Locating regions in a sequence under density constraints

Several biological problems require the identification of regions in a sequence where some feature occurs within a target density range: examples including the location of GC-rich regions, identification of CpG islands, and sequence matching. Mathematically, this corresponds to searching a string of 0s and 1s for a substring whose relative proportion of 1s lies between given lower and upper bounds. We consider the algorithmic problem of locating the longest such substring, as well as other related problems (such as finding the shortest substring or a maximal set of disjoint substrings). For locating the longest such substring, we develop an algorithm that runs in O(n) time, improving upon the previous best-known O(n log n) result. For the related problems we develop O(n log log n) algorithms, again improving upon the best-known O(n log n) results. Practical testing verifies that our new algorithms enjoy significantly smaller time and memory footprints, and can process sequences that are orders of magnitude longer as a result.Comment: 17 pages, 8 figures; v2: minor revisions, additional explanations; to appear in SIAM Journal on Computin

Tuning Nanocrystal Surface Depletion by Controlling Dopant Distribution as a Route Toward Enhanced Film Conductivity

Electron conduction through bare metal oxide nanocrystal (NC) films is hindered by surface depletion regions resulting from the presence of surface states. We control the radial dopant distribution in tin-doped indium oxide (ITO) NCs as a means to manipulate the NC depletion width. We find in films of ITO NCs of equal overall dopant concentration that those with dopant-enriched surfaces show decreased depletion width and increased conductivity. Variable temperature conductivity data shows electron localization length increases and associated depletion width decreases monotonically with increased density of dopants near the NC surface. We calculate band profiles for NCs of differing radial dopant distributions and, in agreement with variable temperature conductivity fits, find NCs with dopant-enriched surfaces have narrower depletion widths and longer localization lengths than those with dopant-enriched cores. Following amelioration of NC surface depletion by atomic layer deposition of alumina, all films of equal overall dopant concentration have similar conductivity. Variable temperature conductivity measurements on alumina-capped films indicate all films behave as granular metals. Herein, we conclude that dopant-enriched surfaces decrease the near-surface depletion region, which directly increases the electron localization length and conductivity of NC films

Genital Pain and Numbness and Female Sexual Dysfunction in Adult Bicyclists.

IntroductionBicycle seat pressure on the perineum may impair arousal and clitoral erection, likely contributing to genital pain and numbness experienced by female cyclists.AimWe aimed to identify the association between genital pain and numbness experienced by female cyclists and female sexual dysfunction (FSD).MethodsFemale cyclists were recruited to complete an online survey using the Female Sexual Function Index (FSFI), a validated questionnaire to assess FSD. Cyclist demographics, experience, preferred riding style, use of ergonomic cycle modifications, and genital discomfort while riding were also queried. Multivariate logistic regression analysis was used to evaluate risk factors of FSD.Main outcome measuresThe main outcome was FSFI score, which is used to diagnose FSD when the FSFI score is <26.55.ResultsOf the survey respondents, 178 (53.1%) completed the survey and FSFI questionnaire. Mean age was 48.1 years (±0.8 standard error [SE]), and the average riding experience was 17.1 years (±0.9 SE). Overall, 53.9% of female cyclists had FSD, 58.1% reported genital numbness, and 69.1% reported genital pain. After adjusting for age, body mass index, relationship status, smoking history, comorbidities, and average time spent cycling per week, females who reported experiencing genital numbness half the time or more were more likely to have FSD (adjusted odds ratio [aOR], 6.0; 95% CI, 1.5-23.6; P = .01), especially if localized to the clitoris (aOR, 2.5; 95% CI, 1.2-5.5; P = .02). Females that reported genital pain half the time or more while cycling also were more likely to have FSD (aOR, 3.6; 95% CI, 1.2-11.1; P = .02). Cyclists experiencing genital pain within the first hour of their ride were more likely to have FSD (aOR, 12.6; 95% CI, 2.5-63.1; P = .002). Frequency and duration of cycling were not associated with FSD. Analysis of FSFI domains found that the frequency of numbness was correlated with decreased arousal, orgasm, and satisfaction during intercourse, whereas the frequency of pain significantly reduced arousal, orgasm, and genital lubrication.Clinical implicationsFemale cyclists that experience numbness and/or pain have higher odds of reporting FSD.Strengths & limitationsOur study includes a validated questionnaire to assess FSD and queries specific characteristics and symptoms of genital pain and genital numbness; however, the study is limited by its cross-sectional survey design.ConclusionThis study highlights the need for cyclists to address genital pain and numbness experienced while cycling, and future studies are required to determine if alleviating these symptoms can reduce the impact of cycling on female sexual function. Greenberg GR, Khandwala YS, Breyer BN, et al. Genital Pain and Numbness and Female Sexual Dysfunction in Adult Bicyclists. J Sex Med 2019; 16:1381-1389

Searching a bitstream in linear time for the longest substring of any given density

Given an arbitrary bitstream, we consider the problem of finding the longest substring whose ratio of ones to zeroes equals a given value. The central result of this paper is an algorithm that solves this problem in linear time. The method involves (i) reformulating the problem as a constrained walk through a sparse matrix, and then (ii) developing a data structure for this sparse matrix that allows us to perform each step of the walk in amortised constant time. We also give a linear time algorithm to find the longest substring whose ratio of ones to zeroes is bounded below by a given value. Both problems have practical relevance to cryptography and bioinformatics.Comment: 22 pages, 19 figures; v2: minor edits and enhancement

Neuroimaging Correlates of Suicidality in Decision-Making Circuits in Posttraumatic Stress Disorder

In depression, brain and behavioral correlates of decision-making differ between individuals with and without suicidal thoughts and behaviors. Though promising, it remains unknown if these potential biomarkers of suicidality will generalize to other high-risk clinical populations. To preliminarily assess whether brain structure or function tracked suicidality in individuals with posttraumatic stress disorder (PTSD), we measured resting-state functional connectivity and cortical thickness in two functional networks involved in decision-making, a ventral fronto-striatal reward network and a lateral frontal cognitive control network. Neuroimaging data and self-reported suicidality ratings, and suicide-related hospitalization data were obtained from 50 outpatients with PTSD and also from 15 healthy controls, and all were subjected to seed-based resting-state functional connectivity and cortical thickness analyses using a priori seeds from reward and cognitive control networks. First, general linear models (GLM) were used to evaluate whether ROI-to-ROI functional connectivity was predictive of self-reported suicidality after false discovery rate (FDR)-correction for multiple comparisons and covariance of age and depression symptoms. Next, regional cortical thickness statistics were included as predictors of ROI-to-ROI functional connectivity in follow-up GLMs evaluating structure-function relationships. Functional connectivity between reward regions was positively correlated with suicidality (p-FDR ≤ 0.05). Functional connectivity of the lateral pars orbitalis to anterior cingulate/paracingulate control regions also tracked suicidality (p-FDR ≤ 0.05). Furthermore, cortical thickness in anterior cingulate/paracingulate was associated with functional correlates of suicidality in the control network (p-FDR < 0.05). These results provide a preliminary demonstration that biomarkers of suicidality in decision-making networks observed in depression may generalize to PTSD and highlight the promise of these circuits as transdiagnostic biomarkers of suicidality

Model of the Quark Mixing Matrix

The structure of the Cabibbo-Kobayashi-Maskawa (CKM) matrix is analyzed from the standpoint of a composite model. A model is constructed with three families of quarks, by taking tensor products of sufficient numbers of spin-1/2 representations and imagining the dominant terms in the mass matrix to arise from spin-spin interactions. Generic results then obtained include the familiar relation $|V_{us}| = (m_d/m_s)^{1/2} - (m_u/m_c)^{1/2}$, and a less frequently seen relation $|V_{cb}| = \sqrt{2} [(m_s/m_b) - (m_c/m_t)]$. The magnitudes of $V_{ub}$ and $V_{td}$ come out naturally to be of the right order. The phase in the CKM matrix can be put in by hand, but its origin remains obscure.Comment: Presented by Mihir P. Worah at DPF 92 Meeting, Fermilab, November, 1992. 3 pages, LaTeX fil

Deflationary tactics with the archive of life: contemporary Jewish art and popular culture

This paper discusses art works by Suzanne Treister, Deborah Kass and Doug Fishbone. It considers the importance of their work for contemporary Jewish identity within the terms of wider conceptual questions that preoccupy contemporary art. These concerns are challenging the perceived structures of power, the “performance” of subjectivity and the questioning of authenticity. A deflationary aesthetic is central to the critique of these structures of thinking fuelled by an interest in the relationship between Jewish subjectivity and popular culture that underpins all of these art works. I argue that popular culture plays a key role as a constituting factor in the production of contemporary Anglophone subjectivity. I use the case studies to develop the argument in the three artists’ specificities and the way they all question the idea of authenticity as a stable source of self-understanding. Suzanne Treister questions history and our relationship with historical events, specifically the Holocaust. She also explores questions of the relationship between structures of power and narratives of history. Debora Kass considers the representation of Jewish women, power and iconicity. Doug Fishbone, a younger artist, takes on self-hate as a transformative tool and as a motif that destabilizes Jewishness as a category, especially in an age of the accelerated post-internet-derived subjectivity