Miracle-dz/UniFAR-FTUs huggingface dataset:
Distinguishing Intraspecific Geographic Variation from Distinct Species Boundaries

52 Copyright © Notice: Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) As the accompanying articles in this issue indicate, Charles M. Bogert and Charles H. Lowe did not always see eye-to-eye about taxonomic issues. One apparent flashpoint in their relationship revolved around the recognition of taxa of Patch-nosed Snakes (Salvadora), which Bogert (1939) had studied for his Master’s thesis. In truth, one could say that Bogert was self-conflicted about Salvadora taxonomy, as he treated certain populations of Arizona Patch-nosed Snakes in at least three distinct ways at various points in his career: as intergrades between S. hexalepis and S. grahamiae (Bogert 1939); as a subspecies of S. hexalepis, which he called S. h. deserticola (Bogert 1945); and finally, as a distinct species, S. deserticola (Bogert and Degenhardt 1961, Bogert 1985). Unfortunately, however, although Bogert used the name S. deserticola in print across nearly a quarter of a century (from 1961-1985), he never published his evidence that the taxon was specifically distinct. At least in part, this may be because of his limited access to specimens in the University of Arizona herpetology collection, which was controlled by Lowe (see Bradley, this issue). As a result, this taxonomic case is controversial and undecided to this day. Various authors either consider the taxon deserticola a distinct species (e.g., Hernández-Jiménez et al. 2019, Hernández-Jiménez et al. 2021) or as a subspecies within S. hexalepis (e.g., Jones et al. 2020, Holycross et al. 2022). Why do different herpetologists continue to disagree on this issue, and what are the criteria that we use to recognize taxa as species versus subspecies?
Learning Ontology Classes from Text by

Many tools for knowledge management and the Semantic Web presuppose the existence of an arrangement of instances into classes, i.e. an ontology. Creating such an ontology, however, is a labor-intensive task. We present an unsupervised method to learn an ontology from text. We rely on pre-trained language models to generate lexical substitutes of given entities and then use matrix factorization to induce new classes and their entities. Our method differs from previous approaches in that (1) it captures the polysemy of entities; (2) it produces interpretable labels of the induced classes; (3) it does not require any particular structure of the text; (4) no re-training is required. We evaluate our method on German and English WikiNER corpora and demonstrate the improvements over state of the art approaches.
Degradation Attacks on Certifiably Robust Neural Networks

Certiﬁably robust neural networks protect against adversarial examples by employing run-time defenses that check if the model is certiﬁably locally robust at the input under evaluation. We show through examples and experiments that any defense (whether complete or incomplete) based on checking local robustness is inherently over-cautious. Speciﬁcally, such defenses ﬂag inputs for which local robustness checks fail, but yet that are not adversarial; i.e., they are classiﬁed consistently with all valid inputs within a distance of (cid:15) . As a result, while a norm-bounded adversary cannot change the classiﬁcation of an input, it can use norm-bounded changes to degrade the utility of certiﬁably robust networks by forcing them to reject otherwise correctly classiﬁable inputs. We empirically demonstrate the eﬃcacy of such attacks against state-of-the-art certiﬁable defenses. Our code is available at https://github.com/ravimangal/degradation-attacks .
InGaAs-based bow-tie diode for spectroscopic terahertz imaging

Suitability of InGaAs-based bow-tie diodes for a spectroscopic terahertz imaging is demonstrated by inspecting explosive simulators packed in a thick plastic container. The transmission images were obtained within the frequency range of 0.58-2.52 THz at room temperature using optimized bow-tie diode connection scheme. Content of sucrose and tartaric acid in the test samples was discriminated. Measured absorbance was found to be in a good correlation with Fourier spectroscopy data. Performance of room temperature THz imaging using the bow-tie diode was compared versus a commercial pyro-electric sensor.
Machine Learning on diagnostic imaging data of systemic sclerosis patients based on lower-dimensional image representations Name :

Systemic sclerosis or Scleroderma is a rheumatic autoimmune disease, characterized by blood vessel abnormalities, and skin and internal organs fibrosis. Due to the complex and varied symptoms that define the disorder, the therapeutic scheme applied to each patient has to be highly personalized. In this work, we explore ways of detecting similarly developed cases, with the potential of helping with the design of individual treatments. Our input data contain high-dimensional fluorescent cellular images of endothelial cells exposed to Systemic sclerosis perturbations. Usually, this kind of analysis starts with segmenting individual cells from the input image and extracting a set of morphological characteristics or measurements for each object. These values are aggregated on an image level to create its signature. The resulting morphological profiles are finally clustered based on similarity. We will deviate from this standard approach and investigate whether compressing the input images into a lower-dimensional space can result in information-rich representations, that could benefit the final patients clustering. We demonstrate that even with a limited amount of data, we can isolate cases of Sceloderma with comparable severity levels.
Serial Increases in Human Leukocyte Antigen-DR Expression and Decreases in Interleukin-10 Expression in Alveolar Monocytes of Survivors of Pneumonia-Related Acute Respiratory Distress Syndrome

Simple Summary Patients with acute respiratory distress syndrome (ARDS) have high mortality. It is important to understand the complex immune interactions in ARDS, which may help identify potential therapeutic targets. In this study, we tried to determine the trends of human leukocyte antigen (HLA)-DR and cytokine expression in alveolar monocytes in patients with pneumonia-related ARDS. We found that alveolar monocyte HLA-DR expression (mHLA-DR) in survivors increased remarkably after seven days, and alveolar monocyte IL-10 expression in survivors decreased substantially after seven days. These findings highlighted the importance of serial increases in HLA-DR expression and decreases in IL-10 expression in alveolar monocytes of survivors. Abstract ARDS is a potentially lethal syndrome. HLA-DR expression in monocytes reflects their activation and antigen-presenting capacity. However, the correlation between clinical outcomes and HLA-DR expression in alveolar monocytes/macrophages in patients with pneumonia-related ARDS remains unclear. Thus, we determined the trends of HLA-DR and cytokine expressions in alveolar monocytes using repeated measurements to answer this question. Thirty-one pneumonia patients with respiratory failure and ARDS without coronavirus disease 2019 between November 2019 and November 2021 were enrolled in our intensive care unit and three without complete data were excluded. Interleukin (IL)-10, IL-12, and HLA-DR expression in bronchoalveolar lavage (BAL) monocytes were determined on days one and eight. Monocyte HLA-DR expression (mHLA-DR) and CD4 T lymphocytes percentages in BAL cells of survivors increased remarkably after seven days. Monocyte IL-10 expression and monocytes percentages in BAL cells of survivors decreased substantially after seven days. The mHLA-DR was negatively correlated with disease severity scores on day one and eight. In conclusion, serial increases in HLA-DR expression and decreases in IL-10 expression were observed in BAL monocytes of survivors of pneumonia-related ARDS. More studies are needed to confirm this point of view, and then development of a therapeutic agent restoring mHLA-DR and preventing IL-10 production can be considered.
FDG-PET in Autoimmune Encephalitis: Utility, Pattern of Abnormalities, and Correlation with Autoantibodies

Background: Fluorodeoxyglucose-positron emission tomography (FDG-PET) in autoimmune encephalitis (AE) as an adjunctive investigation helps in characterizing the type of AE based on characteristic metabolic patterns. Objectives: We aimed to study the following: (i) the sensitivity of FDG-PET in the diagnosis of AE, (ii) describe abnormal patterns of metabolism of various subtypes of AE, and (iii) correlate serum serology with FDG-PET abnormalities. Materials and Methods: This study was conducted at a tertiary university hospital in South India. The demographic profile, clinical features, and investigations (FDG-PET, magnetic resonance imaging (MRI) brain, electroencephalography (EEG), cerebrospinal fluid (CSF)) were reviewed. The nuclear medicine physician performed blinded qualitative visual and semi-quantitative analysis of the 18-FDG-PET (fluorine 18-FDG-PET) findings of these patients. Results: Twenty-nine (M:F: 11:18) patients were recruited; among them, 22 (75.8%) patients had autoimmune antibodies; the rest seven (24.1%) patients were seronegative. Among the 22 seropositive patients, 9 (31%) patients were positive for anti-N-methyl-D-aspartate receptor (NMDAR), 8 (28%) for anti-leucine-rich glioma inactivated 1 (LGI-1), 4 (14%) for anti-contactin-associated protein 2 (CASPR2), 1 (3%) for anti-glutamic acid decarboxylase (GAD)-65, and rest 7 (24%) patients were seronegative. The patterns most commonly observed were isolated hypermetabolism (41%), isolated hypometabolism (41%), and combined hypermetabolism with hypometabolism (18%). The fraction of abnormalities was lower for MRI (17/22; 73.9%) than for FDG-PET (27/29; 93.1%). FDG-PET correlated with serology in 10 (34%) cases [NMDAR: 6 (60%) and LGI-1: 4 (40%)]. The sensitivity of FDG-PET was 94.1% when compared with MRI. Discussion and Conclusion: FDG-PET correlated with serology in only one-third of patients. The most consistent pattern in both seropositive and seronegative AE is characterized by parieto-occipital hypometabolism and fronto-temporal with basal ganglia hypermetabolism.
The field of a focusing source

An analytical description for the field of a focusing source is derived. It is valid for spherically concave sources with small aperture angle and large ka (radius a, wavenumber k.) The solution furnishes easy access to the sound distribution along the axis and in the focal plane, as well as to parameters such as focusing gain, width of the focal spot, and phase shifting in the focal region. Experiments conducted with an f/2 lens coupled to a planar array are discussed. The results support the utility of the analytical model for describing the distribution of sound along the acoustic axis and across the focal plane.
Environment Associated with Deep Moist Convection under SALLJ Conditions: A Case Study

Abstract The present work focuses on the study of the environmental conditions preceding the development of a group of subtropical mesoscale convective systems over central and northern Argentina on 6–7 February 2003 during the South American Low Level Jet Experiment. This period was characterized by an extreme northerly low-level flow along the eastern Andes foothills [South American low-level jet (SALLJ)]. The entire studied episode was dominated by the presence of a very unstable air mass over northern Argentina and a frontal zone near 40°S. The SALLJ generated an important destabilization of the atmosphere due to the strong humidity and differential temperature advection. Orography provided an extra lifting motion to the configuration of the regional wind field, which was efficient in forcing the initiation of convection. Once convection developed, it moved and regenerated in regions where the convective instability was horizontally homogeneous and stronger.
Surface Roughness, Appearance and Identification of AGFA-Gevaert Photograph Samples

The age of digital imaging is rapidly pushing traditional photographic methods into the background. Furthermore, the replacement of discolored analogue photographic prints has become museum display policy, as it is seen as a solution in conservation, and is sometimes promoted by artists. There is therefore an urgent need for methods to characterize photographic materials while they are still available and/or in relatively good condition. Surface properties are some of the most important because they determine the appearance and perception of photographs as works of art. These properties are also valuable for identification and authentication purposes. In particular, the micro-roughness of the surface of a photograph determines the glossiness, but also affects the perception of color. Moreover, a surface’s physical character situates the print in time
Local model uncertainty and incomplete‐data bias (with discussion)

Summary. Problems of the analysis of data with incomplete observations are all too familiar in statistics. They are doubly difficult if we are also uncertain about the choice of model. We propose a general formulation for the discussion of such problems and develop approximations to the resulting bias of maximum likelihood estimates on the assumption that model departures are small. Loss of efficiency in parameter estimation due to incompleteness in the data has a dual interpretation: the increase in variance when an assumed model is correct; the bias in estimation when the model is incorrect. Examples include non‐ignorable missing data, hidden confounders in observational studies and publication bias in meta‐analysis. Doubling variances before calculating confidence intervals or test statistics is suggested as a crude way of addressing the possibility of undetectably small departures from the model. The problem of assessing the risk of lung cancer from passive smoking is used as a motivating example.
Estimation of Tropical Cyclone Wind Hazard for Darwin: Comparison with Two Other Locations and the Australian Wind-Loading Code

The passage of three Australian Category 5 cyclones within 350 km of Darwin (Northern Territory), Australia, during the last decade indicates that that city should have a high wind hazard. In this paper, the wind hazard for Darwin was compared with that for Port Hedland (Western Australia) and Townsville (Queensland) using data from a coupled ocean‐atmosphere simulation model and from historical and satelliteera records of tropical cyclones. According to the authoritative statement on wind hazard in Australia, Darwin’s wind hazard is the same as Townsville’s but both locations’ hazards are much less than that of Port Hedland. However, three different estimates in this study indicate that Darwin’s wind hazard at the long return periods relevant to engineering requirements is higher than for both Port Hedland and Townsville. The discrepancy with previous studies may result from the inadequate cyclone records in the low-latitude north of Australia, from accumulated errors from estimates of wind speeds from wind fields and wind‐pressure relationships, and from inappropriate extrapolations of short-period records based on assumed probability distributions. It is concluded that the current wind-hazard zoning of northern Australia seriously underestimates the hazard near Darwin and that coupled ocean‐atmosphere simulation models could contribute to its revision.
Sleep disturbances in HIV-infected patients associated with depression and high risk of obstructive sleep apnea

Objective: To evaluate sleep disturbances in a diverse, contemporary HIV-positive patient cohort and to identify demographic, clinical, and immune correlates. Methods: A convenience sample of 176 patients from a racially and ethnically diverse HIV-positive patient cohort in an urban population. This was a cross-sectional, epidemiologic study. We surveyed participants using multiple standardized instruments to assess depression, sleep quality, and risk for sleep apnea. We analyzed demographic, behavioral, and clinical correlates. Results: A total of 56% of participants were female, 75% Black and 64% had heterosexual HIV risk. The median age was 49 years. Poor sleep quality (Pittsburgh Sleep Quality Index > 5) was reported by 73% of patients and 52% met insomnia diagnosis criteria. A single question about self-reported sleep problems predicted a Pittsburgh Sleep Quality Index > 5 with a sensitivity and specificity of 82% and 81%, respectively. Female sex was significantly associated with higher risk of poor sleep quality, depression, and insomnia, whereas higher risk of obstructive sleep apnea was significantly associated with older age, male sex, obesity (body mass index ⩾ 30 kg/m2), and metabolic comorbidities. High risk for obstructive sleep apnea, high rate of depression, and poor sleep hygiene represent treatment targets for sleep problems in HIV patients. Conclusion: Sleep disturbances were common in this patient cohort, although largely undiagnosed and untreated. Sleep problems are linked to worse disease progression and increased cardiovascular mortality. Screening for sleep problems with a single question had high sensitivity and specificity. In those patients with self-reported sleep problems, screening for obstructive sleep apnea, depression, and sleep hygiene habits should be part of routine HIV care.
The asymptotic iteration method for the eigenenergies of the Schrödinger equation with the potential V(r) = −Z/r + gr + λr2

The eigenenergies of the Schrödinger equation with Coulomb potential plus linear and harmonic radial terms are investigated using the perturbation technique within the framework of the asymptotic iteration method. The obtained eigenenergies are compared with those obtained from the shifted 1/N expansion method, the moment method and also with the exact values obtained from the super-symmetric method. It is found that asymptotically this method gives accurate results for arbitrary g, Z and λ.
Computer Simulation of Realistic Three-Dimensional Cemented Hip Arthroplasty : Thermal Osteonecrosis Analysis

Many current bone cements have proprietary minor ingredients that affect the chemical kinetics and heat transfer modeling of the exothermic reaction during bone cement polymerization. The geometry and the method of cooling or curing the bone cement can vary by application. We applied a complete numerical model using finite volume methods to investigate temperature history and thermal osteonecrosis analysis during and after bone cement polymerization for a commercial femoral component used in hip arthroplasty. Using a phenomenological kinetic model for energy generation, during bone cement exothermic reaction the effects of precooling and preheating parts of the femoral component before implantation were simulated. Numerical evidence shows that the temperature distribution along the bone depends upon the position of the stem with respect to the exterior bone boundary. Additionally, by precooling the stem, thermal osteonecrosis can be reduced in the bone through evidence of a thermal necrotic plane map of bone. Preheating the stem to above body temperature produces minimal thermal damage of the bone due to limited exposure time.
Identification of New Eruptive Cataclysmic Variables toward the Galactic Bulge and Magellanic Clouds Using the OGLE‐II Database

We have performed a search in the OGLE‐II light‐curve database in order to find new cataclysmic variables. The objects were selected from Magellanic Clouds and Galactic bulge variables, using photometric amplitude as the primary criterion. Nova or dwarf nova–type eruptions were recognized in many candidates, yielding a total of 33 new dwarf novae and two new classical novae identifications. All selected target positions were cross‐correlated against X‐ray survey databases in a search for possible point‐source identifications. The main light‐curve characteristics of each cataclysmic variable identified are described; when possible, a classification in a subtype was assigned to the system. We also find possible candidates to symbiotics, R Coronae Borealis, and RV Tauri. The detected dwarf novae in the direction of the bulge are likely members of the Galactic disk. Using our sample, one may derive an upper limit for the dwarf nova spatial density of 5 × 10-7 pc -3.
The Effects on Parameter Estimation of Correlated Dimensions and a Distribution-Restricted Trait in a Multidimensional Item Response Model

This study was designed to assess the effects on parameter estimation of correlated dimensions and a distribution-restricted trait on one dimension using a two-dimensional item response theory model. Multidimensional analysis of simulated two-dimensional item response data fitting a multi dimensional two-parameter logistic item response theory model (McKinley & Reckase, 1983a; Reckase & McKinley, 1991) was done using the program MIRTE (Carlson, 1987). Six datasets (2 trait distri butions x 3 levels of correlation between dimen sions) of 2,000 trait vectors over 104 items were generated. Each dataset was analyzed and repli cated 100 times. Trait and item parameters generally were recovered adequately in the datasets in which both traits were normally distributed over the full range. In the datasets with a restricted range of trait level on the second dimension, recovery of the trait and item parameters was affected adversely. The results indicated that MIRTE recovers the struc ture of a multidimensional correlated space better than reported in earlier studies, especially when items are multidimensional.
The spectrum and an index formula for the Neumann $p-$Laplacianand multiple solutions for problems with a crossing nonlinearity

In this paper we first conduct a study of the spectrum of the negative $p$-Laplacian with Neumann boundary conditions. More precisely we investigate the first nonzero eigenvalue. We produce alternative variational characterizations, we examine its dependence on $p\in( 1,\infty) $ and on the weight function $m\in L^{\infty}(Z) _{+}$ and we prove that the isolation of the principal eigenvalue $\lambda_{0}=0,$ is uniform for all $p$ in a bounded closed interval. All these results are then used to prove an index formula (jumping theorem) for the $d_{( S)_{+}}-$degree map at the first nonzero eigenvalue. Finally the index formula is used to prove a multiplicity result for problems with a multivalued crossing nonlinearity.
Probing the Galactic thick disc vertical properties and interfaces

Aims. This work investigates the properties (metallicity and kinematics) and interfaces of the Galactic thick disc as a function of height above the Galactic plane. The main aim is to study the thick disc in a place where it is the main component of the sample. Methods. We take advantage of former astrometric work in two fields of several square degrees in which accurate proper motions were measured down to V-magnitudes of 18.5 in two directions, one near the north galactic pole and the other at a galactic latitude of 46 ◦ and galactic longitude near 0 ◦ . Spectroscopic observations have been acquired in these two fields for a total of about 400 stars down to magnitude 18.0, at spectral resolutions of 3.5 to 6.25 A. The spectra have been analysed with the code ETOILE, comparing the target stellar spectra with a grid of 1400 reference stellar spectra. This comparison allowed us to derive the parameters effective temperature, gravity, [Fe/H] and absolute magnitude for each target star. Results. The Metallicity Distribution Function (MDF) of the thin-thick-disc-halo system is derived for several height intervals between 0 and 5 kpc above the Galactic plane. The MDFs show a decrease of the ratio of the thin to thick disc stars between the first and second kilo-parsec. This is consistent with the classical modelling of the vertical density profile of the disc with 2 populations with different scale heights. A vertical metallicity gradient, ∂[Fe/H]/∂z = −0.068 ± 0.009 dex kpc −1 , is observed in the thick disc. It is discussed in terms of scenarios of formation of the thick disc.