Miracle-dz/UniFAR-FTUs huggingface dataset:
Deep Synthetic Noise Generation for RGB-D Data Augmentation

Deep Synthetic Noise Generation for RGB-D Data Augmentation Patrick Douglas Hammond Department of Computer Science, BYU Master of Science Considerable effort has been devoted to finding reliable methods of correcting noisy RGB-D images captured with unreliable depth-sensing technologies. Supervised neural networks have been shown to be capable of RGB-D image correction, but require copious amounts of carefully-corrected ground-truth data to train effectively. Data collection is laborious and time-intensive, especially for large datasets, and generation of ground-truth training data tends to be subject to human error. It might be possible to train an effective method on a relatively smaller dataset using synthetically damaged depth-data as input to the network, but this requires some understanding of the latent noise distribution of the respective camera. It is possible to augment datasets to a certain degree using naive noise generation, such as random dropout or Gaussian noise, but these tend to generalize poorly to real data. A superior method would imitate real camera noise to damage input depth images realistically so that the network is able to learn to correct the appropriate depth-noise distribution. We propose a novel noise-generating CNN capable of producing realistic noise customized to a variety of different depth-noise distributions. In order to demonstrate the effects of synthetic augmentation, we also contribute a large novel RGB-D dataset captured with the Intel RealSense D415 and D435 depth cameras. This dataset pairs many examples of noisy depth images with automatically completed RGB-D images, which we use as proxy for ground-truth data. We further provide an automated depth-denoising pipeline which may be used to produce proxy ground-truth data for novel datasets. We train a modified sparseto-dense depth-completion network on splits of varying size from our dataset to determine reasonable baselines for improvement. We determine through these tests that adding more noisy depth frames to each RGB-D image in the training set has a nearly identical impact on depth-completion training as gathering more ground-truth data. We leverage these findings to produce additional synthetic noisy depth images for each RGB-D image in our baseline training sets using our noise-generating CNN. Through use of our augmentation method, it is possible to achieve greater than 50% error reduction on supervised depth-completion training, even for small datasets.
Corporate Environmentalism in Malaysia : Exploring the Media ’ s Pressure on Businesses

A business pertaining to the environment has three basic issues. First, in order to produce products it takes too much from the environment and does so in a harmful way; second, the product it makes require excessive amounts of energy, toxins, and pollutants; and finally, the method of manufacture and the products themselves produce extraordinary waste and cause harm to present and future generations of all species including humans. The only way out of the unsustainability of business practices is through re-engineering business activities inline with the principle of ecology. Hence, it is crucial for businesses to take a fresh look at the damages that they have done to the natural environment and their far-reaching impacts to human survival. Businesses will not do so, unless there is an increasing pressure from the stakeholders including the public and the government alike to improve their corporate environmentalism. In order to exert an influence on the industry, the media needs to be more proactive in reporting and investigating environmental issues pertaining to business activities. This paper tries to unfold the efficacy and the role of the media in Malaysia as a pressure group towards corporate environmentalism in the Malaysian businesses. This report involves a qualitative study of four major newspaper agencies in the country – two vernacular daily newspapers, one daily English newspaper and a bi-monthly newspaper. Four senior reporters involved in the face-to-face interviews. The conversations were audio-taped and then were analysed using the NVivo Version 7 software programme. This report highlights amongst other things the media challenges pertaining to environmental issues, and the media approaches to exert pressure on businesses. It also investigates the efficacy of the media to exert influence on the Malaysian industries to be more environmentally responsible and forward ways to improve media pressure against unscrupulous business activities.
Unraveling the complexity of amyloid polymorphism using gold nanoparticles and cryo-EM

Significance The ability of proteins to self-assemble into different types of fibrils with distinct morphologies has been linked to the pathological and clinical heterogeneity of amyloid diseases such as Alzheimer’s disease and Parkinson’s disease. Here, we describe nanoparticles (NPs) that efficiently label amyloid fibrils produced in vitro or isolated from postmortem tissues, under hydrating conditions and in such a way as to unmask their polymorphism and morphological features. Using these NPs, we show that pathological aggregates exhibit exceptional morphological homogeneity compared with amyloid fibrils produced in vitro, consistent with the emerging view that the physiologic milieu is a key determinant of amyloid fibril strains. These advances pave the way for elucidating the structural basis of amyloid strains and toxicity. Increasing evidence suggests that amyloid polymorphism gives rise to different strains of amyloids with distinct toxicities and pathology-spreading properties. Validating this hypothesis is challenging due to a lack of tools and methods that allow for the direct characterization of amyloid polymorphism in hydrated and complex biological samples. Here, we report on the development of 11-mercapto-1-undecanesulfonate-coated gold nanoparticles (NPs) that efficiently label the edges of synthetic, recombinant, and native amyloid fibrils derived from different amyloidogenic proteins. We demonstrate that these NPs represent powerful tools for assessing amyloid morphological polymorphism, using cryogenic transmission electron microscopy (cryo-EM). The NPs allowed for the visualization of morphological features that are not directly observed using standard imaging techniques, including transmission electron microscopy with use of the negative stain or cryo-EM imaging. The use of these NPs to label native paired helical filaments (PHFs) from the postmortem brain of a patient with Alzheimer’s disease, as well as amyloid fibrils extracted from the heart tissue of a patient suffering from systemic amyloid light-chain amyloidosis, revealed a high degree of homogeneity across the fibrils derived from human tissue in comparison with fibrils aggregated in vitro. These findings are consistent with, and strongly support, the emerging view that the physiologic milieu is a key determinant of amyloid fibril strains. Together, these advances should not only facilitate the profiling and characterization of amyloids for structural studies by cryo-EM, but also pave the way to elucidate the structural basis of amyloid strains and toxicity, and possibly the correlation between the pathological and clinical heterogeneity of amyloid diseases.
Ice injected into the tropopause by deep convection – Part 2: Over the Maritime Continent

Abstract. The amount of ice injected into the tropical tropopause layer has a strong radiative impact on climate. A companion paper (Part 1) used the amplitude of the diurnal cycle of ice water content (IWC) as an estimate of ice injection by deep convection, showed that the Maritime Continent (MariCont) region provides the largest injection to the upper troposphere (UT; 146 hPa) and to the tropopause level (TL; 100 hPa). This study focuses on the MariCont region and extends that approach to assess the processes, the areas and the diurnal amount and duration of ice injected over islands and over seas during the austral convective season. The model presented in the companion paper is again used to estimate the amount of ice injected (ΔIWC) by combining ice water content (IWC) measured twice a day by the Microwave Limb Sounder (MLS; Version 4.2) from 2004 to 2017 and precipitation (Prec) measurements from the Tropical Rainfall Measurement Mission (TRMM; Version 007) binned at high temporal resolution (1 h). The horizontal distribution of ΔIWC estimated from Prec (ΔIWCPrec) is presented at 2∘×2∘ horizontal resolution over the MariCont. ΔIWC is also evaluated by using the number of lightning events (Flash) from the TRMM-LIS instrument (Lightning Imaging Sensor, from 2004 to 2015 at 1 h and 0.25∘ × 0.25∘ resolution). ΔIWCPrec and ΔIWC estimated from Flash (ΔIWCFlash) are compared to ΔIWC estimated from the ERA5 reanalyses (ΔIWCERA5) with the vertical resolution degraded to that of MLS observations (ΔIWCERA5). Our study shows that the diurnal cycles of Prec and Flash are consistent with each other in phase over land but different over offshore and coastal areas of the MariCont. The observational ΔIWC range between ΔIWCPrec and ΔIWCFlash, interpreted as the uncertainty of our model in estimating the amount of ice injected, is smaller over land (where ΔIWCPrec and ΔIWCFlash agree to within 22 %) than over ocean (where differences are up to 71 %) in the UT and TL. The impact of the MLS vertical resolution on the estimation of ΔIWC is greater in the TL (difference between ΔIWCERA5 and 〈ΔIWCERA5〉 of 32 % to 139 %, depending on the study zone) than in the UT (difference of 9 % to 33 %). Considering all the methods, in the UT, estimates of ΔIWC span 4.2 to 10.0 mg m−3 over land and 0.4 to 4.4 mg m−3 over sea, and in the TL estimates of ΔIWC span 0.5 to 3.9 mg m−3 over land and 0.1 to 0.7 mg m−3 over sea. Finally, based on IWC from MLS and ERA5, Prec and Flash, this study highlights that (1) at both levels, ΔIWC estimated over land can be more than twice that estimated over sea and (2) small islands with high topography present the largest ΔIWC (e.g., island of Java).
A systematic analysis of human transmembrane E3-RING proteins

The reversible covalent conjugation of the small highly conserved ubiquitin protein modifier to selective substrates plays central roles in countless proteolytic and non-proteolytic cellular functions. Substrate protein ubiquitination is co-ordinated by the sequential activity of three distinct classes of proteins: (i) E1-activating enzymes, (ii) E2-conjugating enzymes, and (iii) E3-protein ligases. Really Interesting New Gene (RING) proteins represent the largest family of E3-proteins comprising over half of predicted human E3-ligases. As such, E3-RING proteins play pivotal roles in controlling both specificity and functionality within the ubiquitin system. E3-RING proteins function as catalytically inactive molecular scaffolds that position Ub~E2 and substrate proteins in close proximity for ubiquitination to occur. Within the active ligase complex, E3-RING proteins and E2 conjugating enzymes are believed to select protein substrate(s) and the form of conjugated ubiquitin upon them, respectively. Whilst E3-RING/E2 partners have been investigated in recent HTP screen approaches, a key area of data paucity exists for integral membrane E3-RING (TM-E3-RING) proteins. As such, high throughput yeast-two-hybrid assays were performed for the entire complement of TM-E3-RING proteins and E2-conjugating enzymes. A broad subset of TM-E3-RING/E2 positive and negative Y2H interactions was re-tested in secondary luciferase protein complementation assays (PCAs), which increased confidence in Y2H-derived interactions and extended network coverage. Data from these studies was collated with previously published binary TM-E3-RING/E2 interaction data to provide a high-confidence TM-E3-RING/E2 network consisting of 312 unique binary interactions. In vitro auto-ubiquitination assays were employed to assign functional activity to TM-E3-RING/E2 protein pairs, revealing high verification rates for both positive and negative Y2H or PCA binary interaction data. Furthermore, novel trends in the generation of different forms of ubiquitin modifications were identified between selective TM-E3-RING/E2 pairs. Finally, Y2H screens were also performed to identify TM-E3-RING dimerization events, which represent an emerging theme in ubiquitin system regulation. In total 71 TM-E3-RING/TM-E3-RING interactions were reported demonstrating high incidence of these binding events. Novel data was combined with known interactions to generate a TM-E3-RING network containing >500 binary interactions, encompassing both components of the core ubiquitin cascade and non-ubiquitome proteins. This TM-E3-RINGcentric network provides a valuable tool for the investigation of specificity and regulation of TM-E3-RING proteins and specific ubiquitin cascades.
Efficacy and Acceptability Comparisons of Cognitive Behavior Therapy, Drugs, and Their Combination for Panic Disorder in Adults: a Network Meta-analysis

To compare 22 oral drugs, cognitive behavior therapy (CBT), and their combination treatments for the acute treatment of adults with panic disorder in terms of remission rate and acceptability.Systematic review and network meta-analysisPubMed, Web of Science, Cochrane Central Register of Controlled Trials, and Embase databases from their inception up to May 26, 2019.Randomized controlled clinical trials (RCTs) of any oral drugs, CBT, CBT combined with any drug, or placebo in the acute treatment of adults with panic disorder diagnosed according to standard operationalized criteria. The primary outcomes were efficacy (remission rate) and acceptability (treatment discontinuations due to any cause). We identified 6585 reports that included 68 full-text RCTs involving 11101 patients. In terms of efficacy, 13 (68%) of 19 interventions were associated with higher remission rates than those of for placebo, with ORs ranging from 2.1 (95% credible interval [CrI] = 1.1 to 4.0) for sertraline to 13 (CrI = 4.5 to 44) for CBT combined with any drug. Regarding acceptability, alprazolam, imipramine, and etizolam were associated with lower dropout rates, with ORs ranging from 0.23 (CrI = 0.15 to 0.33) for alprazolam to 0.076 (CrI = 0.0021 to 0.77) for etizolam. Most of the differences between the other interventions were unclear. In head-to-head analyses, CBT combined with any drug was more effective than the other interventions, but it was no associated with an improvement in acceptability (OR = 0.12 to 0.219). CBT combined with any drug was more effective than the other interventions analyzed in this study. CBT alone did not differ significantly from other drugs alone. We found that most drugs are effective against panic disorder, but they exhibit different acceptability and tolerability profiles.Some randomized controlled trials indicated that combined therapy are more effective than drug alone or cognitive behavior therapy alone. Nevertheless, drug monotherapy, cognitive behavior therapy, and combination therapy had never been compared in a comprehensive network meta-analysis. With this evidence gap remaining, the availability of reliable evidence of the relative merits of multiple interventions is essential to ensuring that clinicians choose the best option for each individual patient.This network meta-analysis is the first to evaluate the relative merits of cognitive behavior therapy, cognitive behavior therapy combined with any drug, and 22 oral drugs in the field of panic disorder. The results showed a significant higher remission rates for cognitive behavior therapy combined with any drug than those of the other interventions. Cognitive behavior therapy alone was superior to placebo but did not differ significantly from other active drugs. Additionally, paroxetine, venlafaxine, fluoxetine, sertraline, and clonazepam are more recommendable than the other drugs based on their remission rates, scores on panic-symptoms scales, and acceptability.
Immunopeptidomic Analysis Reveals That Deamidated HLA-bound Peptides Arise Predominantly from Deglycosylated Precursors

A predominance of HLA-I bound Asn deamidated peptides have been found to be generated through the ERAD pathway by quantitative MS-based proteomics. The Asn deamidated peptides in the peptidome of HLA-I, but not in HLA-II peptidomes or shotgun proteolysis, bear a concensus the N-glycosylation motif. The results reported provide new insights into the generation deamidated peptide antigens and provides a strategy for predicting deamidated T cell epitopes derived from glycoproteins. Graphical Abstract Highlights A predominance of HLA-I bound deamidated peptides are generated through ERAD pathway. Deamidation of peptides with N-glycosylation motifs not in peptidome of HLA-II or proteolysis. Many precursors of ERAD generated deamidated peptides are glycoproteins. The presentation of post-translationally modified (PTM) peptides by cell surface HLA molecules has the potential to increase the diversity of targets for surveilling T cells. Although immunopeptidomics studies routinely identify thousands of HLA-bound peptides from cell lines and tissue samples, in-depth analyses of the proportion and nature of peptides bearing one or more PTMs remains challenging. Here we have analyzed HLA-bound peptides from a variety of allotypes and assessed the distribution of mass spectrometry-detected PTMs, finding deamidation of asparagine or glutamine to be highly prevalent. Given that asparagine deamidation may arise either spontaneously or through enzymatic reaction, we assessed allele-specific and global motifs flanking the modified residues. Notably, we found that the N-linked glycosylation motif NX(S/T) was highly abundant across asparagine-deamidated HLA-bound peptides. This finding, demonstrated previously for a handful of deamidated T cell epitopes, implicates a more global role for the retrograde transport of nascently N-glycosylated polypeptides from the ER and their subsequent degradation within the cytosol to form HLA-ligand precursors. Chemical inhibition of Peptide:N-Glycanase (PNGase), the endoglycosidase responsible for the removal of glycans from misfolded and retrotranslocated glycoproteins, greatly reduced presentation of this subset of deamidated HLA-bound peptides. Importantly, there was no impact of PNGase inhibition on peptides not containing a consensus NX(S/T) motif. This indicates that a large proportion of HLA-I bound asparagine deamidated peptides are generated from formerly glycosylated proteins that have undergone deglycosylation via the ER-associated protein degradation (ERAD) pathway. The information herein will help train deamidation prediction models for HLA-peptide repertoires and aid in the design of novel T cell therapeutic targets derived from glycoprotein antigens.
Harmonic Functions and Riesz-Newtonian Potentials on 'Noisy' or Random Domains:Stochastic Extensions of Some Classical Theorems and Estimates

Let $\psi:{\mathcal{D}}\rightarrow{\mathrm{R}}$ be a harmonic function such that $\Delta \psi(x)=0$ for all $x\in\mathcal{D}\subset{\mathrm{R}}^{n}$. There are then many well-established classical results:the Dirichlet problem and Poisson formula, Harnack inequality, the Maximum Principle, the Mean Value Property etc. Here, a 'noisy' or random domain is one for which there also exists a classical scalar Gaussian random field (GRF) ${\mathrm{I\! F}(x)}$ defined for all $x\in{\mathcal{D}}$ or $x\in\partial {\mathcal{D}}$ with respect to a probability space $[\Omega,\mathscr{F},{\mathsf{P}}]$. The GRF has vanishing mean value $\mathsf{E}[\! [\mathrm{I\! F}(x)]\! ] = 0$ and a regulated covariance ${\mathsf{E}}[\! [{\mathrm{I\! F}(x)} \otimes {\mathrm{I\! F}(y)}]\! ] = \alpha K(x,y;\xi)$ for all $(x,y)\in{\mathcal{D}}$, with correlation length $\xi$ and ${\mathsf{E}}[\! [{\mathrm{I\! F}(x)} \otimes {\mathrm{I\! F}}(x)]\! ] = \alpha<\infty$. The gradient $\nabla{\mathrm{I\! F}(x)}$ and integrals $\int_{\mathcal{D}}{\mathrm{I\! F}}(x) d\mu(x)$ also exist on ${\mathcal{D}}$. Harmonic functions and potentials can become randomly perturbed GRFs of the form $\overline{\psi(x)}=\psi(x)+\lambda{\mathrm{I\! F}}(x)$. Physically, this scenario arises from noisy sources or random fluctuations in mass/charge density, noisy or random boundary/surface data; and introducing turbulence/randomness into smooth fluid flows, steady state diffusions or heat flow. This leads to stochastic modifications of classical theorems for randomly perturbed harmonic functions and Riesz and Newtonian potentials; and to stability estimates for the growth and decay of their volatility and moments.
Computer Simulation of the Crystal Growth and Dissolution of Natural Gas Hydrates a

Natural gas hydrates are icelike solids in which the water molecules or “hosts” form a rigid cagelike structure enclosing voids in which light hydrocarbons or other small molecules, known as “guests,” are contained. These solids belong to a class of crystals known as clufhrutes. ’ Gas hydrates are nonstoichiometric crystals. The number of water molecules per gas molecule, the hydration number, depends on the conditions in which the crystal was formed and the type of gas molecule in the hydrate. Usually, hydration numbers range from 5.75 to 19, as quoted by Sloan.2 There arc two types of well-characterized natural gas hydrate denoted as hydrate type I and hydrate type 11. The main factor deciding the type of gas hydrate formed is the diameter of the guest molecule. Propane forms the type I1 hydrate (with the larger cavity), while methane forms the type I (in which the cavity is smaller). Hydrates are important industrially since they form spontaneously in natural gas lines, even at temperatures above O’C, forming plugs that can reduce and stop the flow of gas. These plugs are difficult to remove. To avoid their formation, inhibitors like methanol are injected in the lines, increasing the cost of operation. Hence there is considerable economical incentive to try to understand how hydrates form and how to inhibit their growth. To do this, one needs to understand both the thermodynamics and the kinetics of hydrate growth and dissolution. There are extensive data on hydrate thermodynamic properties, and the phase diagram is well known. However, there are much fewer kinetic data available. Some hydrates exhibit an induction period, i.e., even when conditions are favorable for their formation, some time elapses before the hydrate forms. In contrast, if the hydrate is melted and the conditions reestablished for hydrate formation, there is essentially no induction period and the hydrate will form almost immediately.2 This hysteresis effect suggests that the water remembers its past hydrate history, presumably through the existence of subcritical sized hydrate crystal nuclei in the fluid. A hypothesis has been proposed for the existence of the induction period and the memory but this has yet to be proved.