Consensus opinion from an international group of experts on measurable residual disease in hairy cell leukemia

A significant body of literature has been generated related to the detection of measurable residual disease (MRD) at the time of achieving complete remission (CR) in patients with hairy cell leukemia (HCL). However, due to the indolent nature of the disease as well as reports suggesting long-term survival in patients treated with a single course of a nucleoside analog albeit without evidence of cure, the merits of detection of MRD and attempts to eradicate it have been debated. Studies utilizing novel strategies in the relapse setting have demonstrated the utility of achieving CR with undetectable MRD (uMRD) in prolonging the duration of remission. Several assays including immunohistochemical analysis of bone marrow specimens, multi-parameter flow cytometry and molecular assays to detect the mutant BRAF V600E gene or the consensus primer for the immunoglobulin heavy chain gene (IGH) rearrangement have been utilized with few comparative studies. Here we provide a consensus report on the available data, the potential merits of MRD assessment in the front-line and relapse settings and recommendations on future role of MRD assessment in HCL

The energy penalty of post-combustion CO2 capture & storage and its implications for retrofitting the U.S. installed base

A review of the literature has found a factor of 4 spread in the estimated values of the energy penalty for post-combustion capture and storage of CO2 from pulverized-coal (PC) fired power plants. We elucidate the cause of that spread by deriving an analytic relationship for the energy penalty from thermodynamic principles and by identifying which variables are most difficult to constrain. We define the energy penalty for CCS to be the fraction of fuel that must be dedicated to CCS for a fixed quantity of work output. That penalty can manifest itself as either the additional fuel required to maintain a power plant's output or the loss of output for a constant fuel input. Of the 17 parameters that constitute the energy penalty, only the fraction of available waste heat that is recovered for use and the 2nd-law separation efficiency are poorly constrained. We provide an absolute lower bound for the energy penalty of ~11%, and we demonstrate to what degree increasing the fraction of available-waste-heat recovery can reduce the energy penalty from the higher values reported. It is further argued that an energy penalty of ~40% will be easily achieved while one of ~29% represents a decent target value. Furthermore, we analyze the distribution of PC plants in the U.S. and calculate a distribution for the additional fuel required to operate all these plants with CO2 capture and storage (CCS).Earth and Planetary SciencesEngineering and Applied Science

Proteogenomics refines the molecular classification of chronic lymphocytic leukemia

Cancer heterogeneity at the proteome level may explain differences in therapy response and prognosis beyond the currently established genomic and transcriptomic-based diagnostics. The relevance of proteomics for disease classifications remains to be established in clinically heterogeneous cancer entities such as chronic lymphocytic leukemia (CLL). Here, we characterize the proteome and transcriptome alongside genetic and ex-vivo drug response profiling in a clinically annotated CLL discovery cohort (n = 68). Unsupervised clustering of the proteome data reveals six subgroups. Five of these proteomic groups are associated with genetic features, while one group is only detectable at the proteome level. This new group is characterized by accelerated disease progression, high spliceosomal protein abundances associated with aberrant splicing, and low B cell receptor signaling protein abundances (ASB-CLL). Classifiers developed to identify ASB-CLL based on its characteristic proteome or splicing signature in two independent cohorts (n = 165, n = 169) confirm that ASB-CLL comprises about 20% of CLL patients. The inferior overall survival in ASB-CLL is also independent of both TP53- and IGHV mutation status. Our multi-omics analysis refines the classification of CLL and highlights the potential of proteomics to improve cancer patient stratification beyond genetic and transcriptomic profiling

Elucidation of tonic and activated B-cell receptor signaling in Burkitt's lymphoma provides insights into regulation of cell survival.

Burkitt's lymphoma (BL) is a highly proliferative B-cell neoplasm and is treated with intensive chemotherapy that, because of its toxicity, is often not suitable for the elderly or for patients with endemic BL in developing countries. BL cell survival relies on signals transduced by B-cell antigen receptors (BCRs). However, tonic as well as activated BCR signaling networks and their relevance for targeted therapies in BL remain elusive. We have systematically characterized and compared tonic and activated BCR signaling in BL by quantitative phosphoproteomics to identify novel BCR effectors and potential drug targets. We identified and quantified ∼16,000 phospho-sites in BL cells. Among these sites, 909 were related to tonic BCR signaling, whereas 984 phospho-sites were regulated upon BCR engagement. The majority of the identified BCR signaling effectors have not been described in the context of B cells or lymphomas yet. Most of these newly identified BCR effectors are predicted to be involved in the regulation of kinases, transcription, and cytoskeleton dynamics. Although tonic and activated BCR signaling shared a considerable number of effector proteins, we identified distinct phosphorylation events in tonic BCR signaling. We investigated the functional relevance of some newly identified BCR effectors and show that ACTN4 and ARFGEF2, which have been described as regulators of membrane-trafficking and cytoskeleton-related processes, respectively, are crucial for BL cell survival. Thus, this study provides a comprehensive dataset for tonic and activated BCR signaling and identifies effector proteins that may be relevant for BL cell survival and thus may help to develop new BL treatments

reliability and applicability of modern numerical analyses of dams

Relevance. At present the application of numerical analyses to real problems of dam engineering has suffered at times from the gaps between the specialists of mathematical modeling and dam engineers and managers. The first group usually includes information system specialists because they are able to develop the computer models to their full potential. The professionals belonging to the second group often prefer to revert to traditional methods of calculation and empirical methods based on their proven experience. The aim of the work - based on recommendations of International workshops seminars, organized by the ICOLD Committee on Computational Aspects of Dam Analysis and Design, help dam engineers to interact with mathematical modeling specialists and to work with them without language barriers or gaps in knowledge. In this relation the assessment of reliability and applicability of numerical analyses of dams allows engineers to develop the optimal dam design. Methods. Assessment of the reliability of numerical methods of analyses of dam behavior was based on data of 10 International benchmark-workshop seminars, organized by the Committee in Italy (1991 and 1992), France (1994 and 2009), Spain (1996), USA (1999), Austria (2001), Romania (2003), China (2005), Russia (2007), in which specialists of these countries also took part

An ultra-deep sequencing strategy to detect sub-clonal TP53 mutations in presentation chronic lymphocytic leukemia cases using multiple polymerases

Chronic lymphocytic leukaemia (CLL) is the most common clonal B-cell disorder characterized by clonal diversity, a relapsing and remitting course, and in its aggressive forms remains largely incurable. Current front-line regimes include agents such as fludarabine, which act primarily via the DNA damage response pathway. Key to this is the transcription factor p53. Mutations in the TP53 gene, altering p53 functionality, are associated with genetic instability, and are present in aggressive CLL. Furthermore, the emergence of clonal TP53 mutations in relapsed CLL, refractory to DNA-damaging therapy, suggests that accurate detection of sub-clonal TP53 mutations prior to and during treatment may be indicative of early relapse. In this study, we describe a novel deep sequencing workflow using multiple polymerases to generate sequencing libraries (MuPol-Seq), facilitating accurate detection of TP53 mutations at a frequency as low as 0.3%, in presentation CLL cases tested. As these mutations were mostly clustered within the regions of TP53 encoding DNA-binding domains, essential for DNA contact and structural architecture, they are likely to be of prognostic relevance in disease progression. The workflow described here has the potential to be implemented routinely to identify rare mutations across a range of diseases

Theory of excited state absorptions in phenylene-based π\pi-conjugated polymers

Within a rigid-band correlated electron model for oligomers of poly-(paraphenylene) (PPP) and poly-(paraphenylenevinylene) (PPV), we show that there exist two fundamentally different classes of two-photon A$_g$ states in these systems to which photoinduced absorption (PA) can occur. At relatively lower energies there occur A$_g$ states which are superpositions of one electron - one hole (1e--1h) and two electron -- two hole (2e--2h) excitations, that are both comprised of the highest delocalized valence band and the lowest delocalized conduction band states only. The dominant PA is to one specific member of this class of states (the mA$_g$). In addition to the above class of A$_g$ states, PA can also occur to a higher energy kA$_g$ state whose 2e--2h component is {\em different} and has significant contributions from excitations involving both delocalized and localized bands. Our calculated scaled energies of the mA$_g$ and the kA$_g$ agree reasonably well to the experimentally observed low and high energy PAs in PPV. The calculated relative intensities of the two PAs are also in qualitative agreement with experiment. In the case of ladder-type PPP and its oligomers, we predict from our theoretical work a new intense PA at an energy considerably lower than the region where PA have been observed currently. Based on earlier work that showed that efficient charge--carrier generation occurs upon excitation to odd--parity states that involve both delocalized and localized bands, we speculate that it is the characteristic electronic nature of the kA$_g$ that leads to charge generation subsequent to excitation to this state, as found experimentally.Comment: Revtex4 style, 2 figures inserted in the text, three tables, 10 page

Study of CP violation in Dalitz-plot analyses of B0 --> K+K-KS, B+ --> K+K-K+, and B+ --> KSKSK+

We perform amplitude analyses of the decays $B^0 \to K^+K^-K^0_S$, $B^+ \rightarrow K^+K^-K^+$, and $B^+ \to K^0_S K^0_S K^+$, and measure CP-violating parameters and partial branching fractions. The results are based on a data sample of approximately $470\times 10^6$ $B\bar{B}$ decays, collected with the BABAR detector at the PEP-II asymmetric-energy $B$ factory at the SLAC National Accelerator Laboratory. For $B^+ \to K^+K^-K^+$, we find a direct CP asymmetry in $B^+ \to \phi(1020)K^+$ of $A_{CP}= (12.8\pm 4.4 \pm 1.3)$, which differs from zero by $2.8 \sigma$. For $B^0 \to K^+K^-K^0_S$, we measure the CP-violating phase $\beta_{\rm eff} (\phi(1020)K^0_S) = (21\pm 6 \pm 2)^\circ$. For $B^+ \to K^0_S K^0_S K^+$, we measure an overall direct CP asymmetry of $A_{CP} = (4 ^{+4}_{-5} \pm 2)$. We also perform an angular-moment analysis of the three channels, and determine that the $f_X(1500)$ state can be described well by the sum of the resonances $f_0(1500)$, $f_2^{\prime}(1525)$, and $f_0(1710)$.Comment: 35 pages, 68 postscript figures. v3 - minor modifications to agree with published versio

Truncated and Helix-Constrained Peptides with High Affinity and Specificity for the cFos Coiled-Coil of AP-1

Protein-based therapeutics feature large interacting surfaces. Protein folding endows structural stability to localised surface epitopes, imparting high affinity and target specificity upon interactions with binding partners. However, short synthetic peptides with sequences corresponding to such protein epitopes are unstructured in water and promiscuously bind to proteins with low affinity and specificity. Here we combine structural stability and target specificity of proteins, with low cost and rapid synthesis of small molecules, towards meeting the significant challenge of binding coiled coil proteins in transcriptional regulation. By iteratively truncating a Jun-based peptide from 37 to 22 residues, strategically incorporating i-->i+4 helix-inducing constraints, and positioning unnatural amino acids, we have produced short, water-stable, alpha-helical peptides that bind cFos. A three-dimensional NMR-derived structure for one peptide (24) confirmed a highly stable alpha-helix which was resistant to proteolytic degradation in serum. These short structured peptides are entropically pre-organized for binding with high affinity and specificity to cFos, a key component of the oncogenic transcriptional regulator Activator Protein-1 (AP-1). They competitively antagonized the cJun–cFos coiled-coil interaction. Truncating a Jun-based peptide from 37 to 22 residues decreased the binding enthalpy for cJun by ~9 kcal/mol, but this was compensated by increased conformational entropy (TDS ≤ 7.5 kcal/mol). This study demonstrates that rational design of short peptides constrained by alpha-helical cyclic pentapeptide modules is able to retain parental high helicity, as well as high affinity and specificity for cFos. These are important steps towards small antagonists of the cJun-cFos interaction that mediates gene transcription in cancer and inflammatory diseases