PMLB v1.0: an open-source dataset collection for benchmarking machine learning methods.

MOTIVATION: Novel machine learning and statistical modeling studies rely on standardized comparisons to existing methods using well-studied benchmark datasets. Few tools exist that provide rapid access to many of these datasets through a standardized, user-friendly interface that integrates well with popular data science workflows. RESULTS: This release of PMLB (Penn Machine Learning Benchmarks) provides the largest collection of diverse, public benchmark datasets for evaluating new machine learning and data science methods aggregated in one location. v1.0 introduces a number of critical improvements developed following discussions with the open-source community. AVAILABILITY AND IMPLEMENTATION: PMLB is available at https://github.com/EpistasisLab/pmlb. Python and R interfaces for PMLB can be installed through the Python Package Index and Comprehensive R Archive Network, respectively.

The cognitive aspects of sexual intimacy in dementia patients: a neurophysiological review.

Changes in higher-order cognitive behaviors such as reward recognition, salience processing, novelty perception, decision-making, emotional contagion, motivation, and empathy may contribute to intimacy dysfunction. Network circuitry underlying these cognitive functions is often activated in sexually intimate behavior. We propose that sexual dysfunction in AD and bvFTD is more nuanced than is commonly believed, and propose how AD and bvFTD atrophy may correlate neuroanatomically to brain regions and networks that contribute to the higher-order cognitive aspects of intimacy. The characterization of sexual intimacy in dementias must be expanded to meet the needs of our dementia patients and their romantic partners.

Cytoplasmic dynein and LIS1 are required for microtubule advance during growth cone remodeling and fast axonal outgrowth.

Recent evidence has implicated dynein and its regulatory factors dynactin and LIS1 in neuronal and non-neuronal cell migration. In the current study we sought to test whether effects on neuronal cell motility might reflect, in part, a role for these proteins in the growth cone. In chick sensory neurons subjected to acute laminin treatment dynein, dynactin, and LIS1 were mobilized strikingly and rapidly to the leading edge of the growth cone, where they were seen to be associated with microtubules converging into the laminin-induced axonal outgrowths. To interfere acutely with LIS1 and dynein function and to minimize secondary phenotypic effects, we injected antibodies to these proteins just before axon initiation. Antibody to both proteins produced an almost complete block of laminin-induced growth cone remodeling and the underlying reorganization of microtubules. Penetration of microtubules into the peripheral zone of differentiating axonal growth cones was decreased dramatically by antibody injection, as judged by live analysis of enhanced green fluorescent protein-tubulin and the microtubule tip-associated EB3 (end-binding protein 3). Dynein and LIS1 inhibition had no detectable effect on microtubule assembly but reduced the ability of microtubules to resist retrograde actin flow. In hippocampal neurons dynein, dynactin, and LIS1 were enriched in axonal growth cones at stage 3, and both growth cone organization and axon elongation were altered by LIS1 RNA interference. Together, our data indicate that dynein and LIS1 play a surprisingly prominent role in microtubule advance during growth cone remodeling associated with axonogenesis. These data may explain, in part, the role of these proteins in brain developmental disease and support an important role in diverse aspects of neuronal differentiation and nervous system development.

Initiating morphological changes associated with long-term facilitation in Aplysia is independent of transcription or translation in the cell body.

In Aplysia, the growth of axonal arbor and the formation of new presynaptic varicosities are thought to contribute to long-term facilitation (LTF) produced by serotonin (5-HT). While it is known that there is a requirement for both transcription and translation in LTF and in the accompanying morphological changes, the mechanisms mediating the initiation and maintenance of these changes are poorly understood. We used long-term labeling of the presynaptic sensory neuron to carry out repeated imaging of axonal morphology, coupled with electrophysiology, to further elucidate the macromolecular requirements of this process. Robust synaptic facilitation, axonal growth, and the formation of axonal varicosities were elicited by 5-HT even when transcription was blocked with actinomycin. Increases in synaptic efficacy and varicosity number were detected 12 h after exposure to 5-HT but did not persist to 24 h. Even when sensory neuron cell bodies were removed, eliminating the contributions of both somal transcription and translation, 5-HT elicited these transient morphological and electrophysiological responses. New sensory varicosities contacting the postsynaptic neuron were filled with the neuropeptide sensorin. Under all conditions, global inhibition of protein synthesis completely blocked the formation of new axonal branches and varicosities. These results demonstrate that neither transcription nor somal translation is required to initiate the axonal growth that often accompanies long-term synaptic plasticity-protein synthesis in the axon is sufficient. Macromolecular synthesis in the cell body is, however, required to maintain the enlarged arbor.

Microtubule and Rac 1-dependent F-actin in growth cones.

Extracellular cues control the rate and direction of growth of neuronal processes in large part by regulating the cytoskeleton of the growth cone. The actin filament network of the peripheral region is thought to be the primary target for these cues, with consequences for the advance and organization of microtubules. Binding of laminin to integrin receptors is a cue that accelerates the growth of processes from many types of neurons. It was applied acutely to sympathetic neurons in culture to study its effects on the cytoskeleton of the growth cone. Microtubules advance to the edge of the growth cone and bundle in response to laminin, and it was found that small veils of membrane appear near the ends of some of those microtubules. To examine more clearly the relationship between the microtubules and the appearance of actin-rich structures at the periphery, a low dose of cytochalasin D was used to deplete the peripheral region of the growth cone of pre-existing F-actin. The subsequent addition of laminin resulted in the bundling of ends of dynamic (tyrosinated) microtubules at the distal edge of the growth cone, most of which were associated with foci of F-actin. Observations of labeled actin within living growth cones confirmed that these foci formed in response to laminin. Suppression of microtubule dynamics with drugs eliminated the actin foci; washout of drug restored them. Rac 1 did not co-concentrate with F-actin in the peripheral region of the growth cone in the absence of laminin, but did co-concentrate with the foci of F-actin that formed in response to laminin. Inhibition of Rac 1 functioning prevented the formation of the foci and also inhibited laminin-induced neurite growth with or without cytochalasin. These results indicate that extracellular cues can affect actin in the growth cone via microtubules, as well as affect microtubules via actin. They also point to the mediation of microtubule-dependent accumulation of F-actin at the front of the growth cone as a role of Rac 1 in neurite growth.