Measurement of atmospheric neutrino oscillations with IceCube

We present the first statistically significant detection of neutrino oscillations in the high-energy regime (>20 GeV) from an analysis of IceCube Neutrino Observatory data collected in 2010 and 2011. This measurement is made possible by the low-energy threshold of the DeepCore detector (~20 GeV) and benefits from the use of the IceCube detector as a veto against cosmic-ray-induced muon background. The oscillation signal was detected within a low-energy muon neutrino sample (20-100 GeV) extracted from data collected by DeepCore. A high-energy muon neutrino sample (100 GeV-10 TeV) was extracted from IceCube data to constrain systematic uncertainties. The disappearance of low-energy upward-going muon neutrinos was observed, and the nonoscillation hypothesis is rejected with more than 5σ significance. In a two-neutrino flavor formalism, our data are best described by the atmospheric neutrino oscillation parameters |Δm(32)(2)|=(2.3(-0.5)(+0.6))×10(-3) eV(2) and sin(2)(2θ(23))>0.93, and maximum mixing is favored.

First observation of PeV-energy neutrinos with IceCube

We report on the observation of two neutrino-induced events which have an estimated deposited energy in the IceCube detector of 1.04±0.16 and 1.14±0.17 PeV, respectively, the highest neutrino energies observed so far. These events are consistent with fully contained particle showers induced by neutral-current ν(e,μ,τ) (ν(e,μ,τ)) or charged-current ν(e) (ν(e)) interactions within the IceCube detector. The events were discovered in a search for ultrahigh energy neutrinos using data corresponding to 615.9 days effective live time. The expected number of atmospheric background is 0.082±0.004(stat)(-0.057)(+0.041)(syst). The probability of observing two or more candidate events under the atmospheric background-only hypothesis is 2.9×10(-3) (2.8σ) taking into account the uncertainty on the expected number of background events. These two events could be a first indication of an astrophysical neutrino flux; the moderate significance, however, does not permit a definitive conclusion at this time.

Measurement of the atmospheric νe flux in IceCube

We report the first measurement of the atmospheric electron neutrino flux in the energy range between approximately 80 GeV and 6 TeV, using data recorded during the first year of operation of IceCube's DeepCore low-energy extension. Techniques to identify neutrinos interacting within the DeepCore volume and veto muons originating outside the detector are demonstrated. A sample of 1029 events is observed in 281 days of data, of which 496±66(stat)±88(syst) are estimated to be cascade events, including both electron neutrino and neutral current events. The rest of the sample includes residual backgrounds due to atmospheric muons and charged current interactions of atmospheric muon neutrinos. The flux of the atmospheric electron neutrinos is consistent with models of atmospheric neutrinos in this energy range. This constitutes the first observation of electron neutrinos and neutral current interactions in a very large volume neutrino telescope optimized for the TeV energy range.

Search for dark matter annihilations in the sun with the 79-string IceCube detector

We have performed a search for muon neutrinos from dark matter annihilation in the center of the Sun with the 79-string configuration of the IceCube neutrino telescope. For the first time, the DeepCore subarray is included in the analysis, lowering the energy threshold and extending the search to the austral summer. The 317 days of data collected between June 2010 and May 2011 are consistent with the expected background from atmospheric muons and neutrinos. Upper limits are set on the dark matter annihilation rate, with conversions to limits on spin-dependent and spin-independent scattering cross sections of weakly interacting massive particles (WIMPs) on protons, for WIMP masses in the range 20-5000  GeV/c2. These are the most stringent spin-dependent WIMP-proton cross section limits to date above 35  GeV/c2 for most WIMP models.

Study design and baseline description of the BMI2 trial: reducing paediatric obesity in primary care practices

OBJECTIVES

This study will test the efficacy of motivational interviewing (MI) conducted by primary care providers and dieticians among children ages 2-8 years old with a body mass index (BMI) ≥ 85th and ≤ 97th percentile.

METHODS

Forty-two practices from the American Academy of Pediatrics, Pediatric Research in Office Settings Network were assigned to one of three groups. Group 1 (usual care) measures BMI percentile at baseline, and at 1- and 2-year follow-ups and receives standard health education materials. Group 2 providers deliver three proactive MI counselling sessions with a parent of the index child in Year 1 and one additional 'booster' visit in Year 2. Group 3 adds six MI counselling sessions from a trained dietician. The primary outcome is the child's BMI percentile at 2-year follow-up. Secondary outcomes include parent report of the child's screen time, physical activity, intake of fruits and vegetables, and sugar-sweetened beverages.

RESULTS

We enrolled 633 eligible children whose mean BMI percentile was 92.0 and mean age of 5.1. The cohort was 57% female. Almost 70% of parents reported a household income of ≥ $40,000 per year, and 39% had at least a college education. The cohort was 63% white, 23% Hispanic, 7% black and 7% Asian. Parent self-reported confidence that their child will achieve a healthy weight was on average an 8 (out of 10).

CONCLUSION

To date, several aspects of the study can inform similar efforts including our ability to use volunteer clinicians to recruit participants and their willingness to dedicate their time, without pay, to receive training in MI.

Outbreak of Serratia marcescens infections following injection of betamethasone compounded at a community pharmacy

BACKGROUND

In June 2001, following the report of 4 patients with Serratia marcescens meningitis who received epidural injections of betamethasone compounded at a community pharmacy, we initiated an outbreak investigation.

METHODS

All patients who received injections of betamethasone from the production lot common to the 4 patients were evaluated. A case patient was defined as a patient who received compounded betamethasone and had S. marcescens isolated from a sterile site or clinical and laboratory evidence of infection. We cultured all recovered betamethasone, environmental specimens from the pharmacy, and medications recovered from an ambulatory surgery center. The California Board of Pharmacy reviewed the procedures used to prepare the betamethasone.

RESULTS

We identified 11 patients with culture-confirmed S. marcescens (8 patients) or clinical infection (3 patients) following injection of compounded betamethasone from 25 May through 31 May 2001. Case patients had meningitis (5 patients, with 3 deaths), epidural abscesses (5 patients), or an infected hip (1 patient). S. marcescens was isolated from 35 (69%) of 51 betamethasone vials recovered, from pharmacy specimens of 1% carboxymethylcellulose stock solution, from pharmacy surfaces, and from multiple parenteral materials used at the ambulatory surgery center. Pulsed-field gel electrophoresis patterns of S. marcescens isolates of representative specimens from patients, the betamethasone, the pharmacy, and the ambulatory surgery center were identical. Deficient practices in compounding of betamethasone included inadequate autoclaving temperatures and failure to perform terminal sterilization.

CONCLUSIONS

This outbreak of serious S. marcescens infection followed improper compounding of betamethasone in a community pharmacy. Enforceable national standards for pharmaceutical compounding are needed to reduce the risk of such outbreaks.

Changes in haemoglobin during interferon alpha-2b plus ribavirin combination therapy for chronic hepatitis C virus infection

Interferon alpha and ribavirin (RBV) combination therapy is associated with decreases in haemoglobin (Hb) concentrations and anaemia. The aim of this analysis was to better characterize the magnitude and frequency of Hb changes and risk factors. This retrospective analysis evaluated treatment-related changes in Hb in 677 patients who participated in either of two interferon alpha-2b plus RBV studies for chronic hepatitis C virus (HCV) infection. Study 1 included 192 interferon alpha-naïve patients randomized to receive RBV 1000-1200 mg/day plus interferon alpha-2b 3 million IU daily or three times weekly for 48 weeks. Study 2 included 485 interferon alpha-experienced patients randomized to receive RBV 1000-1200 mg daily plus interferon alpha-2b 3 million IU daily or three times weekly for 4 weeks, followed by three times weekly dosing for 44 weeks. More than 50% of all patients experienced a decrease in Hb > or =30 g/L. Women were 4.4 times as likely as men to experience a Hb level of <100 g/L; however, men were at a 40% higher risk to experience a Hb decline of >30 g/L from baseline. Daily use of interferon alpha-2b did not impact the magnitude of Hb decrease. In this pooled analysis, RBV dose reduction resulted in increases in Hb concentration of approximately 10 g/L. Lower baseline creatinine clearance, higher baseline Hb levels and increased age were independently associated with increased risk of Hb decreases of >27.7%. Lower baseline weight was not associated with increased risk of Hb decrease. Substantial Hb decreases occur frequently with interferon alpha/RBV combination therapy. Sex, the magnitude of the Hb decline and renal function are potentially important factors to consider in patients receiving RBV. Further research is needed to determine the impact on virological response and to develop strategies to manage the medical consequences.

Response by B cell precursors to pre-B receptor assembly: differences between fetal liver and bone marrow

The expression of different sets of immunoglobulin specificities by fetal and adult B lymphocytes is a longstanding puzzle in immunology. In the past few years it has become clear that production of mu heavy chain and subsequent assembly with surrogate light chain to form the pre-B cell receptor complex is critical to promote development of adult B cell precursors in mouse bone marrow. Recently we found that instead of promoting pre-B cell expansion as in adult bone marrow, this complex inhibits pre-B cell growth in fetal liver, providing a previously unrecognized mechanism for alteration of the B cell repertoire with age. The consequence is very distinct primary repertoires for development of fetal B1 cells and adult bone marrow B2 cells.

Primary care treatment of pediatric psychosocial problems: A study from pediatric research in office settings and ambulatory sentinel practice network

OBJECTIVE

Psychosocial problems cause much of the morbidity among children, and their frequency of presentation in primary care is growing. How is primary care treatment of children's psychosocial problems affected by child symptoms, physician training, practice structure, insurance, physician/patient relationship, and family demographics?

DESIGN

Questionnaire study of treatment of psychosocial problems during office visits by children.

SETTINGS

At total of 401 primary care offices from 44 US states, Puerto Rico, and Canada.

PATIENTS

From 21 150 children seen in office visits, we selected children with an identified psychosocial problem but who were not already receiving specialty mental health services (n = 2618 children).

OUTCOME MEASURES

Clinicians' decisions to counsel families, to refer children to mental health specialists, or to prescribe medication.

RESULTS

The treatment choices of primary care clinicians (PCCs) were generally independent of patients' demographics or insurance status. Clinicians' training, beliefs about mental health, and practice structure had no effect on treatment choices. However, clinicians seeing their own patients were more likely to prescribe medications for attention problems. The clinician's perception about whether the parent agreed with the treatment choice was important for every treatment modality. Counseling and referral were more common and medication was less common when a problem was newly recognized at the visit.

CONCLUSIONS

Structural factors such as practice type, insurance coverage, and physician training were less important for treatment than were process factors, such as whether the visit was a psychosocial problem visit, whether the problem was newly or previously recognized, and whether the family and clinician were familiar with each other and in accord about treatment.

Stable enterovirus 5' nontranslated region over a 7-year period in a patient with agammaglobulinemia and chronic infection

Cerebrospinal fluid samples obtained 7 years apart from a patient with chronic meningoencephalitis and underlying agammaglobulinemia were examined to determine enteroviral genotypic variability. From each sample, amplicons spanning 496 nucleotides within the 5' nontranslated region were generated directly from the cerebrospinal fluid and analyzed. A consensus sequence derived from 3 clones of each amplicon revealed only 7 nucleotide changes over the 7-year period within the region studied. The observed 5' nontranslated region mutation rate in this patient ( approximately 0.2% per year) was significantly lower than mutation rates reported for the poliovirus genome.

Peer group training of pragmatic skills in adolescents with acquired brain injury

OBJECTIVE

To empirically evaluate a method of treating adolescents with cognitive communication disorders, including pragmatic deficits, secondary to acquired brain injury (ABI) in a group setting by objectively measuring outcomes before treatment and immediately after treatment and at 6 months posttreatment.

DESIGN

A before-after trial with follow-up in a consecutive sample, with no control group.

SETTING

Inpatient and outpatient pediatric rehabilitation center.

SUBJECTS

Adolescents who demonstrated pragmatic deficits and scored a rating of 3 or less on each subdomain of the Rehabilitation Institute of Chicago Rating Scale of Pragmatic Communication Skills (RICE-RSPCS) were eligible for the study. Eight subjects were recruited into the study, and two subjects were lost to follow-up. Thus, six of the eight completed the study.

MAIN OUTCOME MEASURES

RICE-RSPCS, Communication Performance Scale (CPS).

RESULTS

Clinically relevant and statistically significant (P <.01) changes occurred during the treatment and were maintained at follow-up for the four RICE-RSPCS subscales and the CPS.

CONCLUSION

These results suggest that the potential and often typical long-term pragmatic and subsequent social difficulties associated with ABI can possibly be lessened through effective intervention.

The fetal origin of B-precursor leukemia in the E-mu-ret mouse

Before the clinical onset of B-precursor lymphoblastic leukemia, E-mu-ret mice have an expansion of late pro-B cells (CD45R+CD43(+)CD24(+)BP-1(+)) within the bone marrow. To characterize the early effects of the transgene product on lymphopoiesis, we initially sequenced the Ig heavy chain (IgH) rearrangements within the late pro-B cells in 24-day-old E-mu-ret and transgene negative mice. In both mouse populations, the IgH rearrangements were polyclonal, predominately nonproductive, and exhibited similar V, D, and J gene usage. However, the frequency of N regions, a marker of postnatal lymphopoiesis, was notably different. At the VD junction, N regions were found in 25 of 25 (100. 0%) rearrangements from transgene-negative mice compared with 12 of 36 (33.3%) rearrangements from Emicro-ret mice. At the DJ junction, N regions were found in 21 of 25 (84.0%) rearrangements from transgene negative mice compared with 4 of 36 (11.1%) rearrangements from E-mu-ret mice. Subsequently, we sequenced the clonal IgH rearrangements from 9 leukemias that developed in 10-to 38-week-old mice and found that 7 leukemias had a least 1 rearrangement that lacked N regions at the DJ junction. In addition, V replacement events were observed in the 1 leukemia studied in detail. Terminal deoxynucleotidyl transferase, the enzyme responsible for N region addition, was expressed at markedly lower levels in late pro-B cells from 7- to 10-day-old E-mu-ret mice compared with transgene-negative mice. Examination of fetal lymphopoiesis in E-mu-ret mice identified a relative increase in early (CD45R+CD43(+)CD24(+)BP-1(-)) and late pro-B cells and a decrease in more differentiated CD43(-) B-lineage cells. Fetal early pro-B cells from Emicro-ret mice proliferated threefold to fivefold greater but differentiated to a lesser extent than those from transgene negative mice when cultured in vitro with interleukin-7. These data suggest that the B precursor leukemias in adult E-mu-ret mice arise from the progeny of pro-B cells generated in utero.

The evolution of B precursor leukemia in the Emu-ret mouse

Emu-ret mice carrying an RFP/RET fusion gene under the transcriptional control of the immunoglobulin heavy chain enhancer develop B lineage leukemias/lymphomas. We have characterized B-cell development in these mice before the onset of clinical disease to determine the steps involved in leukemogenesis. Flow cytometry reveals that the CD45R+CD43(+)CD24(+)BP-1(+) late pro-B-cell population is markedly expanded in the bone marrow of 3- to 5-week-old Emu-ret mice. Compared with late pro-B cells from transgene-negative mice, Emu-ret late pro-B cells have a limited capacity to differentiate in interleukin (IL)-7 and a higher incidence of VDJ rearrangements, but a similar cell cycle profile. In contrast, CD45R+CD43(+)CD24(+)BP-1(-) early pro-B cells from 3- to 5-week-old Emu-ret mice, which also express the RFP/RET transgene, differentiate in IL-7 similarly to their normal counterparts. Furthermore, early pro-B cells from Emu-ret and transgene-negative mice have an identical pattern of growth inhibition when exposed to interferons (IFNs)-alpha/beta and -gamma, whereas, pro-B-cell leukemia lines derived from Emu-ret mice are markedly less sensitive to growth inhibition by these IFNs. In 13-week-old well-appearing Emu-ret mice, late pro-B cells upregulate CYCLIN D1 expression and downregulate CASPASE-1 expression in a pattern that correlates with the emergence of B precursor cells in the peripheral blood and the loss of other B lineage subsets in the bone marrow. Taken together, these results suggest that the expression of the RFP/RET transgene initially prevents the normal elimination of late pro-B cells with nonproductive rearrangements. Secondary events that simultaneously disturb the normal transcriptional regulation of genes involved in the control of the cell cycle and apoptosis may allow for subsequent malignant transformation within the expanded late pro-B-cell population.

A novel mechanism for B cell repertoire maturation based on response by B cell precursors to pre-B receptor assembly

The expression of different sets of immunoglobulin specificities by fetal and adult B lymphocytes is a long-standing puzzle in immunology. Recently it has become clear that production of immunoglobulin mu heavy chain and subsequent assembly with a surrogate light chain to form the pre-B cell receptor complex is critical for development of B cells. Here we show that instead of promoting pre-B cell progression as in adult bone marrow, this complex inhibits pre-B cell growth in fetal liver. Curiously, we identify a fetal-associated VH11 mu heavy chain that allows continued pre-B proliferation in fetal liver. Interestingly, this heavy chain does not associate efficiently with a surrogate light chain, providing a previously unrecognized mechanism for skewing the expression of distinctive VH genes toward fetal through early neonatal life.

The human PD-1 gene: complete cDNA, genomic organization, and developmentally regulated expression in B cell progenitors

We report the complete cDNA sequence and the genomic structure of the human PD-1 homologue. An analysis of the expression pattern of the human PD-1 gene (hPD-1) and the murine PD-1 gene (mPD-1) in developing bone marrow B-lineage cells was also undertaken. The full length hPD-1 cDNA is 2106 nucleotides long and encodes a predicted protein of 288 amino acid residues. The hPD-1 and mPD-1 genes share 70% homology at the nucleotide level and 60% homology at the amino acid level. Four potential sites for N-linked glycosylation are conserved, as are a stretch of amino acids between two cysteine residues resembling a V-set immunoglobulin domain, and another region containing a motif similar to an immunoreceptor tyrosine-based inhibitory motif. Isolation of the genomic locus of the hPD-1 gene reveals that the gene is composed of five exons located on human chromosome 2 at band q37. The 5' flanking region lacks TATA and CAAT cis-acting elements, but includes a number of potential transcription factor binding sites and a dominant transcription start site. The mPD-1 gene was preferentially expressed in pro-B cells from murine adult bone marrow. Although hPD-1 was not preferentially expressed in pro-B cells from human fetal bone marrow, treatment of isolated pro-B cells with interleukin-7 resulted in a dramatic increase in expression. These data suggest that PD-1 may play a role in B-cell differentiation during the pro-B cell stage.

Down-regulation of terminal deoxynucleotidyl transferase by Ig heavy chain in B lineage cells

The enzyme terminal deoxynucleotidyl transferase (TdT) adds nontemplate-derived nucleotides (N regions) to the junctions between recombining variable, diversity, and joining segments of Ig genes. The relative paucity of N regions in Ig light chains, together with the down-regulation of TdT transcription in pre-B cells (prior to light chain production), suggested that production of IgM heavy chain (mu) protein might negatively regulate TdT expression. In this study, we examined the effect of mu production on TdT gene expression in B lineage subsets from normal mice, from recombination-deficient mice (SCID and Rag-1-) carrying mu transgenes, and in transformed pro-B cell lines transfected with mu constructs. In normal mice, TdT is sharply down-regulated at the early pre-B stage in which cells have just completed productive mu rearrangement. Furthermore, the expression of mu transgenes in pro-B stage cells from recombination-deficient mice results in a similar decrease. Finally, transfection of genomic constructs encoding mu into pro-B cell lines results in a marked reduction of TdT expression. Taken together, these findings indicate that mu protein production results in the down-regulation of TdT. The ability of mu transgenes to alter TdT expression in cell lines also suggests that signaling through the pre-B receptor does not necessarily require interaction with an external stromal cell-derived ligand.

The influence of provider behavior, parental characteristics, and a public policy initiative on the immunization status of children followed by private pediatricians: a study from Pediatric Research in Office Settings

OBJECTIVES

To determine the relative impact of parental characteristics, provider behavior, and the provision of free vaccines through state-sponsored vaccine volume programs (VVPs) on the immunization status of children followed by private pediatricians.

STUDY DESIGN

Retrospective and cross-sectional surveys of immunization data.

SETTING

The offices of 15 private pediatricians, from 11 states, who were members of the Pediatric Research in Office Settings network. Seven of these physicians used vaccines provided through VVPs.

PATIENTS

Children 2 to 3 years old followed by the participating physicians.

METHODS

The immunization status of children was assessed from two separate samples. For sample 1, immunization data were abstracted from the medical records of 60 consecutive eligible children seen in each office. Parents of the selected children indicated the method of payment for immunizations and the education levels of the mothers. Because this cross-sectional survey might have oversampled frequent health care users, a retrospective chart review of up to 75 randomly selected children in each pediatrician's practice was also conducted (sample 2). Additional data were collected from the parents of children in sample 2 by telephone interviews. For both samples, patients were considered to be fully immunized if they had received four diphtheria-tetanus-pertussis/diphtheria-tetanus vaccines, three oral poliovirus/inactivated poliovirus vaccines, and one measles-mumps-rubella vaccine before their second birthdays. Before collecting vaccination data, pediatricians completed a survey detailing their immunization beliefs and practices. Logistic regression was used to identify factors that were independently associated with a child being fully immunized.

RESULTS

For sample 1, 81.7% of the 857 children surveyed were fully immunized. Practitioner-specific immunization rates varied widely, ranging from 51% to 97%. The immunization rate of children who received vaccines provided by VVPs was similar to that of children whose immunizations were not provided by VVPs (81.2% vs 82.2%; odds ratio [OR] for a VVP as a predictor for being fully immunized, 0.94, 95% confidence interval [CI], 0.66 to 1.32). In addition, parents who paid for immunizations out of pocket were as likely to have fully immunized children as those who had little or no out-of-pocket expenditures for vaccines (OR, 1.13; 95% CI, 0.75 to 1.13). In the logistic model, only individual pediatrician and size of the metropolitan area in which the pediatrician's practice was located were significant predictors of a child's immunization status. The results from sample 2 were similar; 82.1% of the 772 surveyed patients were fully immunized. With sample 2, individual pediatrician and age of the child at the time of the survey were the only predictors of immunization status. The OR of a VVP as a predictor of a child being fully immunized was 1.37 (95% CI, 0.65 to 2.90).

CONCLUSIONS

Individual provider behavior may be the most important determinant of the immunization status of children followed by private pediatricians. In our samples, the effect of parental characteristics was limited. State-sponsored VVPs were not associated with higher immunization rates, perhaps because cost of vaccines did not seem to be a significant barrier to immunization in this population.

Down-regulation of terminal deoxynucleotidyl transferase by Ig heavy chain in B lineage cells

The enzyme terminal deoxynucleotidyl transferase (TdT) adds nontemplate-derived nucleotides (N regions) to the junctions between recombining variable, diversity, and joining segments of Ig genes. The relative paucity of N regions in Ig light chains, together with the down-regulation of TdT transcription in pre-B cells (prior to light chain production), suggested that production of IgM heavy chain (mu) protein might negatively regulate TdT expression. In this study, we examined the effect of mu production on TdT gene expression in B lineage subsets from normal mice, from recombination-deficient mice (SCID and Rag-1-) carrying mu transgenes, and in transformed pro-B cell lines transfected with mu constructs. In normal mice, TdT is sharply down-regulated at the early pre-B stage in which cells have just completed productive mu rearrangement. Furthermore, the expression of mu transgenes in pro-B stage cells from recombination-deficient mice results in a similar decrease. Finally, transfection of genomic constructs encoding mu into pro-B cell lines results in a marked reduction of TdT expression. Taken together, these findings indicate that mu protein production results in the down-regulation of TdT. The ability of mu transgenes to alter TdT expression in cell lines also suggests that signaling through the pre-B receptor does not necessarily require interaction with an external stromal cell-derived ligand.

Identification of the earliest B lineage stage in mouse bone marrow

We have identified a very early stage of B lineage cells in the CD45R (B220)+CD24 (HSA) pre-pro-B fraction of mouse bone marrow delineated by expression of AA4.1, a molecule found on stem cells and early B lineage cells. These cells are B lineage precursors based on their capacity to generate B lineage cells rapidly in stromal-dependent culture and their expression of high levels of germline IgH transcripts in the absence of Rag-1/2. Half of these AA4.1+ precursors express low levels of CD4, characteristic of lymphoid progenitors, but few if any have up-regulated CD19, a molecule expressed very early in the B lineage. Furthermore, expression of genes encoding pre-B and B cell receptor components (mb-1, B29, and lambda 5) and transcription factors necessary for B lineage differentiation (BSAP, E12, E47, and Id) provide further support for designating these cells as the earliest B cell precursors.

A patient-specific in vivo tumor model

A significant body of research, spanning approximately the last 25 years, has focused upon the task of developing a better understanding of tumor growth through the use of in vitro mathematical models. Although such models are useful for simulation, in vivo growth differs in significant ways due to the variety of competing biological, biochemical, and mechanical factors present in a living biological system. An in vivo, macroscopic, primary brain tumor growth model is developed, incorporating previous in vitro growth pattern research as well as scientific investigations into the biological and biochemical factors that affect in vivo neoplastic growth. The tumor growth potential model presents an integrated, universal framework that can be employed to predict the direction and extent of spread of a primary brain tumor with respect to time for a specific patient. This framework may be extended as necessary to include the results of current and future research into parameters affecting neoplastic proliferation. The patient-specific primary brain tumor growth model is expected to have multiple clinical uses, including: predictive modeling, tumor boundary delineation, growth pattern research, improved radiation surgery planning, and expert diagnostic assistance.

Clonal expansion of germline B-lineage acute lymphoblastic leukemia in severe combined immunodeficient mice

CD19+ B lineage acute lymphoblastic leukemias (ALLs) with unrearranged Ig and TCR genes are designated germline B lineage ALLs. We used CDR3 PCR to determine whether pediatric germline B lineage ALLs contain minor subclones with rearranged Ig H V genes. In six of seven cases there were no PCR detectable CDR3 rearrangements. One case with a smear pattern on CDR3 PCR contained multiple unique CDR3 sequences at frequencies of 1-2 per 2,600, suggesting that polyclonal B cells were present at low frequency. To verify that the germline patterns were from leukemic cells and evaluate in vivo subclone differentiation, a germline B lineage ALL with the t(4;11) translocation was propagated in severe combined immunodeficient SCID) mice. The Ig and TCR genes in the leukemic cells recovered from mouse tissues were germline by Southern blot analysis except for single rearrangements that suggested subclone evolution at the Ig H and lambda loci in addition to the germline population. No CDR3 sequences were detected, indicating that the observed Ig H gene rearrangement most likely was a DJ joining. This study suggests that the transformed cell in germline B lineage ALL represents an early pro-B cell with limited tendency to further differentiate.

Differential expression of the blk and ret tyrosine kinases during B lineage development is dependent on Ig rearrangement

Expression of Ig transgenes in recombination-deficient mutant scid and Rag-1-mice results in the generation of pre-B and B cells, which are normally absent from these animals. In screening for protein tyrosine kinases (PTKs) that may play a role in this progression beyond the pro-B stage, we have identified five differentially regulated PTKs and compared their gene expression in defined stages of early B-lineage cells from normal, mutant, and Ig-transgenic mutant mice. Three PTKs (fgr, flk2/flt3, and tsk) show a comparable decrease at an early stage in all mice. In contrast, the decreasing expression of ret and the increasing expression of blk seen in differentiating B cells from normal mice are not observed in the mutant mice, unless they carry Ig transgenes. Therefore, our results show that the expression of certain PTKs is dependent on productive Ig rearrangement and suggest important roles for both Ret and Blk at distinct stages in the Ig-dependent progression of B cell differentiation.

Differential expression of the blk and ret tyrosine kinases during B lineage development is dependent on Ig rearrangement

Expression of Ig transgenes in recombination-deficient mutant scid and Rag-1-mice results in the generation of pre-B and B cells, which are normally absent from these animals. In screening for protein tyrosine kinases (PTKs) that may play a role in this progression beyond the pro-B stage, we have identified five differentially regulated PTKs and compared their gene expression in defined stages of early B-lineage cells from normal, mutant, and Ig-transgenic mutant mice. Three PTKs (fgr, flk2/flt3, and tsk) show a comparable decrease at an early stage in all mice. In contrast, the decreasing expression of ret and the increasing expression of blk seen in differentiating B cells from normal mice are not observed in the mutant mice, unless they carry Ig transgenes. Therefore, our results show that the expression of certain PTKs is dependent on productive Ig rearrangement and suggest important roles for both Ret and Blk at distinct stages in the Ig-dependent progression of B cell differentiation.

Biomedical imaging modalities: a tutorial

The introduction of advanced imaging technologies has improved significantly the quality of medical care available to patients. Non-invasive imaging modalities allow a physician to make increasingly accurate diagnoses and render precise and measured modes of treatment. Current uses of imaging technologies include laboratory medicine, surgery, radiation therapy, nuclear medicine, and diagnostic radiology. This paper provides an overview of most of the popular imaging modalities currently in clinical use. It is hoped that a general understanding of the modality from which an image is derived will help researchers in the subsequent analysis of the image data.

Differentiation stages of childhood acute lymphoblastic leukemias with p53 mutations

Based upon in vitro evidence of p53 involvement in lymphoid differentiation, we assessed immunoglobulin (Ig) and T-cell receptor (TCR) genes in five acute lymphoblastic leukemias (ALLs) with, and 24 ALLs without p53 mutations to compare their genotypic stages. Using Southern blot analysis and complementarity determining region III polymerase chain reaction (CDRIII PCR), 18 cases of B-lineage ALL and 11 cases of T-ALL were studied. Of 20 specimens from 18 B-lineage ALLs, two of four with p53 mutation and two of 16 without mutation had an unrearranged Ig and TCR genotype (p = 0.16; Fisher's exact test). Of 11 cases of T-ALL, the one case with p53 mutation had a rearranged TCR and Ig genotype and a case without mutation was unrearranged. The study indicates that p53 mutation is an infrequent feature of ALL found, nonetheless, in every genotypic subset. The p53 mutations in cases that do not further rearrange may support p53 involvement in lymphoid differentiation, but the heterogeneity in differentiation stages in cases both with and without p53 mutations suggests that regulation of early lymphoid maturation is multifactorial.

Polymorphism at codon 36 of the p53 gene

A polymorphism at codon 36 in exon 4 of the p53 gene was identified by single strand conformation polymorphism (SSCP) analysis and direct sequencing of genomic DNA PCR products. The polymorphic allele, present in the heterozygous state in genomic DNAs of four of 100 individuals (4%), changes the codon 36 CCG to CCA, eliminates a FinI restriction site and creates a BccI site. Including this polymorphism there are four known polymorphisms in the p53 coding sequence.

Identification of an altered immunoglobulin heavy-chain gene rearrangement in the central nervous system in B-precursor acute lymphoblastic leukemia

In B-precursor acute lymphoblastic leukemia (ALL), the nucleotide sequence of the complementarity determining region III (CDRIII) in the rearranged immunoglobulin heavy chain gene (IgH) has been used as a molecular fingerprint to identify the leukemic cells. In a child with B-precursor ALL without central nervous system (CNS) disease at diagnosis and a subsequent isolated CNS relapse, we examined the stability of the rearranged IgH by comparing the nucleotide sequences of the CDRIII in the leukemic cells from the marrow at diagnosis to the sequences in the leukemic cells from the cerebrospinal fluid at relapse. Whereas two of the three IgH sequences isolated from the leukemic cells at CNS relapse were identical to sequences originally isolated from the marrow lymphoblasts at diagnosis, the third CNS sequence was similar but not identical to the third marrow sequence. The third IgH sequence identified in the CNS differed from the marrow sequence only at the variable gene segment adjoining the CDRIII. Using a detection method based on the polymerase chain reaction, the altered IgH sequence identified in the leukemic cells from the cerebrospinal fluid was noted to be present in the CNS at a higher frequency than the related diagnostic sequence and was not detected in the marrow either at diagnosis or at CNS relapse. These findings indicate that the clonal pattern of leukemia in the CNS may differ from that in the marrow.

Molecular residual disease status at the end of chemotherapy fails to predict subsequent relapse in children with B-lineage acute lymphoblastic leukemia

PURPOSE

We have investigated whether the extent of residual leukemia in the marrows obtained at the completion of chemotherapy can predict subsequent relapse in children with B-lineage acute lymphoblastic leukemia (ALL).

PATIENTS AND METHODS

Marrow samples of 24 patients were examined for residual disease at the end of treatment using a quantitative method based on the polymerase chain reaction (PCR) amplification of the complementarity determining region-3 of the immunoglobulin heavy chain.

RESULTS

Of the 15 patients who remain in continuous bone marrow remission (range, 41 to 98 months), 14 had no detectable leukemic cells; one patient had a very low level (one in approximately 335,000 marrow cells) of residual leukemic cells that underwent clonal evolution. Among the nine patients who had a marrow relapse after the completion of treatment, eight patients whose relapses occurred 4 to 54 months from the end of therapy had no detectable leukemic cells, whereas only the one patient who relapsed 2 months after the completion of therapy had detectable residual disease.

CONCLUSION

These observations indicate that the absence of detectable residual leukemia by PCR at the end of chemotherapy is not sufficient to assure that the patient is cured and suggest that frequent serial monitoring is required for the early prediction of relapse off therapy.

Predominance of fetal type DJH joining in young children with B precursor lymphoblastic leukemia as evidence for an in utero transforming event

The presence of N sequences in the complementarity determining region 3 (CDR3) of the rearranged immunoglobulin H chain is developmentally regulated: N regions are generally present in the DJH joinings of adult B cells but are often absent in fetal B cells. Analysis of the CDR3 in 61 B precursor acute lymphoblastic leukemias indicated that 87.5% of the leukemias obtained from children < or = 3 yr old lacked N regions at the DJH junction. In contrast, in children > 3 yr old, only 11.1% of the leukemias lacked N regions at this junction, a frequency similar to what we have observed in B cells from children and adults. These findings suggest that the majority of leukemias presenting within the first 3 yr of age arise from an in utero transforming event.

Residual disease at the end of induction therapy as a predictor of relapse during therapy in childhood B-lineage acute lymphoblastic leukemia

PURPOSE

More than 95% of children with B-lineage acute lymphoblastic leukemia (ALL) achieve a clinical remission after the induction phase of chemotherapy (first 28 days) as evaluated by morphologic criteria. However, relapse occurs in approximately 30% of these children. The objective of this study was to determine whether the outcome of patients in clinical remission at the end of induction therapy could be predicted using a highly sensitive method to detect residual disease.

PATIENTS AND METHODS

All children diagnosed with B-lineage ALL at the Children's Hospital of Philadelphia during a 2-year period were eligible. The extent of residual leukemia was quantitated in remission marrow samples obtained at the end of induction therapy in 44 children using a phage clonogenic assay in association with complementarity-determining-region 3 (CDR3)-polymerase chain reaction (PCR).

RESULTS

Residual disease was a significant predictor of outcome independent of WBC count, age, or sex. The estimated relapse-free survival (RFS) during therapy was 50.4% (+/- 12.6%) for patients with high residual disease (> or = 0.6% leukemia cells among total marrow B cells) versus 91.9% (+/- 5.5%) for those with lower levels (P < .002). There were no significant differences in off-treatment RFS between patients with high or low residual disease who completed therapy in continuous remission (P = .82). The overall estimated RFS was 32.3% (+/- 11.6%) for patients with high residual disease versus 62.6% (+/- 10.7%) for patients with lower levels of residual leukemia cells, with a median follow-up of 5.3 years for patients in continuous remission (P < .008).

CONCLUSION

PCR detection of high residual disease at the end of induction therapy identifies patients at increased risk for relapse during therapy.

Amsacrine and etoposide hypersensitivity of yeast cells overexpressing DNA topoisomerase II

Increasing the cellular concentration of DNA topoisomerase II in yeast by expressing constitutively a plasmid-borne TOP2 gene encoding the enzyme greatly increases the sensitivity of the cells to amsacrine and etoposide (VP-16). This increased drug sensitivity at a higher intracellular DNA topoisomerase II level is observed in both RAD52+ repair-proficient strains and rad52 mutants that are defective in the repair of double-stranded breaks. These results provide strong support of the hypothesis that the cellular target of these drugs is DNA topoisomerase II, and that these drugs kill cells by converting DNA topoisomerase II into a DNA damaging agent.

The pattern of joining (JH) gene usage in the human IgH chain is established predominantly at the B precursor cell stage

Preferential utilization of JH and D genes has been demonstrated in the rearranged IgH chain in human peripheral B cells. We report here that the same hierarchy of JH gene usage is observed in leukemic cells arrested in the B precursor stage of differentiation. Specifically, JH4 and JH6 accounted for 42.9% and 35.7%, respectively, of the JH gene usage in the leukemias compared with an expected frequency of 16.7% assuming unbiased gene usage. Within the D gene families, the DN1 gene appears to be overutilized in both populations, representing about 15% of the total gene usage compared with an expected frequency of 3.2%. Because 21 of the 36 leukemias contained only nonproductive IgH rearrangements, the preferential gene usage could not have arisen from pre-B cells that have undergone clonal selection after a productive rearrangement but before surface Ig expression. Nonproductive rearrangements exhibited the biased gene usage seen for productive rearrangements. These findings suggest that a recombination bias favoring certain segments may be the actual mechanism responsible for the apparent preferential utilization of JH and D genes.

The pattern of joining (JH) gene usage in the human IgH chain is established predominantly at the B precursor cell stage

Preferential utilization of JH and D genes has been demonstrated in the rearranged IgH chain in human peripheral B cells. We report here that the same hierarchy of JH gene usage is observed in leukemic cells arrested in the B precursor stage of differentiation. Specifically, JH4 and JH6 accounted for 42.9% and 35.7%, respectively, of the JH gene usage in the leukemias compared with an expected frequency of 16.7% assuming unbiased gene usage. Within the D gene families, the DN1 gene appears to be overutilized in both populations, representing about 15% of the total gene usage compared with an expected frequency of 3.2%. Because 21 of the 36 leukemias contained only nonproductive IgH rearrangements, the preferential gene usage could not have arisen from pre-B cells that have undergone clonal selection after a productive rearrangement but before surface Ig expression. Nonproductive rearrangements exhibited the biased gene usage seen for productive rearrangements. These findings suggest that a recombination bias favoring certain segments may be the actual mechanism responsible for the apparent preferential utilization of JH and D genes.

VH gene rearrangement events can modify the immunoglobulin heavy chain during progression of B-lineage acute lymphoblastic leukemia

The presence of multiple VHDJH joinings in upwards of 30% of acute lymphoblastic leukemias (ALL) suggests a relative instability of the rearranged immunoglobulin heavy chain (IgH) gene, but the mechanisms involved are not completely understood. An investigation of the structure of the VHDJH joinings using complementarity determining region (CDR)3 polymerase chain reaction (PCR) in 12 leukemias at both diagnosis and relapse indicates that this instability may increase as a function of time. In only one of seven cases in which relapse occurred within 3 years from diagnosis was a new VHDJH joining identified and this coexisted with the original diagnostic joining. Most strikingly, new VHDJH joinings were identified in four of five cases in which relapse occurred more than 5 years from diagnosis. In this latter population, the instability of the joinings was generated from VH----VH gene replacement events in two cases, since the new joinings retained the original DJH sequences and partial N region homology at the VHD junction, and probably in a third case from a VH gene rearrangement to a common DJH precursor. Furthermore, in five of 23 (21.7%) additional cases studied at diagnosis, subclones were identified that had similar modifications of the VH-N region. These data indicate that VH gene replacement events and VH gene rearrangements to a common DJH joining contribute to the instability of the VHDJH joining in ALL. This phenomenon should be taken into consideration in those methodologies that exploit IgH rearrangements for detection of minimal residual disease.

Preferential utilization of specific immunoglobulin heavy chain diversity and joining segments in adult human peripheral blood B lymphocytes

We have examined at the molecular level the CDR3 and adjacent regions in peripheral blood B lymphocytes of normal individuals. A total of 111 sequences (12-28 sequences from six individuals) were obtained after cloning of the polymerase chain reaction-amplified segments into plasmids or phage. The average length of the VDJ joining was 109 nucleotides, with a range from 79 to 151. Approximately 75% of the sequences were in frame when translated into amino acids. Among the JH segments, JH4 was found most frequently (in 52.5% of the sequences), and JH1 and JH2 segments the least frequently (approximately 1% of the clones). A polymorphic JH6 gene with a one-codon deletion accompanied by a base change was present in two of six patients. Preferential breakpoints were found for JH2, JH3, JH4, and JH5, although the breakpoints of JH6 were distributed more heterogenously. In approximately 90% of the cases, significant homology of the D regions with published D sequences was found. Preferential usage of a particular coding frame was observed in in-frame sequences utilizing DA, D21/9, and DM1 segments. However, in general, all coding frames of germline D genes were used to generate CDR3s. Eight sequences that have a DN1-like D sequence with two base changes at the same positions were identified, suggesting the likely existence of a new germ line D gene belonging to the DN families. Using probes specific for a particular CDR3, the frequency of a specific B cell clone in the peripheral blood of normal individuals was estimated to be at most as high as 1/20,000.

Minimal residual disease in childhood B-lineage lymphoblastic leukemia. Persistence of leukemic cells during the first 18 months of treatment

BACKGROUND

Whether patients in clinical remission for acute lymphoblastic leukemia (ALL) continue to harbor leukemic cells is not known, because methods of detecting residual malignant cells have not been sufficiently sensitive. This information might be useful for predicting recurrence and determining the duration of therapy.

METHODS

Using a sensitive new method--identifying complementarity-determining region III sequences with the polymerase chain reaction--we estimated the number of residual leukemic cells in the bone marrow of eight children with B-lineage lymphoblastic leukemia before and after remission.

RESULTS

Induction chemotherapy produced a 3-to-4-log reduction in the number of leukemic cells. In all samples obtained up to 18 months after diagnosis, however, 0.004 to 2.6 percent of bone marrow nucleated cells were residual leukemic cells. Among the four patients studied more than 18 months after diagnosis, three had no detectable leukemic cells in marrow samples. Despite this, one of them, who was no longer receiving therapy, had a central nervous system relapse. In one patient receiving maintenance chemotherapy, there was a 60-fold increase in leukemic cells three months before bone marrow relapse.

CONCLUSIONS

The complete disappearance of leukemic cells (or their reduction below our method's threshold of detection, 1 in 100,000 cells) may be necessary to achieve a cure of ALL. The quantification of residual leukemic cells in serial marrow aspirates during therapy may allow the early detection of relapse.

Viral infections in pediatric bone marrow transplant patients

The records of 96 pediatric patients with aplastic anemia or a malignancy who underwent bone marrow transplantation between 1979 and 1986 at The Children's Hospital of Philadelphia were reviewed for laboratory evidence of viral infections. The most common viral diseases identified were herpes simplex virus (HSV), cytomegalovirus and adenoviruses, which were found in 19 (20%), 17 (18) and 17 (18) patients, respectively. HSV was more common in patients with than without graft vs. host disease (GVHD) (9 of 30; 30% vs. 10 of 66; 15%), but the difference did not reach statistical significance. Late or prolonged isolation of HSV occurred in patients with chronic GVHD. Cytomegalovirus was significantly more common in patients with than without GVHD (10 of 30; 33% vs. 7 of 66; 11%). The presence of pretransplant antibody to cytomegalovirus or HSV was a good predictor of subsequent infection. Adenoviruses were isolated from all 3 patients with Burkitt's lymphoma. Adenovirus type 12, a serotype uncommon in man and known to be highly tumorigenic in young hamsters, was recovered from 4 patients. Adenoviruses were not notably more common in patients with GVHD (6 of 30; 20% vs. 11 of 66; 17%). Other viral infections demonstrated included 5 parainfluenza, 4 enteroviruses, 3 human immunodeficiency virus, 1 respiratory syncytial virus, 1 influenza B and 1 rhinovirus.