Miracle-dz/UniFAR-FTUs huggingface dataset:
Visual Acuity and Over-refraction in Myopic Children Fitted with Soft Multifocal Contact Lenses.

SIGNIFICANCE Practitioners fitting contact lenses for myopia control frequently question whether a myopic child can achieve good vision with a high-add multifocal. We demonstrate that visual acuity is not different than spectacles with a commercially available, center-distance soft multifocal contact lens (MFCL) (Biofinity Multifocal "D"; +2.50 D add). PURPOSE To determine the spherical over-refraction (SOR) necessary to obtain best-corrected visual acuity (BCVA) when fitting myopic children with a center-distance soft MFCL. METHODS Children (n = 294) aged 7 to 11 years with myopia (spherical component) of -0.75 to -5.00 diopters (D) (inclusive) and 1.00 D cylinder or less (corneal plane) were fitted bilaterally with +2.50 D add Biofinity "D" MFCLs. The initial MFCL power was the spherical equivalent of a standardized subjective refraction, rounded to the nearest 0.25 D step (corneal plane). An SOR was performed monocularly (each eye) to achieve BCVA. Binocular, high-contrast logMAR acuity was measured with manifest spectacle correction and MFCLs with over-refraction. Photopic pupil size was measured with a pupilometer. RESULTS The mean (±SD) age was 10.3 ± 1.2 years, and the mean (±SD) SOR needed to achieve BCVA was OD: -0.61 ± 0.24 D/OS: -0.58 ± 0.27 D. There was no difference in binocular high-contrast visual acuity (logMAR) between spectacles (-0.01 ± 0.06) and best-corrected MFCLs (-0.01 ± 0.07) (P = .59). The mean (±SD) photopic pupil size (5.4 ± 0.7 mm) was not correlated with best MFCL correction or the over-refraction magnitude (both P ≥ .09). CONCLUSIONS Children achieved BCVA with +2.50 D add MFCLs that was not different than with spectacles. Children typically required an over-refraction of -0.50 to -0.75 D to achieve BCVA. With a careful over-refraction, these +2.50 D add MFCLs provide good distance acuity, making them viable candidates for myopia control.
Impact of food quantity and quality on the biochemical risk of renal stone formation

Abstract Objective: This study evaluated the role of body mass index (BMI) and dietary potential renal acid load (PRAL) with urinary saturation for calcium oxalate (US-CaOx), calcium phosphate (US-CaP) and uric acid (US-UA) in renal stone formers. Materials and methods: A retrospective analysis was conducted of laboratory data collected on 442 renal stone-forming patients. Demographic information, BMI and 24 h urinary samples were collected from patients on their regular diets. PRAL was calculated as the Load of Acid to Kidney Evaluation (LAKE) score through a short questionnaire. Results: Urinary risk factors, but also inhibitors of calcium stone formation such as magnesium, tended to increase in relation to BMI (p = .000). Urinary pH (p = .002) and ammonium/sulfate ratio (p = .000) were negatively related to BMI. This resulted in a positive correlation between BMI and US-UA (p = .000), whereas US-CaOx and US-CaP were not influenced by BMI. LAKE score was positively correlated with US-CaOx (p = .022) and US-CaP (p = .000) as a consequence of the inverse relationship between LAKE score and citrate (p = .000). Multiple linear regression analysis identified BMI (p = .009) and male gender (p = .002) as independent predictors of US-UA, and LAKE score (p = .004) and age (p = .001) as independent predictors of US-CaP. Conclusions: BMI, which depends on excessive intake of energy from food, is not related to an increased biochemical risk of calcium stone formation, which is more dependent on the renal acid load of the diet. In contrast, obesity is associated with an increased risk of uric acid stone formation due to insulin resistance, impaired ammoniagenesis and low urinary pH.
A method to improve dose gradient for robotic radiosurgery

For targets with substantial volume, collimators of relatively large size are usually selected to minimize the treatment time in robotic radiosurgery. Their large penumbrae may adversely affect the dose gradient around the target. In this study, we implement and evaluate an inner‐shell planning method to increase the dose gradient and reduce dose to normal tissues. Ten patients previously treated with CyberKnife M6 system were randomly selected with the only criterion being that PTV be larger than 2 cm3. A new plan was generated for each patient in which the PTV was split into two regions: a 5 mm inner shell and a core, and a 7.5 mm Iris collimator was exclusively applied to the shell, with other appropriate collimators applied to the core depending on its size. The optimization objective, functions, and constraints were the same as in the corresponding clinical plan. The results were analyzed for V12 Gy, V9 Gy, V5 Gy, and gradient index (GI). Volume reduction was found for the inner‐shell method at all studied dose levels as compared to the clinical plans. The absolute dose‐volume reduction ranged from 0.05 cm3 to 18.5 cm3 with a mean of 5.6 cm3 for 12 Gy, from 0.2 cm3 to 38.1 cm3 with a mean of 9.8 cm3 for 9 Gy, and from 1.5 cm3 to 115.7 cm3 with a mean of 24.8 cm3 for 5 Gy, respectively. The GI reduction ranged from 3.2% to 23.6%, with a mean of 12.6%. Paired t‐test for GI has a p‐value of 0.0014. The range for treatment time increase is from ‐3 min to 20 min, with a mean of 7.0 min. We conclude that irradiating the PTV periphery exclusively with the 7.5 mm Iris collimator, rather than applying mixed collimators to the whole PTV, can substantially improve the dose gradient, while maintaining good coverage, conformity, and reasonable treatment time. PACS number: 87.55. de
An investigation of the mechanical properties of metallic lattice structures fabricated using selective laser melting

Metallic lattice structures manufactured using selective laser melting are widely used in fields such as aerospace and automobile industries in order to save material and reduce energy consumption. An essential element of metallic lattice structures design is determining their mechanical behaviors under loading conditions. Theoretical method based on beam theory has been proposed for evaluating the behaviors of the commonly used body-centered cubic lattice structures. However, it is difficult to predict theoretically the properties of the uniaxially reinforced lattice structures based on the body-centered cubic structures. Since the reinforced structures have superior strength to weight ratio and are deemed promising in lightweight-design applications, this article proposed a force-method-based theoretical method to calculate the mechanical properties of the body-centered cubic structure and its two types of uniaxially reinforced structures fabricated via selective laser melting. The finite element analysis and compression experiment study of selective laser melting samples made using Ti6Al4V powders demonstrated the validity of the proposed analytical method.
Intensity modulated radiation therapy versus three‐dimensional conformal radiation therapy for the treatment of high grade glioma: a dosimetric comparison

The present study compared the dosimetry of intensity‐modulated radiation therapy (IMRT) and three‐dimensional conformal radiation therapy (3D‐CRT) techniques in patients treated for high‐grade glioma. A total of 20 patients underwent computed tomography treatment planning in conjunction with magnetic resonance imaging fusion. Prescription dose and normal‐tissue constraints were identical for the 3D‐CRT and IMRT plans. The prescribed dose was 59.4 Gy delivered at 1.8 Gy per fraction using 4 – 10 MV photons. Normal‐tissue dose constraints were 50 – 54 Gy for the optic chiasm and nerves, and 55 – 60 Gy for the brainstem. The IMRT plan yielded superior target coverage as compared with the 3D‐CRT plan. Specifically, minimum and mean planning target volume cone down doses were 54.52 Gy and 61.74 Gy for IMRT and 50.56 Gy and 60.06 Gy for 3D‐CRT (p≤0.01). The IMRT plan reduced the percent volume of brainstem receiving a dose greater than 45 Gy by 31% (p=0.004) and the percent volume of brain receiving a dose greater than 18 Gy, 24 Gy, and 45 Gy by 10% (p=0.059), 14% (p=0.015), and 40% (p≤0.0001) respectively. With IMRT, the percent volume of optic chiasm receiving more than 45 Gy was also reduced by 30.40% (p=0.047). As compared with 3D‐CRT, IMRT significantly increased the tumor control probability (p≤0.005) and lowered the normal‐tissue complication probability for brain and brainstem (p<0.033). Intensity‐modulated radiation therapy improved target coverage and reduced radiation dose to the brain, brainstem, and optic chiasm. With the availability of new cancer imaging tools and more effective systemic agents, IMRT may be used to intensify tumor doses while minimizing toxicity, therefore potentially improving outcomes in patients with high‐grade glioma. PACs number: 87.53 Tf
Suppression of Type I Interferon Signaling by E1A via RuvBL1/Pontin

ABSTRACT Suppression of interferon signaling is of paramount importance to a virus. Interferon signaling significantly reduces or halts the ability of a virus to replicate; therefore, viruses have evolved sophisticated mechanisms that suppress activation of the interferon pathway or responsiveness of the infected cell to interferon. Adenovirus has multiple modes of inhibiting the cellular response to interferon. Here, we report that E1A, previously shown to regulate interferon signaling in multiple ways, inhibits interferon-stimulated gene expression by modulating RuvBL1 function. RuvBL1 was previously shown to affect type I interferon signaling. E1A binds to RuvBL1 and is recruited to RuvBL1-regulated promoters in an interferon-dependent manner, preventing their activation. Depletion of RuvBL1 impairs adenovirus growth but does not appear to significantly affect viral protein expression. Although RuvBL1 has been shown to play a role in cell growth, its depletion had no effect on the ability of the virus to replicate its genome or to drive cells into S phase. E1A was found to bind to RuvBL1 via the C terminus of E1A, and this interaction was important for suppression of interferon-stimulated gene transcriptional activation and recruitment of E1A to interferon-regulated promoters. Here, we report the identification of RuvBL1 as a new target for adenovirus in its quest to suppress the interferon response. IMPORTANCE For most viruses, suppression of the interferon signaling pathway is crucial to ensure a successful replicative cycle. Human adenovirus has evolved several different mechanisms that prevent activation of interferon or the ability of the cell to respond to interferon. The viral immediate-early gene E1A was previously shown to affect interferon signaling in several different ways. Here, we report a novel mechanism reliant on RuvBL1 that E1A uses to prevent activation of interferon-stimulated gene expression following infection or interferon treatment. This adds to the growing knowledge of how viruses are able to inhibit interferon and identifies a novel target used by adenovirus for modulation of the cellular interferon pathway.
Feline Immunodeficiency Virus Cross-Species Transmission: Implications for Emergence of New Lentiviral Infections

ABSTRACT Owing to a complex history of host-parasite coevolution, lentiviruses exhibit a high degree of species specificity. Given the well-documented viral archeology of human immunodeficiency virus (HIV) emergence following human exposures to simian immunodeficiency virus (SIV), an understanding of processes that promote successful cross-species lentiviral transmissions is highly relevant. We previously reported natural cross-species transmission of a subtype of feline immunodeficiency virus, puma lentivirus A (PLVA), between bobcats (Lynx rufus) and mountain lions (Puma concolor) for a small number of animals in California and Florida. In this study, we investigate host-specific selection pressures, within-host viral fitness, and inter- versus intraspecies transmission patterns among a larger collection of PLV isolates from free-ranging bobcats and mountain lions. Analyses of proviral and viral RNA levels demonstrate that PLVA fitness is severely restricted in mountain lions compared to that in bobcats. We document evidence of diversifying selection in three of six PLVA genomes from mountain lions, but we did not detect selection among 20 PLVA isolates from bobcats. These findings support the hypothesis that PLVA is a bobcat-adapted virus which is less fit in mountain lions and under intense selection pressure in the novel host. Ancestral reconstruction of transmission events reveals that intraspecific PLVA transmission has occurred among panthers (Puma concolor coryi) in Florida following the initial cross-species infection from bobcats. In contrast, interspecific transmission from bobcats to mountain lions predominates in California. These findings document outcomes of cross-species lentiviral transmission events among felids that compare to the emergence of HIV from nonhuman primates. IMPORTANCE Cross-species transmission episodes can be singular, dead-end events or can result in viral replication and spread in the new species. The factors that determine which outcome will occur are complex, and the risk of new virus emergence is therefore difficult to predict. We used molecular techniques to evaluate the transmission, fitness, and adaptation of puma lentivirus A (PLVA) between bobcats and mountain lions in two geographic regions. Our findings illustrate that mountain lion exposure to PLVA is relatively common but does not routinely result in communicable infections in the new host. This is attributed to efficient species barriers that largely prevent lentiviral adaptation. However, the evolutionary capacity for lentiviruses to adapt to novel environments may ultimately overcome host restriction mechanisms over time and under certain ecological circumstances. This phenomenon provides a unique opportunity to examine cross-species transmission events leading to new lentiviral emergence.
miRNA activation is an endogenous gene expression pathway

ABSTRACT Transfection of small non-coding RNAs (sncRNAs) molecules has become a routine technique widely used for silencing gene expression by triggering post-transcriptional and transcriptional RNA interference (RNAi) pathways. Moreover, in the past decade, small activating (saRNA) sequences targeting promoter regions were also reported, thereby a RNA-based gene activation (RNAa) mechanism has been proposed. In this regard, Turner and colleagues recently discovered an endogenous microRNA (miRNA) which binds its promoter in order to upregulate its own expression. Interestingly, several miRNA-induced RNA activation (miRNAa) phenomena have since then been identified. My objective here is to introduce the reader into the emergent miRNAa research field, as well as bring together important discoveries about this unexplored transcriptional activation pathway.
Design and implementation of an affordable, public sector electronic medical record in rural Nepal

Introduction Globally, electronic medical records are central to the infrastructure of modern healthcare systems. Yet, the vast majority of electronic medical records have been designed for resource-rich environments and are not feasible in settings of poverty. Here, we describe the design and implementation of an electronic medical record at a public sector district hospital in rural Nepal and its subsequent expansion to an additional public sector facility. Development The electronic medical record was designed to solve for the following elements of public sector healthcare delivery: 1) integration of the systems across inpatient, surgical, outpatient, emergency, laboratory, radiology and pharmacy sites of care; 2) effective data extraction for impact evaluation and government regulation; 3) optimization for longitudinal care provision and patient tracking and 4) effectiveness for quality improvement initiatives. Application For these purposes, we adapted Bahmni, a product built with open-source components for patient tracking, clinical protocols, pharmacy, laboratory, imaging, financial management and supply logistics. In close partnership with government officials, we deployed the system in February of 2015, added on additional functionality and iteratively improved the system over the following year. This experience enabled us then to deploy the system at an additional district-level hospital in a different part of the country in under four weeks. We discuss the implementation challenges and the strategies we pursued to build an electronic medical record for the public sector in rural Nepal. Discussion Over the course of 18 months, we were able to develop, deploy and iterate upon the electronic medical record, and then deploy the refined product at an additional facility within only four weeks. Our experience suggests the feasibility of an integrated electronic medical record for public sector care delivery even in settings of rural poverty.
Completely Unsupervised Phoneme Recognition by Adversarially Learning Mapping Relationships from Audio Embeddings

Unsupervised discovery of acoustic tokens from audio corpora without annotation and learning vector representations for these tokens have been widely studied. Although these techniques have been shown successful in some applications such as query-by-example Spoken Term Detection (STD), the lack of mapping relationships between these discovered tokens and real phonemes have limited the down-stream applications. This paper represents probably the first attempt towards the goal of completely unsupervised phoneme recognition, or mapping audio signals to phoneme sequences without phoneme-labeled audio data. The basic idea is to cluster the embedded acoustic tokens and learn the mapping between the cluster sequences and the unknown phoneme sequences with a Generative Adversarial Network (GAN). An unsupervised phoneme recognition accuracy of 36% was achieved in the preliminary experiments.
Uplink Area Spectral Efficiency Analysis for Multichannel Heterogeneous Cellular Networks With Interference Coordination

The deployment of small cells (SCs) in heterogeneous cellular networks (HCNs) has been shown to be a promising approach to increase the system capacities of wireless communications. However, the bandwidth sharing and densification of the SCs cause co-tier and cross-tier interferences that limit the system spectral efficiency. In this paper, a framework of an uplink area spectral efficiency (ASE) analysis for multichannel HCNs using a proposed biased cell association scheme with coordinated subchannel allocation and channel inversion power control for mitigating the interferences is developed. The coordinated subchannel allocation is proposed to alleviate the severe cross-tier interference caused by macrocell users around the edges of the SCs. By incorporating the coordinated subchannel allocation into the biased cell association scheme with a bias factor, the proposed scheme is able to design the bias factor to reshape the coverage areas of the SCs providing an effective tradeoff between user offloading and cross-tier interference avoidance. By applying the tools of stochastic geometry, the uplink ASE is analytically derived as a function of the bias factor for the multichannel HCNs. The optimal bias factor can be obtained numerically by maximizing the system ASE. It is shown that the ASE performance analysis agrees with computer simulation very well. The results demonstrate that the proposed scheme can substantially improve the ASE performance of the multichannel HCNs for different small cell densities and outperform upon an existing biased cell association scheme.
Comparison of automatic image registration uncertainty for three IGRT systems using a male pelvis phantom

A series of phantom images using the CIRS Virtual Human Male Pelvis was acquired across available dose ranges for three image‐guided radiotherapy (IGRT) imaging systems: Elekta XVI CBCT, Varian TrueBeam CBCT, and TomoTherapy MV CT. Each image was registered to a fan‐beam CT within the XVI software 100 times with random initial offsets. The residual registration error was analyzed to assess the role of imaging hardware and reconstruction in the uncertainty of the IGRT process. Residual translation errors were similar for all systems and <0.5 mm. Over the clinical dose range for prostate IGRT images (10–25 mGy), all imaging systems provided acceptable matches in >90% of registrations when incorporating residual rotational error using a dual quaternion derived distance metric. Outside normal dose settings, large uncertainties were observed at very low and very high dose levels. No trend between initial offset and residual registration error was observed. Patient images may incur higher uncertainties than this phantom study; however, these results encourage automatic matching for standard dose settings with review by treatment staff. PACS number(s): 87.55. km, 87.55. ne, 87.56. Da
Impact of Inflammatory Bowel Disease and High-Dose Steroid Exposure on Pupillary Responses to Negative Information in Pediatric Depression

Objective: To better understand emotional information processing in pediatric inflammatory bowel disease (IBD) and its relationship with depression. Pediatric IBD is associated with higher rates of depression than seen in other physical diseases and in community samples. In systemic inflammation, proinflammatory cytokines have been implicated in altering activity in brain regions known to affect emotion processing and emotion regulation in depression. Methods: We examined differences in pupillary responses as a marker of brain function in response to negative emotional information in youths (ages, 8–17 years) with IBD both with (n = 8) and without (n = 15) comorbid depression and who were receiving high-dose steroid treatment. We compared their responses to each other and to depressed youths without IBD (n = 20) and healthy youths (n = 22). Results: Youths with IBD demonstrated greater pupillary responses to the initial presentation of negative emotional stimuli, regardless of their depression status (p = .05). In contrast, depressed youths, regardless of their IBD status, demonstrated a greater constriction of the pupil 10 seconds to 12 seconds after exposure to negative stimuli. This constriction was associated with greater depressive severity and lower albumin levels. Conclusions: IBD may be associated with increased sensitivity to negative emotional stimuli above and beyond depression diagnosis. Depressed youths potentially demonstrate affective blunting, emotional avoidance, or a failure to regulate emotion after exposure to negative emotional information. Thus, there seem to be unique contributions of medical disease and depression to physiological indications of emotional reactivity, but these factors do not seem to interact. CD = Crohn's disease; CNS = central nervous system; DSM-IV = Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition; ESR = erythrocyte sedimentation rate; IBD = inflammatory bowel disease; PCDAI = Pediatric Crohn's Disease Activity Index; PUCDAI = Pediatric Ulcerative Colitis Disease Activity Index; UC = ulcerative colitis.