Automatic Data for Applied Railway Management

In 2009, London Overground management implemented a new tactical plan for a.m. and p.m. peak service on the North London Line (NLL). This paper documents that tactical planning intervention and evaluates its outcomes in terms of certain aspects of service delivery (the operator's perspective on system performance) and service quality (the passenger's perspective). Analyses of service delivery and quality and of passenger demand contributed to the development, proposal, and implementation of the new tactical plan. NLL trains were delayed routinely en route, with excessive dwell time a major cause. Near-random passenger incidence behavior suggested that an even headway service for NLL might have been more appropriate. The confluence of these analyses was confirmed by the corresponding excess journey time results. On the basis of longitudinal analysis, an evaluation showed that on-time performance increased substantially and observed journey time decreased with the introduction of the new plan. Overall, the effects of this implementation appeared to have been positive on balance. This case study thus demonstrated the applicability of automatic data generally, and certain measures and techniques in the London Overground specifically, to support the tactical planning of an urban railway.Transport for London (Organization

Predicting odor perceptual similarity from odor structure

To understand the brain mechanisms of olfaction we must understand the rules that govern the link between odorant structure and odorant perception. Natural odors are in fact mixtures made of many molecules, and there is currently no method to look at the molecular structure of such odorant-mixtures and predict their smell. In three separate experiments, we asked 139 subjects to rate the pairwise perceptual similarity of 64 odorant-mixtures ranging in size from 4 to 43 mono-molecular components. We then tested alternative models to link odorant-mixture structure to odorant-mixture perceptual similarity. Whereas a model that considered each mono-molecular component of a mixture separately provided a poor prediction of mixture similarity, a model that represented the mixture as a single structural vector provided consistent correlations between predicted and actual perceptual similarity (r≥0.49, p<0.001). An optimized version of this model yielded a correlation of r = 0.85 (p<0.001) between predicted and actual mixture similarity. In other words, we developed an algorithm that can look at the molecular structure of two novel odorant-mixtures, and predict their ensuing perceptual similarity. That this goal was attained using a model that considers the mixtures as a single vector is consistent with a synthetic rather than analytical brain processing mechanism in olfaction

Genomic analysis of 6,000-year-old cultivated grain illuminates the domestication history of barley

The cereal grass barley was domesticated about 10,000 years ago in the Fertile Crescent and became a founder crop of Neolithic agriculture. Here, we report genome sequences of five 6,000-year-old barley grains excavated at a cave in the Judean Desert close to the Dead Sea. Comparison to whole exome sequence data from a diversity panel of present-day barley accessions revealed the close affinity of ancient samples to extant landraces from the Southern Levant and Egypt, consistent with a proposed origin of domesticated barley in the Upper Jordan Valley. Our findings suggest that barley landraces grown in present-day Israel in the past six millennia have not experienced a major lineage turnover although there is evidence for gene flow between cultivated and sympatric wild populations. We show the utility of ancient genomes from desiccated archaeobotanical remains in informing research into the origin, early domestication and subsequent migration of crop species

Bicategories in univalent foundations

We develop bicategory theory in univalent foundations. Guided by the notion of univalence for (1-)categories studied by Ahrens, Kapulkin, and Shulman, we define and study univalent bicategories. To construct examples of those, we develop the notion of "displayed bicategories", an analog of displayed 1-categories introduced by Ahrens and Lumsdaine. Displayed bicategories allow us to construct univalent bicategories in a modular fashion. To demonstrate the applicability of this notion, we prove several bicategories are univalent. Among these are the bicategory of univalent categories with families and the bicategory of pseudofunctors between univalent bicategories. Our work is formalized in the UniMath library of univalent mathematics

Orphan crops of archaeology-based crop history research

Societal Impact Statement: Agrobiodiversity is central to sustainable farming worldwide. Cultivation, conservation and reintroduction of diverse plant species, including ‘forgotten’ and ‘underutilized’ crops, contribute to global agrobiodiversity, living ecosystems and sustainable food production. Such efforts benefit from traditional and historical knowledge of crop plants' evolutionary and cultural trajectories. This review is a first attempt at systematically gauging species representativeness in studies of archaeological plant remains. Results indicate that, in addition to discipline-specific methodological sources of bias, modern agricultural biases may replicate themselves in crop history research and influence understandings of ‘forgotten crops’. Recognizing these biases is an initial stride towards rectifying them and promoting agrobiodiversity in both research and practical applications. // Summary: So-called ‘forgotten’ or ‘orphan’ crops are an important component of strategies aimed at preserving and promoting biodiversity. Knowledge of historical cultivation, usage, and geographic and evolutionary trajectories of plants, that is, crop history research, is important for the long-term success of such efforts. However, research biases in the crops chosen for study may present hurdles. This review attempts to systematically identify patterns in crop species representativeness within archaeology-based crop history research. A meta-analysis and synthesis of archaeobotanical evidence (and lack thereof) is presented for 268 species known to have been cultivated for food prior to 1492 CE from the Mediterranean region to South Asia. We identified 39 genera with known crop plants in this geographical and historical context that are currently absent from its archaeobotanical record, constituting ‘orphan’ crops of archaeobotany. In addition, a worldwide synthesis of crop species studied using geometric morphometric, archaeogenetic and stable isotope analyses of archaeological plant remains is presented, and biases in the species represented in these disciplines are discussed. Both disciplinary methodological biases and economic agenda-based biases affecting species representativeness in crop history research are apparent. This study also highlights the limited geographic diffusion of most crops and the potential for deeper historical perspectives on how crops become marginalized and ‘forgotten’

Orphan crops of archaeology-based crop history research

So-called ‘forgotten’ or ‘orphan’ crops are an important component of strategies aimed at preserving and promoting biodiversity. Knowledge of historical cultivation, usage, and geographic and evolutionary trajectories of plants, that is, crop history research, is important for the long-term success of such efforts. However, research biases in the crops chosen for study may present hurdles. This review attempts to systematically identify patterns in crop species representativeness within archaeology-based crop history research. A meta-analysis and synthesis of archaeo- botanical evidence (and lack thereof) is presented for 268 species known to have been cultivated for food prior to 1492 CE from the Mediterranean region to South Asia. We identified 39 genera with known crop plants in this geographical and histor- ical context that are currently absent from its archaeobotanical record, constituting ‘orphan’ crops of archaeobotany. In addition, a worldwide synthesis of crop species studied using geometric morphometric, archaeogenetic and stable isotope analyses of archaeological plant remains is presented, and biases in the species represented in these disciplines are discussed. Both disciplinary methodological biases and economic agenda-based biases affecting species representativeness in crop history research are apparent. This study also highlights the limited geographic diffusion of most crops and the potential for deeper historical perspectives on how crops become marginal- ized and ‘forgotten’

Neural synchrony indexes disordered perception and cognition in schizophrenia

Current views of schizophrenia suggest that it results from abnormalities in neural circuitry, but empirical evidence in the millisecond range of neural activity has been difficult to obtain. In pursuit of relevant evidence, we previously demonstrated that schizophrenia is associated with abnormal patterns of stimulus-evoked phaselocking of the electroencephalogram in the γ band (30–100 Hz). These patterns may reflect impairments in neural assemblies, which have been proposed to use γ-band oscillations as a mechanism for synchronization. Here, we report the unique finding that, in both healthy controls and schizophrenia patients, visual Gestalt stimuli elicit a γ-band oscillation that is phase-locked to reaction time and hence may reflect processes leading to conscious perception of the stimuli. However, the frequency of this oscillation is lower in schizophrenics than in healthy individuals. This finding suggests that, although synchronization must occur for perception of the Gestalt, it occurs at a lower frequency because of a reduced capability of neural networks to support high-frequency synchronization in the brain of schizophrenics. Furthermore, the degree of phase locking of this oscillation is correlated with visual hallucinations, thought disorder, and disorganization in the schizophrenia patients. These data provide support for linking dysfunctional neural circuitry and the core symptoms of schizophrenia

New approaches to coding information using inverse scattering transform

Remarkable mathematical properties of the integrable nonlinear Schrödinger equation (NLSE) can offer advanced solutions for the mitigation of nonlinear signal distortions in optical fiber links. Fundamental optical soliton, continuous, and discrete eigenvalues of the nonlinear spectrum have already been considered for the transmission of information in fiber-optic channels. Here, we propose to apply signal modulation to the kernel of the Gelfand-Levitan-Marchenko equations that offers the advantage of a relatively simple decoder design. First, we describe an approach based on exploiting the general N-soliton solution of the NLSE for simultaneous coding of N symbols involving 4×N coding parameters. As a specific elegant subclass of the general schemes, we introduce a soliton orthogonal frequency division multiplexing (SOFDM) method. This method is based on the choice of identical imaginary parts of the N-soliton solution eigenvalues, corresponding to equidistant soliton frequencies, making it similar to the conventional OFDM scheme, thus, allowing for the use of the efficient fast Fourier transform algorithm to recover the data. Then, we demonstrate how to use this new approach to control signal parameters in the case of the continuous spectrum

Smaller Left Heschl’s Gyrus Volume in Patients With Schizotypal Personality Disorder

Objective: Individuals with schizophrenia spectrum disorders evince similar genetic, neurotransmitter, neuropsychological, electrophysiological, and structural abnormalities. Magnetic resonance imaging (MRI) studies have shown smaller gray matter volume in patients with schizotypal personality disorder than in matched comparison subjects in the left superior temporal gyrus, an area important for language processing. In a further exploration, the authors studied two components of the superior temporal gyrus: Heschl’s gyrus and the planum temporale. Method: MRI scans were acquired from 21 male, neuroleptic-naive subjects recruited from the community who met DSM-IV criteria for schizotypal personality disorder and 22 male comparison subjects similar in age. Eighteen of the 21 subjects with schizotypal personality disorder had additional comorbid, nonpsychotic diagnoses. The superior temporal gyrus was manually delineated on coronal images with subsequent identification of Heschl’s gyrus and the planum temporale. Exploratory correlations between region of interest volumes and neuropsychological measures were also performed. Results: Left Heschl’s gyrus gray matter volume was 21% smaller in the schizotypal personality disorder subjects than in the comparison subjects, a difference that was not associated with the presence of co-morbid axis I disorders. There were no between-group volume differences in right Heschl’s gyrus or in the right or left planum temporale. Exploratory analyses also showed a correlation between poor logical memory and smaller left Heschl’s gyrus volume. Conclusions: Smaller left Heschl’s gyrus gray matter volume in subjects with schizotypal personality disorder may help to explain the previously reported abnormality in the left superior temporal gyrus and may be a vulnerability marker for schizophrenia spectrum disorders

Winnowing DNA for Rare Sequences: Highly Specific Sequence and Methylation Based Enrichment

Rare mutations in cell populations are known to be hallmarks of many diseases and cancers. Similarly, differential DNA methylation patterns arise in rare cell populations with diagnostic potential such as fetal cells circulating in maternal blood. Unfortunately, the frequency of alleles with diagnostic potential, relative to wild-type background sequence, is often well below the frequency of errors in currently available methods for sequence analysis, including very high throughput DNA sequencing. We demonstrate a DNA preparation and purification method that through non-linear electrophoretic separation in media containing oligonucleotide probes, achieves 10,000 fold enrichment of target DNA with single nucleotide specificity, and 100 fold enrichment of unmodified methylated DNA differing from the background by the methylation of a single cytosine residue