Unsupervised discovery of temporal sequences in high-dimensional datasets, with applications to neuroscience.

Identifying low-dimensional features that describe large-scale neural recordings is a major challenge in neuroscience. Repeated temporal patterns (sequences) are thought to be a salient feature of neural dynamics, but are not succinctly captured by traditional dimensionality reduction techniques. Here, we describe a software toolbox-called seqNMF-with new methods for extracting informative, non-redundant, sequences from high-dimensional neural data, testing the significance of these extracted patterns, and assessing the prevalence of sequential structure in data. We test these methods on simulated data under multiple noise conditions, and on several real neural and behavioral datas. In hippocampal data, seqNMF identifies neural sequences that match those calculated manually by reference to behavioral events. In songbird data, seqNMF discovers neural sequences in untutored birds that lack stereotyped songs. Thus, by identifying temporal structure directly from neural data, seqNMF enables dissection of complex neural circuits without relying on temporal references from stimuli or behavioral outputs

Duality of Bures and Shape Distances with Implications for Comparing Neural Representations

A multitude of (dis)similarity measures between neural network representations have been proposed, resulting in a fragmented research landscape. Most of these measures fall into one of two categories. First, measures such as linear regression, canonical correlations analysis (CCA), and shape distances, all learn explicit mappings between neural units to quantify similarity while accounting for expected invariances. Second, measures such as representational similarity analysis (RSA), centered kernel alignment (CKA), and normalized Bures similarity (NBS) all quantify similarity in summary statistics, such as stimulus-by-stimulus kernel matrices, which are already invariant to expected symmetries. Here, we take steps towards unifying these two broad categories of methods by observing that the cosine of the Riemannian shape distance (from category 1) is equal to NBS (from category 2). We explore how this connection leads to new interpretations of shape distances and NBS, and draw contrasts of these measures with CKA, a popular similarity measure in the deep learning literature

Prevalence of Inherited Hemoglobin Disorders and Relationships with Anemia and Micronutrient Status among Children in Yaoundé and Douala, Cameroon.

Information on the etiology of anemia is necessary to design effective anemia control programs. Our objective was to measure the prevalence of inherited hemoglobin disorders (IHD) in a representative sample of children in urban Cameroon, and examine the relationships between IHD and anemia. In a cluster survey of children 12-59 months of age (n = 291) in Yaoundé and Douala, we assessed hemoglobin (Hb), malaria infection, and plasma indicators of inflammation and micronutrient status. Hb S was detected by HPLC, and α⁺thalassemia (3.7 kb deletions) by PCR. Anemia (Hb < 110 g/L), inflammation, and malaria were present in 45%, 46%, and 8% of children. A total of 13.7% of children had HbAS, 1.6% had HbSS, and 30.6% and 3.1% had heterozygous and homozygous α⁺thalassemia. The prevalence of anemia was greater among HbAS compared to HbAA children (60.3 vs. 42.0%, p = 0.038), although mean Hb concentrations did not differ, p = 0.38). Hb and anemia prevalence did not differ among children with or without single gene deletion α⁺thalassemia. In multi-variable models, anemia was independently predicted by HbAS, HbSS, malaria, iron deficiency (ID; inflammation-adjusted ferritin <12 µg/L), higher C-reactive protein, lower plasma folate, and younger age. Elevated soluble transferrin receptor concentration (>8.3 mg/L) was associated with younger age, malaria, greater mean reticulocyte counts, inflammation, HbSS genotype, and ID. IHD are prevalent but contribute modestly to anemia among children in urban Cameroon

The relationship between Modic changes and intervertebral disc degeneration

BACKGROUND: Recent reported results have added to the weight of evidence supporting association between disc degeneration and Modic changes. Endplate or Modic changes are also associated with increased body mass index. The most recent study from Teichtahl et al. titled 'Modic changes in the lumbar spine and their association with body composition, fat distribution and intervertebral disc height - a 3.0 T-MRI study' showed associations of Modic changes with quantitatively measured reduced disc height and fat mass index. However, there were some facts, which we would like to address in this Correspondence to their article. DISCUSSION: The different components of intervertebral disc degeneration such as loss of disc height and disc signal intensity have already been shown associated with endplate changes - but not disc height if it is assessed using newer more precise methods of quantitation of disc height. A possible protective effect of different adiposity distribution in the body to Modic change development would be of interest if observed in a longitudinal study in the future. Modic changes have been associated with different components of intervertebral disc degeneration such as loss of disc height and disc signal intensity previously. The influence of body fat distribution on endplate changes would be interesting to study longitudinally

Representational dissimilarity metric spaces for stochastic neural networks

Quantifying similarity between neural representations -- e.g. hidden layer activation vectors -- is a perennial problem in deep learning and neuroscience research. Existing methods compare deterministic responses (e.g. artificial networks that lack stochastic layers) or averaged responses (e.g., trial-averaged firing rates in biological data). However, these measures of deterministic representational similarity ignore the scale and geometric structure of noise, both of which play important roles in neural computation. To rectify this, we generalize previously proposed shape metrics (Williams et al. 2021) to quantify differences in stochastic representations. These new distances satisfy the triangle inequality, and thus can be used as a rigorous basis for many supervised and unsupervised analyses. Leveraging this novel framework, we find that the stochastic geometries of neurobiological representations of oriented visual gratings and naturalistic scenes respectively resemble untrained and trained deep network representations. Further, we are able to more accurately predict certain network attributes (e.g. training hyperparameters) from its position in stochastic (versus deterministic) shape space

Utilizing x-ray computed tomography for heritage conservation : the case of megalosaurus bucklandii

Of key importance to any cultural institution is the practice of conservation, the method by which specimens at risk of severe degradation or destruction are treated to ensure that they survive into the future. However, surface inspection is often insufficient to properly inform conservators of the best treatment approach, and where there is little to no record of the conservational history of an object it can be difficult to identify exactly what form of conservation has been undertaken. X-Ray Computed Tomography (XCT) grants a way to overcome these issues by allowing conservators to non-destructively investigate the subsurface details of an artefact to provide essential information on condition of a specimen. Here, the potential of this approach is demonstrated using the first XCT scans of the iconic dentary of Megalosaurus bucklandii Mantell, 1827 (1); the first dinosaur ever named and described scientifically. XCT analysis reveals that the degree of repair is less extensive than previously thought and also elucidates two different material types, M1 and M2, thought to be representative of at least two phases of repair. Finally the potential of this approach is further explored, highlighting its importance for conservation practice, identifying forgeries and hoaxes in addition to potential applications in public engagement