On the representation theory of finite J-trivial monoids

In 1979, Norton showed that the representation theory of the 0-Hecke algebra admits a rich combinatorial description. Her constructions rely heavily on some triangularity property of the product, but do not use explicitly that the 0-Hecke algebra is a monoid algebra. The thesis of this paper is that considering the general setting of monoids admitting such a triangularity, namely J-trivial monoids, sheds further light on the topic. This is a step to use representation theory to automatically extract combinatorial structures from (monoid) algebras, often in the form of posets and lattices, both from a theoretical and computational point of view, and with an implementation in Sage. Motivated by ongoing work on related monoids associated to Coxeter systems, and building on well-known results in the semi-group community (such as the description of the simple modules or the radical), we describe how most of the data associated to the representation theory (Cartan matrix, quiver) of the algebra of any J-trivial monoid M can be expressed combinatorially by counting appropriate elements in M itself. As a consequence, this data does not depend on the ground field and can be calculated in O(n^2), if not O(nm), where n=|M| and m is the number of generators. Along the way, we construct a triangular decomposition of the identity into orthogonal idempotents, using the usual M\"obius inversion formula in the semi-simple quotient (a lattice), followed by an algorithmic lifting step. Applying our results to the 0-Hecke algebra (in all finite types), we recover previously known results and additionally provide an explicit labeling of the edges of the quiver. We further explore special classes of J-trivial monoids, and in particular monoids of order preserving regressive functions on a poset, generalizing known results on the monoids of nondecreasing parking functions.Comment: 41 pages; 4 figures; added Section 3.7.4 in version 2; incorporated comments by referee in version

BISON: bio-interface for the semi-global analysis of network patterns

BACKGROUND: The large amount of genomics data that have accumulated over the past decade require extensive data mining. However, the global nature of data mining, which includes pattern mining, poses difficulties for users who want to study specific questions in a more local environment. This creates a need for techniques that allow a localized analysis of globally determined patterns. RESULTS: We developed a tool that determines and evaluates global patterns based on protein property and network information, while providing all the benefits of a perspective that is targeted at biologist users with specific goals and interests. Our tool uses our own data mining techniques, integrated into current visualization and navigation techniques. The functionality of the tool is discussed in the context of the transcriptional network of regulation in the enteric bacterium Escherichia coli. Two biological questions were asked: (i) Which functional categories of proteins (identified by hidden Markov models) are regulated by a regulator with a specific domain? (ii) Which regulators are involved in the regulation of proteins that contain a common hidden Markov model? Using these examples, we explain the gene-centered and pattern-centered analysis that the tool permits. CONCLUSION: In summary, we have a tool that can be used for a wide variety of applications in biology, medicine, or agriculture. The pattern mining engine is global in the way that patterns are determined across the entire network. The tool still permits a localized analysis for users who want to analyze a subportion of the total network. We have named the tool BISON (Bio-Interface for the Semi-global analysis Of Network patterns)

The Development of Techie Times

Summer 2020 provided the motivation and opportunity to move summer outreach programs into the virtual world. Faculty and students in the Purdue University School of Engineering Technology moved face-to-face programs into a middle school program called Techie Times. This program was designed to provide students with an organized platform occurring just before the school year started, allowing them to learn at home, working with family, or independently. The program was designed to take place nonconsecutively over eight days, covering five various STEM topics. Some of these activities were already a part of the middle school curriculum; others were not. That provided an opportunity to engage students and teach them principles that support various engineering technology curricula. Students were recruited from across the country. Students were placed into three cohorts sorted by biological age and then into smaller groups to enhance interactions. Volunteers moderated the smaller groups representing corporate engineering retirees, university professors, and others interested in helping. The volunteers were provided with information to support the principles being learned in the activity of the day. They asked the students to demonstrate what they did at home and then asked them questions about what they learned from the activity. In the older age groups, volunteers generated hypotheses and tested them to see if they worked, thus providing a challenge for the older and more experienced students. This camp proved to be well-timed on the summer calendar. Parents expressed their pleasure in their students becoming a bit more disciplined as they transitioned from their summer activities to the upcoming school year. This paper will review the program’s curriculum, observations by the parents/guardians, and feedback from the students. The program is an example of a well-transformed outreach program that engaged and enlightened students

Polydispersity and ordered phases in solutions of rodlike macromolecules

We apply density functional theory to study the influence of polydispersity on the stability of columnar, smectic and solid ordering in the solutions of rodlike macromolecules. For sufficiently large length polydispersity (standard deviation $\sigma>0.25$) a direct first-order nematic-columnar transition is found, while for smaller $\sigma$ there is a continuous nematic-smectic and first-order smectic-columnar transition. For increasing polydispersity the columnar structure is stabilized with respect to solid perturbations. The length distribution of macromolecules changes neither at the nematic-smectic nor at the nematic-columnar transition, but it does change at the smectic-columnar phase transition. We also study the phase behaviour of binary mixtures, in which the nematic-smectic transition is again found to be continuous. Demixing according to rod length in the smectic phase is always preempted by transitions to solid or columnar ordering.Comment: 13 pages (TeX), 2 Postscript figures uuencode

Vitamin and mineral supplementation for maintaining cognitive function in cognitively healthy people in mid and late life

Vitamins and minerals play multiple functions within the central nervous system which may help to maintain brain health and optimal cognitive functioning. Supplementation of the diet with various vitamins and minerals has been suggested as a means of maintaining cognitive function, or even of preventing dementia, in later life

Population-level impact and herd effects following the introduction of human papillomavirus vaccination programmes: updated systematic review and meta-analysis

Background More than 10 years have elapsed since human papillomavirus (HPV) vaccination was implemented. We did a systematic review and meta-analysis of the population-level impact of vaccinating girls and women against human papillomavirus on HPV infections, anogenital wart diagnoses, and cervical intraepithelial neoplasia grade 2+ (CIN2+)to summarise the most recent evidence about the effectiveness of HPV vaccines in real-world settings and to quantify the impact of multiple age-cohort vaccination.Methods In this updated systematic review and meta-analysis, we used the same search strategy as in our previous paper. We searched MEDLINE and Embase for studies published between Feb 1, 2014, and Oct 11, 2018. Studies were eligible if they compared the frequency (prevalence or incidence) of at least one HPV-related endpoint (genital HPV infections, anogenital wart diagnoses, or histologically confirmed CIN2+) between pre-vaccination and post-vaccination periods among the general population and if they used the same population sources and recruitment methods before and after vaccination. Our primary assessment was the relative risk (RR) comparing the frequency (prevalence or incidence) of HPV-related endpoints between the pre-vaccination and post-vaccination periods. We stratified all analyses by sex, age, and years since introduction of HPV vaccination. We used random-effects models to estimate pooled relative risks.Findings We identified 1702 potentially eligible articles for this systematic review and meta-analysis, and included 65 articles in 14 high-income countries: 23 for HPV infection, 29 for anogenital warts, and 13 for CIN2+.After 5\u20138 years of vaccination, the prevalence of HPV 16 and 18 decreased significantly by 83% (RR 0\ub717, 95% CI 0\ub711\u20130\ub725) among girls aged 13\u201319 years, and decreased significantly by 66% (RR 0\ub734, 95% CI 0\ub723\u20130\ub749) among women aged 20\u201324 years. The prevalence of HPV 31, 33, and 45 decreased significantly by 54% (RR 0\ub746, 95% CI 0\ub733\u20130\ub766) among girls aged 13\u201319 years. Anogenital wart diagnoses decreased significantly by 67% (RR 0\ub733, 95% CI 0\ub724\u20130\ub746) among girls aged 15\u201319 years, decreased significantly by 54% (RR 0\ub746, 95% CI 0.36\u20130.60) among women aged 20\u201324 years, and decreased significantly by 31% (RR 0\ub769, 95% CI 0\ub753\u20130\ub789) among women aged 25\u201329 years. Among boys aged 15\u201319 years anogenital wart diagnoses decreased significantly by 48% (RR 0\ub752, 95% CI 0\ub737\u20130\ub775) and among men aged 20\u201324 years they decreased significantly by 32% (RR 0\ub768, 95% CI 0\ub747\u20130\ub798). After 5\u20139 years of vaccination, CIN2+ decreased significantly by 51% (RR 0\ub749, 95% CI 0\ub742\u20130\ub758) among screened girls aged 15\u201319 years and decreased significantly by 31% (RR 0\ub769, 95% CI 0\ub757\u20130\ub784) among women aged 20\u201324 years.Interpretation This updated systematic review and meta-analysis includes data from 60 million individuals and up to 8 years of post-vaccination follow-up. Our results show compelling evidence of the substantial impact of HPV vaccination programmes on HPV infections and CIN2+ among girls and women, and on anogenital warts diagnoses among girls, women, boys, and men. Additionally, programmes with multi-cohort vaccination and high vaccination coverage had a greater direct impact and herd effects

Comprehensive analysis of the major histocompatibility complex in systemic sclerosis identifies differential HLA associations by clinical and serological subtypes

Objective: The greatest genetic effect reported for systemic sclerosis (SSc) lies in the major histocompatibility complex (MHC) locus. Leveraging the largest SSc genome-wide association study, we aimed to fine-map this region to identify novel human leucocyte antigen (HLA) genetic variants associated with SSc susceptibility and its main clinical and serological subtypes. Methods: 9095 patients with SSc and 17 584 controls genome-wide genotyped were used to impute and test single-nucleotide polymorphisms (SNPs) across the MHC, classical HLA alleles and their composite amino acid residues. Additionally, patients were stratified according to their clinical and serological status, namely, limited cutaneous systemic sclerosis (lcSSc), diffuse cutaneous systemic sclerosis (dcSSc), anticentromere (ACA), antitopoisomerase (ATA) and anti-RNApolIII autoantibodies (ARA). Results: Sequential conditional analyses showed nine SNPs, nine classical alleles and seven amino acids that modelled the observed associations with SSc. This confirmed previously reported associations with HLA-DRB1*11:04 and HLA-DPB1*13:01, and revealed a novel association of HLA-B*08:01. Stratified analyses showed specific associations of HLA-DQA1*02:01 with lcSSc, and an exclusive association of HLA-DQA1*05:01 with dcSSc. Similarly, private associations were detected in HLA-DRB1*08:01 and confirmed the previously reported association of HLA-DRB1*07:01 with ACA-positive patients, as opposed to the HLA-DPA1*02:01 and HLA-DQB1*03:01 alleles associated with ATA presentation. Conclusions: This study confirms the contribution of HLA class II and reveals a novel association of HLA class I with SSc, suggesting novel pathways of disease pathogenesis. Furthermore, we describe specific HLA associations with SSc clinical and serological subtypes that could serve as biomarkers of disease severity and progression.Funding: This work was supported by the Spanish Ministry of Science and Innovation (grant ref. SAF2015-66761-P and RTI20181013 (32-B-100)), Red de Investigación en Inflamación y Enfermedades Reumáticas from Instituto de Salud Carlos III (RD16/0012/0013) and grants from National Institutes of Health (R01AR073284) and DoD (W81XWH-16-1-0296). MAH was funded by the Spanish Ministry of Science and Innovation through the Juan de la Cierva Incorporacion program (ref. IJC2018-035131-I). GO, AB and ALH were supported by the NIHR Manchester Biomedical Research Centre and Versus Arthritis (grant ref 21754)

Relating gene expression data on two-component systems to functional annotations in Escherichia coli

<p>Abstract</p> <p>Background</p> <p>Obtaining physiological insights from microarray experiments requires computational techniques that relate gene expression data to functional information. Traditionally, this has been done in two consecutive steps. The first step identifies important genes through clustering or statistical techniques, while the second step assigns biological functions to the identified groups. Recently, techniques have been developed that identify such relationships in a single step.</p> <p>Results</p> <p>We have developed an algorithm that relates patterns of gene expression in a set of microarray experiments to functional groups in one step. Our only assumption is that patterns co-occur frequently. The effectiveness of the algorithm is demonstrated as part of a study of regulation by two-component systems in <it>Escherichia coli</it>. The significance of the relationships between expression data and functional annotations is evaluated based on density histograms that are constructed using product similarity among expression vectors. We present a biological analysis of three of the resulting functional groups of proteins, develop hypotheses for further biological studies, and test one of these hypotheses experimentally. A comparison with other algorithms and a different data set is presented.</p> <p>Conclusion</p> <p>Our new algorithm is able to find interesting and biologically meaningful relationships, not found by other algorithms, in previously analyzed data sets. Scaling of the algorithm to large data sets can be achieved based on a theoretical model.</p

Serum Neurotrophin Profile in Systemic Sclerosis

International audienceBACKGROUND: Neurotrophins (NTs) are able to activate lymphocytes and fibroblasts; they can modulate angiogenesis and sympathic vascular function. Thus, they can be implicated in the three pathogenic processes of systemic sclerosis (SSc). The aims of this study are to determine blood levels of Nerve Growth Factor (NGF), Brain-Derived Neurotrophic Factor (BDNF) and Neurotrophin-3 (NT-3) in SSc and to correlate them with clinical and biological data.METHODS: Serum samples were obtained from 55 SSc patients and 32 control subjects to measure NTs levels by ELISA and to determine their relationships with SSc profiles. FINDINGS: Serum NGF levels were higher in SSc patients (288.26 ± 170.34 pg/mL) than in control subjects (170.34 ± 50.8 pg/mL, p<0.001) and correlated with gammaglobulins levels and the presence of both anti-cardiolipin and anti-Scl-70 antibodies (p<0.05). In contrast, BDNF levels were lower in SSc patients than in controls (1121.9 ± 158.1 vs 1372.9 ± 190.9 pg/mL, p<0.0001), especially in pulmonary arterial hypertension and diffuse SSc as compared to limited forms (all p<0.05). NT-3 levels were similar in SSc and in the control group (2657.2 ± 2296 vs 2959.3 ± 2555 pg/mL, NS). BDNF levels correlated negatively with increased NGF levels in the SSc group (and not in controls). CONCLUSION: Low BDNF serum levels were not previously documented in SSc, particularly in the diffuse SSc subset and in patients with pulmonary hypertension or anti-Scl-70 antibodies. The negative correlation between NGF and BDNF levels observed in SSc and not in healthy controls could be implicated in sympathic vascular dysfunction in SSc