Identification of an Efficient Gene Expression Panel for Glioblastoma Classification.

We present here a novel genetic algorithm-based random forest (GARF) modeling technique that enables a reduction in the complexity of large gene disease signatures to highly accurate, greatly simplified gene panels. When applied to 803 glioblastoma multiforme samples, this method allowed the 840-gene Verhaak et al. gene panel (the standard in the field) to be reduced to a 48-gene classifier, while retaining 90.91% classification accuracy, and outperforming the best available alternative methods. Additionally, using this approach we produced a 32-gene panel which allows for better consistency between RNA-seq and microarray-based classifications, improving cross-platform classification retention from 69.67% to 86.07%. A webpage producing these classifications is available at http://simplegbm.semel.ucla.edu

Dielasma or Tunethyris? A Taxonomic Conundrum

A new species of a dielasmid brachiopod from the Triassic Saharonim Formation of Makhtesh Ramon, southern Israel, was discovered in Anisian-Ladinian limestones that alternate with calcareous shales. The environment of deposition was an open shelf with normal salinity. The new species is homeomorphic with Paleozoic forms, but may not belong to the genus Dielasma; however, it may be a species of Tunethyris, a Triassic genus from Tunisia. If the Triassic specimens belong to the Paleozoic genus Dielasma, an important new Lazarus genus is added to the systematic literature. However, if the specimens belong to the Triassic Tunethyris, there are important paleobiogeographic considerations to be noted, such as the significance of the enigmatic Ladinian crisis and the influence of the Hispanic Corridor, an immature seaway connecting the western Tethys with eastern Panthalassa that may have been open sporadically during the Late Triassic and affected brachiopod distribution. Points favoring the selection of Tunethyris are: 1. The orientation of the crura in the new species is slightly different from Paleozoic dielasmids, especially D. elongatum from the Permian of Germany; 2. the anatomy of Tunethyris punica from the Norian of Tunisia is very similar to the new species and the anterior commissure of both is sulicplicate, a feature not found in Paleozoic forms; 3. The loop of the Israeli brachiopods is acuminate. In addition to other anatomical characters that support the erection of a new species, Tunethyris calzada has a septalium supported by a median septum whereas the septalium in the brachiopods from Makhtesh Ramon rests on the valve floor

Metal-insulator transition in EuO

It is shown that the spectacular metal-insulator transition in Eu-rich EuO can be simulated within an extended Kondo lattice model. The different orders of magnitude of the jump in resistivity in dependence on the concentration of oxygen vacancies as well as the low-temperature resistance minimum in high-resistivity samples are reproduced quantitatively. The huge colossal magnetoresistance (CMR) is calculated and discussed

Emerging Role of Immune Checkpoint Blockade in Pancreatic Cancer

Immune checkpoint blockade (ICB) with programmed cell death protein-1(PD-1)/programmed death ligand -1(PD-L1) antibodies has revolutionized the management of several cancers, especially non-small cell lung cancer, melanoma, urothelial, and renal cancer. Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive cancers associated with high morbidity and mortality. Based on available data, it’s obvious that ICB has limited success in PDACs, which can be explained by the low immunogenicity and immunosuppressive tumor microenvironment of these tumors. In this review article, we focus on PD-L1 expression and microsatellite instability (MSI) in PDAC, and their roles as prognostic and predictive markers. We also discuss data supporting combination therapies to augment cancer immunity cycle. Combining anti-PD-1/PD-L1 agents with other modalities such as vaccines, chemotherapy, and radiation could potentially overcome resistance patterns and increase immune responsiveness in PDA

Comparison of quantification methods for the condensed tannin content of extracts of Pinus pinaster bark

Bark from Pinus Pinaster is an interesting source of polyphenolic natural compounds, that can be used successful1y as total or partial replacement of conventional phenolic resins. These compounds, among other applications, are used as adhesives in the wood agglomerate industry. In this kind of application some problems remain to be solved in order to obtain a Pine extract of commercial value. It is necessary to optimise tije extraction procedure and select a suitable method for the quantification of the tannin content of the bark. In order to study these problems, the tannin extraction from the Pine bark was tested with an alkaline solution (NaOH), and with a fractionation procedure based on a sequence of an organic (ethanol) and aqueous extraction. The phenolic content of each extract or fraction was evaluated by the FolinCiocalteu colorimetric assay for total phenols and two procedures using the Stiasny reaction: the gravimetric Stiasny method and the indirect colorimetric procedure that uses the Folin-Ciocalteu reagent to evaluate the total phenols present in the extract solution before and after it condenses with formaldehyde. The yield value when the alkaline extraction is used is substantially higher than the values obtained with organic or aqueous solutions. However, the selectivity of the process is low. In fact, it was found that the alkaline extract Formaldehyde Condensable Phenolic Material (FCPM) content represents 9596 % of the total phenols content of the extract but this fraction is only ~ 40 % of the total mass of extract. So, the alkaline extract is relatively poor in phenolic material, exhibiting a large variety of non-phenolic extractives. On the other end, ethanol provides a very rich phenolic extract, in which 96 % of total phenols are condensable with formaldehyde, but exhibits a relatively low extraction yield. The aqueous extract presents the lowest extraction yield with low content either in phenolic material as in FCPM, but, as most of the phenolics had already been extracted by the previous organic extraction, especially the low molecular weight fractions, this result was predictable

High-Dose Chemotherapy with Autologous Hematopoietic Stem-Cell Rescue for Pediatric Brain Tumor Patients: A Single Institution Experience from UCLA

Background. Dose-dependent response makes certain pediatric brain tumors appropriate targets for high-dose chemotherapy with autologous hematopoietic stem-cell rescue (HDCT-AHSCR). Methods. The clinical outcomes and toxicities were analyzed retrospectively for 18 consecutive patients ≤19 y/o treated with HDCT-AHSCR at UCLA (1999–2009). Results. Patients' median age was 2.3 years. Fourteen had primary and 4 recurrent tumors: 12 neural/embryonal (7 medulloblastomas, 4 primitive neuroectodermal tumors, and a pineoblastoma), 3 glial/mixed, and 3 germ cell tumors. Eight patients had initial gross-total and seven subtotal resections. HDCT mostly consisted of carboplatin and/or thiotepa ± etoposide (n = 16). Nine patients underwent a single AHSCR and nine ≥3 tandems. Three-year progression-free and overall survival probabilities were 60.5% ± 16 and 69.3% ± 11.5. Ten patients with pre-AHSCR complete remissions were alive/disease-free, whereas 5 of 8 with measurable disease were deceased (median followup: 2.3 yrs). Nine of 13 survivors avoided radiation. Single AHSCR regimens had greater toxicity than ≥3 AHSCR (P < .01). Conclusion. HDCT-AHSCR has a definitive, though limited role for selected pediatric brain tumors with poor prognosis and pretransplant complete/partial remissions

Management recommendations for pancreatic manifestations of von Hippel–Lindau disease

Von Hippel–Lindau disease (VHL) is a multineoplasm inherited disease manifesting with hemangioblastoma of the central nervous system and retina, adrenal pheochromocytoma, renal cell carcinoma, pancreatic neuroendocrine tumors and cysts, and neoplasms/cysts of the ear, broad ligament, and testicles. During 2018-2020, the VHL Alliance gathered several committees of experts in the various clinical manifestations of VHL to review the literature, gather the available evidence on VHL, and develop recommendations for patient management. The current report details the results of the discussion of a group of experts in the pancreatic manifestations of VHL along with their proposed recommendations for the clinical surveillance and management of patients with VHL. The recommendations subcommittee performed a comprehensive systematic review of the literature and conducted panel discussions to reach the current recommendations. The level of evidence was defined according to the Shekelle variation of the Grading of Recommendations, Assessment, Development, and Evaluation grading system. The National Comprehensive Cancer Network Categories of Evidence and Consensus defined the committee members' interpretation of the evidence and degree of consensus. The recommendations encompass the main aspects of VHL-related pancreatic manifestations and their clinical management. They are presented in a clinical orientation, including general planning of screening and surveillance for pancreatic neuroendocrine tumors, utility of biochemical biomarkers, the optimal choice for imaging modality, indirect risk stratification, indications for tissue sampling of VHL-related pancreatic neuroendocrine tumors, and interventions. These recommendations are designed to serve as the reference for all aspects of the screening, surveillance, and management of VHL-related pancreatic manifestations

Cation- and vacancy-ordering in Li_xCoO_2

Using a combination of first-principles total energies, a cluster expansion technique, and Monte Carlo simulations, we have studied the Li/Co ordering in LiCoO_2 and Li-vacancy/Co ordering in CoO_2. We find: (i) A ground state search of the space of substitutional cation configurations yields the (layered) CuPt structure as the lowest-energy state in the octahedral system LiCoO_2 (and CoO_2), in agreement with the experimentally observed phase. (ii) Finite temperature calculations predict that the solid-state order- disorder transitions for LiCoO_2 and CoO_2 occur at temperatures (~5100 K and ~4400 K, respectively) much higher than melting, thus making these transitions experimentally inaccessible. (iii) The energy of the reaction E(LiCoO_2) - E(CoO_2) - E(Li) gives the average battery voltage V of a Li_xCoO_2/Li cell. Searching the space of configurations for large average voltages, we find that CuPt (a monolayer superlattice) has a high voltage (V=3.78 V), but that this could be increased by cation randomization (V=3.99 V), partial disordering (V=3.86 V), or by forming a 2-layer Li_2Co_2O_4 superlattice along (V=4.90 V).Comment: 12 Pages, RevTeX galley format, 5 figures embedded using epsf Phys. Rev. B (in press, 1998

Mindfulness-based interventions for people diagnosed with a current episode of an anxiety or depressive disorder: a meta-analysis of randomised controlled trials

Objective Mindfulness-based interventions (MBIs) can reduce risk of depressive relapse for people with a history of recurrent depression who are currently well. However, the cognitive, affective and motivational features of depression and anxiety might render MBIs ineffective for people experiencing current symptoms. This paper presents a meta-analysis of randomised controlled trials (RCTs) of MBIs where participants met diagnostic criteria for a current episode of an anxiety or depressive disorder. Method Post-intervention between-group Hedges g effect sizes were calculated using a random effects model. Moderator analyses of primary diagnosis, intervention type and control condition were conducted and publication bias was assessed. Results Twelve studies met inclusion criteria (n = 578). There were significant post-intervention between-group benefits of MBIs relative to control conditions on primary symptom severity (Hedges g = −0.59, 95% CI = −0.12 to −1.06). Effects were demonstrated for depressive symptom severity (Hedges g = −0.73, 95% CI = −0.09 to −1.36), but not for anxiety symptom severity (Hedges g = −0.55, 95% CI = 0.09 to −1.18), for RCTs with an inactive control (Hedges g = −1.03, 95% CI = −0.40 to −1.66), but not where there was an active control (Hedges g = 0.03, 95% CI = 0.54 to −0.48) and effects were found for MBCT (Hedges g = −0.39, 95% CI = −0.15 to −0.63) but not for MBSR (Hedges g = −0.75, 95% CI = 0.31 to −1.81). Conclusions This is the first meta-analysis of RCTs of MBIs where all studies included only participants who were diagnosed with a current episode of a depressive or anxiety disorder. Effects of MBIs on primary symptom severity were found for people with a current depressive disorder and it is recommended that MBIs might be considered as an intervention for this population

Effects of anharmonic strain on phase stability of epitaxial films and superlattices: applications to noble metals

Epitaxial strain energies of epitaxial films and bulk superlattices are studied via first-principles total energy calculations using the local-density approximation. Anharmonic effects due to large lattice mismatch, beyond the reach of the harmonic elasticity theory, are found to be very important in Cu/Au (lattice mismatch 12%), Cu/Ag (12%) and Ni/Au (15%). We find that is the elastically soft direction for biaxial expansion of Cu and Ni, but it is for large biaxial compression of Cu, Ag, and Au. The stability of superlattices is discussed in terms of the coherency strain and interfacial energies. We find that in phase-separating systems such as Cu-Ag the superlattice formation energies decrease with superlattice period, and the interfacial energy is positive. Superlattices are formed easiest on (001) and hardest on (111) substrates. For ordering systems, such as Cu-Au and Ag-Au, the formation energy of superlattices increases with period, and interfacial energies are negative. These superlattices are formed easiest on (001) or (110) and hardest on (111) substrates. For Ni-Au we find a hybrid behavior: superlattices along and like in phase-separating systems, while for they behave like in ordering systems. Finally, recent experimental results on epitaxial stabilization of disordered Ni-Au and Cu-Ag alloys, immiscible in the bulk form, are explained in terms of destabilization of the phase separated state due to lattice mismatch between the substrate and constituents.Comment: RevTeX galley format, 16 pages, includes 9 EPS figures, to appear in Physical Review