Miracle-dz/UniFAR-FTUs huggingface dataset:
Weight Loss Interventions for Breast Cancer Survivors: Impact of Dietary Pattern

Body weight management is not emphasized in clinical practice guidelines for breast cancer survivors, reflecting the lack of evidence that weight loss improves prognosis. Even if this situation changes, the optimal design for weight loss interventions is unclear. We conducted a 6-month non-randomized, controlled weight loss intervention in 249 post-menopausal breast cancer survivors. This paper reports effects on two secondary endpoints, change in body weight and composition. Participants were predominantly non-Hispanic whites (89%) with a mean age of 54.9 ± 9.2 years, a mean BMI of 29.0 ± 2.6 kg/m: 2 and an average of 43 ± 5% body fat. Two dietary interventions, low fat or low carbohydrate, were investigated and consisted of a 42 day cycle of menus and recipes. Weight loss counseling and anthropometric assessment were provided at monthly clinic visits. One hundred ninety-two women completed the trial (77% retention). In comparison to the nonintervention control, both intervention arms achieved significant decreases in body weight (12.5%), body fat (27.5%), waist circumference (9.5%), and hip circumference (7.8%) (all p < 0.001) with minimal effects on lean mass (1.3% decrease). Median time to 5 and 10% weight loss was 2 (95% confidence interval = 1 to 3) and 4 (95% confidence interval = 3 to 5) months, respectively, and 23% of participants experienced ≥ 15% weight loss. Loss of body weight and fat mass was rapid and substantial irrespective of dietary approach when a structured program was provided with monthly anthropometric assessment and weight loss counseling. Trial Registration ClinicalTrials.gov NCT01315483
Active Data Collection for Efficient Estimation and Comparison of Nonlinear Neural Models

The stimulus-response relationship of many sensory neurons is nonlinear, but fully quantifying this relationship by a complex nonlinear model may require too much data to be experimentally tractable. Here we present a theoretical study of a general two-stage computational method that may help to significantly reduce the number of stimuli needed to obtain an accurate mathematical description of nonlinear neural responses. Our method of active data collection first adaptively generates stimuli that are optimal for estimating the parameters of competing nonlinear models and then uses these estimates to generate stimuli online that are optimal for discriminating these models. We applied our method to simple hierarchical circuit models, including nonlinear networks built on the spatiotemporal or spectral-temporal receptive fields, and confirmed that collecting data using our two-stage adaptive algorithm was far more effective for estimating and comparing competing nonlinear sensory processing models than standard nonadaptive methods using random stimuli.
An Arabidopsis Mutant with Enhanced Resistance to Powdery Mildew

We have identified an Arabidopsis mutant that displays enhanced disease resistance to the fungus Erysiphe cichoracearum, causal agent of powdery mildew. The edr1 mutant does not constitutively express the pathogenesis-related genes PR-1, BGL2, or PR-5 and thus differs from previously described disease-resistant mutants of Arabidopsis. E. cichoracearum conidia (asexual spores) germinated normally and formed extensive hyphae on edr1 plants, indicating that the initial stages of infection were not inhibited. Production of conidiophores on edr1 plants, however, was <16% of that observed on wild-type Arabidopsis. Reduction in sporulation correlated with a more rapid induction of defense responses. Autofluorescent compounds and callose accumulated in edr1 leaves 3 days after inoculation with E. cichoracearum, and dead mesophyll cells accumulated in edr1 leaves starting 5 days after inoculation. Macroscopic patches of dead cells appeared 6 days after inoculation. This resistance phenotype is similar to that conferred by “late-acting” powdery mildew resistance genes of wheat and barley. The edr1 mutation is recessive and maps to chromosome 1 between molecular markers ATEAT1 and NCC1. We speculate that the edr1 mutation derepresses multiple defense responses, making them more easily induced by virulent pathogens.
The double bind of validation: distant reading and the digital humanities' “trough of disillusionment”

University of Toronto Correspondence Adam Hammond, University of Toronto. Email: adam.hammond@utoronto.ca Abstract The digital humanities (DH) is currently in the phase of the “hype cycle” known as the “trough of disillusionment. ” Franco Moretti, perhaps the most prominent practitioner of the most prominent discipline of DH—“distant reading,” the computational analysis of large quantities of literary texts—recently expressed his exasperation with the state of DH, reflecting “our work could have been better” and asking why, “considering the amount of energy, talent, and tools, going into [DH], that we have such difficulty producing great results. ” Surveying leading recent work in distant reading by Moretti, Matthew L. Jockers, Laura Mandell, Ryan Heuser, Long Le‐Khac, and Joanna Swafford, this paper provides a twofold explanation to the field's failure to produce “great results. ” Both explanations relate to “validation,” the process by which quantitative results are shown to be reliable and trustworthy. Many distant reading projects have produced disappointing results because they have been more interested in validating their tools—showing that their computational methods are able to confirm existing stereotypes—than in pursuing genuine discoveries. Many others, meanwhile, produce provocative results that cannot be meaningfully validated. Although the double bind of validation is real, I propose collaboration and “interdisciplinary adaptation” as promising solutions.
Mental Health Monitoring During Basic Military Training: Psychometric Properties of the Outcome Questionnaire-30.2

This study examined the psychometric properties of the Outcome Questionnaire-30.2 (OQ-30.2; designed to measure patient progress throughout mental health treatment) in a sample of United States Air Force active duty basic military trainees who were evaluated for mental health concerns during the course of basic training. Findings indicate that the OQ-30.2 was internally consistent and Total scores decreased with more contact with mental health professionals. Previously reported 1- and 3-factor structures were not replicated; rather, results suggested the use of a broad 27-item general psychological distress subscale and a separate subscale of 3 critical items assessing substance use concerns. Present findings support the utility of the OQ-30.2 as a tool for repeated monitoring of patient progress in military mental health settings. Recommendations for future directions in the development of alternate calculations of the clinical cut score and reliable change index are discussed.
Diabetes and Breast Cancer Subtypes

Background Women with diabetes have a worse survival after breast cancer diagnosis compared to women without diabetes. This may be due to a different etiological profile, leading to the development of more aggressive breast cancer subtypes. Our aim was to investigate whether insulin and non-insulin treated women with diabetes develop specific clinicopathological breast cancer subtypes compared to women without diabetes. Methods and Findings This cross-sectional study included randomly selected patients with invasive breast cancer diagnosed in 2000–2010. Stratified by age at breast cancer diagnosis (≤50 and >50 years), women with diabetes were 2:1 frequency-matched on year of birth and age at breast cancer diagnosis (both in 10-year categories) to women without diabetes, to select ~300 patients with tumor tissue available. Tumor MicroArrays were stained by immunohistochemistry for estrogen and progesterone receptor (ER, PR), HER2, Ki67, CK5/6, CK14, and p63. A pathologist scored all stains and revised morphology and grade. Associations between diabetes/insulin treatment and clinicopathological subtypes were analyzed using multivariable logistic regression. Morphology and grade were not significantly different between women with diabetes (n = 211) and women without diabetes (n = 101), irrespective of menopausal status. Premenopausal women with diabetes tended to have more often PR-negative (OR = 2.44(95%CI:1.07–5.55)), HER2-negative (OR = 2.84(95%CI:1.11–7.22)), and basal-like (OR = 3.14(95%CI:1.03–9.60) tumors than the women without diabetes, with non-significantly increased frequencies of ER-negative (OR = 2.48(95%CI:0.95–6.45)) and triple negative (OR = 2.60(95%CI:0.88–7.67) tumors. After adjustment for age and BMI, the associations remained similar in size but less significant. We observed no evidence for associations of clinicopathological subtypes with diabetes in postmenopausal women, or with insulin treatment in general. Conclusions We found no compelling evidence that women with diabetes, treated with or without insulin, develop different breast cancer subtypes than women without diabetes. However, premenopausal women with diabetes tended to develop breast tumors that do not express hormonal receptors, which are typically associated with poor prognosis.
Are therapists likely to use a new empirically supported treatment if required?

Summary There continues to be a movement to address the gap between empirically supported treatment research and social services practice. While the general social services field values services based in science, many therapists’ practices are not grounded in and directed by empirical evidence. This study was a secondary analysis of data collected from 17 (N = 17) social service organizations. The final sample consisted of 440 frontline therapists. Findings We find that about one-third (32.7%) of therapists are reluctant to use a new intervention if required by their state, agency, or supervisor. These reluctant empirically supported treatment users had higher levels of field experience (aOR = 1.02, 95% CI = 1.00, 1.05, p = .002) and more years at their present job (aOR = 1.05, 95% CI = 1.01, 1.09, p = .001). We also find an association between race (white versus nonwhite) and the likelihood of being reluctant to using empirically supported treatments, with nonwhites being more likely to be reluctant to use empirically supported treatments (aOR = 1.72, 95% CI = 1.00, 2.95, p = .001). Applications Outcomes indicate that there is a cohort of frontline clinical therapists who are reluctant to use new, empirically supported interventions even if mandated to do so. Organizational leaders may need to consider barriers such as therapist demographics (e.g. years in the field or at the agency), client demographics (e.g. race/ethnicity concordance), and the perceived level of cultural appropriateness of empirically supported treatments by therapists when determining strategies to achieve increased use of empirically supported treatments.
A Framework for Characterization, Planning, and Evaluation of Safe, Comfortable and Customizable Motion of Assistive Mobile Robots (Dissertation Proposal)

An MO disk includes a readout layer, an intermediate layer and a recording layer each of which is made of a rare earth-transition metal amorphous material. The MO disk also includes a fourth magnetic layer formed on the recording layer and made of a rare earth-transition metal amorphous magnetic material containing Gd. The fourth magnetic layer has a rare earth metal magnetization-dominant composition and an axis of easy magnetization oriented longitudinally at room temperature. The axis of easy magnetization is changed to be oriented perpendicularly to the fourth magnetic layer as the temperature of the fourth magnetic layer rises to the Curie temperature of the fourth magnetic layer.
Growing dens. On re-grounding the child–nature relationship through a new materialist approach to children’s dens

ABSTRACT This paper contributes to the dawning disruption of the prevailing notion of the child–nature relationship through a new materialist reading of children’s dens, and proffers a re-grounded and worldly gaze on the relationship with implications for the promotion of children’s outdoor lives. The study is an ethnographical field study among 10–12-year-old boys in a Danish school. Data were generated through participant observation, and include video recordings and photographs of children’s dens. Drawing on a flat ontology and plugging in key Ingoldian concepts of meshwork and growing (Ingold 2011a, 2013), the analysis suggests that children’s relations to dens cut across taken-for-granted subject–object binaries and go beyond common notions of nature as inert materials. I find that dens are growing in an ever-becoming meshwork comprised by human and non-human intra-actions, and that agency or vitality can be ascribed broadly to the material world. Possible implications for planning are considered.
Flexible Parametric Alternatives to the Cox Model, and more

Since its introduction to a wondering public in 1972, the Cox proportional hazards regression model has become an overwhelmingly popular tool in the analysis of censored survival data. However, some features of the Cox model may cause problems for the analyst or an interpreter of the data. They include the restrictive assumption of proportional hazards for covariate effects, and “loss” (non-estimation) of the baseline hazard function induced by conditioning on event times. In medicine, the hazard function is often of fundamental interest since it represents an important aspect of the time course of the disease in question. In the present article, the Stata implementation of a class of flexible parametric survival models recently proposed by Royston and Parmar (2001) will be described. The models start by assuming either proportional hazards or proportional odds (user-selected option). The baseline distribution function is modeled by restricted cubic regression spline in log time, and parameter estimation is by maximum likelihood. Model selection and choice of knots for the spline function are discussed. Interval-censored data and models in which one or more covariates have nonproportional effects are also supported by the software. Examples based on a study of prognostic factors in breast cancer are given.
Effects of Starvation on Physiological Activity and Chlorine Disinfection Resistance in Escherichia coliO157:H7

ABSTRACT Escherichia coli O157:H7 can persist for days to weeks in microcosms simulating natural conditions. In this study, we used a suite of fluorescent, in situ stains and probes to assess the influence of starvation on physiological activity based on membrane potential (rhodamine 123 assay), membrane integrity (LIVE/DEADBacLight kit), respiratory activity (5-cyano-2,3-di-4-tolyl-tetrazolium chloride assay), intracellular esterase activity (ScanRDI assay), and 16S rRNA content. Growth-dependent assays were also used to assess substrate responsiveness (direct viable count [DVC] assay), ATP activity (MicroStar assay), and culturability (R2A agar assay). In addition, resistance to chlorine disinfection was assessed. After 14 days of starvation, the DVC values decreased, while the values in all other assays remained relatively constant and equivalent to each other. Chlorine resistance progressively increased through the starvation period. After 29 days of starvation, there was no significant difference in chlorine resistance between control cultures that had not been exposed to the disinfectant and cultures that had been exposed. This study demonstrates that E. coli O157:H7 adapts to starvation conditions by developing a chlorine resistance phenotype.
Population structure, sex ratio and growth of the seabob shrimp Xiphopenaeus kroyeri (Decapoda, Penaeidae) from coastal waters of southern Brazil

Abstract This study evaluated the growth and population structure of Xiphopenaeus kroyeri in Babitonga Bay, southern Brazil. Monthly trawls were conducted from July 2010 through June 2011, using a shrimp boat outfitted with double-rig nets, at depths from 5 to 17 m. Differences from the expected 0.5 sex ratio were determined by applying a Binomial test. A von Bertalanffy growth model was used to estimate the individual growth, and longevity was calculated using its inverted formula. A total of 4,007 individuals were measured, including 1,106 juveniles (sexually immature) and 2,901 adults. Females predominated in the larger size classes. Males and females showed asymptotic lengths of 27.7 mm and 31.4 mm, growth constants of 0.0086 and 0.0070 per day, and longevities of 538 and 661 days, respectively. The predominance of females in larger size classes is the general rule in species of Penaeidae. The paradigm of latitudinal-effect does not appear to apply to seabob shrimp on the southern Brazilian coast, perhaps because of the small proportion of larger individuals, the occurrence of cryptic species, or the intense fishing pressure in this region. The longevity values are within the general range for species of Penaeidae. The higher estimates for longevity in populations at lower latitudes may have occurred because of the growth constants observed at these locations, resulting in overestimation of this parameter.
Neuroprotective effect of mild hypothermia in the temporary brain ischemia in cats.

OBJECTIVE To evaluate the neuroprotective effect of mild hypothermia during temporary focal ischemia in cats. METHOD 20 cats underwent middle cerebral artery 60 minutes occlusion and 24 hours reperfusion: 10 under normothermia and 10 under mild hypothermia (32 masculine C). Brain coronal sections 2mm thick were stained with 2,3,5-triphenyltetrazolium hydrochloride, photographed and evaluated with software for volume calculation. RESULTS Cortical ischemia was found in 7 and basal ganglia ischemia in 8 animals of group 1 and in both regions in 5 animals of group 2 (no difference: p=0.6499 for cortical; p=0.3498 for basal ganglia). No ischemia was found in 5 animals of group 2 and in none of group 1 (significant difference, p=0.0325). The infarct volume was greater in group 1 than 2 (p=0.0433). CONCLUSION Mild hypothermia did not interfere with location of ischemia, but it was effective for reducing the infarct volume.
Intelligent Global Face Recognition

Face recognition by humans is a natural process that we perform on daily basis. A quick glance at a face and we are able to recognize the face and, most of the time, name the person. Such a process occurs so quickly that we never think of what exactly we looked at in that face. Some of us may take a longer time while trying to name the person, however, the recognition of the familiar face is usually instantaneous. The complexity of a human face arises from the continuous changes in the facial features that take place over time. Despite these changes, we humans are still able to recognize faces and identify the persons. Of course, our natural recognition ability extends beyond face recognition, where we are equally able to quickly recognize patterns, sounds and smells. Unfortunately, this natural ability does not exist in machines, thus the need for artificially simulating recognition in our attempts to create intelligent autonomous machines. Face recognition by machines can be invaluable and has various important applications in real life, such as, electronic and physical access control, national defense and international security. Simulating our face recognition natural ability in machines is a difficult task, but not impossible. Throughout our life time, many faces are seen and stored naturally in our memories forming a kind of database. Machine recognition of faces requires also a database which is usually built using facial images, where sometimes different face images of a one person are included to account for variations in facial features. Current face recognition methods rely on: detecting local facial features and using them for face recognition or on globally analyzing a face as a whole. The first approach (local face recognition systems) uses facial features within the face such as (eyes, nose and mouth) to associate the face with a person. The second approach (global face recognition systems) uses the whole face for identifying the person. This chapter reviews some known existing face recognition methods and presents one case study of a recently developed intelligent face recognition system that uses global pattern averaging for facial data encoding prior to training a neural network using the averaged patterns. The development of intelligent systems that use neural networks is fascinating and has lately attracted more researchers into exploring the potential applications of such systems. The idea of simulating the human perceptions and modeling our senses using machines is great and may help humankind in medical advancement, space exploration, finding alternative energy resources or providing national and international security and peace. Intelligent systems are being increasingly developed aiming to simulate our perception of
Morphology of the Galaxy Distribution from Wavelet Denoising

We have developed a method based on wavelets to obtain the true underlying smooth density from a point distribution. The goal has been to reconstruct the density field in an optimal way, ensuring that the morphology of the reconstructed field reflects the true underlying morphology of the point field, which, as the galaxy distribution, has a genuinely multiscale structure, with near-singular behavior on sheets, filaments, and hot spots. If the discrete distributions are smoothed using Gaussian filters, the morphological properties tend to be closer to those expected for a Gaussian field. The use of wavelet denoising provides us with a unique and more accurate morphological description.
Detection of Temporal Changes in Insect Body Reflectance in Response to Killing Agents

Computer vision and reflectance-based analyses are becoming increasingly important methods to quantify and characterize phenotypic responses by whole organisms to environmental factors. Here, we present the first study of how a non-destructive and completely non-invasive method, body reflectance profiling, can be used to detect and time stress responses in adult beetles. Based on high-resolution hyperspectral imaging, we acquired time series of average reflectance profiles (70 spectral bands from 434-876 nm) from adults in two beetle species, maize weevils (Sitophilus zeamais) and larger black flour beetles (Cynaus angustus). For each species, we acquired reflectance data from untreated controls and from individuals exposed continuously to killing agents (an insecticidal plant extract applied to maize kernels or entomopathogenic nematodes applied to soil applied at levels leading to ≈100% mortality). In maize weevils (exposed to hexanic plant extract), there was no significant effect of the on reflectance profiles acquired from adult beetles after 0 and 12 hours of exposure, but a significant treatment response in spectral bands from 434 to 550 nm was detected after 36 to 144 hours of exposure. In larger black flour beetles, there was no significant effect of exposure to entomopathogenic nematodes after 0 to 26 hours of exposure, but a significant response in spectral bands from 434-480 nm was detected after 45 and 69 hours of exposure. Spectral bands were used to develop reflectance-based classification models for each species, and independent validation of classification algorithms showed sensitivity (ability to positively detect terminal stress in beetles) and specificity (ability to positively detect healthy beetles) of about 90%. Significant changes in body reflectance occurred at exposure times, which coincided with published exposure times and known physiological responses to each killing agent. The results from this study underscore the potential of hyperspectral imaging as an approach to non-destructively and non-invasively quantify stress detection in insects and other animals.