Miracle-dz/UniFAR-FTUs huggingface dataset:
The Difference in Prognostic Outcomes Between De Novo Stage IV and Recurrent Metastatic Patients with Hormone Receptor-positive, HER2-negative Breast Cancer.

BACKGROUND/AIM Patients with de novo stage IV and recurrent metastatic breast cancer are often treated with the same strategies, although the difference in prognostic outcomes remains unclear. The objective of this retrospective chart review study was to compare the prognostic outcomes between two types of patients with hormone receptor-positive (HR+), HER2-negative (HER2-) breast cancer. PATIENTS AND METHODS We estimated overall survival of the two groups and evaluated the progressive course of the disease using disease-free interval (DFI) and interval from the end of adjuvant treatment to the first recurrence (AFI). RESULTS We studied 172 patients with HR+/HER2- breast cancer, of which 65 were de novo and 107 were recurrent. Median OS between de novo and recurrent BC was 4.85 and 3.45 years, respectively (p=0.046). Recurrent patients with a DFI<2 years were found to have a significantly poorer prognosis than recurrent patients with a DFI≥2 years (p=0.016) and de novo patients (p=0.002). Similarly, recurrent patients with an AFI<1 year had a significantly poorer prognosis compared to de novo patients (p=0.026). CONCLUSION De novo patients had better prognoses than recurrent patients with DFI<2 years or AFI<1 year, likely due to their therapy-naïve status or lower resistance to systemic treatment.
Towards a Uniform Template-based Architecture for Accelerating 2D and 3D CNNs on FPGA

Three-dimensional convolutional neural networks (3D CNNs) are used efficiently in many computer vision applications. Most previous work in this area has concentrated only on designing and optimizing accelerators for 2D CNN, with few attempts made to accelerate 3D CNN on FPGA. We find accelerating 3D CNNs on FPGA to be challenge due to their high computational complexity and storage demands. More importantly, although the computation patterns of 2D and 3D CNNs are analogous, the conventional approaches adopted for accelerating 2D CNNs may be unfit for 3D CNN acceleration. In this paper, in order to accelerate 2D and 3D CNNs using a uniform framework, we propose a uniform template-based architecture that uses templates based on the Winograd algorithm to ensure fast development of 2D and 3D CNN accelerators. Furthermore, we also develop a uniform analytical model to facilitate efficient design space explorations of 2D and 3D CNN accelerators based on our architecture. Finally, we demonstrate the effectiveness of the template-based architecture by implementing accelerators for real-life 2D and 3D CNNs (VGG16 and C3D) on multiple FPGA platforms. On S2C VUS440, we achieve up to 1.13 TOPS and 1.11 TOPS under low resource utilization for VGG16 and C3D, respectively. End-to-end comparisons with CPU and GPU solutions demonstrate that our implementation of C3D achieves gains of up to 13x and 60x in performance and energy relative to a CPU solution, and a 6.4x energy efficiency gain over a GPU solution.
Germline TP53 mutations result into a constitutive defect of p53 DNA binding and transcriptional response to DNA damage

Abstract Li-Fraumeni Syndrome (LFS) results from heterozygous germline mutations of TP53, encoding a key transcriptional factor activated in response to DNA damage. We have recently shown, from a large LFS series, that dominant-negative missense mutations are the most clinically severe and, thanks to a new p53 functional assay in lymphocytes, that they alter the p53 transcriptional response to DNA damage more drastically than null mutations. In this study, we first confirmed this observation by performing the p53 functional assay in lymphocytes from 56 TP53 mutation carriers harbouring 35 distinct alterations. Then, to compare the impact of the different types of germline TP53 mutations on DNA binding, we performed chromatin immunoprecipitation-sequencing (ChIP-Seq) in lymphocytes exposed to doxorubicin. ChIP-Seq performed in wild-type TP53 control lymphocytes accurately mapped 1287 p53-binding sites. New p53-binding sites were validated using a functional assay in yeast. ChIP-Seq analysis of LFS lymphocytes carrying TP53 null mutations (p.P152Rfs*18 or complete deletion) or the low penetrant ‘Brazilian’ p.R337H mutation revealed a moderate decrease of p53-binding sites (949, 580 and 620, respectively) and of ChIP-Seq peak depths. In contrast, analysis of LFS lymphocytes with TP53 dominant-negative missense mutations p.R273H or p.R248W revealed only 310 and 143 p53-binding sites, respectively, and the depths of the corresponding peaks were drastically reduced. Altogether, our results show that TP53 mutation carriers exhibit a constitutive defect of the transcriptional response to DNA damage and that the clinical severity of TP53 dominant-negative missense mutations is explained by a massive and global alteration of p53 DNA binding.
Maternal Infections, Antibiotics, and Paracetamol in Pregnancy and Offspring Celiac Disease: A Cohort Study

Objectives: Infections in pregnancy are common, may affect fetal development, and have been linked to offspring autoimmunity. We aimed to determine whether maternal infections, the use of antibiotics, and use of paracetamol in pregnancy are associated with the risk of offspring celiac disease (CD). Methods: The nationwide Norwegian Mother and Child Cohort Study includes 84,274 children born in the period from 2000 to 2009 with prospectively collected questionnaire data on maternal infections and medication use in pregnancy. CD was identified through questionnaires and the Norwegian Patient Register. Logistic regression yielded odds ratios adjusted for age and sex (aORs). Results: During a median follow-up of 8.5 years, 617 children (0.7%) were diagnosed with CD. The aOR for offspring CD per increase in number of maternal infections was 1.07 (95% confidence interval [CI] = 1.01–1.13), but not significantly increased for categories 1 infection (1.01 [95% CI = 0.82–1.25]) and ≥2 infections (1.22 [95% CI = 1.00–1.49]) versus no infection. We found the same pattern for respiratory tract infections, but not for gastrointestinal infections. The aORs were broadly consistent across pregnancy periods of exposure. The use of antibiotics and paracetamol was, compared with no use, not associated with offspring CD (aOR = 1.16 [95% CI = 0.94–1.43] and aOR = 1.13 [95% CI = 0.96–1.33], respectively; P values for trend >0.2). Conclusions: In this large pregnancy cohort we found no clear association between maternal infections in pregnancy and offspring CD, but considering the marginal significance in some of our results maternal infections cannot be ruled out as a risk factor. Reassuringly for both parents-to-be and clinicians, the use of antibiotics and paracetamol in pregnancy was not a significant risk factor.
Comparative Proteomic Analysis of Hymenolepis diminuta Cysticercoid and Adult Stages

Cestodiases are common parasitic diseases of animals and humans. As cestodes have complex lifecycles, hexacanth larvae, metacestodes (including cysticercoids), and adults produce proteins allowing them to establish invasion and to survive in the hostile environment of the host. Hymenolepis diminuta is the most commonly used model cestode in experimental parasitology. The aims of the present study were to perform a comparative proteomic analysis of two consecutive developmental stages of H. diminuta (cysticercoid and adult) and to distinguish proteins which might be characteristic for each of the stages from those shared by both stages. Somatic proteins of H. diminuta were isolated from 6-week-old cysticercoids and adult tapeworms. Cysticercoids were obtained from experimentally infected beetles, Tenebrio molitor, whereas adult worms were collected from experimentally infected rats. Proteins were separated by GeLC-MS/MS (one dimensional gel electrophoresis coupled with liquid chromatography and tandem mass spectrometry). Additionally protein samples were digested in-liquid and identified by LC-MS/MS. The identified proteins were classified according to molecular function, cellular components and biological processes. Our study showed a number of differences and similarities in the protein profiles of cysticercoids and adults; 233 cysticercoid and 182 adult proteins were identified. From these proteins, 131 were present only in the cysticercoid and 80 only in the adult stage samples. Both developmental stages shared 102 proteins; among which six represented immunomodulators and one is a potential drug target. In-liquid digestion and LC-MS/MS complemented and confirmed some of the GeLC-MS/MS identifications. Possible roles and functions of proteins identified with both proteomic approaches are discussed.
Analysis and comparison of numerical methods for design and development of small Diffuser-Augmented Wind Turbine (DAWT)

The paper discusses results of examination of various wind turbine rotor models implemented in numerical simulations, with particular emphasis on the interaction of a rotor with the surrounding airflow. The study concerns a wind turbine placed at the inlet of a divergent duct, a solution known as Diffuser-Augmented Wind Turbine. This type of wind energy converter has recently been an object of numerous studies at the Institute of Turbomachinery of Lodz University of Technology. The study focuses on the search of wind turbine evaluation method combining high accuracy and tolerable time-to-results factor. The examined models include: FRM (Fully-resolved Rotor Model), ADM (Actuator Disk Model) and authors' modified approach to ALM (Actuator Line Model). The study covers: the implementation of the above mentioned method(s) into a commercial solver ANSYS CFX 15.0, the comparison of the obtained results with available experimental data, the analysis of the results obtained from simulations and the discussion. The paper is characterised by the wide spectrum of actuator models compared with 3D accurate rotor modelling for the estimation of turbine performance, the authors' proposal of the ALM variant, and the comparison of the models also from the viewpoint of the numerical effort (computation time and resources necessary) they require.
Meta-Learning for Semi-Supervised Few-Shot Classification

In few-shot classification, we are interested in learning algorithms that train a classifier from only a handful of labeled examples. Recent progress in few-shot classification has featured meta-learning, in which a parameterized model for a learning algorithm is defined and trained on episodes representing different classification problems, each with a small labeled training set and its corresponding test set. In this work, we advance this few-shot classification paradigm towards a scenario where unlabeled examples are also available within each episode. We consider two situations: one where all unlabeled examples are assumed to belong to the same set of classes as the labeled examples of the episode, as well as the more challenging situation where examples from other distractor classes are also provided. To address this paradigm, we propose novel extensions of Prototypical Networks (Snell et al., 2017) that are augmented with the ability to use unlabeled examples when producing prototypes. These models are trained in an end-to-end way on episodes, to learn to leverage the unlabeled examples successfully. We evaluate these methods on versions of the Omniglot and miniImageNet benchmarks, adapted to this new framework augmented with unlabeled examples. We also propose a new split of ImageNet, consisting of a large set of classes, with a hierarchical structure. Our experiments confirm that our Prototypical Networks can learn to improve their predictions due to unlabeled examples, much like a semi-supervised algorithm would.
The diverse expression of the WT1 gene in patients with acquired bone marrow failure syndromes

Abstract Acquired bone marrow failure syndromes (aBMFS) encompass a wide range of diseases. A study to investigate WT1 expression in BM was conducted in 387 patients with aBMFS in China. The WT1 level in patients with aplastic anemia (AA) was significantly lower than that in patients with paroxysmal nocturnal hemoglobinuria (PNH, p = .023) and myelodysplastic syndrome (MDS, p < .001). In addition, the WT1 level in patients with MDS significantly increased as the disease progressed to an advanced stage. Patients with hypoplastic MDS had a differentiated expression level of WT1 compared with that of NSAA (p < .001). Furthermore, post-treatment patients of AA with partial response (PR) or complete response (CR) status had relatively higher WT1 levels than those with naive AA (p = .017, p = .003, respectively). Thus, the WT1 expression level could be a useful genetic marker for routine clinical work in aBMFS.
Precoder Design for Multiuser MIMO ISI Channels Based on Iterative LMMSE Detection

Precoding has been widely investigated for multiple-input multiple-output (MIMO) and inter-symbol interference (ISI) channels. Most related work so far has been on uncoded systems and the impact of forward-error-correction (FEC) codes has not been well studied. In this paper, we present an optimized precoding technique that takes into account iterative joint LMMSE detection and FEC decoding. The proposed scheme has some interesting features. First, the design problem is convex. Second, the proposed scheme achieves water-filling gain when channel state information at the transmitter (CSIT) is available and diversity gain when CSIT is not available, as well as multi-user gain in multi-user environments. Third, the water-filling gain is achieved using a single code (instead of multiple codes as in conventional approaches), which greatly simplifies the design and implementation problems. Both simulation and evolution analyses are provided to show that significant performance improvement can be achieved with the proposed scheme.
Induction machine faults detection based on a constant false alarm rate detector

This paper presents a novel approach for induction machine condition monitoring using stator current measurements. The proposed method, based on hypothesis testing, specifically investigates a binary detection problem: the machine is healthy or faulty. The Generalized Likelihood Ratio Test (GLRT) is used to address this statistical detection problem with unknown signal and noise parameters. It is indeed a Constant False Alarm Rate (CFAR) detector. Decision is obtained according to a threshold, which is set to reach a desired false alarm probability. The proposed detector implementation needs estimations that are based on the Maximum Likelihood Estimator (MLE). In particular, Total Least Squares-Estimation of Signal Parameters via Rotational Invariance Techniques (TLS-ESPRIT) estimates frequencies. The proposed CFAR detector is tested on experimental data of bearings faults and broken rotor bars that clearly show it effectiveness.
The Classifications and Some Correlations for Fermi Blazars

In a recent paper, we constructed the spectral energy distributions (SEDs) for 1425 Fermi blazars. We classify them as low synchrotron peak sources (LSPs) if log ν p ( Hz ) ≤ 14.0, intermediate synchrotron peak sources (ISPs) if 14.0 15.3 . We obtain an empirical relation to estimate the synchrotron peak frequency, ν p Eq . from effective spectral indexes α o x and α r o as log ν p Eq . = 16 + 4.238 X if X 0 , where X = 1.0 − 1.262 α r o − 0.623 α o x and Y = 1.0 + 0.034 α r o − 0.978 α o x . In the present work, we investigate the correlation between the peak frequency and the radio-to-X-ray spectral index, between peak luminosity (bolometric luminosity) and γ-ray/optical luminosity, and between peak luminosity and bolometric luminosity. Some discussion is presented.
Stable Schizophrenia Patients Learn Equally Well as Age-Matched Controls and Better than Elderly Controls in Two Sensorimotor Rotary Pursuit Tasks

Objective: To compare sensorimotor performance and learning in stable schizophrenia patients, healthy age- and sex-matched controls and elderly controls on two variations of the rotary pursuit: circle pursuit (true motor learning) and figure pursuit (motor and sequence learning). Method: In the circle pursuit, a target circle, rotating with increasing speed along a predictable circular path on the computer screen, must be followed by a cursor controlled by a pen on a writing tablet. In the eight-trial figure pursuit, subjects learn to draw a complex figure by pursuing the target circle that moves along an invisible trajectory between and around several goals. Tasks were administered thrice (day 1, day 2, day 7) to 30 patients with stable schizophrenia (S), 30 healthy age- and sex-matched controls (C), and 30 elderly participants (>65 years; E) and recorded with a digitizing tablet and pressure-sensitive pen. The outcome measure accuracy (% of time that cursor is within the target) was used to assess performance. Results: We observed significant group differences in accuracy, both in circle and figure pursuit tasks (E < S < C, p < 0.01). Strong learning effects were found in each group. Learning curves were similar in circle pursuit but differed between groups in figure pursuit. When corrected for group differences in starting level, the learning gains over the three sessions of schizophrenia patients and age-matched controls were equal and both were larger than those of the elderly controls. Conclusion: Despite the reduced sensorimotor performance that was found in the schizophrenia patients, their sensorimotor learning seems to be preserved. The relevance of this finding for the evaluation of procedural learning in schizophrenia is discussed. The better performance and learning rate of the patients compared to the elderly controls was unexpected and deserves further study.
Flagella-Mediated Adhesion and Extracellular DNA Release Contribute to Biofilm Formation and Stress Tolerance of Campylobacter jejuni

Campylobacter jejuni is a leading cause of foodbourne gastroenteritis, despite fragile behaviour under standard laboratory conditions. In the environment, C. jejuni may survive within biofilms, which can impart resident bacteria with enhanced stress tolerance compared to their planktonic counterparts. While C. jejuni forms biofilms in vitro and in the wild, it had not been confirmed that this lifestyle confers stress tolerance. Moreover, little is understood about molecular mechanisms of biofilm formation in this pathogen. We previously found that a ΔcprS mutant, which carries a deletion in the sensor kinase of the CprRS two-component system, forms enhanced biofilms. Biofilms were also enhanced by the bile salt deoxycholate and contained extracellular DNA. Through more in-depth analysis of ΔcprS and WT under conditions that promote or inhibit biofilms, we sought to further define this lifestyle for C. jejuni. Epistasis experiments with ΔcprS and flagellar mutations (ΔflhA, ΔpflA) suggested that initiation is mediated by flagellum-mediated adherence, a process which was kinetically enhanced by motility. Lysis was also observed, especially under biofilm-enhancing conditions. Microscopy suggested adherence was followed by release of eDNA, which was required for biofilm maturation. Importantly, inhibiting biofilm formation by removal of eDNA with DNase decreased stress tolerance. This work suggests the biofilm lifestyle provides C. jejuni with resilience that has not been apparent from observation of planktonic bacteria during routine laboratory culture, and provides a framework for subsequent molecular studies of C. jejuni biofilms.
American Journal of Epidemiology Original Contribution a Population-based Longitudinal Study on Work Environmental Factors and the Risk of Major Depressive Disorder

which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. To investigate the relation between work environmental factors and the risk of major depressive disorder (MDD) over 1 year, the authors conducted a population-based longitudinal study of randomly selected employees in Alberta, Canada (January 2008 to November 2011). Participants without a current or lifetime diagnosis of MDD at baseline (n ¼ 2,752) were followed for 1 year. The relations between work environmental factors and MDD differed by sex. In men, high job strain increased the risk of MDD in those who worked 35–40 hours per week; job insecurity and family-to-work conflict were predictive of MDD. Women who worked 35–40 hours per week and reported job insecurity, a high effort-reward imbalance, and work-to-family conflict were at a higher risk of developing MDD. Job strain, effort-reward imbalance, job insecurity, and work-to-family conflicts are important risk factors for the onset of MDD and should be targets of primary prevention. However, these work environmental factors appear to operate differently in men and in women. Major depression is a significant public health and societal issue. It imposes considerable burden on health care systems and employers and negatively affects people's quality of life and productivity (1–5). In recent decades, there have been an increasing number of studies indicating that work environmental factors might precipitate the onset of major depression (1, 6–11). In general occupational health research, 3 theoretical models have been widely used: the demand-control model (12), the effort-reward imbalance (ERI) model (13), and the work-to-family conflicts model (14). The demand-control model posits that negative health outcomes, such as fatigue, depression, and other physical illnesses, result from situations in which one's control over one's work is low and the psychological demands imposed by one's work are high (12). Large longitudinal studies have shown that high job strain is associated with an increased risk of psychiatric syndromes (7, 8) and major depression (10, 11, 15). However , research has shown that not all of the domains of the demand-control model are associated with mental disorders, and some domains seem to affect men and women differently in terms of the risk of mental disorders (7, 15). Using national data from Canada, Wang et al. (16) found that a combination of high demand and low control at work was associated major depression in men but not in women. The ERI model …
A discrete log-Sobolev inequality under a Bakry-Emery type condition

We consider probability mass functions $V$ supported on the positive integers using arguments introduced by Caputo, Dai Pra and Posta, based on a Bakry--\'{E}mery condition for a Markov birth and death operator with invariant measure $V$. Under this condition, we prove a modified logarithmic Sobolev inequality, generalizing and strengthening results of Wu, Bobkov and Ledoux, and Caputo, Dai Pra and Posta. We show how this inequality implies results including concentration of measure and hypercontractivity, and discuss how it may extend to higher dimensions.
Differential relationships of internal and external networking behaviors with turnover

Porter, Caitlin M. M.S., Purdue University, May 2013. Differential Relationships of Internal and External Networking Behaviors With Turnover. Major Professor: Sang Eun Woo. Although networking behaviors are proven to be beneficial for career success, less is known about how networking influences organizational outcomes such as turnover. Using a professional and an academic sample of “stayers” and “leavers”, the present study addresses how two types of networking behaviors, networking focused either internal or external to the organization, differentially influence the voluntary turnover process. Data gathered from “stayers” suggested that internal networking behaviors were positively associated with perceived desirability of movement (i.e., job satisfaction), whereas external networking behaviors were associated with perceived (i.e., perceived employment opportunity) and actual (i.e., job offers) ease of movement. For “leavers”, external networking positively related to attitude-driven turnover, whereas internal networking positively related to opportunity-driven turnover. Theoretical and practical implications are discussed.