Miracle-dz/UniFAR-FTUs huggingface dataset:
Deformable ProtoPNet: An Interpretable Image Classifier Using Deformable Prototypes

We present a deformable prototypical part network (Deformable ProtoPNet), an interpretable image classifier that integrates the power of deep learning and the interpretability of case-based reasoning. This model classifies input images by comparing them with prototypes learned during training, yielding explanations in the form of “this looks like that. ” However, while previous methods use spatially rigid prototypes, we address this shortcoming by proposing spatially flexible prototypes. Each prototype is made up of several prototypical parts that adaptively change their relative spatial positions depending on the input image. Consequently, a Deformable ProtoPNet can explicitly capture pose variations and context, improving both model accuracy and the richness of explanations provided. Compared to other case-based interpretable models using prototypes, our approach achieves state-of-the-art accuracy and gives an explanation with greater context. The code is available at https://github.com/jdonnelly36IDeformable-ProtoPNet.
A framework to measure the robustness of programs in the unpredictable environment

Due to the diffusion of IoT, modern software systems are often thought to control and coordinate smart devices in order to manage assets and resources, and to guarantee efficient behaviours. For this class of systems, which interact extensively with humans and with their environment, it is thus crucial to guarantee their correct behaviour in order to avoid unexpected and possibly dangerous situations. In this paper we will present a framework that allows us to measure the robustness of systems. This is the ability of a program to tolerate changes in the environmental conditions and preserving the original behaviour. In the proposed framework, the interaction of a program with its environment is represented as a sequence of random variables describing how both evolve in time. For this reason, the considered measures will be defined among probability distributions of observed data. The proposed framework will be then used to define the notions of adaptability and reliability. The former indicates the ability of a program to absorb perturbation on environmental conditions after a given amount of time. The latter expresses the ability of a program to maintain its intended behaviour (up-to some reasonable tolerance) despite the presence of perturbations in the environment. Moreover, an algorithm, based on statistical inference, is proposed to evaluate the proposed metric and the aforementioned properties. We use two case studies to the describe and evaluate the proposed approach.
A Census of Stars and Disks in Corona Australis

We have performed a census of the young stellar populations near the Corona Australis molecular cloud using photometric and kinematic data from several sources, particularly Gaia EDR3, and spectroscopy of hundreds of candidate members. We have compiled a catalog of 393 members of Corona Australis, (39 at >M6), 293 (36) of which are spectroscopically classified for the first time in this work. We find that Corona Australis can be described in terms of two stellar populations, a younger one (a few megayears) that is partially embedded in the cloud (the Coronet Cluster) and an older one (∼15 Myr) that surrounds and extends beyond the cloud (Upper Corona Australis). These populations exhibit similar space velocities, and we find no evidence for distinct kinematic populations in Corona Australis, in contrast to a recent study based on Gaia DR2. The distribution of spectral types in Corona Australis reaches a maximum at M5 (∼0.15 M ⊙), indicating that the initial mass function has a similar characteristic mass as other nearby star-forming regions. Finally, we have compiled mid-infrared photometry from the Wide-field Infrared Survey Explorer and the Spitzer Space Telescope for the members of Corona Australis, and we have used those data to identify and classify their circumstellar disks. Excesses are detected for 122 stars, one-third of which are reported for the first time in this work.
NGC 5846-UDG1: A Galaxy Formed Mostly by Star Formation in Massive, Extremely Dense Clumps of Gas

It has been shown that ultra-diffuse galaxies (UDGs) have higher specific frequencies of globular clusters, on average, than other dwarf galaxies with similar luminosities. The UDG NGC 5846-UDG1 is among the most extreme examples of globular cluster–rich galaxies found so far. Here we present new Hubble Space Telescope observations and analysis of this galaxy and its globular cluster system. We find that NGC 5846-UDG1 hosts 54 ± 9 globular clusters, three to four times more than any previously known galaxy with a similar luminosity and higher than reported in previous studies. With a galaxy luminosity of L V,gal ≈ 6 × 107 L ⊙ (M ⋆ ≈ 1.2 × 108 M ⊙) and a total globular cluster luminosity of L V,GCs ≈ 7.6 × 106 L ⊙, we find that the clusters currently comprise ∼13% of the total light. Taking into account the effects of mass loss from clusters during their formation and throughout their lifetime, we infer that most of the stars in the galaxy likely formed in globular clusters, and very little to no “normal” low-density star formation occurred. This result implies that the most extreme conditions during early galaxy formation promoted star formation in massive and dense clumps, in contrast to the dispersed star formation observed in galaxies today.
Supermode Si/III-V Lasers and Circular Bragg Lasers

Semiconductor lasers are arguably the most important component in optical communications. This thesis investigates two types of semiconductor lasers that are useful in integrated optics. Part I focuses on supermode Si/III–V lasers and Part II discusses circular Bragg lasers for the application as surface-emitting lasers. Just as optical fibers have largely replaced the traditional copper wires in long-distance applications, people started to consider incorporating optical communication onto chips, primarily because the increased ohmic heating and RC delay associated with the metal interconnection prevent further increase in the data-processing rate. Si is well known to be the integration platform for electronics, and III–V materials (GaAs, InP, etc.) are efficient light emitters. It is natural to bring them together to realize the on-chip optical communication. Among various Si/III–V integration schemes the most promising is the hybrid Si evanescent platform in which a wafer-bonding technique that is compatible with current CMOS processing is used to bring Si and III–V materials together. Part I of this thesis focuses on the application of a novel mode-control method to such hybrid waveguide system to enhance the modal gain, which makes for more efficient and, most importantly, shorter devices that may hold the key to the photonics/electronics integration. The supermode theory is derived, the shortest adiabatic mode transformer is theoretically and numerically studied, and the device design and fabrication are presented, followed by the experimental demonstration of the performance enhancement in the mode-controlled Si/InGaAsP laser devices. Vertical cavity surface emitting lasers are a commercial light source for optical communications, but their single-modedness and good emission pattern are guaranteed only over a very small mode area (diameter of several microns) thus they have limitations in high-power applications. As an alternative, circular Bragg lasers can be designed as a superior surface emitting laser that produces high output power with good beam quality. Part II of this thesis presents a comprehensive and systematic theoretical study on the surface-emitting Hankel-phased circular Bragg lasers in various geometries. The analytical and numerical mode-solving methods will be described, followed by near- and above-threshold modal analyses.
A LOFAR view into the stormy environment of the galaxy cluster 2A0335+096

Context. Radio observations represent a powerful probe of the physics occurring in the intracluster medium (ICM) because they trace the relativistic cosmic rays in the cluster magnetic ﬁelds, or within galaxies themselves. By probing the low-energy cosmic rays, low-frequency radio observations are especially interesting because they unveil emission powered by low-e ﬃ ciency particle acceleration processes, which are believed to play a crucial role in the origin of di ﬀ use radio emission. Aims. We investigate the origin of the radio mini-halo at the centre of the galaxy cluster 2A0335 + 096 and its connection to the central galaxy and the sloshing cool core. We also study the properties of the head-tail galaxy GB6 B0335 + 096 hosted in the cluster to explore the life cycle of the relativistic electrons in its radio tails. Methods. We used new LOw Frequency ARray (LOFAR) observations from the LOFAR Two-meter Sky Survey at 144MHz to map the low-frequency emission with a high level of detail. The new data were combined with archival Giant Metrewave Radio Telescope and Chandra observations to carry out a multi-wavelength study. Results. We have made the ﬁrst measurement of the spectral index of the mini-halo ( α = − 1 . 2 ± 0 . 1 between 144MHz and 1.4GHz) and the lobes of the central source ( α (cid:39) − 1 . 5 ± 0 . 1 between 144 and 610MHz). Based on the low-frequency radio emission morphology with respect to the thermal ICM, we propose that the origin of the di ﬀ use radio emission is linked to the sloshing of the cool core. The new data reveal the presence of a megaparsec-long radio tail associated with GB6 B0335 + 096. The observed projected length is a factor 3 longer than the expected cooling length, with evidence of ﬂattening in the spectral index trend along the tail. Therefore, we suggest that the electrons towards the end of the tail are kept alive by the ICM gentle re-acceleration.
Both negative and positive task-irrelevant stimuli contract attentional breadth in individuals with high levels of negative affect

ABSTRACT Emotionally-salient stimuli can capture attention to their spatial location, even when they are not relevant to a prescribed task. Here we tested whether they can influence the spatial breadth of attention. Experiment 1 tested whether small task-irrelevant emotionally-salient stimuli contracted attentional breadth when the task required a broad focus, while Experiment 2 tested whether large task-irrelevant emotionally-salient stimuli expanded attentional breadth when the task required a narrow focus. Both experiments compared the effect of negative and positive emotionally-salient images against neutral, and examined the role of participants’ self-reported experiences of negative affect. Both experiments revealed slower responses following large emotionally-salient images, an effect unrelated to attentional breadth. Experiment 1 demonstrated an interaction between accuracy and negative affect, such that individuals with high levels of negative affect were less accurate at identifying global targets following both negative and positive small images, but not following neutral small images. This suggests that these small task-irrelevant emotionally-salient images contracted attentional breadth. Experiment 2 suggested that large task-irrelevant emotionally-salient images did not expand attentional breadth. We discuss how these results cannot be explained by existing models of emotion-based effects on attention and cognition, and the important implications they have for the practicalities of model-testing.
Numerical simulation of the early-time high altitude electromagnetic pulse

In this paper, the finite difference method is used to develop the Fortran software MCHII. The physical process in which the electromagnetic signal is generated by the interaction of nuclear-explosion-induced Compton currents with the geomagnetic field is numerically simulated. The electromagnetic pulse waveforms below the burst point are investigated. The effects of the height of burst, yield and the time-dependence of γ-rays are calculated by using the MCHII code. The results agree well with those obtained by using the code CHAP.
SARS-CoV-2–specific memory B cells can persist in the elderly who have lost detectable neutralizing antibodies

Memory B cells (MBCs) can provide a recall response able to supplement waning antibodies (Abs) with an affinity-matured response better able to neutralize variant viruses. We studied a cohort of elderly care home residents and younger staff (median age of 87 years and 56 years, respectively), who had survived COVID-19 outbreaks with only mild or asymptomatic infection. The cohort was selected because of its high proportion of individuals who had lost neutralizing antibodies (nAbs), thus allowing us to specifically investigate the reserve immunity from SARS-CoV-2–specific MBCs in this setting. Class-switched spike and receptor-binding domain (RBD) tetramer–binding MBCs persisted 5 months after mild or asymptomatic SARS-CoV-2 infection, irrespective of age. The majority of spike- and RBD-specific MBCs had a classical phenotype, but we found that activated MBCs, indicating possible ongoing antigenic stimulation or inflammation, were expanded in the elderly group. Spike- and RBD-specific MBCs remained detectable in the majority of individuals who had lost nAbs, although at lower frequencies and with a reduced IgG/IgA isotype ratio. Functional spike-, S1 subunit of the spike protein– (S1-), and RBD-specific recall was also detectable by enzyme-linked immune absorbent spot (ELISPOT) assay in some individuals who had lost nAbs, but was significantly impaired in the elderly. Our findings demonstrate that a reserve of SARS-CoV-2–specific MBCs persists beyond the loss of nAbs but highlight the need for careful monitoring of functional defects in spike- and RBD-specific B cell immunity in the elderly.
Metabolomics Signature of Patients With Narcolepsy

Background and Objectives Narcolepsy type 1 (NT1) is an orphan brain disorder caused by the irreversible destruction of orexin neurons. Metabolic disturbances are common in patients with NT1 who have a body mass index (BMI) 10% to 20% higher than the general population, with one-third being obese (BMI >30 kg/m2). Besides the destruction of orexin neurons in NT1, the metabolic alterations in obese and nonobese patients with NT1 remain unknown. The aim of this study was to identify possible differences in plasma metabolic profiles between patients with NT1 and controls as a function of their BMI status. Methods We used a targeted liquid chromatography–mass spectrometry metabolomics approach to measure 141 circulating, low-molecular-weight metabolites in drug-free fasted plasma samples from 117 patients with NT1 (including 41 obese individuals) compared with 116 BMI-matched controls (including 57 obese individuals). Results Common metabolites driving the difference between patients with NT1 and controls, regardless of BMI, were identified, namely sarcosine, glutamate, nonaylcarnitine (C9), 5 long-chain lysophosphatidylcholine acyls, 1 sphingolipid, 12 phosphatidylcholine diacyls, and 11 phosphatidylcholine acyl-akyls, all showing increased concentrations in NT1. Metabolite concentrations significantly affected by NT1 (n = 42) and BMI category (n = 40) showed little overlap (n = 5). Quantitative enrichment analysis revealed common metabolic pathways that were implicated in the NT1/control differences in both normal BMI and obese comparisons, namely glycine and serine, arachidonic acid, and tryptophan metabolism. The metabolites driving these differences were glutamate, sarcosine, and ornithine (glycine and serine metabolism); glutamate and PC aa C34:4 (arachidonic acid metabolism); and glutamate, serotonin, and tryptophan (tryptophan metabolism). Linear metabolite-endophenotype regression analyses highlight that as part of the NT1 metabolic phenotype, most of the relationships between the sleep parameters (i.e., slow-wave sleep duration, sleep latency, and periodic leg movement) and metabolite concentrations seen in the controls were lost. Discussion These results represent the most comprehensive metabolic profiling of patients with NT1 as a function of BMI and propose some metabolic diagnostic biomarkers for NT1, namely glutamate, sarcosine, serotonin, tryptophan, nonaylcarnitine, and some phosphatidylcholines. The metabolic pathways identified offer, if confirmed, possible targets for treatment of obesity in NT1. Classification of Evidence This study provides Class II evidence that a distinct metabolic profile can differentiate patients with NT1 from patients without the disorder.
Progestin Significantly Inhibits Carcinogenesis in the Mogp-TAg Transgenic Mouse Model of Fallopian Tube Cancer

The fallopian tube is thought to harbor the cell of origin for most ovarian cancers. We show in a mouse model of fallopian tube cancer that progestin eradicates the earliest known precancerous lesions and markedly inhibits fallopian tube carcinogenesis, adding to growing preclinical evidence supporting progestins as potent ovarian cancer chemopreventive agents. Recent studies suggest that the fallopian tube epithelium (FTE) harbors the precursor for high-grade ovarian cancer, creating opportunities for targeting the FTE for ovarian cancer prevention. Preclinical evidence supports progestins as ovarian cancer preventives, but the effect of progestins on the FTE is not well characterized. The murine oviduct–specific glycoprotein promotor-driven simian virus 40 large T-Antigen (mogp-TAg) transgenic mouse model develops neoplastic lesions in the fallopian tube in a manner similar to that described in human fallopian tube and ovarian cancers. In this study, we investigated the inhibitory effects of the progestin depo-medroxyprogesterone acetate (DMPA) on fallopian tube carcinogenesis following treatment for 3 and 7 weeks in 5-week-old mogp-TAg mice. Overall, compared with vehicle-treated mice, the fallopian tube of DMPA-treated mice was significantly smaller (P < 0.0005), accumulated fewer p53-positive cells, had normal distribution of ciliated cells, less nuclear pleomorphism and epithelial tufting, and had a significantly lower proliferative index (P = 0.001). Accumulation of p53 signatures and serous tubal intraepithelial carcinomas (STIC) in the fallopian tube was significantly reduced in the DMPA (P < 0.0005) treatment group. Moreover, the fallopian tube of the DMPA-treated mice developed significantly less adenocarcinoma compared with vehicle (P < 0.005) at both treatment time points. DMPA treatment significantly induced cleaved caspase-3 (P < 0.0005) in the FTE compared with vehicle suggesting that apoptosis is involved in DMPA-related clearance of abnormal cells from the fallopian tube. These data demonstrate that DMPA targets early events in fallopian tube carcinogenesis by clearing genetically damaged cells, leading to marked reduction in adenocarcinoma, supporting progestins as chemopreventive agents for fallopian tube and ovarian cancers. Prevention Relevance: The fallopian tube is thought to harbor the cell of origin for most ovarian cancers. We show in a mouse model of fallopian tube cancer that progestin eradicates the earliest known precancerous lesions and markedly inhibits fallopian tube carcinogenesis, adding to growing preclinical evidence supporting progestins as potent ovarian cancer chemopreventive agents.
Detection of psychosocial distress in cancer patients: A survey of Mexican oncologists

Abstract Purpose: Identification of patients’ distress is relevant for an on-time referral to psychosocial treatment. The objective was to assess the implementation of the guidelines for distress managing in Mexican oncologists based on the NCCN guidelines. Design: The study was non-experimental and cross-sectional. Sample: Two hundred thirty-one oncologists participated with an average age of 38 ± 11 years. Methods: The likelihood of distress assessment was quantitatively evaluated. Findings: A high percentage of oncologists knew and used procedures to assess psychosocial discomfort. However, a smaller percentage used a valid and reliable instrument. Factors associated with performing distress identification procedures were knowing the distress guidelines and lack of time. Factors for questionnaire usage are the availability of brief instruments and the percentage of patients suffering from stress. Implications for Psychosocial Providers: Psychosocial providers should develop strategies to educate and ensure that oncologists are familiar with guidelines on distress in oncology. More dissemination of screening procedures and referral to psychosocial programs in oncology is required. Integrating a distress screening program involving psychosocial providers and oncologists should be approached as a routine in high-quality cancer care, to reduce the stigma associated with mental health services.
BIOMECHANICS OF STANDING LONG JUMP WITH HADNHELD WEIGHT

INTRODUCTION: Many studies had proved that extra weights was held in the hands of the athletes during the long jump competition(Minetti A Lenoir, Clercq & Laporte, 2005), and some researchers found that extra weights would increase the jump distance, but those studies did not point out the joint moment and power. The purpose of this study was to investigate the biomechanical difference between unloaded and loaded groups, and to understand the joint moment and power of standing long jump.
Family History of Psychiatric Disorders and Clinical Factors Associated With a Schizophrenia Diagnosis

Background Schizophrenia (SCH) and bipolar disorder (BD) have both shared and unique genetic risk factors and clinical characteristics. The aim of the present study was to identify potential risk factors significantly associated with SCH, relative to a BD reference group. Methods Data were obtained from medical records of patients that entered a major Mexico City hospital during 2009–2010 presenting psychotic symptoms (n = 1132; 830 cases of SCH, 302 cases of BD; 714 men and 418 women). SCH and BD diagnoses were compared with respect to a number of family and clinical characteristics. Logistic and linear regression analyses were used to respectively identify factors selectively associated with the SCH diagnosis relative to the BD diagnosis and explore the relationship between PANSS scores and parental age at time of birth to the age of SCH onset. Results Patients with SCH showed greater functional impairment than those with BD. Family history of mental illness, premorbid schizoid-like personality, and obstetric trauma were significantly associated with the SCH diagnosis. The association of obstetric trauma with SCH was greatest in male patients with a family history of mental illness. In women, increased paternal and decreased maternal age at time of the patient’s birth were associated with an earlier age of SCH onset. Conclusion Male gender, showing premorbid schizoid-like personality, familial SCH, and obstetric trauma are risk factors that distinguish SCH from BD. Additionally, our results suggest that risk for SCH relative to BD may be importantly influenced by interactions between familial risk, gender, and obstetric trauma.
Expenditure on complementary and alternative medicine and productivity losses in patients with primary dysmenorrhea: A survey of women in Korea

Abstract In women with primary dysmenorrhea (PD), the use of complementary and alternative medicine (CAM) and productivity losses at both workplaces and schools have not been comprehensively assessed. In this study, researchers evaluated the disease burden in women with PD in patients’ perspective in two categories: direct cost (the use of CAM and associated costs) and indirect cost (productivity losses). Women with PD aged 16–49 years were asked to fill an online survey in 2017. The survey consisted of 49 questions. CAM included traditional Korean medicines, over-the-counter products, dietary supplements, and traditional remedies. All costs were expressed in US dollars in this study. The survey data from 86 patients with PD were analyzed. The total mean annual cost per patient with PD was $4053, comprising direct costs ($1245) and indirect costs ($2807). PD causes considerable expenditure on CAM and impairs work productivity (especially in presenteeism).