bluuebunny/crossref_metadata_2025_split huggingface dataset:
Corneal Total and Epithelial Thickness Measured by Sonogage Ultrasound Pachometry and High-resolution Optical Coherence Tomography
Authors: Swarbrick Helen A. , Kang Pauline , Peguda Rajini 
Published: May 2020

SIGNIFICANCE
This research questions the validity of using the Sonogage ultrasound (US) pachometer to measure corneal epithelial thickness and coincidentally provides confirmation for the conventional view of the mechanism of orthokeratology (OK) based on central epithelial thinning.

PURPOSE
The Sonogage (Corneo-Gage Plus 1) pachometer uses A-scan US to measure total corneal thickness. It is claimed that this instrument can also measure corneal epithelial thickness. We sought to validate this claim by comparing total and epithelial thickness measurements with the Sonogage with those obtained with high-resolution optical coherence tomography (OCT).

METHODS
Fourteen non–contact lens wearers and 14 subjects who had worn Paragon CRT OK lenses overnight for greater than 1 month were recruited. Three OCT and five US measurements were taken in one eye of each subject. Depending on normality of data, paired t tests or Wilcoxon tests were used to compare total and epithelial thicknesses measured with the Sonogage pachometer and the Tomey Casia OCT. Pearson or Spearman correlation analyses were used to examine relationships between measurements obtained with the two instruments.

RESULTS
There was a significant difference in total corneal thickness measurements between the two instruments. Although a significant correlation was found (r = 0.916, P < .001), the Sonogage consistently measured greater total corneal thickness than did the OCT (+19.5 ± 9.2 μm; P < .001). Epithelial thickness using the Sonogage showed little variation (range, 46.4 to 50.0 μm), whereas epithelial thickness using the OCT ranged from 30.7 to 54.7 μm. There was no significant correlation between epithelial thicknesses obtained with the two instruments (r = −0.135, P = .49). Epithelial thickness measured by OCT was significantly thinner in OK wearers (35.8 ± 2.8 μm) than in nonlens wearers (46.7 ± 4.5 μm, P < .001).

CONCLUSIONS
The Sonogage is not able to measure epithelial thickness in vivo, returning essentially identical measurements over a range of epithelial thicknesses. Optical coherence tomography measurements confirm the conventional view of the mechanism of OK based on central epithelial thinning.
Baseline and Clinical Factors Associated with Response to Amblyopia Treatment in a Randomized Clinical Trial
Authors: Birch Eileen E. , Jost Reed M. , Kelly Krista R. , Leffler Joel N. , Dao Lori , Beauchamp Cynthia L. 
Published: May 2020

SIGNIFICANCE
We sought to identify baseline and clinical factors that were predictive of the response to amblyopia treatment. We report that binocular amblyopia treatment may be especially effective for moderate amblyopia in orthotropic children.

PURPOSE
We previously reported results from the primary cohort (n = 28) enrolled in a randomized clinical trial (NCT02365090), which found that binocular amblyopia treatment was more effective than patching. Enrollment of an additional 20 children was pre-planned to provide the opportunity to examine factors that may be predictive of response to amblyopia treatment.

METHODS
Forty-eight children (4 to 10 years old) were enrolled, with 24 randomized to contrast-rebalanced binocular game treatment (1 hour a day, 5 days a week) and 24 to patching treatment (2 hours a day, 7 days a week). The primary outcome was change in amblyopic eye best-corrected visual acuity at the 2-week visit. Baseline factors examined were age at enrollment, visual acuity, stereoacuity, and suppression. Clinical factors were etiology, age at diagnosis, prior treatment, and ocular alignment.

RESULTS
At 2 weeks, visual acuity improvement was significantly greater with the binocular game than patching. Children with moderate amblyopia and orthotropia had more visual acuity improvement with binocular game play than did those with severe amblyopia. In addition, children who spent more time playing the binocular game had more improvement. We were not able to confidently identify any baseline or clinical factors that were associated with response to patching treatment.

CONCLUSIONS
Binocular amblyopia treatment was more effective among orthotropic children with moderate amblyopia than among children with microtropia or severe amblyopia.
Timely Delivery of Discharge Medications to Patients’ Bedsides: A Patient-centered Quality Improvement Project
Authors: Katz Daphna T. , Fernandez-Sanchez Josaura V. , Loeffler Leah A. , Chang Simone M. , Puertolas-Lopez Mora V. , Ramdial Faizal R. , Fisher Gabrielle R. , Gutierrez Susan A. , Mahajan Neha , Keerthy Divya R. , Cavallaro Stephania P. , Landaeta Claudia E. , Pascall Akilah S. , Acevedo Kristina T. , Chan-Poon Kwai T. , Abraham Benjamin R. , Siri Matthew , Reynolds Kimberly L. , Van Kirk Kendra , Bayes Santos Liz Y. 
Published: May 2020

Introduction:
Patients who are unable to fill prescriptions after discharge are at risk of hospital readmission. Ensuring that patients have prescriptions in hand at the time of discharge is a critical component of a safe and effective discharge process. Using a “Meds to Beds” program, we aimed to increase the percentage of patients discharged from Holtz Children’s Hospital with medications in hand from 49% to 80%, reduce turnaround time (TAT) from electronic prescription signature to bedside delivery from 4.9 hours (±2.6 hours) to 2 hours, and increase caregiver satisfaction.

Methods:
We formed a multidisciplinary team and implemented 4 patient-centered interventions through iterative plan-do-study-act cycles. Statistical process control charts were used to understand the impact of the interventions over 10 months. Hospital length of stay and discharges before 2:00 pm were used as balancing measures. We measured caregiver satisfaction using a telephone survey administered by pediatric residents within 7 days after discharge.

Results:
The mean percentage of patients discharged with medications in hand increased to 76%. TAT decreased to 3.5 hours (±1.8 hours). Length of stay did not significantly increase, whereas the percentage of patients discharged before 2:00 pm did. Caregivers of patients who had prescriptions delivered to their bedside reported high levels of satisfaction.

Conclusions:
Using a “Meds to Beds” program, we increased the percentage of patients discharged with medications in hand, decreased TAT with reduced variability, and achieved high levels of caregiver satisfaction. Importantly, there was a shift in the culture of the institution toward improved medication access for patients.
Assisting Scalable Diagnosis Automatically via CT Images in the Combat against COVID-19
Authors: Liu Bohan , Liu Pan , Dai Lutao , Yang Yanlin , Xie Peng , Tan Yiqing , Du Jicheng , Shan Wei , Zhao Chenghui , Zhong Qin , Lin Xixiang , Guan Xizhou , Xing Ning , Sun Yuhui , Wang Wenjun , Zhang Zhibing , Fu Xia , Fan Yanqing , Li Meifang , Zhang Na , Li Lin , Liu Yaou , Xu Lin , Du Jingbo , Zhao Zhenhua , Hu Xuelong , Fan Weipeng , Wang Rongpin , Wu Chongchong , Nie Yongkang , Cheng Liuquan , Ma Lin , Li Zongren , Jia Qian , Liu Minchao , Guo Huayuan , Huang Gao , Shen Haipeng , An Weimin , Li Hao , Zhou Jianxin , He Kunlun 
Published: May 2020

Introductory paragraphThe pandemic of coronavirus Disease 2019 (COVID-19) caused enormous loss of life globally. 1-3 Case identification is critical. The reference method is using real-time reverse transcription PCR (rRT-PCR) assays, with limitations that may curb its prompt large-scale application. COVID-19 manifests with chest computed tomography (CT) abnormalities, some even before the onset of symptoms. We tested the hypothesis that application of deep learning (DL) to the 3D CT images could help identify COVID-19 infections. Using the data from 920 COVID-19 and 1,073 non-COVID-19 pneumonia patients, we developed a modified DenseNet-264 model, COVIDNet, to classify CT images to either class. When tested on an independent set of 233 COVID-19 and 289 non-COVID-19 patients. COVIDNet achieved an accuracy rate of 94.3% and an area under the curve (AUC) of 0.98. Application of DL to CT images may improve both the efficiency and capacity of case detection and long-term surveillance.
Haplotype-based analysis distinguishes maternal-fetal genetic contribution to pregnancy-related outcomes
Authors: Srivastava Amit K. , Juodakis Julius , Sole-Navais Pol , Chen Jing , Bacelis Jonas , Teramo Kari , Hallman Mikko , Njølstad Pal R. , Evans David M. , Jacobsson Bo , Muglia Louis J. , Zhang Ge 
Published: May 2020

AbstractGenotype-based approaches for the estimation of SNP-based narrow-sense heritabilityhave limited utility in pregnancy-related outcomes due to confounding by the shared alleles between mother and child. Here, we propose a haplotype-based approach to estimate the genetic variance attributable to three haplotypes – maternal transmitted, maternal non-transmittedand paternal transmittedin mother-child pairs. We show through extensive simulations that our haplotype-based approach outperforms the conventional and contemporary approaches for resolving the contribution of maternal and fetal effects, particularly when m1 and p1 have different effects in the offspring. We apply this approach to estimate the explicit and relative maternal-fetal genetic contribution to the phenotypic variance of gestational duration and gestational duration adjusted fetal size measurements at birth in 10,375 mother-child pairs. The results reveal that variance of gestational duration is mainly attributable to m1 and m2 (= 17.3%, S. E. = 5.2%;= 12.2%, S. E. = 5.2%;= 0.0%, S. E. = 5.0%). In contrast, variance of fetal size measurements at birth are mainly attributable to m1 and p1 (= 18.6 − 36.4%,= 0.0 − 5.2% and= 4.4 − 13.6%). Our results suggest that gestational duration and fetal size measurements are primarily genetically determined by the maternal and fetal genomes, respectively. In addition, a greater contribution of m1 as compared to m2 and p1to birth length and head circumference suggests a substantial influence of correlated maternal-fetal genetic effects on these traits. Our newly developed approach provides a direct and robust alternative for resolving explicit maternal and fetal genetic contributions to the phenotypic variance of pregnancy-related outcomes.
A normative account of confirmation bias during reinforcement learning
Authors: Lefebvre Germain , Summerfield Christopher , Bogacz Rafal 
Published: May 2020

AbstractReinforcement learning involves updating estimates of the value of states and actions on the basis of experience. Previous work has shown that in humans, reinforcement learning exhibits a confirmatory bias: when updating the value of a chosen option, estimates are revised more radically following positive than negative reward prediction errors, but the converse is observed when updating the unchosen option value estimate. Here, we simulate performance on a multi-arm bandit task to examine the consequences of a confirmatory bias for reward harvesting. We report a paradoxical finding: that confirmatory biases allow the agent to maximise reward relative to an unbiased updating rule. This principle holds over a wide range of experimental settings and is most influential when decisions are corrupted by noise. We show that this occurs because on average, confirmatory biases lead to overestimating the value of more valuable bandits, and underestimating the value of less valuable bandits, rendering decisions overall more robust in the face of noise. Our results show how apparently suboptimal learning policies can in fact be reward-maximising if decisions are made with finite computational precision.
Rewiring of peatland plant-microbe networks outpaces species turnover
Authors: Robroek Bjorn J.M. , Martí Magalí , Svensson Bo H. , Dumont Marc G. , Veraart Annelies J. , Jassey Vincent E.J. 
Published: May 2020

AbstractEnviro-climatological changes are thought to be causing alterations in ecosystem processes through shifts in plant and microbial communities; however, how links between plant and microbial communities change with enviro-climatological change is likely to be less straightforward but may be fundamental for many ecological processes. To address this, we assessed the composition of the plant community and the prokaryotic community –using amplicon-based sequencing– of three European peatlands that were distinct in enviro-climatological conditions. Bipartite networks were used to construct site-specific plant-prokaryote co-occurrence networks. Our data show that between sites, plant and prokaryotic communities differ and that turnover in interactions between the communities was complex. Essentially, turnover in plant-microbial interactions is much faster than turnover in the respective communities. Our findings suggest that network rewiring does largely result from novel associations between species that are common and shared across the networks. Turnover in network composition is largely driven by novel interactions between a core community of plants and microorganisms. Taken together our results indicate that plant-microbe associations are context dependent, and that changes in enviro-climatological conditions will likely lead to network rewiring. Integrating turnover in plant-microbe interactions into studies that assess the impact of enviro-climatological change on peatland ecosystems is essential to understand ecosystem dynamics and must be combined with studies on the impact of these changes on ecosystem processes.
Key traits and genes associate with salinity tolerance independent from vigor in cultivated sunflower (Helianthus annuusL.)
Authors: Temme Andries A. , Kerr Kelly L. , Masalia Rishi R. , Burke John M. , Donovan Lisa A. 
Published: May 2020

AbstractWith rising food demands, crop production on salinized lands is increasingly necessary. Sunflower, a moderately salt tolerant crop, exhibits a trade-off where more vigorous, high-performing genotypes have a greater proportional decline in biomass under salinity stress. Prior research has found deviations from this relationship across genotypes; the magnitude and direction of these deviations provides a useful metric of tolerance. Here, we identified the traits and genomic regions underlying variation in this expectation-deviation tolerance. We grew a diversity panel under control and salt-stressed conditions and measured a suite of morphological (growth, allocation, plant and leaf morphology) and leaf ionomic traits. The genetic basis of variation in these traits and their plasticity was investigated via genome-wide association studies, which also enabled the identification of genomic regions (i.e., haplotypic blocks) influencing multiple traits. We found that the magnitude of plasticity in whole root mass fraction, fine root mass fraction, and chlorophyll content, as well as leaf Na and K content under saline conditions, were the traits most strongly correlated with expectation-deviation tolerance. Additionally, we identified multiple genomic regions underlying these traits as well as a single gene directly associated with this tolerance metric. Our results show that, by taking the vigor-salinity effect trade-off into account, we can identify unique traits and genes associated with salinity tolerance. Since these traits and genomic regions are distinct from those associated with high vigor (i.e., growth in benign conditions), they provide an avenue for increasing salinity tolerance in high-performing sunflower genotypes without compromising vigor.Single sentence summaryDespite a trade-off between vigor and salinity-induced decline in biomass, distinct traits and genomic regions exist that could modulate this trade-off in cultivated sunflower.
Investigating the role of N-terminal domain in phosphodiesterase 4B-inhibition by molecular dynamics simulation
Authors: Sharma Vidushi , Wakode Sharad 
Published: May 2020

AbstractPhosphodiesterase 4B (PDE4B) is a potential therapeutic target for the inflammatory respiratory diseases such as congestive obstructive pulmonary disease (COPD) and asthma. The sequence identity of ∼88% with its isoform PDE4D is the key barrier in developing selective PDE4B inhibitors which may help to overcome associated side effects. Despite high sequence identity, both isoforms differ in few residues present in N-terminal (UCR2) and C-terminal (CR3) involved in catalytic site formation. Previously, we designed and tested specific PDE4B inhibitors considering N-terminal residues as a part of the catalytic cavity. In continuation, current work thoroughly presents an MD simulation-based analysis of N-terminal residues and their role in ligand binding. The various parameters viz. root mean square deviation (RMSD), radius of gyration (Rg), root mean square fluctuation (RMSF), principal component analysis (PCA),dynamical cross-correlation matrix(DCCM) analysis, secondary structure analysis, and residue interaction mapping were investigated to establish rational. Results showed that UCR2 reduced RMSF values for the metal binding pocket (31.5±11 to 13.12±6 Å2) and the substrate-binding pocket (38.8±32 to 17.3±11 Å2). UCR2 enhanced anti-correlated motion at the active site region that led to the improved ligand-binding affinity of PDE4B from −24.57±3 to −35.54±2 kcal/mol. Further, the atomic-level analysis indicated that T-pi and π-π interactions between inhibitors and residues are vital forces that regulate inhibitor association to PDE4B with high affinity. In conclusion, UCR2, the N-terminal domain, embraces the dynamics of PDE4B active site and stabilizes PDE4B inhibitor interactions. Therefore the N-terminal domain needs to be included by designing next-generation, selective PDE4B-inhibitors as potential anti-inflammatory drugs.
Differential myoblast and tenoblast affinity to collagen, fibrin and mixed threads in the prospect of muscle-tendon junction modelisation
Authors: Rieu Clément , Rose Nicolas , Taleb Anissa , Mosser Gervaise , Haye Bernard , Coradin Thibaud , Le Grand Fabien , Trichet Léa 
Published: May 2020

AbstractThe myotendinous junction transfers forces from muscle to tendon. As such, it must hold two tissues of completely different biological and cellular compositions as well as mechanical properties (kPa-MPa to MPa-GPa) and is subject to frequent stresses of high amplitude. This region remains a weak point of the muscle-tendon unit and is involved in frequent injuries. We here produce fibrin (40 mg/mL, E0 =0.10 ± 0.02 MPa) and collagen (60 mg/mL, E0=0.57 ± 0.05 MPa) threads as well as mixed collagen:fibrin threads (3:2 in mass, E0 = 0.33 ± 0.05 MPa) and investigate the difference of affinity between primary murine myoblasts and tenoblasts. We demonstrate a similar behavior of cells on mixed and fibrin threads with high adherence of tenoblasts and myoblasts, in comparison to collagen threads that promote high adherence and proliferation of tenoblasts but not of myoblasts. Besides, we show that myoblasts on threads differentiate but do not fuse, on the contrary to 2D control substrates, raising the question of the effect of substrate curvature on the ability of myoblasts to fusein vitro.
Evolution of body size and wing shape trade-offs in arsenurine silkmoths
Authors: Hamilton Chris A. , Winiger Nathalie , Rubin Juliette J. , Breinholt Jesse , Rougerie Rodolphe , Kitching Ian J. , Barber Jesse R. , Kawahara Akito Y. 
Published: May 2020

AbstractOne of the key objectives in biological research is understanding how evolutionary processes have produced Earth’s biodiversity. These processes have led to a vast diversity of wing shapes in insects; an unanswered question especially pronounced in moths. As one of the major predators of nocturnal moths, bats are thought to have been involved in a long evolutionary arms race with their prey. In response, moths are thought to have evolved many counter strategies, such as diverse wing shapes and large body sizes. However, the tradeoffs between body size and wing shape are not well understood. Here we examined the evolution of wing shape in the wild silkmoth subfamily Arsenurinae (Saturniidae). By using phylogenomics and geometric morphometrics, we established the framework to evaluate potential evolutionary relationships between body size and wing shape. The phylogeny was inferred based on 781 loci from target capture data of 42 arsenurine species representing all 10 recognized genera.We found there are evolutionary trade-offs between body size, wing shape, and the interaction of fore- and hindwing shape. Namely, body size decreases with increasing hindwing length, but increases as forewing shape becomes more complex. Additionally, hindwing shape has a significant effect on forewing shape complexity. The complex wing shapes that make Arsenurinae, and silkmoths as a whole, so charismatic are likely driven by the strong forces of natural selection and genomic constraints.One other important outcome was discovering within our data one of the most vexing problems in phylogenetic inference – a region of a tree that possesses short branches and no “support” for relationships (i.e., a polytomy). These parts of the Tree of Life are often some of the most interesting from an evolutionary standpoint. To investigate this problem, we used reciprocal illumination to determine the most probable generic relationships within the Arsenurinae by inspecting differing phylogenetic inferences, alternative support values, quartets, and phylogenetic networks to reveal hidden phylogenetic signal.
Medial Orbitofrontal Cortex Regulates Instrumental Conditioned Punishment, but not Pavlovian Conditioned Fear
Authors: Ma Cassandra , Jean-Richard-dit-Bressel Philip , Roughley Stephanie , Vissel Bryce , Balleine Bernard W. , Killcross Simon , Bradfield Laura A. 
Published: May 2020

AbstractBidirectionally aberrant medial orbitofrontal cortical (mOFC) activity has been consistently linked with compulsion and compulsive disorders. Although rodent studies have established a causal link between mOFC excitation and compulsive-like actions, no such link has been made with mOFC inhibition. Here we use excitotoxic lesions of mOFC to investigate its role in sensitivity to punishment; a core characteristic of many compulsive disorders. In our first experiment, we demonstrated that mOFC lesions prevented instrumental conditioned punishment learning in a manner that could not be attributed to differences in Pavlovian conditioned fear. We then showed that increasing the frequency of punishing outcomes allowed mOFC-lesioned animals to overcome their initial deficit. Our second experiment demonstrated that the retrieval of instrumental punishment is also mOFC-dependent, as mOFC lesions prevented the extended retrieval of punishment contingencies relative to shams. In contrast, mOFC lesions did not prevent the re-acquisition of conditioned punishment that was learned prior to lesions being administered. Together, these results reveal that the mOFC does indeed regulate punishment learning and retrieval in a manner that is disassociated from any role in Pavlovian fear learning. These results imply that aberrant mOFC activity may contribute to the punishment insensitivity that is observed across multiple compulsive disorders.