Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploring the intersection of executive function and medication adherence in school-age children with asthma

ABSTRACT Asthma is one of the most common chronic diseases of childhood. For children with persistent asthma, asthma control is largely related to controller medication adherence. With increasing calls for children to be involved in their own asthma management, there is a gap in our knowledge about the executive functioning of children with asthma. Objective: The purpose of this study was to explore the relationship between executive function, asthma, and medication adherence among school-age children with asthma. Methods: Thirty-one children ages 7 to 11 years (M = 8.9 ± 1.51) and one of their parents were enrolled in this study. Parents reported on asthma control while children reported on asthma control, medication beliefs, medication adherence, and completed an executive function battery that assessed inhibition, updating, shifting and planning. Results: Compared to the reference sample, children in this study had significantly lower composite scores in inhibition, t (31) = −3.84, p =. 001, and shifting, t (30) = −3.73, p =. 001. Controlling for age and asthma control, hierarchical regression analyses revealed that shifting accounted for 16% of the variance in child-reported medication adherence. Conclusions: This study revealed lowered executive functioning scores among school-age children with persistent asthma. Furthermore, it appears executive functioning and controller medication adherence are intertwined and warrant future exploration.
A CFD model of laser cladding: From deposition head to melt pool dynamics

The laser metal deposition process continues to receive attention from researchers and industry due to its unique capabilities in applications such as surface coating or rapid manufacture. The development of numerical models has proven useful for improving the process. However, most models have focused on analyzing individual stages of the deposition process and have required the introduction of a number of assumptions at their limits. This paper describes a complete CFD model that, starting from particles in the deposition head, simulates all interactions that govern the dynamics of a deposition melt pool. Individual phenomena that are included in the gasphase stage of the model include the ricocheting of particles within the head, the flow of powder particles, their interaction with the laser and powder catchment/bouncing. Phenomena in the liquid phase (melt pool) stage of the model include particle enthalpy effects, buoyancy, temperature-dependant material properties and Marangoni forces. The model is demonstrated using the actual geometry and gas flows found in a typical coaxial nozzle. The method, using a single technique to capture all phenomena, allows simulation of the melt pool dynamics from input parameters in a single model.
Immediate autologous breast reconstruction after neoadjuvant chemoradiotherapy for breast cancer: initial results of the first 29 patients

Breast reconstruction after mastectomy in the treatment of locally advanced breast cancer is often done in stages and before radiotherapy. We have previously published an algorithm for immediate free autologous reconstruction after neoadjuvant chemotherapy and preoperative radiotherapy. This protocol was designed to provide a shorter and simpler reconstructive path whilst improving cosmesis and maintaining oncological efficiency.
Microenvironment-driven resistance to B-Raf inhibition in a melanoma patient is accompanied by broad changes of gene methylation and expression in distal fibroblasts

The incidence of malignant melanoma is rapidly increasing and current medicine is offering only limited options for treatment of the advanced disease. For B-Raf mutated melanomas, treatment with mutation-specific drug inhibitors may be used. Unfortunately, tumors frequently acquire resistance to the treatment. Tumor microenvironment, namely cancer-associated fibroblasts, largely influence this acquired resistance. In the present study, fibroblasts were isolated from a patient suffering from acrolentiginous melanoma (Breslow, 4.0 mm; Clark, IV; B-Raf V600E mutated). The present study focused on the expression of structural and functional markers of fibroblast activation in melanoma-associated fibroblasts (MAFs; isolated prior to therapy initiation) as well as in autologous control fibroblasts (ACFs) of the same patient isolated during B-Raf inhibitor therapy, yet before clinical progression of the disease. Analysis of gene transcription was also performed, as well as DNA methylation status analysis at the genomic scale of both isolates. MAFs were positive for smooth muscle actin (SMA), which is a marker of myofibroblasts and the hallmark of cancer stoma. Surprisingly, ACF isolated from the distant uninvolved skin of the same patient also exhibited strong SMA expression. A similar phenotype was also observed in control dermal fibroblasts (CDFs; from different donors) exclusively following stimulation by transforming growth factor (TGF)-β1. Immunohistochemistry confirmed that melanoma cells potently produce TGF-β1. Significant differences were also identified in gene transcription and in DNA methylation status at the genomic scale. Upregulation of SMA was observed in ACF cells at the protein and transcriptional levels. The present results support recent experimental findings that tumor microenvironment is driving resistance to B-Raf inhibition in patients with melanoma. Such an activated microenvironment may be viable for the growth of circulating melanoma cells.
Support for Relatives Bereaved by Psychiatric Patient Suicide: National Confidential Inquiry Into Suicide and Homicide Findings.

OBJECTIVES International suicide prevention strategies recommend providing support to families bereaved by suicide. The study objectives were to measure the proportion of cases in which psychiatric professionals contact next of kin after a patient's suicide and to investigate whether specific, potentially stigmatizing patient characteristics influence whether the family is contacted. METHODS Annual survey data from England and Wales (2003-2012) were used to identify 11,572 suicide cases among psychiatric patients. Multivariate regression analysis was used to describe the association between specific covariates (chosen on the basis of clinical judgment and the published literature) and the probability that psychiatric staff would contact bereaved relatives of the deceased. RESULTS Relatives were not contacted after the death in 33% of cases. Contrary to the hypothesis, a violent method of suicide was independently associated with greater likelihood of contact with relatives (adjusted odds ratio=1.67). Four patient factors (forensic history, unemployment, and primary diagnosis of alcohol or drug dependence or misuse) were independently associated with less likelihood of contact with relatives. Patients' race-ethnicity and recent alcohol or drug misuse were not associated with contact with relatives. CONCLUSIONS Four stigmatizing patient-related factors reduced the likelihood of contacting next of kin after patient suicide, suggesting inequitable access to support after a potentially traumatic bereavement. Given the association of suicide bereavement with suicide attempt, and the possibility of relatives' shared risk factors for suicide, British psychiatric services should provide more support to relatives after patient suicide.
Molecular mobility and activity in an intravital imaging setting – implications for cancer progression and targeting

ABSTRACT Molecular mobility, localisation and spatiotemporal activity are at the core of cell biological processes and deregulation of these dynamic events can underpin disease development and progression. Recent advances in intravital imaging techniques in mice are providing new avenues to study real-time molecular behaviour in intact tissues within a live organism and to gain exciting insights into the intricate regulation of live cell biology at the microscale level. The monitoring of fluorescently labelled proteins and agents can be combined with autofluorescent properties of the microenvironment to provide a comprehensive snapshot of in vivo cell biology. In this Review, we summarise recent intravital microscopy approaches in mice, in processes ranging from normal development and homeostasis to disease progression and treatment in cancer, where we emphasise the utility of intravital imaging to observe dynamic and transient events in vivo. We also highlight the recent integration of advanced subcellular imaging techniques into the intravital imaging pipeline, which can provide in-depth biological information beyond the single-cell level. We conclude with an outlook of ongoing developments in intravital microscopy towards imaging in humans, as well as provide an overview of the challenges the intravital imaging community currently faces and outline potential ways for overcoming these hurdles. Summary: Intravital imaging approaches in mice are reviewed with a focus on cancer progression and treatment, where it offers detailed insight into the dynamic interactions between cancer cells and their microenvironment in vivo.
Effects of Pre-exposure Prophylaxis for the Prevention of Human Immunodeficiency Virus Infection on Sexual Risk Behavior in Men Who Have Sex With Men: A Systematic Review and Meta-analysis

Background Human immunodeficiency virus (HIV) pre-exposure prophylaxis (PrEP) is effective in reducing HIV risk in men who have sex with men (MSM). However, concerns remain that risk compensation in PrEP users may lead to decreased condom use and increased incidence of sexually transmitted infections (STIs). We assessed the impact of PrEP on sexual risk outcomes in MSM. Methods We conducted a systematic review of open-label studies published to August 2017 that reported sexual risk outcomes in the context of daily oral PrEP use in HIV-negative MSM and transgender women. Pooled effect estimates were calculated using random-effects meta-analysis, and a qualitative review and risk of bias assessment were performed. Results Sixteen observational studies and 1 open-label trial met selection criteria. Eight studies with a total of 4388 participants reported STI prevalence, and 13 studies with a total of 5008 participants reported change in condom use. Pre-exposure prophylaxis use was associated with a significant increase in rectal chlamydia (odds ratio [OR], 1.59; 95% confidence interval [CI], 1.19-2.13) and an increase in any STI diagnosis (OR, 1.24; 95% CI, .99-1.54). The association of PrEP use with STI diagnoses was stronger in later studies. Most studies showed evidence of an increase in condomless sex among PrEP users. Conclusion Findings highlight the importance of efforts to minimize STIs among PrEP users and their sexual partners. Monitoring of risk compensation among MSM in the context of PrEP scale-up is needed to assess the impact of PrEP on the sexual health of MSM and to inform preventive strategies.
Quality control of assembly-defective U1 snRNAs by decapping and 5′-to-3′ exonucleolytic digestion

Significance Cellular RNAs undergo assembly with various proteins, which leads to the formation of functional ribonucleoprotein (RNP) complexes. Kinetic defects in the RNP assembly pathway, which affect the rate of RNP formation, can lead to a reduction in the levels of functional RNPs in the cell, and can lead to a disease state, which we classify as an “RNP assembly disease. ” One example of this class of diseases is spinal muscular atrophy (SMA), where mutations in the assembly factor survival motor neuron lead to reduced small nuclear (sn)RNA and snRNP levels. Here we describe the decay pathways that regulate snRNA levels and function in the cell, prevention of which could be pertinent as a therapy for SMA. The accurate biogenesis of RNA–protein complexes is a key aspect of eukaryotic cells. Defects in Sm protein complex binding to snRNAs are known to reduce levels of snRNAs, suggesting an unknown quality control system for small nuclear ribonucleoprotein (snRNP) assembly. snRNA quality control may also be relevant in spinal muscular atrophy, which is caused by defects in the survival motor neuron (SMN)1 gene, an assembly factor for loading the Sm complex on snRNAs and, when severely reduced, can lead to reduced levels of snRNAs and splicing defects. To determine how assembly-defective snRNAs are degraded, we first demonstrate that yeast U1 Sm-mutant snRNAs are degraded either by Rrp6- or by Dcp2-dependent decapping/5′-to-3′ decay. Knockdown of the decapping enzyme DCP2 in mammalian cells also increases the levels of assembly-defective snRNAs and suppresses some splicing defects seen in SMN-deficient cells. These results identify a conserved mechanism of snRNA quality control, and also suggest a general paradigm wherein the phenotype of an “RNP assembly disease” might be suppressed by inhibition of a competing RNA quality control mechanism.
Estimating the Production Function when Firms Are Constrained

Behind many production function estimators lies a crucial assumption that the firm’s choice of intermediate inputs depends only on observed choices of other inputs and on unobserved productivity. I show that this assumption fails when firms are constrained or face other market distortions. I derive a test for the assumption, which is rejected in several industries. I show that when firms are constrained a simple autoregressive estimator becomes viable and is complementary to choice-based methods, in that it requires choices to be distorted. I propose criteria for choosing between estimators, which in simulations yields lower error than either estimator alone. (JEL Codes: C52, D24) ∗University of California, Santa Cruz; email at azshenoy@ucsc.edu. Phone: (831) 359-3389. Postal Address: Rm. E2455, University of California, M/S Economics Department, 1156 High Street, Santa Cruz CA, 95064. I am grateful to Salvador Navarro for providing code, data, and encouragement. I also thank Dan Ackerberg for helpful comments and suggestions. I thank Liam Rose for excellent research assistance. This paper benefited greatly from the suggestions of Natalia Lazzati, Alan Spearot, and seminar participants at U.C. Santa Cruz, Stanford, SIDE, Michigan State, NYU, Yale, Brown, BU, Columbia, NEUDC (Tufts), and Dartmouth.
Multi-class segmentation of neuronal electron microscopy images using deep learning

Study of connectivity of neural circuits is an essential step towards a better understanding of functioning of the nervous system. With the recent improvement in imaging techniques, high-resolution and high-volume images are being generated requiring automated segmentation techniques. We present a pixel-wise classification method based on Bayesian SegNet architecture. We carried out multi-class segmentation on serial section Transmission Electron Microscopy (ssTEM) images of Drosophila third instar larva ventral nerve cord, labeling the four classes of neuron membranes, neuron intracellular space, mitochondria and glia / extracellular space. Bayesian SegNet was trained using 256 ssTEM images of 256 x 256 pixels and tested on 64 different ssTEM images of the same size, from the same serial stack. Due to high class imbalance, we used a class-balanced version of Bayesian SegNet by re-weighting each class based on their relative frequency. We achieved an overall accuracy of 93% and a mean class accuracy of 88% for pixel-wise segmentation using this encoder-decoder approach. On evaluating the segmentation results using similarity metrics like SSIM and Dice Coefficient, we obtained scores of 0.994 and 0.886 respectively. Additionally, we used the network trained using the 256 ssTEM images of Drosophila third instar larva for multi-class labeling of ISBI 2012 challenge ssTEM dataset.
Effects of group versus individual therapy for patients with memory disorder after an acquired brain injury: A randomized, controlled study

ABSTRACT Introduction: This randomized, controlled, single-blind study compared the efficacy of group versus individual memory rehabilitation therapy for patients with acquired brain injury (ABI). Subjects (N = 65) were assigned to individual (IT), group (GT), or no (NT) therapy during the three-week rehabilitation program. A neuropsychological assessment was conducted before treatment, immediately after completing treatment, and 4 months after completing treatment. Three levels of functioning were assessed: participation, disability, and impairment. The primary outcome measure was the Rivermead Behavioural Memory Test (RBMT). The results of the cognitive measures in the three groups at subsequent assessments were compared, and the effect sizes were calculated to investigate the magnitude of improvement. Results: There were no significant changes in self-reported patient memory problems for the participation-level measures. However, relatives of participants in the GT group reported a decreased frequency of memory failures (p = .026). According to the ability-level measure (RBMT), both therapeutic groups had similar significant improvements (p < .001), and the effect sizes were large in both groups. Although the NT group also improved (p = .015), the effect size was small. The differences between the three groups were not significant according to analysis of variance (ANOVA). However, after therapy was completed, only the GT group continued to improve (p = .013). For the impairment-level measures, the IT group showed significant improvement post treatment in three out of four measures (p < .05). This group had medium effect sizes, while the other groups showed a small or marginal effect. Conclusions: Cognitive rehabilitation – either in a group or individually – led to equally enhanced memory functioning in ABI patients, but the effects were not significantly different from those for patients in the NT group. GT and IT had specific effects on different levels of functioning.
Combined Smoking Cues Enhance Reactivity and Predict Immediate Subsequent Smoking

Introduction Cue reactivity (CR) research has reliably demonstrated robust cue-induced responding among smokers exposed to common proximal smoking cues (eg, cigarettes, lighter). More recent work demonstrates that distal stimuli, most notably the actual environments in which smoking previously occurred, can also gain associative control over craving. In the real world, proximal cues always occur within an environment; thus, a more informative test of how cues affect smokers might be to present these two cue types simultaneously. Methods Using a combined-cue counterbalanced CR paradigm, the present study tested the impact of proximal (smoking and neutral) + personal environment (smoking and nonsmoking places) pictorial cues, on smokers' subjective and behavioral CR; as well as the extent to which cue-induced craving predicts immediate subsequent smoking in a within-subjects design. Results As anticipated, the dual smoking cue combination (ProxS + EnvS) led to the greatest cue-induced craving relative to the other three cue combinations (ProxS + EnvN, ProxN + EnvS, and ProxN ± EnvN), ps < . 004. Dual smoking cues also led to significantly shorter post-trial latencies to smoke, ps < . 01. Overall CR difference score (post-trial craving minus baseline craving) was predictive of subsequent immediate smoking indexed by: post-trial latency to smoke [B = -2.69, SE = 9.02; t(143) = -2.98, p = . 003]; total puff volume [B = 2.99, SE = 1.13; t(143) = 2.65, p = . 009]; and total number of puffs [B = . 053, SE = . 027; t(143) = 1.95, p = . 05]. Conclusions The implications of these findings for better understanding the impact of cues on smoking behavior and cessation are discussed. Implications This novel cue reactivity study examined smokers' reactivity to combined proximal and distal smoking cues. Exposure to a combination of two smoking cues (proximal and environment) led to the greatest increases in cue-induced craving and smoking behavior compared to all other cue combinations. Further, the overall magnitude of cue-induced craving was found to significantly predict immediate subsequent smoking. This work provides new insight on how exposure to various cues and cue combinations directly affect smokers' craving and actual smoking behavior, as well as the relationship between those two indices of reactivity.
Efficient event-driven reactive control for large scale robot skin

In this work we present a novel efficient event-driven reactive skin controller for large scale robot skin. The novel event-driven controller derives from a standard Jacobian torque controller and fully takes advantage of our multi-modal event-driven robot skin. Event-driven systems only sample, transmit and process information when the novelty of the information is guaranteed. This increases their efficiency in comparison to synchronous systems. We also use the new event-driven controller formulation to design a new synchronous reactive skin controller. We compare both controllers in a comprehensive performance evaluation with our robot TOMM. TOMM has two UR5 robot arms, each covered with 253 multi-modal skin cells. Each skin cell samples 4 different modalities and supports data mode and event mode. The results show that the event-driven reactive skin controller always outperforms the synchronous reference controller while both controllers show exactly the same response. When the robot is not moving then the event-driven controller reduces the CPU usage by 78% in comparison to the synchronous reference controller. When the robot is responding to contacts then the CPU usage reduces by 66%.
Postgres-R(SI): combining replica control with concurrency control based on snapshot isolation

Replicating data over a cluster of workstations is a powerful tool to increase performance, and provide fault-tolerance for demanding database applications. The big challenge in such systems is to combine replica control (keeping the copies consistent) with concurrency control. Most of the research so far has focused on providing the traditional correctness criteria serializability. However, more and more database systems, e.g., Oracle and PostgreSQL, use multi-version concurrency control providing the isolation level snapshot isolation. In this paper, we present Postgres-R(SI), an extension of PostgreSQL offering transparent replication. Our replication tool is designed to work smoothly with PostgreSQL's concurrency control providing snapshot isolation for the entire replicated system. We present a detailed description of the replica control algorithm, and how it is combined with PostgreSQL's concurrency control component. Furthermore, we discuss some challenges we encountered when implementing the protocol. Our performance analysis based on the TPC-W benchmark shows that this approach exhibits excellent performance for real-life applications even if they are update intensive.