Miracle-dz/UniFAR-FTUs huggingface dataset:
Ph-Net: Parallelepiped Microstructure Homogenization Via 3d Convolutional Neural Networks

Microstructures are attracting academic and industrial interests with the rapid development of additive manufacturing. The numerical homogenization method has been well studied for analyzing mechanical behaviors of microstructures; however, it is too time-consuming to be applied to online computing or applications requiring high-frequency calling, e.g., topology optimization. Data-driven homogenization methods emerge as a more efficient choice but limit the microstructures into a cubic shape, which are infeasible to the periodic microstructures with a more general shape, e.g., parallelepiped. This paper introduces a fine-designed 3D convolutional neural network (CNN) for fast homogenization of parallel-shaped microstructures, named PH-Net. Superior to existing data-driven methods, PH-Net predicts the local displacements of microstructures under specified macroscope strains instead of direct homogeneous material, motivating us to present a label-free loss function based on minimal potential energy. For dataset construction, we introduce a shape-material transformation and voxel-material tensor to encode microstructure type,base material and boundary shape together as the input of PH-Net, such that it is CNN-friendly and enhances PH-Net on generalization in terms of microstructure type, base material, and boundary shape. PH-Net predicts homogenized properties with hundreds of acceleration compared to the numerical homogenization method and even supports online computing. Moreover, it does not require a labeled dataset and thus is much faster than current deep learning methods in training processing. Benefiting from predicting local displacement, PH-Net provides both homogeneous material properties and microscopic mechanical properties, e.g., strain and stress distribution, yield strength, etc. We design a group of physical experiments and verify the prediction accuracy of PH-Net.
AJA2000055 851..861

Purpose: This retrospective study used a cochlear implant registry to determine how performing speech recognition candidacy testing in quiet versus noise influenced patient selection, speech recognition, and self-report outcomes. Method: Database queries identified 1,611 cochlear implant recipients who were divided into three implant candidacy qualifying groups based on preoperative speech perception scores (≤ 40% correct) on the AzBio sentence test: quiet qualifying group, +10 dB SNR qualifying group, and +5 dB SNR qualifying group. These groups were evaluated for demographic and preoperative hearing characteristics. Repeated-measures analysis of variance was used to compare preand postoperative performance on the AzBio in quiet and noise with qualifying group as a between-subjects factor. For a subset of recipients, preto postoperative changes on
Histone Tail

Backbone (N) NMR relaxation is one of the main sources of information on dynamics of disordered proteins. Yet, we do not know very well what drives N relaxation in such systems, i.e., how different forms of motion contribute to the measurable relaxation rates. To address this problem, we have investigated, both experimentally and via molecular dynamics simulations, the dynamics of a 26-residue peptide imitating the N-terminal portion of the histone protein H4. One part of the peptide was found to be fully flexible, whereas the other part features some transient structure (a hairpin stabilized by hydrogen bonds). The following motional modes proved relevant for N relaxation. 1) Sub-picosecond librations attenuate relaxation rates according to S 0.85–0.90. 2) Axial peptide-plane fluctuations along a stretch of the peptide chain contribute to relaxation-active dynamics on a fast timescale (from tens to hundreds of picoseconds). 3) 4/j backbone jumps contribute to relaxation-active dynamics on both fast (from tens to hundreds of picoseconds) and slow (from hundreds of picoseconds to a nanosecond) timescales. The major contribution is from polyproline II (PPII) 4 b transitions in the Ramachandran space; in the case of glycine residues, the major contribution is from PPII 4 (b) 4 rPPII transitions, in which rPPII is the mirror-image (right-handed) version of the PPII geometry, whereas b geometry plays the role of an intermediate state. 4) Reorientational motion of certain (sufficiently long-lived) elements of transient structure, i.e., rotational tumbling, contributes to slow relaxation-active dynamics on 1-ns timescale (however, it is difficult to isolate this contribution). In conclusion, recent advances in the area of force-field development have made it possible to obtain viable Molecular Dynamics models of protein disorder. After careful validation against the experimental relaxation data, these models can provide a valuable insight into mechanistic origins of spin relaxation in disordered peptides and proteins.
Subconjunctival dendrimer-drug therapy for the treatment of dry eyein rabbits with induced autoimmune dacryoadenitis

Purpose: To investigate the efficacy of a single subconjunctival injection of dendrimerdexamethasone to treat dry eye in a rabbit model of induced autoimmune dacryoadenitis (AID). Method: Dendrimer biodistribution after subconjuntival injection in AID animals was evaluated using Cy5-labelled dendrimer (D-Cy5) and confocal microscopy. Diseased animals were treated with free dexamethasone (Free-Dex), dendrimer-dexamethasone (DDex), or saline via a single subconjunctival injection. The efficacy was evaluated using various clinical evaluations, such as Schirmer’s test, tear breakup time (TBUT), and fluorescein and rose bengal staining. Histopathology was evaluated by H&E staining and immunostaining. Levels of inflammatory cytokines and aquaporin proteins in the LGs were determined by real-time PCR. Result: Subconjunctivally administered dendrimers selectively localized in the inflamed LGs, and were taken up by the infiltrated cells. At two weeks post-treatment, the D-Dex group showed improved clinical evaluations. No significant changes were observed in other groups. H&E staining demonstrated, less inflammatory cell infiltration and fewer atrophic acini in D-Dex group, compared to those treated with saline or Free-Dex. Immunohistochemistry demonstrated that the intensity of CD-18 (+) and RTLA (+) was weaker in LGs in the D-Dex group than in other treatment rabbits. Pro-inflammatory gene expression levels of MMP9, IL6, IL8, and TNFα were significantly decreased in the D-Dex group compared to the saline group. Conclusion: The dendrimer exhibits pathology-dependent biodistribution in the inflamed LGs. Subconjunctivally administered D-Dex suppressed LG inflammation, leading to partial recovery of # Corresponding authors: Samuel C. Yiu, M.D., Ph.D, and Rangaramanujam M. Kannan, Ph.D., 400 N. Broadway, Baltimore, MD, 21231, United States, Tel: 1-443-287-4890; syiu2@jhmi.edu, krangar1@jhmi.edu. Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. The authors declare no conflict of interest and financial or business interest related to this study. HHS Public Access Author manuscript Ocul Surf. Author manuscript; available in PMC 2020 February 27. Published in final edited form as: Ocul Surf. 2018 October ; 16(4): 415–423. doi:10.1016/j.jtos. 2018.05. 004. A uhor M anscript
A-to-I RNA editing of Alu dsRNAs is markedly decreased in MS; unedited Alu dsRNAs but not edited Alu dsRNAs are potent activators of pro-inflammatory transcriptional responses

Sensors that detect double stranded RNA stimulate IFN-responses as a defense against viral infection. IFN-responses are also well documented in a variety of human autoimmune diseases including relapsing remitting multiple sclerosis in which increased IFN-responses result from increased levels of double-stranded endogenous Alu RNAs. Mechanisms underlying increases in double-stranded Alu RNAs in multiple sclerosis are obscure. We find widespread loss of A-to-I editing of Alu RNAs in multiple sclerosis. Unedited Alu RNAs are potent activators of both IFNand NF-κB responses via the dsRNA sensors, RIG-I and TLR3. Minor editing of highly active Alu elements abrogates ability to activate both transcriptional responses. Thus, A-to-I editing may also represent an important defense against autoimmune diseases, such as multiple sclerosis.
Lung cancer screening eligibility, risk perceptions and clinician delivery of tobacco cessation in schizophrenia

Objective: Individuals with schizophrenia experience increased lung cancer mortality and decreased access to cancer screening and tobacco cessation. Screening promotes early lung cancer detection and can decrease mortality among high-risk populations, yet this screening remains underutilized. To promote screening among individuals with schizophrenia we need to investigate the proportion who meet screening criteria, and examine smoking behaviors, cancer risk perceptions, receipt of primary care and tobacco cessation interventions. Methods: A cross-sectional survey and medical record review of 112 adults with schizophrenia treated with clozapine in a CMHC. Results: Among older participants (aged 55–77) with schizophrenia, 34% met criteria for screening based on smoking history (heavy current and former smokers); over half believed they had a low risk of developing lung cancer. 88% of all participants visited their PCP in the past year; PCPs represented 35 different practices. Among all current smokers, only 1 in 3 reported that their PCPs and/or psychiatrists assisted with medications for tobacco cessation. Corresponding Author: Kelly E. Irwin, MD, MPH, Massachusetts General Hospital Cancer Center, Center for Psychiatric Oncology and Behavioral Sciences, 55 Fruit St, Boston, Massachusetts 02114; Fax: 617-643-9913; Kirwin1@partners.org. HHS Public Access Author manuscript Psychiatr Serv. Author manuscript; available in PMC 2021 August 25. Published in final edited form as: Psychiatr Serv. 2019 October 01; 70(10): 927–934. doi:10.1176/appi.ps. 201900044. A uhor M anscript
Enhancing Fetal ECG Using Gaussian Process

This paper investigates the problem of the extraction of fetal ECG from the noisy abdominal channel. The method which is presented here is a multi-channel one which uses two data channels: one is the abdominal channel and the other is the reference channel. The reference channel, which is recorded from the chest of the mother, can well define the covariance function to model the maternal ECG contribution in the abdominal channel. The maternal ECG can then be extracted using this model which proposes a non-linear extraction. The reference signal is also proposed to be replaced with a 1-bit thoracic signal which can be cheaply recorded and has less time complexity to be processed.
Orosomucoid Like 3 (ORMDL3) Supports Rhinovirus Replication in Human Epithelial Cells.

Polymorphism at the 17q21 gene locus and wheezing responses to rhinovirus (RV) early in childhood conspire to increase the risk of developing asthma. However, the mechanisms mediating this gene-environment interaction remain unclear. In this study, we investigated the impact of one of the 17q21 encoded genes, ORMDL3 on RV replication in human epithelial cells. ORMDL3 knockdown inhibited RV-A16 replication in HeLa, BEAS-2B, A549, NCI-H358 epithelial cell lines, and primary nasal and bronchial epithelial cells. Inhibition varied by RV species, as both minor and major group RV-A subtypes, RV-B52 and RV-C2 were inhibited, but not RV-C15 or RV-C41. ORMDL3 siRNA did not affect expression of the major group RV-A receptor ICAM-1 or initial internalization of RV-A16. The two major outcomes of ORMDL3 activity, serine palmitoyl-CoA transferase (SPT) inhibition and endoplasmic reticulum (ER) stress induction were further examined: silencing ORMDL3 decreased RV-induced ER stress and IFN- mRNA expression. However, pharmacologic induction of ER stress and concomitant increased IFN- inhibited RV-A16 replication. Conversely, blockade of ER stress with tauroursodeoxycholic acid augmented replication, pointing to an alternative mechanism for the effect of ORMDL3 knockdown on RV replication. In comparison, the SPT inhibitor myriocin increased RV-A16 but not RV-C15 replication, and negated the inhibitory effect of ORMDL3 knockdown. Further, lipidomics analysis revealed opposing regulation of specific sphingolipid species (downstream of SPT) by myriocin and ORMDL3 siRNA, correlating with the effect of these treatments on RV replication. Together this data revealed a requirement for ORMDL3 in supporting RV replication in epithelial cells via SPT inhibition.
Riluzole augmentation in treatment-refractory obsessive- compulsive disorder: a pilot placebo-controlled trial

Objective—Obsessive-compulsive disorder (OCD) affects approximately 2.5% of the population and is associated with significant morbidity. Many patients receive little benefit from the best available treatments, and even those who do respond often suffer from significant residual symptoms. Convergent evidence suggests that abnormalities in glutamate homeostasis and neurotransmission may contribute to OCD and that glutamate-modulating medications may be of benefit in patients whose symptoms are refractory to standard interventions. Small open-label trials of augmentation of SSRI pharmacotherapy with the glutamate modulator riluzole have suggested benefit in adults with refractory symptoms. We report a pilot placebo-control trial of riluzole augmentation of ongoing SRI treatment in SRI-refractory patients. Method—Outpatients (n = 27) and inpatients (n = 12) with DSM-IV OCD on stable SSRI pharmacotherapy were randomized between 11/2006 and 12/2012 to receive riluzole 50 mg bid or placebo and followed for 12 weeks, after a 2-week placebo lead-in. Results—Riluzole was well tolerated; one patient experienced moderate nausea, but none discontinued treatment due to side effects. While there was nominally greater Y-BOCS improvement in the riluzole group (our primary outcome), it did not reach significance in a mixed model random effects analysis, in the overall analysis or in the outpatient subsample. In the Correspondence: 34 Park Street, W315, New Haven, CT 06519, Christopher.pittenger@yale.edu. Previous presentation: none ClinicalTrials.gov identifier: NCT00523718 Disclosure Statement VC is now a full-time employee of Bristol-Myers Squibb, Inc. He is a paid consultant to New Haven Forensics Consultants, LLC and the Center for Research and Development, Ltd., and a stock shareholder for Bristol Myers Squibb. GS is a paid consultant to AstraZeneca, Avanier Pharmaceuticals, Bristol-Myers Squibb, Eli Lilly & Co., Hoffman La Roche, Merck, Naurex, Noven Pharmaceuticals, and Takeda, and has received research support from AstraZeneca, Bristol-Myers Squibb, Eli Lilly & Co., Johnson & Johnson, Hoffman La Roche, Merck & Co., Naurex, and Servier. VC and GS are originators on the patent Glutamate Agents in the Treatment of Mental Disorders (USPTO No 11/399188; 5 April 2006) and have a financial interest in Biohaven Pharmaceutical Holding Company, a privately held company that has licensed this intellectual property. The other authors have no real or apparent conflict of interest to declare. HHS Public Access Author manuscript J Clin Psychiatry. Author manuscript; available in PMC 2016 August 01. Published in final edited form as: J Clin Psychiatry. 2015 August ; 76(8): 1075–1084. doi:10.4088/JCP.14m09123. A uhor M anscript
Circulating DNA in Systemic Lupus Erythematosus

Immunoprecipitable double-stranded (dsDNA) was previously shown to persist in the circulation ofa clinically recognizable subgroup of patients with systemic lupus erythematosus (SLE). Plasma from 10 such patients was subjected to a DNA isolation procedure that used a combination ofproteolysis, phenol extraction, and hydroxylapatite adsorption and elution in the presence of urea. The isolated dsDNA was radiolabeled by nick translation and then characterized by isopyknic ultracentrifugation in CsCl under both neutral and alkaline conditions, as well as after digestion with S,-endonuclease. These experiments demonstrated essential identity in nucleotide base composition between the plasma-derived DNA and human genomic DNA. The presence of specific human base sequences in the plasma DNA was demonstrated by finding that authentic human genomic DNA accelerated the renaturation of plasma DNA when compared with the effect of nonhuman, control DNA. The proportion of such sequences in plasma DNA was estimated by attempting to renature the plasma DNA in the presence ofhuman DNA under conditions shown to result in complete renaturation of human DNA in model experiments. In this way, a minimum of 47% of plasma DNA base sequences could be shown also to be present in human genomic DNA. However, an average of 1020% ofthe plasma-derived DNA failed to renature under these conditions, a result that was further confirmed by comparing the renaturation ofthe tritium-labeled plasma DNA specimens, in double-label experiments, with inThis work was presented in preliminary form at the 43rd Annual Meeting ofThe American Rheumatism Association, May 30, 1979 and published in abstract form (1979. Arthritis Rheum. 22:664). Received for publication 30 August 1982 and in revisedform 7 November 1983. ternal controls consisting of '4C-labeled authentic human DNA. Attempts to drive the reaction to completion with human DNA led to a similar conclusion. The relative nonrenaturability of this fraction ofplasma DNA did not appear to be attributable to extensive chain breakage, although adequate analysis of this DNA subfraction was limited by reagent availability. It was therefore concluded that, in this group ofSLE patients, persistently circulating DNA consisted largely of base sequences also found in human genomic DNA. The additional presence in plasma of a DNA subfraction that differed in its renaturation behavior from human genomic DNA was recognized, although its significance could not be established with certainty.
FP 16.3: A 3.5mW 2.5GHz Diversity Receiver and a 1.2mW 3.6GHz VCO in Silicon-On-Anything

A fully-integrated voltage controlled oscillator WCO) and RF diversity receiver are fabricated in a bipolar IC technology called silicon on anything. With this silicon based technology it is possible to fabricate low-power transistors, as well as integrated inductors that have a quality factor >25 at 1GHz. The inductors in the VCO exhibit a maximum quality factor of 29 at 4GHz, with a self-resonance frequency of 10.5GHz. In standard silicon based processes it is difficult to implement fully integrated VCOs because of the limitation in performance of the resonant circuit components, especially the inductors. The main drawbacks for the integration of inductors on silicon are well known; due to the losses associated with the silicon substrate it is very difficult
The Rayleigh prolongation factor at small bubble to wall stand-off distances

Abstract The Rayleigh collapse time is the time it would take to shrink an empty spherical bubble in an infinite liquid domain to zero size, which is a function of ambient pressure and initial bubble radius. If a solid boundary is located in the vicinity of the shrinking or collapsing bubble, then liquid flow is hindered, such that the collapse time is prolonged. This can be quantified with the Rayleigh prolongation factor $k$. Here, we provide $k$ for intermediate to smallest bubble to wall stand-off distances. It is measured with single laser-induced cavitation bubbles in water close to a solid boundary. Maximum bubble radii are determined from microscopic high-speed imaging at one million frames per second. Collapse times are measured acoustically via the acoustic transients emitted during bubble seeding and collapse. The experimental findings are compared, with good agreement, to numerical simulations based on a volume of fluid method. As a result, a polynomial fit of $k$ versus stand-off distance is given for the near-wall bubble collapse in water. Then the influence of the viscosity on $k$ is studied numerically in the near-wall regime.
Combined three-dimensional flow field measurements and motion tracking of freely moving spheres in a turbulent boundary layer

Abstract A combination of time-resolved tomographic particle image velocimetry, refractive index matching technique and machine vision algorithms was used to measure the translational and rotational motion of freely moving, nearly neutrally buoyant spheres in a fully developed turbulent boundary layer (TBL). Located in the buffer and logarithmic layers, the hydrogel spheres ($\sim$70 inner wall units in diameter) were refractive index matched with the water and tagged by ‘spokes’. Besides translational motion, the spheres exhibited significant rotation. The spheres were surrounded by typical coherent structures observed in TBLs, among them hairpin packets and transverse and longitudinal vortices that induced ejections and sweeps. While the majority of instantaneous sphere Reynolds numbers did not exceed 100, and vortex shedding was not observed, the results showed that the spheres may affect the evolution of hairpin packets in TBLs due to their finite size. The instantaneous rotation-, wall- and shear-induced lift forces, as well as the drag forces, acting on the spheres were estimated using available correlations for the lift and drag coefficients. Results hinted at negative shear-induced lift due to flow separation at a smaller critical Reynolds number than incorporated in the correlations that do not include the effect of ambient turbulence. The results indicated further that the drag force aided by the rotation-induced lift force was instrumental in keeping one of the spheres aloft. For the wall-ward moving spheres, lift forces opposed sphere motion. As a result, the spheres approached the wall with velocities lower than their quiescent settling velocity.
The Genetic Diversity of Triploid Celtis pumila and its Diploid Relatives C. occidentalis and C. laevigata (Cannabaceae)

Abstract The genus Celtis in eastern North America shows puzzling patterns of variation. While three species are generally recognized, many authors have suggested hybridization may be blurring the boundaries among them. Suspected hybridization between C. occidentalis and C. pumila has hampered conservation planning for the latter, which is a Threatened species in Canada. Using microsatellite markers and flow cytometry, we assessed the relationship between genetic diversity, ploidy, and morphology in this group. We confirmed the presence of two diploid species, C. occidentalis and C. laevigata, and that they do hybridize where they co-occur in southern Missouri and Illinois. We found two triploid genetic groups. These groups had distinct geographic ranges, but were morphologically very similar, corresponding to C. pumila. Furthermore, the triploid groups were characterized by a small number of heterozygous multi-locus genotypes. A single genotype dominated populations across Ontario, Michigan, Ohio, and Pennsylvania, indicating apomictic reproduction is common in these groups. While the triploid clusters were distinct from each other, they did have strong associations with sympatric diploid species, and also with the western triploid species C. reticulata. However, we found no evidence of hybridization or gene flow between diploid C. occidentalis and triploid C. pumila. This removes hybridization and introgression as a complicating issue for conservation management. The intermediate forms observed are a demonstration of remarkable phenotypic plasticity, with the same triploid genotype variously presenting as dwarf shrubs in xeric, exposed sites, and subcanopy trees in mesic forests.