Not Every Thing Must Go

In The Entangled Brain, Pessoa criticizes standard approaches in cognitive neuroscience in which the brain is seen as a functionally decomposable, modular system with causal operations built up hierarchically. Instead, he advocates for an emergentist perspective whereby dynamic brain networks are associated, not with traditional psychological categories, but with behavioral functions characterized in evolutionary terms. Here, we raise a number of concerns with such a radical approach. We ultimately believe that while much revision to cognitive neuroscience is welcome and needed, Pessoa’s more radical proposals may be counterproductive

A simple approach to preserve keratinized mucosa around implants using a pre-fabricated implant-retained stent: a report of two cases

Purpose: There is no consensus regarding the relationship between the width of keratinized mucosa and the health of periimplant tissues, but clinicians prefer to provide enough keratinized mucosa around dental implants for long-term implant maintenance. An apically positioned flap during second stage implant surgery is the chosen method of widening the keratinized zone in simple procedures. However, the routine suture techniques used with this method tend to apply tension over the provisional abutments and decrease pre-existing keratinized mucosa. To overcome this shortcoming, a pre-fabricated implant-retained stent was designed to apply vertical pressure on the labial flap and stabilize it in a bucco-apical direction to create a wide keratinized mucous zone. Methods: During second stage implant surgery, an apically displaced, partial thickness flap with a lingualized incision was retracted. A pre-fabricated stent was clipped over the abutments after connecting to the provisional abutment. Vertical pressure was applied to displace the labial flap. No suture was required and the stent was removed after 10 days. Results: A clinically relevant amount of keratinized mucosa was achieved around the dental implants. Buccally displaced keratinized mucosa was firmly attached to the underlying periosteum. A slight shrinkage of the keratinized zone was noted after the healing period in one patient, but no discomfort during oral hygiene was reported. Clinically healthy gingiva with enough keratinized mucosa was achieved in both patients. Conclusions: The proposed technique is a simple and time-effective technique for preserving and providing keratinized tissue around dental implantsope

Interplane Transport and Superfluid Density in Layered Superconductors

We report on generic trends in the behavior of the interlayer penetration depth $\lambda_c$ of several different classes of quasi two-dimensional superconductors including cuprates, Sr$_2$RuO$_4$, transition metal dichalcogenides and organic materials of the $(BEDT-TTF)_2X$-series. Analysis of these trends reveals two distinct patterns in the scaling between the values of $\lambda_c$ and the magnitude of the DC conductivity: one realized in the systems with a Fermi liquid (FL) ground state and the other seen in systems with a marked deviation from the FL response. The latter pattern is found primarily in under-doped cuprates and indicates a dramatic enhancement (factor $\simeq 10^2$) of the energy scale $\Omega_C$ associated with the formation of the condensate compared to the data for the FL materials. We discuss implications of these results for the understanding of pairing in high-$T_c$ cuprates.Comment: 4 pages, 2 figure

Analyzing the Impacts of Off-Road Vehicle (ORV) Trails on Watershed Processes in Wrangell-St. Elias National Park and Preserve, Alaska

Trails created by off-road vehicles (ORV) in boreal lowlands are known to cause local impacts, such as denuded vegetation, soil erosion, and permafrost thaw, but impacts on stream and watershed processes are less certain. In Wrangell-St. Elias National Park and Preserve (WRST), Alaska, ORV trails have caused local resource damage in intermountain lowlands with permafrost soils and abundant wetlands and there is a need to know whether these impacts are more extensive. Comparison of aerial photography from 1957, 1981, and 2004 coupled with ground surveys in 2009 reveal an increase in trail length and number and show an upslope expansion of a trail system around points of stream channel initiation. We hypothesized that these impacts could also cause premature initiation and headward expansion of channels because of lowered soil resistance and greater runoff accumulation as trails migrate upslope. Soil monitoring showed earlier and deeper thaw of the active layer in and adjacent to trails compared to reference sites. Several rainfall-runoff events during the summer of 2009 showed increased and sustained flow accumulation below trail crossings and channel shear forces sufficient to cause headward erosion of silt and peat soils. These observations of trail evolution relative to stream and wetland crossings together with process studies suggest that ORV trails are altering watershed processes. These changes in watershed processes appear to result in increasing drainage density and may also alter downstream flow regimes, water quality, and aquatic habitat. Addressing local land-use disturbances in boreal and arctic parklands with permafrost soils, such as WRST, where responses to climate change may be causing concurrent shifts in watershed processes, represents an important challenge facing resource managers

Inferring Pathway Activity toward Precise Disease Classification

The advent of microarray technology has made it possible to classify disease states based on gene expression profiles of patients. Typically, marker genes are selected by measuring the power of their expression profiles to discriminate among patients of different disease states. However, expression-based classification can be challenging in complex diseases due to factors such as cellular heterogeneity within a tissue sample and genetic heterogeneity across patients. A promising technique for coping with these challenges is to incorporate pathway information into the disease classification procedure in order to classify disease based on the activity of entire signaling pathways or protein complexes rather than on the expression levels of individual genes or proteins. We propose a new classification method based on pathway activities inferred for each patient. For each pathway, an activity level is summarized from the gene expression levels of its condition-responsive genes (CORGs), defined as the subset of genes in the pathway whose combined expression delivers optimal discriminative power for the disease phenotype. We show that classifiers using pathway activity achieve better performance than classifiers based on individual gene expression, for both simple and complex case-control studies including differentiation of perturbed from non-perturbed cells and subtyping of several different kinds of cancer. Moreover, the new method outperforms several previous approaches that use a static (i.e., non-conditional) definition of pathways. Within a pathway, the identified CORGs may facilitate the development of better diagnostic markers and the discovery of core alterations in human disease

Protein Networks as Logic Functions in Development and Cancer

Many biological and clinical outcomes are based not on single proteins, but on modules of proteins embedded in protein networks. A fundamental question is how the proteins within each module contribute to the overall module activity. Here, we study the modules underlying three representative biological programs related to tissue development, breast cancer metastasis, or progression of brain cancer, respectively. For each case we apply a new method, called Network-Guided Forests, to identify predictive modules together with logic functions which tie the activity of each module to the activity of its component genes. The resulting modules implement a diverse repertoire of decision logic which cannot be captured using the simple approximations suggested in previous work such as gene summation or subtraction. We show that in cancer, certain combinations of oncogenes and tumor suppressors exert competing forces on the system, suggesting that medical genetics should move beyond cataloguing individual cancer genes to cataloguing their combinatorial logic

A proteome-wide protein interaction map for Campylobacter jejuni

'Systematic identification of protein interactions for the bacterium Campylobacter jejuni using high-throughput yeast two-hybrid screens detected interactions for 80% of the organism's proteins

Development and validation of a unifying pre-treatment decision tool for intracranial and extracranial metastasis-directed radiotherapy

BackgroundThough metastasis-directed therapy (MDT) has the potential to improve overall survival (OS), appropriate patient selection remains challenging. We aimed to develop a model predictive of OS to refine patient selection for clinical trials and MDT.Patients and methodsWe assembled a multi-institutional cohort of patients treated with MDT (stereotactic body radiation therapy, radiosurgery, and whole brain radiation therapy). Candidate variables for recursive partitioning analysis were selected per prior studies: ECOG performance status, time from primary diagnosis, number of additional non-target organ systems involved (NOS), and intracranial metastases.ResultsA database of 1,362 patients was assembled with 424 intracranial, 352 lung, and 607 spinal treatments (n=1,383). Treatments were split into training (TC) (70%, n=968) and internal validation (IVC) (30%, n=415) cohorts. The TC had median ECOG of 0 (interquartile range [IQR]: 0-1), NOS of 1 (IQR: 0-1), and OS of 18 months (IQR: 7-35). The resulting model components and weights were: ECOG = 0, 1, and > 1 (0, 1, and 2); 0, 1, and > 1 NOS (0, 1, and 2); and intracranial target (2), with lower scores indicating more favorable OS. The model demonstrated high concordance in the TC (0.72) and IVC (0.72). The score also demonstrated high concordance for each target site (spine, brain, and lung).ConclusionThis pre-treatment decision tool represents a unifying model for both intracranial and extracranial disease and identifies patients with the longest survival after MDT who may benefit most from aggressive local therapy. Carefully selected patients may benefit from MDT even in the presence of intracranial disease, and this model may help guide patient selection for MDT