divertor conditions to high-density, low-temperature, detached divertor conditions is experimentally observed in DIII-D tokamak plasmas as density is increased. The step transition is only observed in the high confinement mode and only when the B×∇B drift is directed towards the divertor. This work reports for the first time a theoretical explanation and numerical simulations that qualitatively reproduce this bifurcation and its dependence on the toroidal field direction. According to the model, the bifurcation is primarily driven by the interdependence of the E×B-drift fluxes, divertor electric potential structure, and divertor conditions. In the attached conditions, strong potential gradients in the low field side (LFS) divertor drive E×B-drift flux towards the high field side divertor, reinforcing low density, high temperature conditions in the LFS divertor leg. At the onset of detachment, reduction in the potential gradients in the LFS divertor leg reduce the E×B-drift flux as well, such that the divertor plasma evolves nonlinearly to high density, strongly detached conditions. Experimental estimates of the E×B-drift fluxes, based on divertor Thomson scattering measurements, and their dependence on the divertor conditions are qualitatively consistent with the numerical predictions. The implications for divertor power exhaust and detachment control in the next step fusion devices are discussed.

Tuberculosis screening among HIV-infected patients: tuberculin skin test vs. interferon-gamma release assay.

National guidelines recommend screening for latent tuberculosis infection (LTBI) in all HIV-infected patients. Thus, the objective of this study was to measure protocol adherence to national guidelines regarding LTBI screening for HIV-infected patients entering care at an urban primary care clinic specializing in HIV care, identify clinical and other characteristics associated with adherence, and determine whether transitioning from the tuberculin skin test (TST) to the interferon-gamma release assay (IGRA) improved adherence. We conducted a retrospective study using protocol adherence to LTBI screening guidelines within twelve months of entering care at an HIV clinic as the primary outcome. Successful protocol adherence was defined as the placement and reading of a TST, performance of an IGRA, or a note in study clinic records documenting prior testing or treatment for tuberculosis in an outside setting. Multivariable modified Poisson regression models were used in analyses. Overall, 32% (n = 118/372) of patients received LTBI screening within twelve months of entering care. Protocol adherence to LTBI screening guidelines increased from 28% to 37% following the transition from TST to IGRA screening. IGRA screening [adjusted prevalence ratio: 1.45, 95% confidence limits: (1.07, 1.96)], male sex [1.47 (1.05, 2.07)], transfer patient status [1.51 (1.05, 2.18)], and greater than one year of clinic attendance [1.62 (1.06, 2.48)] were independently associated with protocol adherence. Among patients without prior LTBI screening or treatment, patients entering the clinic in 2013 under the IGRA screening protocol were more likely to be screened for LTBI compared to patients entering under the TST screening protocol (34.3% vs. 9.7%, p < 0.001). In conclusion, transitioning from TST to IGRA-based screening improved adherence to screening guidelines. However, further work on improving adherence to LTBI screening guidelines among HIV-infected patients is needed.

Lower Limb Muscles' Activation during Ascending and Descending a Single Step-Up Movement: Comparison between In water and On land Exercise at Different Step Cadences in Young Injury-Free Adults.

(1) Background: Forward step-up (FSU) simulates the stance phase in stair ascension. With the benefits of physical properties of water, aquatic FSU exercise may be more suitable for patients with lower limb weakness or pain. The purpose of this study is to investigate the effect of progressive steps per min on the surface electromyography (sEMG) of gluteus maximus (GM), biceps femoris (BF), rectus femoris (RF), and gastrocnemius (GA), when performing FSU exercise with different steps per min in water and on land. (2) Methods: Participants (N = 20) were instructed to perform FSU exercises at different steps per min (35, 60, and 95 bpm) in water and on land. The sEMG of the tested muscles were collected. The percentage maximum voluntary isometric contraction (%MVIC) of GM, RF, GA and BF at different environments and steps per min was compared. (3) Result: There was a statistically significant difference of %MVIC of RF at all steps per min comparisons regardless of the movement phases and environments (p < 0.01, except for descending phases of 35 bpm vs. 60 bpm). All tested muscles showed a statistically significant lower muscle activation in water (p < 0.05) (4) Conclusion: This study found that the %MVIC of the tested muscle in both investigated environments increase as steps per minute increases. It is also found that the movement pattern of FSU exercise activates RF the most among all the tested muscles. Muscle activation of all tested muscles is also found to be smaller in water due to buoyancy property of water. Aquatic FSU exercise might be applicable to patients with lower limb weakness or knee osteoarthritis to improve their lower limb strength.

Spectrally resolved polarization angle across the motional Stark effect spectrum.

A new diagnostic technique has been developed that couples a spectrometer and an image-intensified camera into the traditional motional Stark effect (MSE) system on DIII-D. The image-intensified camera syncs with the photo-elastic modulators to spectrally resolve the Stokes parameters across the Stark multiplet. Polarization dependent phase shift, likely from a plasma facing mirror, leads to the spectropolarimeter measuring a variation in the polarization angle across the MSE spectrum of ∼8°.

Production of autoantibodies by CD5-expressing B lymphocytes from patients with chronic lymphocytic leukemia.

CD5-expressing B lymphocytes from patients with selected chronic lymphoproliferative disorders were used to determine whether monoclonal populations of CD5+ human B cells produce autoantibodies. CD5+ B cells from 19 patients with chronic lymphocytic leukemia (CLL) and one with diffuse well-differentiated lymphocytic lymphoma (DWDL) were cultured, with and without mitogenic stimulation, to obtain Ig from these cells. 17 of the 20 samples produced Ig in vitro. mAb from nine of the 17 patients were reactive with either IgG, ssDNA, or dsDNA. In every instance, the autoantibodies displayed monotypic L chain usage that correlated precisely with the L chain expressed on the CD5+ leukemic B cell surface. These monoclonal autoantibodies varied in their degree of antigenic specificity; some were quite specific, reacting with only one antigen, whereas others were polyspecific, reacting with two or all three autoantigens tested. Three features distinguish these autoantibodies from those observed in prior studies of CD5+ B cells. First, they are clearly the products of monoclonal populations of CD5+ cells; second, several react with dsDNA, a specificity not previously reported and often seen in association with significant autoimmune disorders; and third, two of the monoclonal autoantibodies secreted by the CD5+ clones were of the IgG class. Although not all of the Ig-producing, CD5-expressing clones elaborated mAbs reactive with the autoantigens tested, greater than 50% did. It is possible that with a broader autoantigenic panel or with larger quantities of CLL/DWDL-derived Ig, even more autoantibody-producing clones might be identified. These studies may have important implications for the antigenic specificity of subsets of human B lymphocytes as well as for lymphoproliferative and autoimmune disorders in general.

Somatic diversification and selection of immunoglobulin heavy and light chain variable region genes in IgG+ CD5+ chronic lymphocytic leukemia B cells.

Chronic lymphocytic leukemia (CLL) is characterized by the clonal expansion of CD5-expressing B lymphocytes. Most studies have found that these leukemic CD5+ B cells, like their normal counterparts, use immunoglobulin (Ig) variable (V) region genes that exhibit minimal, if any, somatic diversity. These and other observations have suggested that CD5+ B cells may be incapable of generating Ig V gene diversity, and therefore may not be able to develop higher affinity binding sites that could be selected by antigen. However, most of the studies of CLL and normal CD5+ B cells have focused on IgM-producing cells. Since somatic mutations are most often seen in B cells that have undergone an isotype class switch, we analyzed the Ig heavy (H) and light (L) chain variable region genes of seven IgG+CD5+ CLL B cells to determine if somatic diversification and antigen selection had occurred. The data derived provide evidence for skewed use, somatic diversification, and antigenic selection of the Ig V region genes. Nonrandom use of both H and L chain V region genes was manifested by an overrepresentation of VH4 and VKI family genes and the underrepresentation of the JH4 gene segment. Furthermore, VH4 gene use was restricted to only two family members (4.21 and 4.18). In four of the seven cases, the VH and VL genes displayed > or = 5% difference from the most homologous known germline counterparts. Polymerase chain reaction and Southern blot analyses performed in two of these patients demonstrated that their unique VH CDR2 and adjacent sequences were not present in their germline DNA. In addition, a significant level of diversity was seen in the rearranged DJH segments and at the VL-JL junctions of every patient that occurred both at the time of recombination and subsequently. The localization of replacement changes to complementarity determining regions of some patients suggested that antigen selection had occurred. Furthermore, the mutations identified in the VH and VL genes of each individual patient were strikingly similar, both in number and location. Collectively, the data indicate that a subset of CD5+ CLL B cells can display Ig V region gene mutations. In addition, they are consistent with the notions that in some cases antigen selection of these mutations may have occurred, and that antigen stimulation may be a promoting factor in the evolution of certain CLL clones.

Comparative analysis of six genome sequences of three novel picornaviruses, turdiviruses 1, 2 and 3, in dead wild birds, and proposal of two novel genera, Orthoturdivirus and Paraturdivirus, in the family Picornaviridae.

In this territory-wide molecular epidemiology study of picornaviruses, involving 6765 dead wild birds from 201 species in 50 families over a 12 month period, three novel picornaviruses, turdiviruses 1, 2 and 3 (TV1, TV2 and TV3), were identified from birds of different genera in the family Turdidae. In contrast to many other viruses in birds of the family Turdidae or viruses of the family Picornaviridae, TV1, TV2 and TV3 were found exclusively in the autumn and winter months. Two genomes each of TV1, TV2 and TV3 were sequenced. Regions P1, P2 and P3 of the three turdiviruses possessed, respectively, <40, <40 and <50 % amino acid identities with those of other picornaviruses. Moreover, P1, P2 and P3 of TV1 also possessed, respectively, <40, <40 and <50 % amino acid identities with those of TV2 and TV3. Phylogenetic analysis revealed that TV1, TV2 and TV3 were distantly related to members of the genus Kobuvirus. Among the three turdiviruses, TV2 and TV3 were always clustered together, with high bootstrap supports of 1000. The genomic features of TV2 and TV3 were also distinct from TV1, including lower G+C contents, shorter leader protein and a preference for codon sequence NNT rather than NNC for amino acids that can use either NNT or NNC as codons (P<0.001 by χ(2)-test). Based on our results we propose two novel genera, Orthoturdivirus for TV1, and Paraturdivirus for TV2 and TV3, in the family Picornaviridae. The type of internal ribosomal entry site for TV1, TV2 and TV3 remains to be determined.

Characterization of avian influenza viruses A (H5N1) from wild birds, Hong Kong, 2004-2008.

From January 2004 through June 2008, surveillance of dead wild birds in Hong Kong, People's Republic of China, periodically detected highly pathogenic avian influenza (HPAI) viruses (H5N1) in individual birds from different species. During this period, no viruses of subtype H5N1 were detected in poultry on farms and in markets in Hong Kong despite intensive surveillance. Thus, these findings in wild birds demonstrate the potential for wild birds to disseminate HPAI viruses (H5N1) to areas otherwise free from the viruses. Genetic and antigenic characterization of 47 HPAI (H5N1) viruses isolated from dead wild birds in Hong Kong showed that these isolates belonged to 2 antigenically distinct virus groups: clades 2.3.4 and 2.3.2. Although research has shown that clade 2.3.4 viruses are established in poultry in Asia, the emergence of clade 2.3.2 viruses in nonpasserine birds from Hong Kong, Japan, and Russia raises the possibility that this virus lineage may have become established in wild birds.

Genomic exclusion: a rapid means for inducing homozygous diploid lines in Tetrahymena pyriformis, syngen 1.

Genomic exclusion is an abnormal form of conjugation occurring between cells with defective micronuclei and normal cells with diploid micronuclei. The progeny are heterocaryons; each cell has an old macronucleus but a new diploid micronucleus derived from one meiotic product of the normal mate. Such cells express genes found in the old macronucleus, are sexually mature, and can be specifically selected. When inbred, they give rise to lines genetically homozygous at all known loci.

Heparin-induced thrombocytopenia complicating hemodialysis.

Hemodialysis complicated by heparin-induced thrombocytopenia (HIT) is a rare event requiring anticoagulation with direct-thrombin inhibitors. Contaminant calcific uremic arteriolopathy (calciphylaxis) further complicates this situation due to the possibility that warfarin anticoagulation may exacerbate skin necrosis. The authors report a patient with renal failure and calciphylaxis who developed HIT after starting hemodialysis. She was successfully treated with Argatroban.

Laser calibration of the DIII-D coherence imaging system.

In this paper, we describe an in situ calibration technique for Coherence Imaging Spectroscopy (CIS) that measures 2-D images of ion flows on DIII-D. A low power CW diode laser that is tuneable in the range 464-468 nm along with a precision wavemeter (10-5 nm resolution) is used to characterize the interferometer phase as a function of wavelength in the region of C iii (465 nm) and He ii (468 nm). The interferometer is stabilized both mechanically and thermally to minimize drift during the calibration. Optical stirring and an integration sphere are used to obtain spatially uniform calibration images. The quality of the calibration data enables a measurement of phase versus wavelength over approximately 10 fringes of the interferometer. These coefficients can also be related to the geometry of the optics and the birefringent crystal of the interferometer. On DIII-D, the integration sphere with the laser light is inserted into the CIS optical system between shots and the laser image and wavelength are automatically recorded, providing a zero velocity reference.

Tomographic analysis of tangential viewing cameras (invited).

Many tokamaks now use visible light cameras to observe plasma-wall interactions and integrated line emission. The DIII-D coherence imaging spectroscopy diagnostic cameras image interferograms that encode line integrated velocity. By modeling the 2D camera image pixels as line of sight integrals through an axisymmetric discrete grid, it is possible to do tomographic analysis to determine the local plasma line emissivity and parallel velocity. Methods to solve the inverse problem posed by these tangential viewing cameras are presented. The inversion begins with calculation of the sparse response matrix that encompasses all the geometry and diagnostic information and reduces the process of image formation to a sparse matrix-vector multiply. This work includes techniques for determining the detailed geometry of the camera views and methods for handling physical quantities that vary spatially. Additionally, the size of the response matrix has driven the development of capability to distribute the coarse parallel calculation across a heterogeneous cluster of computers on the Energy Sciences Network. Iterative techniques are then used to solve the sparse matrix-vector linear system.

Verification of Doppler coherence imaging for 2D ion velocity measurements on DIII-D.

Coherence Imaging Spectroscopy (CIS) has emerged as a powerful tool for investigating complex ion phenomena in the boundary of magnetically confined plasma devices. The combination of Fourier-transform interferometry and high-resolution fast-framing cameras has made it possible to make sensitive velocity measurements that are also spatially resolved. However, this sensitivity makes the diagnostic vulnerable to environmental effects including thermal drifts, vibration, and magnetic fields that can influence the velocity measurement. Additionally, the ability to provide an absolute calibration for these geometries can be impacted by differences in the light-collection geometry between the plasma and reference light source, spectral impurities, and the presence of thin-films on in-vessel optics. This paper discusses the mitigation of these effects and demonstration that environmental effects result in less than 0.5 km/s error on the DIII-D CIS systems. A diagnostic comparison is used to demonstrate agreement between CIS and traditional spectroscopy once tomographic artifacts are accounted for.

The spectrum of molecular alterations in the evolution of chronic myelocytic leukemia.

DNA from 135 patients with chronic myelogenous leukemia (CML) at various clinical stages and Philadelphia (Ph1) chromosome positive acute lymphoblastic leukemia was investigated for alterations in a variety of proto-oncogenes which have been implicated in the evolution of CML from its chronic phase to blast crisis. The most common genetic change found in the evolution of typical Ph1 chromosome positive CML to blast crisis was an alteration of the p53 gene involving either a rearrangement, a deletion, or a point mutation in the coding sequence of the gene. Alterations of the p53 gene were found in the myeloid and the rare megakaryocytic variant of blast crisis but were absent in the lymphoid leukemic transformants. Gross structural alterations were seen in 11 of 54 (20%) of myeloid or unknown phenotypes of blast crisis and in only 1 of 44 chronic phase cases. Eight examples of mutations in the open reading frame of the p53 gene at codons 49, 53, 60, 140, 202, 204, 238, and 239 were observed in blast crisis patients. Mutations in the N-RAS gene were rare in typical blast crisis (2 of 27 cases) but were found in megakaryocytic and Ph1 negative myeloid blast crisis. We concluded that heterogeneous alterations in the p53 gene and occasionally in the N-RAS genes accompany the evolution of chronic phase CML to blast crisis.

Chronic lymphocytic leukemia B cells express restricted sets of mutated and unmutated antigen receptors.

To better understand the stage(s) of differentiation reached by B-type chronic lymphocytic leukemia (B-CLL) cells and to gain insight into the potential role of antigenic stimulation in the development and diversification of these cells, we analyzed the rearranged VH genes expressed by 83 B-CLL cells (64 IgM+ and 19 non-IgM+). Our results confirm and extend the observations of a bias in the use of certain VH, D, and JH genes among B-CLL cells. In addition, they indicate that the VH genes of approximately 50% of the IgM+ B-CLL cells and approximately 75% of the non-IgM+ B-CLL cells can exhibit somatic mutations. The presence of mutation varies according to the VH family expressed by the B-CLL cell (VH3 expressers displaying more mutation than VH1 and VH4 expressers). In addition, the extent of mutation can be sizeable with approximately 32% of the IgM+ cases and approximately 68% of the non-IgM+ cases differing by > 5% from the most similar germline gene. Approximately 20% of the mutated VH genes display replacement mutations in a pattern consistent with antigen selection. However, CDR3 characteristics (D and JH gene use and association and HCDR3 length, composition, and charge) suggest that selection for distinct B cell receptors (BCR) occurs in many more B-CLL cells. Based on these data, we suggest three prototypic BCR, representing the VH genes most frequently encountered in our study. These data suggest that many B-CLL cells have been previously stimulated, placing them in the "experienced" or "memory" CD5(+) B cell subset.

Examples of in vivo isotype class switching in IgM+ chronic lymphocytic leukemia B cells.

Chronic lymphocytic leukemia (CLL) usually involves the expansion of a clone of CD5+ B cells synthesizing IgM antibodies. These B cells appear to be blocked at the antigen receptor-expressing stage of B cell differentiation and are thought not to undergo an isotype class switch to IgG or IgA production. In vivo and in vitro studies suggest, however, that in some instances terminal differentiation and isotype switching can occur. To test the hypothesis that in vivo isotype class switching occurs in IgM+ B-type CLL cells, we analyzed the PBMC of 19 CLL patients for the presence of transcripts encoding the rearranged CLL V(H)DJ(H) associated with either gamma or alpha H chains. The molecular data indicate that approximately 50% of B-CLL patients have amplifications of IgM+ B cells that undergo an isotype class switch. Switching to IgA appears to occur more often than to IgG; also, switching can involve different IgG subclasses in individual patients. In many instances, these CLL-related gamma and alpha transcripts are much more plentiful than those of normal B cells that produce the same isotype. These switched transcripts do not reveal evidence for the accumulation of significant numbers of new V(H) gene mutations. The cellular data indicate that B cells with lesser amounts of surface membrane IgD and higher IgM/IgD ratios are more likely to undergo this switching process. Furthermore, B cells expressing IgG and IgA of the same idiotype or V(H) family and the same CDR3 length as those of the CLL IgM+ clone can be identified in the blood of patients studied using multiparameter immunofluorescence analyses. Collectively, these data suggest that not all members of a B-CLL clone are frozen at the surface membrane Ig-expressing stage of B cell maturation, and that some members can switch to the production of non-IgM isotypes. The occurrence of switching without the accumulation of V gene mutations indicates that the processes of differentiation and diversification are not linked.

Methylation site within a facultatively persistent sequence in the macronucleus of Tetrahymena thermophila.

DNA methylation occurs at the adenines in the somatic macronucleus of Tetrahymena thermophila. We report on a methylation site within a DNA segment showing facultative persistence in the macronucleus. When the site is present, methylation occurs on both strands, although only 50% of the DNA molecules are methylated.

Clinical and laboratory parameters that define clinically relevant B-CLL subgroups.

B cell-type chronic lymphocytic leukemia (B-CLL) is a heterogeneous disease. This is reflected by the very wide-ranging clinical courses that B-CLL patients experience and by the marked variation in laboratory findings between patients. In this chapter, we will review the various clinical and laboratory parameters that divide B-CLL patients into "subgroups," and correlate the parameters that define them. When feasible, we will also link clinical features to the cellular and genetic characteristics recently defined for these leukemic cells. The discussion is limited to parameters that define phenotypes or subgroups that may relate to disease activity and clinical outcome.

Phase I/II study of cyclophosphamide, doxorubicin, fluorouracil, and leucovorin for treatment of metastatic adenocarcinoma.

Leucovorin enhances the cytotoxicity of fluorouracil (5-FU) in patients with colorectal cancer and may increase the efficacy of combination chemotherapy regimens containing 5-FU. To determine the maximum tolerated dose of 5-FU with leucovorin for use in combination with cyclophosphamide and doxorubicin, we conducted a phase I/II trial in 20 patients. The doses of leucovorin (200 mg/m2 on days 1-5), cyclophosphamide (500 mg/m2 on day 1), and doxorubicin (40 mg/m2 on day 1) were held constant, while the dose of 5-FU was escalated in cohorts of patients beginning at 150 mg/m2 on days 1-5. Cycles were repeated every 3 weeks. Significant mucositis, diarrhea, and myelosuppression were infrequently observed in patients receiving up to 250 mg/m2 5-FU on days 1-5. In contrast, at a dose of 300 mg/m2 on days 1-5, three of six patients had granulocyte count nadirs of less than 500/microL during the first cycle of therapy, and two of these three had platelet counts of less than 25,000/microL. In addition, two patients treated at this dose had significant mucosal toxic effects, and three had insufficient recovery to permit a second course by day 22. Among 14 patients with assessable breast cancer, there were one complete and nine partial responses (response rate 71%). Leucovorin modulation of 5-FU can be safely incorporated into combination chemotherapy with cyclophosphamide and doxorubicin and provides a highly active regimen for treatment of metastatic breast cancer. Further study will be required to determine whether the addition of leucovorin significantly enhances the activity of this regimen.

Pharmacokinetic and phase I evaluation of esorubicin (4'-deoxydoxorubicin) by continuous infusion over forty-eight hours in patients with leukemia.

Sixteen patients with previously treated acute nonlymphocytic leukemia or chronic myelogenous leukemia in blast crisis were given one to three courses of esorubicin by continuous infusion over 48 h. Dosage levels extended from 35 to 85 mg/m2. Four patients showed partial responses of short duration. Nonhematological toxicity observed at dosages of 55 to 85 mg/m2 were mucositis, diarrhea, skin rash, transaminitis, nausea, vomiting, and cardiac dysfunction. One patient receiving 85 mg/m2 developed acute florid congestive heart failure within hours of administration of the drug. Pharmacokinetic analysis revealed large interpatient variation in plasma drug levels. At the end of infusion, plasma decay of esorubicin was rapid initially but slow thereafter, with a terminal half-life of 20 to 54 h. The metabolite 4'-deoxy-13-hydroxydoxorubicin reached significant plasma levels. Total body clearance, renal clearance, volume of distribution at steady state, and mean residence time show little variation during dose escalation for both esorubicin and 4'-deoxy-13-hydroxydoxorubicin. Urinary excretion of esorubicin and 4'-deoxy-13-hydroxydoxorubicin accounted for 10.5 and 1.5%, respectively, of the administered dose.