A Partial Least Squares (PLS) carbonate (CO3) prediction model was developed for soils throughout the contiguous United States using mid-infrared (MIR) spectroscopy. Excellent performance was ...achieved over an extensive geographic and chemical diversity of soils. A single model for all soil types performed very well with a root mean square error of prediction (RMSEP) of 12.6 g kg-1 and was further improved if Histosols were excluded (RMSEP 11.1 g kg-1). Exclusion of Histosols was particularly beneficial for accurate prediction of CO3 values when the national model was applied to an independent regional dataset. Little advantage was found in further narrowing the taxonomic breadth of the calibration dataset, but higher precision was obtained by running models for a restricted range of CO3. A model calibrated using only on the independent regional dataset, was unable to accurately predict CO3 content for the more chemically diverse national dataset. Ten absorbance peaks enabling CO3 prediction by mid-infrared (MIR) spectroscopy were identified and evaluated for individual and combined predictive power. A single-band model derived from an absorbance peak centered at 1796 cm-yielded the lowest RMSEP of 13.5 g kg-1 for carbonate prediction compared to other single-band models. This predictive power is attributed to the strength and sharpness of the peak, and an apparent minimal overlap with confounding co-occurring spectral features of other soil components. Drawing from the 10 identified bands, multiple combinations of 3 or 4 peaks were able to predict CO3 content as well as the full-spectrum national models. Soil CO3 is an excellent example of a soil parameter that can be predicted with great effectiveness and generality, and MIR models could replace direct laboratory measurement as a lower cost, high quality alternative.
Patients with relapsed or refractory chronic lymphocytic leukemia (CLL) have profound immune defects and limited treatment options. Given the dramatic activity of lenalidomide in other B-cell ...malignancies and its pleotropic immunomodulatory effects, we conducted a phase II trial of this agent in CLL.
Patients with relapsed or refractory B-cell CLL (B-CLL) were eligible if they required treatment as per the National Cancer Institute Working Group 1996 guidelines. Lenalidomide was administered orally at 25 mg on days 1 through 21 of a 28-day cycle. Response was assessed after each cycle. Patients were to continue treatment until disease progression, unacceptable toxicity, or complete remission. Rituximab was added to lenalidomide on disease progression.
Forty-five patients were enrolled, with a median age of 64 years. Sixty-four percent of the patients had Rai stage III or IV disease, and 51% were refractory to fludarabine. The overall response rate was 47%, with 9% of the patients attaining a complete remission. Fatigue, thrombocytopenia, and neutropenia were the most common adverse effects noted in 83%, 78%, and 78% of the patients, respectively.
Lenalidomide is clinically active in patients with relapsed or refractory B-CLL. These findings are encouraging and warrant further investigation of this agent in the treatment of this disorder.
Adeno-associated viruses (AAV) are promising gene therapy vectors that have little or no acute toxicity. We show that normal mice and mice with mucopolysaccharidosis VII (MPS VII) develop ...hepatocellular carcinoma (HCC) after neonatal injection of an AAV vector expressing b-glucuronidase. AAV proviruses were isolated from four tumors and were all located within a 6-kilobase region of chromosome 12. This locus encodes several imprinted transcripts, small nucleolar RNAs (snoRNAs), and microRNAs. Transcripts from adjacent genes encoding snoRNAs and microRNAs were overexpressed in tumors. Our findings implicate this locus in the development of HCC and raise concerns over the clinical use of AAV vectors.
Animal data indicate that ketogenic diets are associated with improved mitochondrial function, but human data are lacking. We aimed to characterize skeletal muscle mitochondrial changes in response ...to a ketogenic diet combined with exercise training in healthy individuals. Twenty-nine physically active adults completed a 12-wk supervised exercise program after self-selection into a ketogenic diet (KD,
= 15) group or maintenance of their habitual mixed diet (MD,
= 14). Measures of metabolic health and muscle biopsies (vastus lateralis) were obtained before and after the intervention. Mitochondria were isolated from muscle and studied after exposure to carbohydrate (pyruvate), fat (palmitoyl-l-carnitine), and ketone (β-hydroxybutyrate+acetoacetate) substrates. Compared with MD, the KD resulted in increased whole body resting fat oxidation (
< 0.001) and decreased fasting insulin (
= 0.019), insulin resistance homeostatic model assessment of insulin resistance (HOMA-IR),
= 0.022, and visceral fat (
< 0.001). The KD altered mitochondrial function as evidenced by increases in mitochondrial respiratory control ratio (19%,
= 0.009), ATP production (36%,
= 0.028), and ATP/H
O
(36%,
= 0.033) with the fat-based substrate. ATP production with the ketone-based substrate was four to eight times lower than with other substrates, indicating minimal oxidation. The KD resulted in a small decrease in muscle glycogen (14%,
= 0.035) and an increase in muscle triglyceride (81%,
= 0.006). These results expand our understanding of human adaptation to a ketogenic diet combined with exercise. In conjunction with weight loss, we observed altered skeletal muscle mitochondrial function and efficiency, an effect that may contribute to the therapeutic use of ketogenic diets in various clinical conditions, especially those associated with insulin resistance.
Collection of biological samples for DNA is necessary in a variety of disciplines including disease epidemiology, landscape genetics, and forensics. Quantity and quality of DNA varies depending on ...the method of collection or media available for collection (e.g., blood, tissue, fecal). Blood is the most common sample collected in vials or on Whatman Flinders Technology Associates (FTA) cards with short- and long-term storage providing adequate DNA for study objectives. The focus of this study was to determine if biological samples stored on Whatman FTA Elute cards were a reasonable alternative to traditional DNA sample collection, storage, and extraction. Tissue, nasal swabs, and ocular fluid were collected from white-tailed deer (Odocoileus virginianus). Tissue samples and nasal swabs acted as a control to compare extraction and DNA suitability for microsatellite analysis for nasal swabs and ocular fluid extracted from FTA Elute cards. We determined that FTA Elute cards improved the extraction time and storage of samples and that nasal swabs and ocular fluid containing pigmented fluid were reasonable alternatives to traditional tissue DNA extractions.
Estuarine-coastal ecosystems are rich areas of the global ocean with elevated rates of organic matter production supporting major fisheries. Net and gross primary production (NPP, GPP) are essential ...properties of these ecosystems, characterized by high spatial, seasonal, and inter-annual variability associated with climatic effects on hydrology. Over 20 years ago, Nixon defined the trophic classification of marine ecosystems based on annual phytoplankton primary production (APPP), with categories ranging from "oligotrophic" to "hypertrophic". Source data consisting of shipboard measurements of NPP and GPP from 1982 to 2004 for Chesapeake Bay in the mid-Atlantic region of the United States supported estimates of APPP from 300 to 500 g C m
yr
, corresponding to "eutrophic" to "hypertrophic" categories. Here, we developed generalized additive models (GAM) to interpolate the limited spatio-temporal resolution of source data. Principal goals were: (1) to develop predictive models of NPP and GPP calibrated to source data (1982 to 2004); (2) to apply the models to historical (1960s, 1970s) and monitoring (1985 to 2015) data with adjustments for nutrient loadings and climatic effects; (3) to estimate APPP from model predictions of NPP; (4) to test effects of simulated reductions of phytoplankton biomass or nutrient loadings on trophic classification based on APPP. Simulated 40% decreases of euphotic-layer chl-a or TN and NO
+ NO
loadings led to decreasing APPP sufficient to change trophic classification from "eutrophic' to "mesotrophic" for oligohaline (OH) and polyhaline (PH) salinity zones, and from "hypertrophic" to "eutrophic" for the mesohaline (MH) salinity zone of the bay. These findings show that improved water quality is attainable with sustained reversal of nutrient over-enrichment sufficient to decrease phytoplankton biomass and APPP.
Zinc finger nucleases (ZFNs) have been used successfully to create genome-specific double-strand breaks and thereby stimulate gene targeting by several thousand fold. ZFNs are chimeric proteins ...composed of a specific DNA-binding domain linked to a non-specific DNA-cleavage domain. By changing key residues in the recognition helix of the specific DNA-binding domain, one can alter the ZFN binding specificity and thereby change the sequence to which a ZFN pair is being targeted. For these and other reasons, ZFNs are being pursued as reagents for genome modification, including use in gene therapy. In order for ZFNs to reach their full potential, it is important to attenuate the cytotoxic effects currently associated with many ZFNs. Here, we evaluate two potential strategies for reducing toxicity by regulating protein levels. Both strategies involve creating ZFNs with shortened half-lives and then regulating protein level with small molecules. First, we destabilize ZFNs by linking a ubiquitin moiety to the N-terminus and regulate ZFN levels using a proteasome inhibitor. Second, we destabilize ZFNs by linking a modified destabilizing FKBP12 domain to the N-terminus and regulate ZFN levels by using a small molecule that blocks the destabilization effect of the N-terminal domain. We show that by regulating protein levels, we can maintain high rates of ZFN-mediated gene targeting while reducing ZFN toxicity.
The emergence and scope of personal and collective efforts to integrate faith into workplaces is a social movement that includes and extends beyond personal ethics. This paper discusses the ...development of The Integration Profile (TIP) Faith and Work Integration Scale, which is designed to measure the multidimensional nature of faith expressions within workplace settings. TIP measures the manifestations of faith, religion, and spirituality at the individual level. Earlier research theorized that individuals tend to manifest or live out their faith in one of four ways (Miller in God at work: the history and promise of the faith at work movement, Oxford University Press, New York, 2007); TIP expands this to assess eight sub-orientations, nested within the four main manifestations of faith-work integration. The development of the 24-item TIP scale involved exploratory analyses in a sample of 512 employees of a for-profit palliative care organization and a hierarchical confirmatory factor analysis in a sample of 4463 employees in an American multinational food processing organization. Additional analyses were conducted in a third sample of 266 working adults to assess the convergent and discriminant validity of the eight sub-orientations with other faith variables as well as associations with work outcomes.
Lifespan and aging rates vary considerably across taxa; thus, understanding the factors that lead to this variation is a primary goal in biology and has ramifications for understanding constraints ...and flexibility in human aging. Theory predicts that senescence—declining reproduction and increasing mortality with advancing age—evolves when selection against harmful mutations is weaker at old ages relative to young ages or when selection favors pleiotropic alleles with beneficial effects early in life despite late-life costs. However, in many long-lived ectotherms, selection is expected to remain strong at old ages because reproductive output typically increases with age, which may lead to the evolution of slow or even negligible senescence. We show that, contrary to current thinking, both reproduction and survival decline with adult age in the painted turtle, Chrysemys picta, based on data spanning >20 y from a wild population. Older females, despite relatively high reproductive output, produced eggs with reduced hatching success. Additionally, age-specific mark–recapture analyses revealed increasing mortality with advancing adult age. These findings of reproductive and mortality senescence challenge the contention that chelonians do not age and more generally provide evidence of reduced fitness at old ages in nonmammalian species that exhibit long chronological lifespans.
Long-term survival for children with diffuse intrinsic pontine glioma (DIPG) is less than 10%, and new therapeutic targets are urgently required. We evaluated a large cohort of DIPGs to identify ...recurrent genomic abnormalities and gene expression signatures underlying DIPG.
Single-nucleotide polymorphism arrays were used to compare the frequencies of genomic copy number abnormalities in 43 DIPGs and eight low-grade brainstem gliomas with data from adult and pediatric (non-DIPG) glioblastomas, and expression profiles were evaluated using gene expression arrays for 27 DIPGs, six low-grade brainstem gliomas, and 66 nonbrainstem low-grade gliomas.
Frequencies of specific large-scale and focal imbalances varied significantly between DIPGs and nonbrainstem pediatric glioblastomas. Focal amplifications of genes within the receptor tyrosine kinase-Ras-phosphoinositide 3-kinase signaling pathway were found in 47% of DIPGs, the most common of which involved PDGFRA and MET. Thirty percent of DIPGs contained focal amplifications of cell-cycle regulatory genes controlling retinoblastoma protein (RB) phosphorylation, and 21% had concurrent amplification of genes from both pathways. Some tumors showed heterogeneity in amplification patterns. DIPGs showed distinct gene expression signatures related to developmental processes compared with nonbrainstem pediatric high-grade gliomas, whereas expression signatures of low-grade brainstem and nonbrainstem gliomas were similar.
DIPGs comprise a molecularly related but distinct subgroup of pediatric gliomas. Genomic studies suggest that targeted inhibition of receptor tyrosine kinases and RB regulatory proteins may be useful therapies for DIPG.
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