The following sections provide an overview of the papers that were presented and accepted for publication in this supplement. 2 Comparative effectiveness research (CER)/Patient-centered outcomes ...research (PCOR) implementations Choudhry and Shrank present design and implementation issues from a novel, pragmatic cluster randomized trial embedded in a commercial insurance claims data system 4. ...study results are directly applicable to patients and providers in that system, and may be generalizable to other similar systems.
We present a Prototheca wickerhamii wound infection case that failed treatment with ketoconazole but was cured with amphotericin-B plus tetracycline. The patient was immunocompetent but had had local ...steroid injections. We reviewed another 159 cases from the literature. Prototheca has infected many areas of the human body, but most often skin, olecranon bursa, or wounds. Prior treatment with steroids and immune deficiencies are contributing factors. Itraconazole and fluconazole are reasonable initial treatments for patients with mild infections. For serious infections, or for infections that have failed azole treatment, amphotericin-B is the treatment of choice.
Spontaneous generation of complex order in apparently simple systems is both arresting and potentially useful. Here we describe the appearance of complex, ordered structures induced by the buckling ...of thin metal films owing to thermal contraction of an underlying substrate. We deposit the films from the vapour phase on a thermally expanded polymer (polydimethylsiloxane, PDMS). Subsequent cooling of the polymer creates compressive stress in the metal film that is relieved by buckling with a uniform wavelength of 20-50 micrometres. The waves can be controlled and orientated by relief structures in the surface of the polymer, which can set up intricate, ordered patterns over large areas. We can account qualitatively for the size and form of the patterned features in terms of the non-uniform stresses developed in the film near steps on the polymer substrate. This patterning process may find applications in optical devices such as diffraction gratings and optical sensors, and as the basis for methods of strain analysis in materials.
This study investigates the causes for, and distribution of, unimodal versus bimodal seasonal cycle of vegetation greenness in the Southwest United States using extensive site observations, climate ...data, satellite data, and the Lund‐Potsdam‐Jena (LPJ) vegetation model. Peak vegetation greenness is achieved in a clockwise manner across the Southwest, beginning in spring in the Sonoran Desert following winter rains, then in Utah‐Colorado with snowmelt/summer rains, and finally in New Mexico–eastern Arizona with late summer monsoon rains. At high elevations, spring‐summer snowmelt is critical for supplying the necessary soil moisture to trigger vegetation growth. A bimodal seasonal cycle of vegetation greenness is evident in satellite data and LPJ simulations across eastern Arizona and western New Mexico, characterized by peaks during late spring–early summer and late summer–early autumn. This bimodal green‐up remains a pressing paradox for which many competing hypotheses exist. The mechanism for this seasonal pattern is demonstrated using LPJ and observational data and is found to deviate from the traditional pulse‐reserve paradigm. This paradigm states that rainfall events in arid lands produce nearly immediate pulses of vegetation growth and accumulation of reserves but does not consider cold dormancy, time‐lagged vegetation responses, or rainfall seasonality. The following soil moisture based mechanism for bimodal greening is proposed. The initial peak in vegetation greenness during late spring–early summer results from a break in cold dormancy and benefits from the gradual winter‐long accumulation of deep soil moisture from weak synoptic rain events and snowmelt in colder regions. Limited precipitation and ongoing transpiration, from the initial vegetation greening, trigger a midsummer drying of the soil and a consequential minimum in vegetation activity. Later, pulses of monsoon rainfall in late summer–early autumn support the secondary greening, although significant runoff of brief, intense rainstorms and substantial soil evaporation limit moisture to the upper soil layers.
Objectives
Loss‐of‐function mutations in the gene encoding the calcium‐calmodulin (Ca2+‐CaM)‐dependent protein kinase kinase‐2 (CaMKK2) enzyme are linked to bipolar disorder. Recently, a de novo ...arginine to cysteine (R311C) mutation in CaMKK2 was identified from a whole exome sequencing study of bipolar patients and their unaffected parents. The aim of the present study was to determine the functional consequences of the R311C mutation on CaMKK2 activity and regulation by Ca2+‐CaM.
Methods
The effects of the R311C mutation on CaMKK2 activity and Ca2+‐CaM activation were examined using a radiolabeled adenosine triphosphate (ATP) kinase assay. We performed immunoblot analysis to determine whether the R311C mutation impacts threonine‐85 (T85) autophosphorylation, an activating phosphorylation site on CaMKK2 that has also been implicated in bipolar disorder. We also expressed the R311C mutant in CaMKK2 knockout HAP1 cells and used immunoblot analysis and an MTS reduction assay to study its effects on Ca2+‐dependent downstream signaling and cell viability, respectively.
Results
The R311C mutation maps to the conserved HRD motif within the catalytic loop of CaMKK2 and caused a marked reduction in kinase activity and Ca2+‐CaM activation. The R311C mutation virtually abolished T85 autophosphorylation in response to Ca2+‐CaM and exerted a dominant‐negative effect in cells as it impaired the ability of wild‐type CaMKK2 to initiate downstream signaling and maintain cell viability.
Conclusions
The highly disruptive, loss‐of‐function impact of the de novo R311C mutation in human CaMKK2 provides a compelling functional rationale for being considered a potential rare monogenic cause of bipolar disorder.
Background
The Iowa Rectal Surgery Risk Calculator estimates risk for proctectomy procedures. The Iowa Calculator performed well on NSQIP 2010–2011 training and 2005–2009 validation datasets, but was ...not prospectively validated and did not include low anterior resections. This study sought to demonstrate validity on new independent data, to update the calculator to include low anterior resection, and to compare performance to other risk assessment tools.
Methods
Non-emergent ACS-NSQIP proctectomy and low anterior resection data from 2010 to 2015 (
n
= 65,683) were included. The Iowa Calculator generated risk estimates for 30-day morbidity using 2012–2015 data. An Updated Calculator used 2010–2011 training data to include low anterior resection, with validation on 2012–2015 data. NSQIP data provided NSQIP Morbidity Model predictions and a custom web-script collected ACS-NSQIP Online Surgical Risk Calculator predictions for all patients.
Results
Proctectomy morbidity (not including low anterior resection) decreased from 40.4% in 2010–2011 to 37.0% in 2012–2015. Low anterior resection had lower morbidity (22.4% in 2012–15). The Iowa Calculator demonstrated good discrimination and calibration using 2012–2015 data (C-statistic 0.676, deviance + 9.2%). After including low anterior resection, the Updated Iowa Calculator performed well during training (c-statistic 0.696, deviance 0%) and validation (C-statistic 0.706, deviance + 7.9%). The Updated Iowa Calculator had significantly better discrimination and calibration than morbidity predictions from the ACS Online Calculator (C-statistic 0.693,
P
< 0.001, deviance − 28.1%) and NSQIP General/Vascular Surgery Model (C-statistic 0.703,
P
< 0.05, deviance − 40.8%).
Conclusion
When applied to new independent data, the Iowa Calculator supplies accurate risk estimates. The Updated Iowa Calculator includes low anterior resection, and both are prospectively validated. Risk estimation by the Iowa Calculators was superior to ACS-provided risk tools.
Resistances to begomoviruses, including bipartite tomato mottle virus and monopartite tomato yellow leaf curl virus (TYLCV), have been introgressed to cultivated tomato (
Solanum lycopersicum
) from ...wild tomato accessions. A major gene,
Ty
-
2
from
S. habrochaites
f.
glabratum
accession “B6013
,”
that confers resistance to TYLCV was previously mapped to a 19-cM region on the long arm of chromosome 11. In the present study, approximately 11,000 plants were screened and nearly 157 recombination events were identified between the flanking markers C2_At1g07960 (82.5 cM, physical distance 51.387 Mb) and T0302 (89 cM, 51.878 Mb). Molecular marker analysis of recombinants and TYLCV evaluation of progeny from these recombinants localized
Ty
-
2
to an approximately 300,000-bp interval between markers UP8 (51.344 Mb) and M1 (51.645 Mb). No recombinants were identified between TG36 and C2_At3g52090, a region of at least 115 kb, indicating severe recombination suppression in this region. Due to the small interval, fluorescence in situ hybridization analysis failed to clarify whether recombination suppression is caused by chromosomal rearrangements. Candidate genes predicted based on tomato genome annotation were analyzed by RT-PCR and virus-induced gene silencing. Results indicate that the NBS gene family present in the
Ty
-
2
region is likely not responsible for the
Ty
-
2
-conferred resistance and that two candidate genes might play a role in the
Ty
-
2
-conferred resistance. Several markers very tightly linked to the
Ty
-
2
locus are presented and useful for marker-assisted selection in breeding programs to introgress
Ty
-
2
for begomovirus resistance.
Regulation of AMP-activated protein kinase (AMPK) signalling is complex and involves contributions from adenine nucleotides, co-/posttranslational modifications, and isoform composition of the AMPK ...heterotrimer. It is becoming apparent that AMPK activation/inhibition by synthetic drugs involves similar levels of complexity. Major advances in our understanding of these mechanisms have been gained from recombinant expression systems that provide sufficient quantities of highly purified material for structure/function studies. Here, we provide a detailed protocol for transient expression of affinity-tagged AMPK complexes in mammalian cells. We have found this system to be optimal as a source of enzyme possessing regulatory modifications found in vivo.
A complete understanding of the factors that determine selection of antigens recognized by the humoral immune response following infectious agent challenge is lacking. Here we illustrate a systems ...biology approach to identify the antibody signature associated with Brucella melitensis (Bm) infection in humans and predict proteomic features of serodiagnostic antigens. By taking advantage of a full proteome microarray expressing previously cloned 1406 and newly cloned 1640 Bm genes, we were able to identify 122 immunodominant antigens and 33 serodiagnostic antigens. The reactive antigens were then classified according to annotated functional features (COGs), computationally predicted features (e.g., subcellular localization, physical properties), and protein expression estimated by mass spectrometry (MS). Enrichment analyses indicated that membrane association and secretion were significant enriching features of the reactive antigens, as were proteins predicted to have a signal peptide, a single transmembrane domain, and outer membrane or periplasmic location. These features accounted for 67% of the serodiagnostic antigens. An overlay of the seroreactive antigen set with proteomic data sets generated by MS identified an additional 24%, suggesting that protein expression in bacteria is an additional determinant in the induction of Brucella-specific antibodies. This analysis indicates that one-third of the proteome contains enriching features that account for 91% of the antigens recognized, and after B. melitensis infection the immune system develops significant antibody titers against 10% of the proteins with these enriching features. This systems biology approach provides an empirical basis for understanding the breadth and specificity of the immune response to B. melitensis and a new framework for comparing the humoral responses against other microorganisms.
Summary
Brentuximab vedotin (BV) significantly improved progression‐free survival in a phase 3 study in patients with relapsed or refractory Hodgkin lymphoma (RR‐HL) post‐autologous‐haematopoietic ...stem cell transplant (auto‐HSCT); we report the impact of BV on quality of life (QOL) from this trial. The European Quality of Life five dimensions questionnaire was administered at the beginning of each cycle, end of treatment, and every 3 months during follow‐up; index value scores were calculated using the time trade‐off (TTO) method for UK‐weighted value sets. Questionnaire adherence during the trial was 87·5% (N = 329). In an intent‐to‐treat analysis, compared with placebo, TTO scores in the BV arm did not exceed the minimally important difference (MID) of 0·08 except at month 15 (−0·084; 95% confidence interval, −0·143 to −0·025). On‐treatment index scores were similar between arms and did not reach the MID at any time point; mixed‐effect modelling showed that BV treatment effect was not significant (P = 0·2127). BV‐associated peripheral neuropathy did not meaningfully impact QOL. Utility scores for patients who progressed declined compared with those who did not; TTO scores between these patients exceeded the MID beginning at month 15. In conclusion, QOL decreased modestly with BV consolidation treatment in patients with RR‐HL at high risk of relapse after auto‐HSCT.
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