Miracle-dz/UniFAR-FTUs huggingface dataset:
Community Structures of Phytoplankton with Emphasis on Toxic Cyanobacteria in an Ohio Inland Lake during Bloom Season

The community structures of phytoplankton are important factors and indicators of lake water quality. Harmful algal blooms severely impact water supply, recreational activities and wildlife habitat. This study aimed to examine the phytoplankton composition and variations using microscopy, and identify harmful Cyanobacteria in weekly samples taken from four sites at Harsha Lake in southwest Ohio. Over the course of the summer in 2015, the phytoplankton of Harsha Lake consisted mainly of 13 taxa belonging to Bacillariophyta, Chlorophyta, Cryptophyta, Cyanobacteria, Dinophyta and Euglenophyta. Their significant successions started with Bacillariophyta and/or Chlorophyta, then bloomed with Cyanobacteria and ended with Chlorophyta and/or Dinophyta. Cyanobacteria members: Microcystis, Planktothrix, Dolichospermum, Aphanizomenon, Cylindrospermopsis, and Oscillatoria from the Cyanophyceae were identified to be dominant genera. These organisms varied spatially and temporally in similar patterns along with the variations of nutrients and formed the summer bloom with the total biomasses ranging from 0.01 to 114.89 mg L−1 with mean of 22.88 mg L−1. M. aeruginosa and P. rubescens were revealed as the microcystin producers, while A. circinalis and Aphanizomenon sp. were identified as a saxitoxin producer through cloning and sequencing PCR products of mcyA, mcyE and sxtA genes. The biomasses of phytoplankton, Cyanobacteria and Microcystis were positively correlated to nutrients, especially to total nitrogen. The total ELISA measurement for microcystin positively correlated with Cyanobacteria (R2 = 0.66, P < 0.0001), Microcystis (R2 = 0.64, P < 0.0001) and phytoplankton (R2 = 0.59, P < 0.0001). The basic information on the occurrence and biomasses of Cyanobacteria and total phytoplankton, and the analysis for toxic species, which were the first report for the inland water in Ohio, USA, will document the succession patterns of phytoplankton and toxin production over a season and provide data to predict risk occurrence to both human and ecological factors.
Staying Alert? Neural Correlates of the Association Between Grit and Attention Networks

Recent research has demonstrated that heightened motivational levels promote enhanced attention capabilities. However, the relation between attentional systems and the trait-based ability to sustain a motivational state long-term is less understood. Grit refers to one’s ability and willingness to pursue long-term goals despite setbacks. This report presents the results of two studies conducted to examine the relation between facets of Grit–Consistency and Perseverance and attention networks, assessed using the Attention Network Test (ANT). Across both studies Grit–Perseverance was related to performance on the ANT. In Study 1, Grit–Perseverance was negatively related to alerting indicating that individuals who were high on Perseverance were more likely to show a smaller alerting effect. In particular, Grit–Perseverance was negatively correlated with reaction times in the no cue trials. In Study 2, we assessed ERP components associated with attention networks. Individuals with higher scores on Grit–Perseverance were more likely to demonstrate smaller mean difference in N1 amplitudes for double cue relative to no cue trials, suggesting an attenuated alerting effect. Our findings indicate that individuals high on Grit–Perseverance may have enhanced sustained attention. Specifically individuals with high Grit–Perseverance appear to exhibit a more efficient alerting system in the no cue trials. Implications of high levels of Grit on cognitive performance are discussed.
Fault Detection for Fuzzy Systems With Multiplicative Noises Under Periodic Communication Protocols

This paper is concerned with the fault detection problem for a class of networked fuzzy systems with multiplicative noises on both system states and measurement outputs. In view of the limited communication capacity, a periodical communication protocol (i.e., the round-robin protocol) is adopted to undertake the transmission task between the sensors and the fault detection filter, which leads to periodical delays in the overall system. A Takagi–Sugeno fuzzy-model-based fault detection filter is constructed to produce the residual signal and an auxiliary error system is established to facilitate the stability analysis of the error dynamics. With the aid of Lyapunov stability theory, sufficient conditions are obtained that ensure the exponentially mean-square stability of the error dynamics with prescribed $H_{\infty }$ performance constraint. The desired fault detection filter is designed by solving a convex optimization problem via the semidefinite programme method. A finite-time evaluation function and an adjustable threshold are introduced in order to detect the possible faults effectively. The effectiveness of the proposed fault detection scheme is validated by a numerical simulation example.
The dynamics of norm change in the cultural evolution of language

Significance Social conventions, such as shaking hands or dressing formally, allow us to coordinate smoothly and, once established, appear to be natural. But what happens when a new convention replaces an old one? This question has remained largely unanswered so far, due to the lack of suitable data. Here, we investigate the process of norm change by looking at 2,541 linguistic norm shifts occurring over the last two centuries in English and Spanish. We identify different patterns of norm adoption depending on whether the change is spontaneous or driven by a centralized institution, and we propose a simple model that reproduces all of the empirical observations. These results shed light on the cultural evolution of linguistic norms and human collective behavior. What happens when a new social convention replaces an old one? While the possible forces favoring norm change—such as institutions or committed activists—have been identified for a long time, little is known about how a population adopts a new convention, due to the difficulties of finding representative data. Here, we address this issue by looking at changes that occurred to 2,541 orthographic and lexical norms in English and Spanish through the analysis of a large corpora of books published between the years 1800 and 2008. We detect three markedly distinct patterns in the data, depending on whether the behavioral change results from the action of a formal institution, an informal authority, or a spontaneous process of unregulated evolution. We propose a simple evolutionary model able to capture all of the observed behaviors, and we show that it reproduces quantitatively the empirical data. This work identifies general mechanisms of norm change, and we anticipate that it will be of interest to researchers investigating the cultural evolution of language and, more broadly, human collective behavior.
Weather Classification: A new multi-class dataset, data augmentation approach and comprehensive evaluations of Convolutional Neural Networks

Weather conditions often disrupt the proper functioning of transportation systems. Present systems either deploy an array of sensors or use an in-vehicle camera to predict weather conditions. These solutions have resulted in incremental cost and limited scope. To ensure smooth operation of all transportation services in all-weather conditions, a reliable detection system is necessary to classify weather in wild. The challenges involved in solving this problem is that weather conditions are diverse in nature and there is an absence of discriminate features among various weather conditions. The existing works to solve this problem have been scene specific and have targeted classification of two categories of weather. In this paper, we have created a new open source dataset consisting of images depicting three classes of weather i.e rain, snow and fog called RFS Dataset. A novel algorithm has also been proposed which has used super pixel delimiting masks as a form of data augmentation, leading to reasonable results with respect to ten Convolutional Neural Network architectures.
Incomplete penetrance for isolated congenital asplenia in humans with mutations in translated and untranslated RPSA exons

Significance Isolated congenital asplenia (ICA) is characterized by the absence of a spleen at birth without any other developmental defect. ICA predisposes individuals to severe bacterial infections early in childhood. In 2013, we showed that very rare deleterious mutations in the protein-coding region of RPSA, which codes for a protein in the ribosome, caused ICA in 8 of 23 kindreds. We have since enrolled 33 more kindreds and identified 11 new ICA-causing RPSA protein-coding mutations, as well as the first two ICA-causing mutations in the 5′-UTR of this gene. A few individuals carrying one of the new RPSA mutations had a spleen, indicating that mutations in RPSA can cause ICA with incomplete penetrance. Isolated congenital asplenia (ICA) is the only known human developmental defect exclusively affecting a lymphoid organ. In 2013, we showed that private deleterious mutations in the protein-coding region of RPSA, encoding ribosomal protein SA, caused ICA by haploinsufficiency with complete penetrance. We reported seven heterozygous protein-coding mutations in 8 of the 23 kindreds studied, including 6 of the 8 multiplex kindreds. We have since enrolled 33 new kindreds, 5 of which are multiplex. We describe here 11 new heterozygous ICA-causing RPSA protein-coding mutations, and the first two mutations in the 5′-UTR of this gene, which disrupt mRNA splicing. Overall, 40 of the 73 ICA patients (55%) and 23 of the 56 kindreds (41%) carry mutations located in translated or untranslated exons of RPSA. Eleven of the 43 kindreds affected by sporadic disease (26%) carry RPSA mutations, whereas 12 of the 13 multiplex kindreds (92%) carry RPSA mutations. We also report that 6 of 18 (33%) protein-coding mutations and the two (100%) 5′-UTR mutations display incomplete penetrance. Three mutations were identified in two independent kindreds, due to a hotspot or a founder effect. Finally, RPSA ICA-causing mutations were demonstrated to be de novo in 7 of the 23 probands. Mutations in RPSA exons can affect the translated or untranslated regions and can underlie ICA with complete or incomplete penetrance.
Long Term Effects of Pair Programming

<italic>Contribution:</italic> This paper provides evidence for the benefits of pair programming early in the curriculum on student performance later in the curriculum. It also confirms the short term benefits of partnerships at scale. <italic>Background:</italic> Engineers often work in teams, both in industry and in academia. Previous work has shown that partnered programming yields higher student performance during the course in which students partner. <italic>Research Questions:</italic> This paper investigates the long term effects of early curriculum pair programming on student performance in a following course. Specifically, do student partnerships impact long-term student performance in a later course? Are previously observed effects of partner programming robust to a larger sample size? <italic>Methodology:</italic> This quantitative analysis examines 2468 students in an introductory computer science sequence at a large, public research institution. The data set comprises two academic years and includes partnership participation, project and exam scores, withdraw rates, time between courses, GPA, and gender. <italic>Findings:</italic> A positive relationship is observed between partnering in an introductory course, and higher project scores in a future course, where all students worked alone (<inline-formula> <tex-math notation="LaTeX">$N = 1003$ </tex-math></inline-formula>). Students with the lowest GPAs experienced the greatest benefits. Additionally, results with a large population of students confirm the observations of previous research, showing that partnerships are associated with an overall positive grade impact during the course in which the partnership takes place (<inline-formula> <tex-math notation="LaTeX">$N = 2468$ </tex-math></inline-formula>).
Robust Constrained Adaptive Filtering Under Minimum Error Entropy Criterion

Minimum error entropy (MEE), as a robust adaption criterion, has received considerable attention due to its broad applicability, especially in the presence of non-Gaussian noises. In this brief, we propose a constrained adaptive filtering algorithm under MEE criterion, called CMEE, which is derived by incorporating a set of linear equality constrains into MEE to handle a constrained MEE optimization problem. In addition, convergence analysis of the proposed CMEE including the stability and steady-state mean square deviation is studied. Simulation results validate the theoretical conclusions, and confirm the effectiveness of the new algorithm in non-Gaussian noises.
Enhancing ventilation detection during cardiopulmonary resuscitation by filtering chest compression artifact from the capnography waveform

Background During cardiopulmonary resuscitation (CPR), there is a high incidence of capnograms distorted by chest compression artifact. This phenomenon adversely affects the reliability of automated ventilation detection based on the analysis of the capnography waveform. This study explored the feasibility of several filtering techniques for suppressing the artifact to improve the accuracy of ventilation detection. Materials and methods We gathered a database of 232 out-of-hospital cardiac arrest defibrillator recordings containing concurrent capnograms, compression depth and transthoracic impedance signals. Capnograms were classified as non-distorted or distorted by chest compression artifact. All chest compression and ventilation instances were also annotated. Three filtering techniques were explored: a fixed-coefficient (FC) filter, an open-loop (OL) adaptive filter, and a closed-loop (CL) adaptive filter. The improvement in ventilation detection was assessed by comparing the performance of a capnogram-based ventilation detection algorithm with original and filtered capnograms. Results Sensitivity and positive predictive value of the ventilation algorithm improved from 91.9%/89.5% to 97.7%/96.5% (FC filter), 97.6%/96.7% (OL), and 97.0%/97.1% (CL) for the distorted capnograms (42% of the whole set). The highest improvement was obtained for the artifact named type III, for which performance improved from 77.8%/74.5% to values above 95.5%/94.5%. In addition, errors in the measurement of ventilation rate decreased and accuracy in the detection of over-ventilation increased with filtered capnograms. Conclusions Capnogram-based ventilation detection during CPR was enhanced after suppressing the artifact caused by chest compressions. All filtering approaches performed similarly, so the simplicity of fixed-coefficient filters would take advantage for a practical implementation.
Mitochondrial DNA Haplogroups and Breast Cancer Risk Factors in the Avon Longitudinal Study of Parents and Children (ALSPAC)

The relationship between mitochondrial DNA (mtDNA) and breast cancer has been frequently examined, particularly in European populations. However, studies reporting associations between mtDNA haplogroups and breast cancer risk have had a few shortcomings including small sample sizes, failure to account for population stratification and performing inadequate statistical tests. In this study we investigated the association of mtDNA haplogroups of European origin with several breast cancer risk factors in mothers and children of the Avon Longitudinal Study of Parents and Children (ALSPAC), a birth cohort that enrolled over 14,000 pregnant women in the Southwest region of the UK. Risk factor data were obtained from questionnaires, clinic visits and blood measurements. Information on over 40 independent breast cancer risk factor-related variables was available for up to 7781 mothers and children with mtDNA haplogroup data in ALSPAC. Linear and logistic regression models adjusted for age, sex and population stratification principal components were evaluated. After correction for multiple testing we found no evidence of association of European mtDNA haplogroups with any of the breast cancer risk factors analysed. Mitochondrial DNA haplogroups are unlikely to underlie susceptibility to breast cancer that occurs via the risk factors examined in this study of a population of European ancestry.
Nur77 serves as a molecular brake of the metabolic switch during T cell activation to restrict autoimmunity

Significance The role of metabolic processes during T cell activation has been increasingly acknowledged, and recent data suggest an impact of T cell immunometabolism on T cell function and T cell-mediated autoimmunity. The factors regulating metabolic function in T cells are not clear, however. We identify the nuclear receptor Nur77 as central regulator of T cell immunometabolism, controlling oxidative phosphorylation and aerobic glycolysis during T cell activation. Functionally, Nur77 restricts murine and human T cell activation and proliferation and limits inflammation in autoimmune conditions in animal models of CNS autoimmunity, contact dermatitis, and arthritis. These findings identify Nur77 as a central regulator of T cell immunometabolism that restricts T cell-mediated autoimmunity, which might open up new avenues for a more tailored therapeutic approach. T cells critically depend on reprogramming of metabolic signatures to meet the bioenergetic demands during activation and clonal expansion. Here we identify the transcription factor Nur77 as a cell-intrinsic modulator of T cell activation. Nur77-deficient T cells are highly proliferative, and lack of Nur77 is associated with enhanced T cell activation and increased susceptibility for T cell-mediated inflammatory diseases, such as CNS autoimmunity, allergic contact dermatitis and collagen-induced arthritis. Importantly, Nur77 serves as key regulator of energy metabolism in T cells, restricting mitochondrial respiration and glycolysis and controlling switching between different energy pathways. Transcriptional network analysis revealed that Nur77 modulates the expression of metabolic genes, most likely in close interaction with other transcription factors, especially estrogen-related receptor α. In summary, we identify Nur77 as a transcriptional regulator of T cell metabolism, which elevates the threshold for T cell activation and confers protection in different T cell-mediated inflammatory diseases.
The PMEL Gene and Merle in the Domestic Dog: A Continuum of Insertion Lengths Leads to a Spectrum of Coat Color Variations in Australian Shepherds and Related Breeds

Merle is a distinct coat color and pattern found in numerous species, including the domestic dog, characterized by patches of diluted eumelanin (black pigment) interspersed among areas of normal pigmentation. In dogs, this variegated pattern is caused by an insertion of a SINE element into the canine PMEL gene. Although variation in the length of the SINE insertion - due to a variable-length poly(A) tail - has been observed to be associated with variation in merle coat color and patterning, no systematic evaluation of this correlation has been conducted and published in the scientific literature. We performed high-resolution analysis of the SINE insertion lengths in 175 dogs (99 Australian shepherds, 45 miniature Australian shepherds, and 31 miniature American shepherds) and compared the genotypes with the coat phenotypes (when available). SINE insertion lengths varied from 201 to 277 bp, indicating that merle insertion variants can occur in virtually any size along the entire continuum. Genotype-phenotype correlation of 126 dogs with only a single SINE insertion (m/M) identified at least 4 major phenotypic clusters designated as “cryptic,” “atypical,” “classic,” and “harlequin” merle. However, we found several phenotypic outliers that did not cluster within these major groupings, suggesting that insertion size is not the only factor responsible for merle phenotypic variability. In addition, we detected 25 dogs with 2 SINE insertions (M/M) and 24 dogs with more than 2 PMEL (merle) alleles, indicating mosaicism. Genotype-phenotype correlation of M/M dogs suggests that cryptic merle alleles often act like non-merle (m) alleles when combined with atypical, classic, and harlequin-sized alleles. The finding of mosaicism has important implications for the dog's phenotype and the ability to potentially transmit various alleles to its offspring. Furthermore, we identified examples of the SINE insertion poly(A)-tail expansion and contraction between generations, which also has important implications for breeding practices and determining mating pairs to avoid producing double merle dogs. These data demonstrate that there is a continuum of merle insertion lengths associated with a spectrum of coat color and patterns and that genotype-phenotype exceptions and overlap make it difficult to strictly assign certain insertion sizes with an expected coat color, although some generalizations are possible.
Endonasal Endoscopic Resection of Olfactory Neuroblastoma: An 11-Year Experience

OBJECTIVEOlfactory neuroblastoma (ONB) is a rare malignant neoplasm of the sinonasal cavity. Surgery has been and remains a mainstay of treatment for patients with this tumor. Open craniofacial resections have been the treatment of choice for many decades. More recently, experience has been growing with endoscopic approaches in the management of patients with ONB. The object of this study is to report the authors' experience over the past 11 years with ONB patients treated with purely endonasal endoscopic techniques.METHODSThe authors performed a retrospective chart review of 20 consecutive patients with ONB who underwent a completely endonasal endoscopic approach for an oncological tumor resection at their institution between January 2006 and January 2017. Patient demographics, tumor stage, pathological grade, frozen section analysis, permanent margin assessment, perioperative complications, postoperative therapy, length of follow-up, and outcomes at last follow-up were collected and analyzed.RESULTSEighteen patients presented with newly diagnosed disease, with a modified Kadish stage of A in 2 cases, B in 3, C in 11, and D in 2. Two patients presented with recurrent tumors. An average of 25.3 specimens per patient were examined by frozen section analysis. Although analysis of intraoperative frozen section margins was negative in all but 1 case, microscopic foci of tumor were found in 7 cases (35%) on permanent histopathological analysis. Perioperative complications occurred in 7 patients (35%) including 1 patient who developed a cerebrospinal fluid leak; there were no episodes of meningitis. All but 1 patient received postoperative radiotherapy, and 5 patients received postoperative chemotherapy. With a mean follow-up of over 5 years, 19 patients were alive and 1 patient died from an unrelated cause. There were 2 cases of tumor recurrence. The 5-year overall, disease-specific, and recurrence-free survival rates were 92.9%, 100%, and 92.9%, respectively.CONCLUSIONSThe current results provide additional evidence for the continued use of endoscopic procedures in the management of this malignancy.