Miracle-dz/UniFAR-FTUs huggingface dataset:
Co-Operative Pain Education and Self-management (COPES) Expanding Treatment for Real-World Access (ExTRA): Pragmatic Trial Protocol

Abstract Background Given access barriers to cognitive behavioral therapy for chronic pain (CBT-CP), this pragmatic superiority trial will determine whether a remotely delivered CBT-CP intervention that addresses these barriers outperforms in-person and other synchronous forms of CBT-CP for veterans with musculoskeletal pain. Design This pragmatic trial compares an asynchronous form of CBT-CP that uses interactive voice response (IVR) to allow patients to participate from their home (IVR CBT-CP) with synchronous CBT-CP delivered by a Department of Veterans Affairs (VA) clinician. Veterans (n=764; 50% male) with chronic musculoskeletal pain throughout nine VA medical centers will participate. The primary outcome is pain interference after treatment (4 months). Secondary outcomes, including pain intensity, depression symptom severity, sleep, self-efficacy, and global impression of change, are also measured after treatment. Where possible, outcomes are collected via electronic health record extraction, with remaining measures collected via IVR calls to maintain blinding. Quantitative and qualitative process evaluation metrics will be collected to evaluate factors related to implementation. A budget impact analysis will be performed. Summary This pragmatic trial compares the outcomes, cost, and implementation of two forms of CBT-CP as delivered in the real-world setting. Findings from the trial can be used to guide future policy and implementation efforts related to these interventions and their use in the health system. If one of the interventions emerges as superior, resources can be directed to this modality. If both treatments are effective, patient preferences and health care system factors will take precedence when making referrals. Implications of COVID-19 on treatment provision and trial outcomes are discussed.
Positioning of endoplasmic reticulum exit sites around the Golgi depends on BicaudalD2 and Rab6 activity

The endoplasmic reticulum (ER) is involved in biogenesis, modification and transport of secreted and membrane proteins. The ER membranes are spread throughout the cell cytoplasm as well as the export domains known as ER exit sites (ERES). A subpopulation of ERES is centrally localized proximal to the Golgi apparatus. The significance of this subpopulation on ER‐to‐Golgi transport remains unclear. Transport carriers (TCs) form at the ERES via a COPII‐dependent mechanism and move to Golgi on microtubule (MT) tracks. It was shown previously that ERES are distributed along MTs and undergo chaotic short‐range movements and sporadic rapid long‐range movements. The long‐range movements of ERES are impaired by either depolymerization of MTs or inhibition of dynein, suggesting that ERES central concentration is mediated by dynein activity. We demonstrate that the processive movements of ERES are frequently coupled with the TC departure. Using the Sar1a[H79G]‐induced ERES clustering at the perinuclear region, we identified BicaudalD2 (BicD2) and Rab6 as components of the dynein adaptor complex which drives perinuclear ERES concentration at the cell center. BicD2 partially colocalized with ERES and with TC. Peri‐Golgi ERES localization was significantly affected by inhibition of BicD2 function with its N‐terminal fragment or inhibition of Rab6 function with its dominant‐negative mutant. Golgi accumulation of secretory protein was delayed by inhibition of Rab6 and BicD2. Thus, we conclude that a BicD2/Rab6 dynein adaptor is required for maintenance of Golgi‐associated ERES. We propose that Golgi‐associated ERES may enhance the efficiency of the ER‐to‐Golgi transport.
Assessing Perceptual and Recommendation Mutation of Adversarially-Poisoned Visual Recommenders (short paper)

Visually-aware recommendation leverages visual signals of product images extracted through Deep Neural Networks to improve the recommendation performance. However, human-imperceptible adversarial noise can alter recommendation outcomes, e.g., pushing/nuking specific product categories. In this work, we provide 24 combinations of attack/defense strategies, and visual-based recommenders to 1) access performance alteration on recommendation and 2) empirically verify the effect on final users through offline-visual metrics. The results suggest defense is not protecting recommender models as expected, and shed light on the importance of human evaluation to identify visual attacks on recommendations. Source code, data, and experimental parameters are available at https://github.com/sisinflab/ Perceptual-Rec-Mutation-of-Adv-VRs.
Lysosomal Exocytosis: The Extracellular Role of an Intracellular Organelle

Lysosomes are acidic cell compartments containing a large set of hydrolytic enzymes. These lysosomal hydrolases degrade proteins, lipids, polysaccharides, and nucleic acids into their constituents. Materials to be degraded can reach lysosomes either from inside the cell, by autophagy, or from outside the cell, by different forms of endocytosis. In addition to their degradative functions, lysosomes are also able to extracellularly release their contents by lysosomal exocytosis. These organelles move from the perinuclear region along microtubules towards the proximity of the plasma membrane, then the lysosomal and plasma membrane fuse together via a Ca2+-dependent process. The fusion of the lysosomal membrane with plasma membrane plays an important role in plasma membrane repair, while the secretion of lysosomal content is relevant for the remodelling of extracellular matrix and release of functional substrates. Lysosomal storage disorders (LSDs) and age-related neurodegenerative disorders, such as Parkinson’s and Alzheimer’s diseases, share as a pathological feature the accumulation of undigested material within organelles of the endolysosomal system. Recent studies suggest that lysosomal exocytosis stimulation may have beneficial effects on the accumulation of these unprocessed aggregates, leading to their extracellular elimination. However, many details of the molecular machinery required for lysosomal exocytosis are only beginning to be unravelled. Here, we are going to review the current literature on molecular mechanisms and biological functions underlying lysosomal exocytosis, to shed light on the potential of lysosomal exocytosis stimulation as a therapeutic approach.
Side-chain polymers bearing azo-moieties for nonlinear optics

In this paper we present a series of side-chain polymers bearing original azo-moieties, namely: poly(methacrylate)s and poly(maleimide-styrene)s; designed for nonlinear optics (NLO). The different classes of azopolymers are discussed comparatively to one another from the point of view of: solubility, molar weights, glass transition temperatures & thermal stability, chromophore contents, and as well as from the point of view of their third-nonlinear response. The third-order nonlinear absorptive and refractive effect of the polymers containing different substituted azobenzene chromophores were investigated by the Z-scan technique. The effect of substituents on the azobenzene group and the composition of the polymer chain were investigated by UV-Vis spectroscopy.
ColorCells: a database of expression, classification and functions of lncRNAs in single cells

Although long noncoding RNAs (lncRNAs) have significant tissue specificity, their expression and variability in single cells remain unclear. Here, we developed ColorCells (http://rna.sysu.edu.cn/colorcells/), a resource for comparative analysis of lncRNAs expression, classification and functions in single-cell RNA-Seq data. ColorCells was applied to 167 913 publicly available scRNA-Seq datasets from six species, and identified a batch of cell-specific lncRNAs. These lncRNAs show surprising levels of expression variability between different cell clusters, and has the comparable cell classification ability as known marker genes. Cell-specific lncRNAs have been identified and further validated by in vitro experiments. We found that lncRNAs are typically co-expressed with the mRNAs in the same cell cluster, which can be used to uncover lncRNAs' functions. Our study emphasizes the need to uncover lncRNAs in all cell types and shows the power of lncRNAs as novel marker genes at single cell resolution.
Patterning of poly-para-xylylenes by reactive ion etching

Poly‐para‐xylylene family thin films deposited by vapor phase polymerization are pin hole free and are chemically inert to most acids, alkalies, and organic solvents. These properties make this material very attractive as a passivation agent on top of devices. This paper discusses the patterning of such films on planar structures by various masking techniques and the reactive ion etching (RIE) of the poly(monochloro‐p‐xylylene) in an oxygen‐containing plasma, including details like etch rates, control of edge profiles (vertical or tapered), and the process parameters to achieve patterns of 1.5 μm wide and below.
Discussion on Water Condensation in Membrane Pores during CO2 Absorption at High Temperature

Water condensation is a possible cause of membrane wetting in the operation of membrane contactors, especially under high-temperature conditions. In this study, water condensation in pores of polytetrafluoroethylene (PTFE) hollow fiber membranes was investigated during high-pressure CO2 absorption around 70 °C. It was found that the liquid accumulation rate in the treated gas knock-out drum was constant during continuous operation for 24 h when all experimental conditions were fixed, indicating a stable degree of membrane wetting. However, as the operating parameters were changed, the equilibrium vapor pressure of water within membrane pores could change, which may result in a condensation-conducive environment. Water condensation in membrane pores was detected and proven indirectly through the increase in liquid accumulation rate in the treated gas knock-out drum. The Hagen–Poiseuille equation was used to correlate the liquid accumulation rate with the degree of membrane wetting. The degree of membrane wetting increased significantly from 1.8 × 10−15 m3 to 3.9 × 10−15 m3 when the feed gas flow rate was reduced from 1.45 kg/h to 0.40 kg/h in this study due to water condensation in membrane pores. The results of this study provide insights into potential operational limitations of membrane contactor for CO2 absorption under high-temperature conditions.
Ab initio Hartree-Fock calculations of CaO, VO, MnO and NiO

Abstract Ab initio Hartree-Fock calculations are reported of the electronic structures of CaO, VO, MnO and NiO. They are found to be essentially ionic in nature with ground states that are insulating, and, in the case of VO, MnO and NiO, high-spin antiferromagnetic. Calculated lattice parameters, binding energies and bulk moduli compare in accuracy with those for closed-shell oxides such as Li2O, MgO and Al2O3. Differences are found in the upper part of the valence band between VO and MnO and NiO. In VO it is predominantly V(3d) in character, whereas in both MnO and NiO it is O(2p). In the case of NiO this seems to be in accord with oxygen K-edge data for LixNi1−xO.
Ephedrine attenuates cerebral ischemia/reperfusion injury in rats through NF-κB signaling pathway

The inflammation and immune responses are critical in ischemic stroke and contribute to aggravated brain damage. Ephedrine was reported to play an important role in the control of inflammatory responses. This study was to investigate the repairing effects and potential mechanisms of ephedrine on cerebral ischemic injury in a rat model of focal cerebral ischemia. The rat model of cerebral ischemia/reperfusion injury was established using the middle cerebral artery occlusion (MCAO) method and then rats were treated with ephedrine (5 and 10 mg/kg) for 7 days. The neurobehavioral progression was assessed using the neurological scoring method. The pathology of brain tissue was evaluated by hematoxylin and eosin (H&E) staining. The infarct volume was examined by triphenyltetrazolium chloride (TTC) staining. The apoptosis in ischemic brain tissues was detected by terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay. Inflammatory factors were detected by enzyme-linked immunosorbent assay (ELISA). Gene quantification and protein expression were detected by real-time PCR and western blot, respectively. Ephedrine treatment significantly alleviated the cerebral ischemia/reperfusion injury, evidenced by decreased neurological deficit score, infarct volume and water content. Ephedrine also decreased autophagy and apoptosis in brain tissues. Moreover, ephedrine treatment significantly reduced inflammatory responses, associating with decreasing the protein expression of p-NF-κB. These results demonstrated neuroprotective properties of ephedrine and highlighted it as a new potential anti-inflammatory agent against injury of cerebral ischemia/reperfusion.
Molecular Dynamics of Reversible and Irreversible Melting in Chain-Folded Crystals of Short Polyethylene-like Polymer

Crystallization and melting are fundamental thermal processes in crystalline polymers. In contrast to recent considerable efforts to simulate molecular processes of crystallization, investigations of melting in polymer crystals are still rare. The present report deals with molecular dynamics modeling of melting in chain-folded lamellae of short polyethylene-like molecules made of 100 methylene units. We observe two types of melting with distinct molecular mechanisms: equilibrium melting at the fold surface and nonequilibrium melting at the growth front. The former fold-surface melting is very quick and reversible, giving increasingly thinner lamellae at higher temperatures. Large molecular mobility in the crystal is suggested to be the essential prerequisite for this specific mode of melting. The latter type of melting at the growth front is much slower and irreversible, and it becomes apparent right after the end of rapid surface melting. It is found that the rate of the irreversible melting shows intrig.
Nucleotide resolution profiling of m3C RNA modification by HAC-seq

Abstract Cellular RNAs are subject to a myriad of different chemical modifications that play important roles in controlling RNA expression and function. Dysregulation of certain RNA modifications, the so-called ‘epitranscriptome’, contributes to human disease. One limitation in studying the functional, physiological, and pathological roles of the epitranscriptome is the availability of methods for the precise mapping of individual RNA modifications throughout the transcriptome. 3-Methylcytidine (m3C) modification of certain tRNAs is well established and was also recently detected in mRNA. However, methods for the specific mapping of m3C throughout the transcriptome are lacking. Here, we developed a m3C-specific technique, Hydrazine-Aniline Cleavage sequencing (HAC-seq), to profile the m3C methylome at single-nucleotide resolution. We applied HAC-seq to analyze ribosomal RNA (rRNA)-depleted total RNAs in human cells. We found that tRNAs are the predominant m3C-modified RNA species, with 17 m3C modification sites on 11 cytoplasmic and 2 mitochondrial tRNA isoacceptors in MCF7 cells. We found no evidence for m3C-modification of mRNA or other non-coding RNAs at comparable levels to tRNAs in these cells. HAC-seq provides a novel method for the unbiased, transcriptome-wide identification of m3C RNA modification at single-nucleotide resolution, and could be widely applied to reveal the m3C methylome in different cells and tissues.
Surface Effects on Cation Transport across Porous Alumina Membranes

Transport behavior of monovalent and divalent solutes across mesoporous Anopore {gamma}-alumina membranes was investigated as a function of pore diameter, pH, ionic strength, and nature of the salt or complexing species in solutions. Radiotracer {sup 137}Cs, {sup 85}Sr, {sup 22}Na, and {sup 45}Ca were present in the feed solutions at very low concentrations, ranging from 10{sup {minus}9} to 10{sup {minus}12}M and total salt concentrations from 0.1 to 10{sup {minus}4}M. The divalent cations Ca{sup 2+} and Sr{sup 2+} exhibit lower diffusion rates (3--7 times slower) than the monovalent cations Cs{sup +} and Na{sup +} for membranes with 20 nm diameter pores. Differences between monovalent and divalent cation diffusion rates for the membranes can be explained in terms of a Donnan exclusion effect from the positively charged alumina surface. The rate of Sr{sup 2+} transport across the 20 nm alumina membranes was greatly increased by raising the pH (reducing the membrane surface charge) from 5 to 8 for both the feed and receive sides. Increased ionic strengths and the addition of complexing agents or specific salt solutions also facilitated divalent ion transport. Diffusion coefficients for divalent cations increased 3-fold for the 100 nm pore diameter membranes.
Ribosome profiling reveals ribosome stalling on tryptophan codons and ribosome queuing upon oxidative stress in fission yeast

Abstract Translational control is essential in response to stress. We investigated the translational programmes launched by the fission yeast Schizosaccharomyces pombe upon five environmental stresses. We also explored the contribution of defence pathways to these programmes: The Integrated Stress Response (ISR), which regulates translation initiation, and the stress-response MAPK pathway. We performed ribosome profiling of cells subjected to each stress, in wild type cells and in cells with the defence pathways inactivated. The transcription factor Fil1, a functional homologue of the yeast Gcn4 and the mammalian Atf4 proteins, was translationally upregulated and required for the response to most stresses. Moreover, many mRNAs encoding proteins required for ribosome biogenesis were translationally downregulated. Thus, several stresses trigger a universal translational response, including reduced ribosome production and a Fil1-mediated transcriptional programme. Surprisingly, ribosomes stalled on tryptophan codons upon oxidative stress, likely due to a decrease in charged tRNA-Tryptophan. Stalling caused ribosome accumulation upstream of tryptophan codons (ribosome queuing/collisions), demonstrating that stalled ribosomes affect translation elongation by other ribosomes. Consistently, tryptophan codon stalling led to reduced translation elongation and contributed to the ISR-mediated inhibition of initiation. We show that different stresses elicit common and specific translational responses, revealing a novel role in Tryptophan-tRNA availability.
Comparison of direct wet mount, Kato–Katz and formol ether sedimentation technique for the diagnosis of hookworm infection in Debre Elias Woreda, Northwest Ethiopia

Hookworm infection is a neglected parasitic disease. Direct wet mount is the usual method for the diagnosis of hookworm in Ethiopia, but its sensitivity is unsatisfactory. A cross-sectional study was therefore conducted from January to February 2018 among 192 study participants in Debre Elias district. Stool samples were processed by three methods: the prevalence of hookworm was 77.6%, 68.2% and 49.0% by Kato–Katz, formol ether sedimentation technique and direct wet mount, respectively. Direct wet mount had relatively low sensitivity (61.4%) compared to formol ether sedimentation technique (85.6%) and Kato–Katz (97.4%). The latter two compared well with the gold standard method with kappa values of κ = 0.94, κ = 0.71 and κ = 0.39, respectively, and are therefore recommended over against the direct wet mount technique in detecting hookworm.
Analysis of mutations in tumor and normal adjacent tissue via fluorescence detection

Inflammation is a major risk factor for many types of cancer, including colorectal. There are two fundamentally different mechanisms by which inflammation can contribute to carcinogenesis. First, reactive oxygen and nitrogen species (RONS) can damage DNA to cause mutations that initiate cancer. Second, inflammatory cytokines and chemokines promote proliferation, migration, and invasion. Although it is known that inflammation‐associated RONS can be mutagenic, the extent to which they induce mutations in intestinal stem cells has been little explored. Furthermore, it is now widely accepted that cancer is caused by successive rounds of clonal expansion with associated de novo mutations that further promote tumor development. As such, we aimed to understand the extent to which inflammation promotes clonal expansion in normal and tumor tissue. Using an engineered mouse model that is prone to cancer and within which mutant cells fluoresce, here we have explored the impact of inflammation on de novo mutagenesis and clonal expansion in normal and tumor tissue. While inflammation is strongly associated with susceptibility to cancer and a concomitant increase in the overall proportion of mutant cells in the tissue, we did not observe an increase in mutations in normal adjacent tissue. These results are consistent with opportunities for de novo mutations and clonal expansion during tumor growth, and they suggest protective mechanisms that suppress the risk of inflammation‐induced accumulation of mutant cells in normal tissue.
Self-Nano-Emulsifying Drug-Delivery Systems: From the Development to the Current Applications and Challenges in Oral Drug Delivery

Approximately one third of newly discovered drug molecules show insufficient water solubility and therefore low oral bio-availability. Self-nano-emulsifying drug-delivery systems (SNEDDSs) are one of the emerging strategies developed to tackle the issues associated with their oral delivery. SNEDDSs are composed of an oil phase, surfactant, and cosurfactant or cosolvent. SNEDDSs characteristics, their ability to dissolve a drug, and in vivo considerations are determinant factors in the choice of SNEDDSs excipients. A SNEDDS formulation can be optimized through phase diagram approach or statistical design of experiments. The characterization of SNEDDSs includes multiple orthogonal methods required to fully control SNEDDS manufacture, stability, and biological fate. Encapsulating a drug in SNEDDSs can lead to increased solubilization, stability in the gastro-intestinal tract, and absorption, resulting in enhanced bio-availability. The transformation of liquid SNEDDSs into solid dosage forms has been shown to increase the stability and patient compliance. Supersaturated, mucus-permeating, and targeted SNEDDSs can be developed to increase efficacy and patient compliance. Self-emulsification approach has been successful in oral drug delivery. The present review gives an insight of SNEDDSs for the oral administration of both lipophilic and hydrophilic compounds from the experimental bench to marketed products.