Miracle-dz/UniFAR-FTUs huggingface dataset:
Regimen selection in the OPTIONS trial of HIV salvage therapy: drug resistance, prior therapy, and race–ethnicity determine the degree of regimen complexity

Abstract Background: Regimen selection for highly treatment-experienced patients is complicated. Methods: Using a web-based utility, study team members reviewed antiretroviral (ARV) history and resistance data and recommended individual ARV regimens and nucleoside reverse transcriptase inhibitor (NRTI) options for treatment-experienced participants consisting of 3–4 of the following agents: raltegravir (RAL), darunavir (DRV)/ritonavir, tipranavir (TPV)/ritonavir, etravirine (ETR), maraviroc (MVC), and enfuvirtide (ENF). We evaluated team recommendations and site selection of regimen and NRTIs. Associations between baseline factors and the selection of a complex regimen (defined as including four ARV agents or ENF) were explored with logistic regression. Results: A total of 413 participants entered the study. Participants initiated the first or second recommended regimen 86% of the time and 21% of participants started a complex regimen. In a multivariable model, ARV resistance to NRTI (odds ratio [OR] = 2.2), non-nucleoside reverse transcriptase inhibitor (NNRTI, OR = 6.2) or boosted protease inhibitor (PI, OR = 6.6), prior use of integrase strand transfer inhibitor (INSTI, OR = 25), and race–ethnicity (all P ≤ 0.01) were associated with selection of a complex regimen. Black non-Hispanic (OR = 0.5) and Hispanic participants from the continental US (OR = 0.2) were less likely to start a complex regimen, compared to white non-Hispanics. Conclusions: In this multi-center trial, we developed a web-based utility that facilitated treatment recommendations for highly treatment-experienced patients. Drug resistance, prior INSTI use, and race–ethnicity were key factors in decisions to select a more complex regimen.
Differences in Oral Structure and Tissue Interactions during Mouse vs. Human Palatogenesis: Implications for the Translation of Findings from Mice

Clefting of the secondary palate is one of the most common human birth defects and results from failure of the palatal shelves to fuse during embryonic development. Palatogenesis is traditionally considered to be a highly conserved developmental process among mammalian species. However, cleft palate phenotypes in humans are considerably more variable than those seen in mice, the most common animal model for studying palatal development and pathogenesis of cleft palate. In this investigation, we utilized macroscopic observations, histology and 3D imaging techniques to directly compare palate morphology and the oral-nasal cavity during palate closure in mouse embryos and human conceptuses. We showed that mouse and human palates display distinct morphologies attributable to the structural differences of the oral-nasal cavity. We further showed that the palatal shelves interact differently with the primary palate and nasal septum in the hard palate region and with pharyngeal walls in the soft palate region during palate closure in mice and humans. Knowledge of these morphological differences is important for improved translation of findings in mouse models of human cleft lip/palate and, as such, should ultimately enhance our understanding of human palatal morphogenesis and the pathogenesis of cleft lip/palate in humans.
A Simplified Ultrasound Comet Tail Grading Scoring to Assess Pulmonary Congestion in Patients with Heart Failure

Ultrasound lung comets (ULCs) are a nonionizing bedside approach to assess extravascular lung water. We evaluated a protocol for grading ULC score to estimate pulmonary congestion in heart failure patients and investigated clinical and echocardiographic correlates of the ULC score. Ninety-three patients with congestive heart failure, admitted to the emergency department, underwent pulmonary ultrasound and echocardiography. A ULC score was obtained by summing the ULC scores of 7 zones of anterolateral chest scans. The results of ULC score were compared with echocardiographic results, the New York Heart Association (NYHA) functional classification, radiologic score, and N-terminal pro-b-type natriuretic peptide (NT-proBNP). Positive linear correlations were found between the 7-zone ULC score and the following: E/e′, systolic pulmonary artery pressure, severity of mitral regurgitation, left ventricular global longitudinal strain, NYHA functional classification, radiologic score, and NT-proBNP. However, there was no significant correlation between ULC score and left ventricular ejection fraction, left ventricle diameter, left ventricular volume, or left atrial volume. A multivariate analysis identified the E/e′, systolic pulmonary artery pressure, and radiologic score as the only independent variables associated with ULC score increase. The simplified 7-zone ULC score is a rapid and noninvasive method to assess lung congestion. Diastolic rather than systolic performance may be the most important determinant of the degree of lung congestion in patients with heart failure.
Non-Hyper-Singular Boundary Integral Equations for Acoustic Problems, Implemented by the Collocation-Based Boundary Element Method

The weak-form of Helmholtz differential equation, in conjunction with vector test-functions (which are gradients of the fundamental solutions to the Helmholtz differential equation in free space) is utilized as the basis in order to directly derive non-hyper-singular boundary integral equations for the velocity potential, as well as its gradients. Thereby, the presently proposed boundary integral equations, for the gradients of the acoustic velocity potential, involve only O(r−2) singularities at the surface of a 3-D body. Several basic identities governing the fundamental solution to the Helmholtz differential equation for velocity potential, are also derived for the further desingularization of the strongly singular integral equations for the potential and its gradients to be only weakly-singular. These weakly-singular equations are denoted as R-φ-BIE, and R-q-BIE, respectively. [i.e., containing singularities of O(r−1) only at the boundary] Collocation-based boundary-element numerical approaches [denoted as BEM-R-φ-BIE, and BEMR-q−BIE] are implemented to solve these R-φ-BIE, and R-q-BIE. The lower computational costs of BEM-R-φBIE and BEM-R-q-BIE, as compared to the previously published Symmetric Galerkin BEM based solutions of R-φ&q-BIE [Qian, Han and Atluri (2004)] are demonstrated through examples involving acoustic radiation as well as scattering from 3-D bodies. keyword: Boundary integral equations, hypersingularity, collocation
High-Precision Phenotyping of Grape Bunch Architecture Using Fast 3D Sensor and Automation

Wine growers prefer cultivars with looser bunch architecture because of the decreased risk for bunch rot. As a consequence, grapevine breeders have to select seedlings and new cultivars with regard to appropriate bunch traits. Bunch architecture is a mosaic of different single traits which makes phenotyping labor-intensive and time-consuming. In the present study, a fast and high-precision phenotyping pipeline was developed. The optical sensor Artec Spider 3D scanner (Artec 3D, L-1466, Luxembourg) was used to generate dense 3D point clouds of grapevine bunches under lab conditions and an automated analysis software called 3D-Bunch-Tool was developed to extract different single 3D bunch traits, i.e., the number of berries, berry diameter, single berry volume, total volume of berries, convex hull volume of grapes, bunch width and bunch length. The method was validated on whole bunches of different grapevine cultivars and phenotypic variable breeding material. Reliable phenotypic data were obtained which show high significant correlations (up to r2 = 0.95 for berry number) compared to ground truth data. Moreover, it was shown that the Artec Spider can be used directly in the field where achieved data show comparable precision with regard to the lab application. This non-invasive and non-contact field application facilitates the first high-precision phenotyping pipeline based on 3D bunch traits in large plant sets.
Salient Object Detection and Segmentation via Ultra-Contrast

Salient object detection aims at finding the most conspicuous objects in an image that highly catches the user’s attention. The traditional contrast based salient object detection algorithms focus on highlighting the most dissimilar regions and generally fail to detect complex salient objects. In this paper, we propose a salient object detection principle from existing contrast based methods: dissimilarity produces contrast, while contrast leads to saliency. Guided by this principle, we propose a generalized framework to detect complex salient objects. First, we propose a set of region dissimilarity definitions inspired by diverse saliency cues. Then, multiple contrast contexts are encoded to derive dissimilarity matrices. Afterwards, multiple contrast transformations are designed to convert dissimilarity matrices into unified ultra-contrast features. Finally, these ultra-contrast features are mapped to saliency values through logistic regression. The proposed framework is capable of flexibly integrating different kinds of region dissimilarity definitions, region contexts, and contrast transformations. The experimental results demonstrate that our ultra-contrast based saliency detection method outperforms existing contrast based algorithms in terms of three metrics on four datasets.
Therapeutic effects of a recombinant human collagen peptide bioscaffold with human adipose‐derived stem cells on impaired wound healing after radiotherapy

Chronic changes following radiotherapy include alterations in tissue‐resident stem cells and vasculatures, which can lead to impaired wound healing. In this study, novel recombinant human collagen peptide (rhCP) scaffolds were evaluated as a biomaterial carrier for cellular regenerative therapy. Human adipose‐derived stem cells (hASCs) were successfully cultured on rhCP scaffolds. By hASC culture on rhCP, microarray assay indicated that expression of genes related to cell proliferation and extracellular matrix production was upregulated. Pathway analyses revealed that signaling pathways related to inflammatory suppression and cell growth promotion were activated as well as signaling pathways consistent with some growth factors including vascular endothelial growth factor, hepatocyte growth factor, and transforming growth factor beta, although gene expression of these growth factors was not upregulated. These findings suggest the rhCP scaffold showed similar biological actions to cytokines regulating cell growth and immunity. In subsequent impaired wound healing experiments using a locally irradiated (20 Gray) mouse, wound treatment with rhCP sponges combined with cultured hASCs and human umbilical vein endothelial cells accelerated wound closure compared with wounds treated with rhCP with hASCs alone, rhCP only, and control (dressing alone), with better healing observed according to this order. These results indicating the therapeutic value of rhCP scaffolds as a topical biomaterial dressing and a biocarrier of stem cells and vascular endothelial cells for regenerating therapies. The combination of rhCP and functional cells was suggested to be a potential tool for revitalizing stem cell‐depleted conditions such as radiation tissue damage.
Beginning with the application in mind: Designing and planning health behavior change interventions to enhance dissemination

Dissemination of behavior change interventions can be enhanced by considering key elements related to public health impact in the study design and planning phases of research projects. In this article we describe a framework of reach, efficacy/effectiveness, adoption, implementation, and maintenance known as RE-AIM and how it can be used to plan and design studies with features that can strengthen the potential translation of interventions. In describing how RE-AIM concepts were introduced to and adopted by 15 behavior change intervention studies as part of the Behavioral Change Consortium (BCC), we provide an example of practical application of the framework. Recommendations for applying the framework to study planning are based on literature reviews conducted by the RE-AIM workgroup and on discussions with investigators who participated in BCC. Utilizing RE-AIM as a planning framework may have increased attention to issues of external validity among BCC studies and enhanced the potential translation and dissemination of intervention findings into practice.
Under Consideration for Publication in J. Functional Programming the Structure and Interpretation of the Computer Science Curriculum

Twenty years ago Abelson and Sussman's Structure and Interpretation of Computer Programs radically changed the intellectual landscape of introductory computing courses. Instead of teaching some currently fashionable programming language, it employed Scheme and functional programming to teach important ideas. Introductory courses based on the book showed up around the world and made Scheme and functional programming popular. Unfortunately, these courses quickly disappeared again due to shortcomings of the book and the whimsies of Scheme. Worse, the experiment left people with a bad impression of Scheme and functional programming in general. In this pearl, we propose an alternative role for functional programming in the first-year curriculum. Specifically, we present a framework for discussing the first-year curriculum and, based on it, the design rationale for our book and course, dubbed How to Design Programs. The approach emphasizes the systematic design of programs. Experience shows that it works extremely well as a preparation for a course on object-oriented programming. 1 History and critique The publication of Abelson and Sussman's Structure and Interpretation of Computer Programs (sicp) (Abelson et al., 1985) revolutionized the landscape of the introductory computing curriculum in the 1980s. Most importantly, the book liberated the introductory course from the tyranny of syntax. Instead of arranging a course around the syntax of a currently fashionable programming language, sicp focused the first course on the study of important ideas in computing: functional abstraction , data abstraction, streams, data-directed programming, implementation of message-passing objects, interpreters, compilers, and register machines. Over a short period, many universities in the US and around the world switched their first course to sicp and Scheme. The book became a major bestseller for MIT Press.
The use of ceramic matrix composites for metal cutting applications

Abstract Al 2 O 3 ceramics retain their hardness at elevated temperatures, are chemically inert to ferrous workpieces and can be used at high cutting speeds. Early ceramic tools lacked toughness and resistance to mechanical and thermal shocks. The need for tougher and more reliable ceramic tools led to better processing techniques and ceramic matrix composites. Ceramic tools are made by hot pressing, hot isostatic pressing or cold isostatic pressing followed by pressureless sintering. There are four families: (1) Al 2 O 3 -based ceramics, (2) Si 3 N 4 -based ceramics, (3) sialon-based ceramics and (4) cermet tool materials. They are used for metal cutting after strengthening and toughening, e.g., transformation toughening, particle-dispersion toughening, whisker toughening and the use of nanocomposites. Ceramic inserts are used to machine hard-to-cut materials.
Human Micro-Doppler Frequency Estimation Approach for Doppler Radar

Micro-Doppler frequency estimation is an important issue for radar target recognition. In this paper, a novel approach is proposed to accurately estimate the micro-Doppler frequencies of specific target scattering parts, which can be very promising in real-time human sensing applications. For this approach, the adapted linear predictive coding algorithm is first applied to extend the known data in each time window. Then, the Hough transform with a set of new fitting models is used to extract the interested echo components and accurately estimate their micro-Doppler frequencies. Finally, a series of experiments are conducted to illustrate the performance of the proposed approach.
Action understanding based on a combination of one-versus-rest and one-versus-one multi-classification methods

When people observe the actions of others, they naturally try to understand the underlying intentions. This behavior is called action understanding, and it has an important influence on mental development, language comprehension, and socialization. In this study, we used functional near-infrared spectroscopy (fNIRS) to obtain brain signals related to action understanding and then classified different intentions. Aiming to overcome the drawbacks of traditional multiclass classification methods of one-versus-rest (OVR) and one-versus-one (OVO), in this paper, we propose a new effective method to solve multiclass classification that is a combination of OVR and OVO. Compared with OVO, this new method effectively improved the accuracy of four-class classification from 25% to 48%.
A novel length back-calculation approach accounting for ontogenetic changes in the fish length – otolith size relationship during the early life of sprat (Sprattus sprattus)

An individual-based length back-calculation method was developed for juvenile Baltic sprat (Sprattus sprattus), accounting for ontogenetic changes in the relationship between fish length and otolith length. In sprat, metamorphosis from larvae to juveniles is characterized by the coincidence of low length growth, strong growth in body height, and maximal otolith growth. Consequently, the method identifies a point of metamorphosis for an individual as the otolith radius at maximum increment widths. By incorporating this information in our back-calculation method, estimated length growth for the early larval stage was more than 60% higher compared with the result of the biological intercept model. After minimal length growth during metamorphosis, we found the highest increase in length during the early juvenile stage. We thus located the strongest growth potential in the early juvenile stage, which is supposed to be critical in determining recruitment strength in Baltic sprat.
Attachment security as a mechanism linking foster care placement to improved mental health outcomes in previously institutionalized children.

BACKGROUND Children reared in institutions experience elevated rates of psychiatric disorders. Inability to form a secure attachment relationship to a primary caregiver is posited to be a central mechanism in this association. We determined whether the ameliorative effect of a foster care (FC) intervention on internalizing disorders in previously institutionalized children was explained by the development of secure attachment among children placed in FC. Second we evaluated the role of lack of attachment in an institutionalized sample on the etiology of internalizing disorders within the context of a randomized trial. METHODS A sample of 136 children (aged 6-30 months) residing in institutions was recruited in Bucharest, Romania. Children were randomized to FC (n = 68) or to care as usual (CAU; n = 68). Foster parents were recruited, trained, and overseen by the investigative team. Attachment security at 42 months was assessed using the Strange Situation Procedure, and internalizing disorders at 54 months were assessed using the Preschool Age Psychiatric Assessment. RESULTS Girls in FC had fewer internalizing disorders than girls in CAU (OR = 0.17, p = .006). The intervention had no effect on internalizing disorders in boys (OR = 0.47, p = .150). At 42 months, girls in FC were more likely to have secure attachment than girls in CAU (OR = 12.5, p < .001), but no difference was observed in boys (OR = 2.0, p = .205). Greater attachment security predicted lower rates of internalizing disorders in both sexes. Development of attachment security fully mediated intervention effects on internalizing disorders in girls. CONCLUSION Placement into FC facilitated the development of secure attachment and prevented the onset of internalizing disorders in institutionalized girls. The differential effects of FC on attachment security in boys and girls explained gender differences in the intervention effects on psychopathology. Findings provide evidence for the critical role of disrupted attachment in the etiology of internalizing disorders in children exposed to institutionalization.
Overall severities of gastrointestinal symptoms in pediatric outpatients with and without autism spectrum disorder

In order to determine the effectiveness of a Gastrointestinal Severity Index to screen for gastrointestinal disorders, the Gastrointestinal Severity Index was administered to 135 children with autism spectrum disorders and 146 comparisons with and without gastrointestinal disorders. The mean Gastrointestinal Severity Index scores of the groups were 3.53 ± 1.78, 3.15 ± 1.99, 0.81 ± 1.25, and 0.29 ± 0.76 (comparative pediatric patients with gastrointestinal disorder = autism spectrum disorder + gastrointestinal disorder > autism spectrum disorder-gastrointestinal disorder > comparative pediatric patients without gastrointestinal disorder, respectively), Ps < 0.05. Receiver operating characteristic curves and areas under the receiver operating characteristic curves were calculated to ascertain which Gastrointestinal Severity Index cutoff scores yielded the highest sensitivity and specificity rates for the diagnosis of gastrointestinal disorders. The area under the receiver operating characteristic curve (0.97) for the comparison group was higher (P < 0.001) than the area under the receiver operating characteristic curve (0.85) for autism spectrum disorder children indicating that the Gastrointestinal Severity Index was more effective in screening for gastrointestinal disorders in comparisons. However, the same Gastrointestinal Severity Index cutoff score of 2 and above yielded, respectively, sensitivity and specificity rates of 92% and 93% for comparisons and 80% and 79% for autism spectrum disorder children. The negative and positive predictive values based on these sensitivity and specificity rates were calculated for a range of prevalences of gastrointestinal disorders and indicated that the Gastrointestinal Severity Index may be useful for screening children with and without autism spectrum disorder for gastrointestinal symptoms.
Living in the epilepsy treatment gap in rural South India: A focused ethnography of women and problems associated with stigma

ABSTRACT In India, women with epilepsy face unique challenges. A focused ethnography of six women within the epilepsy treatment gap was conducted in rural South India. Women were asked to describe their day-to-day lives. Data were collected through open-ended, semistructured interview questions, participant observation, and field notes. Thematic analysis was done. The disease-related stigma contributed to the women's physical, psychological, and emotional struggles; the women and their family members made every effort to conceal the disease. Educational interventions to create awareness could help women seek effective treatments for their seizures, thereby reducing the stigma and improving the quality of their lives.