Miracle-dz/UniFAR-FTUs huggingface dataset:
Affinity and Structural Analysis of the U1A RNA Recognition Motif with Engineered Methionines to Improve Experimental Phasing

RNA plays a central role in all organisms and can fold into complex structures to orchestrate function. Visualization of such structures often requires crystallization, which can be a bottleneck in the structure-determination process. To promote crystallization, an RNA-recognition motif (RRM) of the U1A spliceosomal protein has been co-opted as a crystallization module. Specifically, the U1-snRNA hairpin II (hpII) single-stranded loop recognized by U1A can be transplanted into an RNA target to promote crystal contacts and to attain phase information via molecular replacement or anomalous diffraction methods using selenomethionine. Herein, we produced the F37M/F77M mutant of U1A to augment the phasing capability of this powerful crystallization module. Selenomethionine-substituted U1A(F37M/F77M) retains high affinity for hpII (KD of 59.7 ± 11.4 nM). The 2.20 Å resolution crystal structure reveals that the mutated sidechains make new S-π interactions in the hydrophobic core and are useful for single-wavelength anomalous diffraction. Crystals were also attained of U1A(F37M/F77M) in complex with a bacterial preQ1-II riboswitch. The F34M/F37M/F77M mutant was introduced similarly into a lab-evolved U1A variant (TBP6.9) that recognizes the internal bulged loop of HIV-1 TAR RNA. We envision that this short RNA sequence can be placed into non-essential duplex regions to promote crystallization and phasing of target RNAs. We show that selenomethionine-substituted TBP6.9(F34M/F37M/F77M) binds a TAR variant wherein the apical loop was replaced with a GNRA tetraloop (KD of 69.8 ± 2.9 nM), laying the groundwork for use of TBP6.9(F34M/F37M/F77M) as a crystallization module. These new tools are available to the research community.
Preparation of Polyrotaxane Fibers. Part I: Influence of Dope Solvents on the Physical Properties of Wet-spun Polyrotaxane Fibers

The preparation of polyrotaxane fibers by wet spinning of polyrotaxane, consisting of poly(ethylene glycol) (PEG) and α-cyclodextrins (α-CDs), was examined using three different types of dope solvents: dimethylacetamide (DMAc) containing 8 wt% lithium chloride (LiCl), dimethylformamide (DMF) containing 8 wt% LiCl, and dimethylsulfoxide (DMSO). In DMSO, polyrotaxane concentrations of 20 and 30 wt% were favorable for the smooth spinning of fibers with sufficient tenacity, while other polyrotaxane concentrations (10, 15, and 40 wt%) were unsuitable for the wet spinning of durable fibers. All of the fibers had nearly identical scanning electron microscopy (SEM) images and X-ray diffraction patterns. Although the values for tenacity at break and initial modulus also were similar for all fibers, elongation at break of fibers from DMSO was higher than the values for the other two fibers. The poorer physical properties of the latter two fibers may be affected by the slight amount of lithium salt remaining in the fibers.
Revised Model for Molecular Diffusion and Advection

Molecular diffusion of fluid constituents currently is most frequently defined as a flux relative to the mean flux. Different interpretations of “mean flux” exist in the literature; usually it refers to the mass average flux of a solution as a whole. The flux of constituents relative to the mean flux must sum to zero, and consequently diffusion, as currently defined, does not exist in a fluid consisting of a single constituent. Diffusion, as understood by the pioneers, applied to the flux of a single‐species fluid as well as the flux of a constituent in a fluid mixture. The purpose of this study was to show that the current definition of diffusion is illogical because “mean flux” is not independent of diffusive flux. Defining diffusion as a flux proportional to a gradient of kinetic energy is consistent with diffusive flux as understood by the early investigators of diffusion, provided the kinetic energy gradients of a particular molecular species are correctly identified. For example, diffusive fluxes of ideal gas constituents are proportional to their partial pressure gradients, and diffusive flux of pure liquid water is proportional to its vapor pressure gradient. Advection is defined here as a volume flux (of a solution as a whole) in response to a pressure gradient and a body force. We evaluate the total flux of a solution as a whole as the vector sum of advection and diffusive fluxes of all constituents.
Antioxidative and Skin Protective Effects of Canarium subulatum Methanol Extract on Keratinocytes

Canarium subulatum is a traditional medical herb used in South Asia. Recently, the anti-inflammatory effects of C. subulatum methanol extract (Cs-ME) have been reported; however, the effect of Cs-ME on skin physiology has not yet been elucidated. Therefore, in this study, we evaluated the protective effect of Cs-ME on UV-induced skin aging and cell death as well as the reinforcing effect on the skin barrier. According to viable cell counting and MTT assays, Cs-ME significantly reduced UV-evoked HaCaT cell death. Cs-ME blocked reactive oxygen species (ROS) generation in UV-irradiated HaCaT cells and showed radical scavenging activity against DPPH and ABTS. In addition, H2O2-induced cell death was inhibited by Cs-ME, indicating that Cs-ME protects cells from UV-derived cell death through the suppression of ROS. PCR analysis revealed that Cs-ME diminished the expression of aging-related HYAL-1 and MMP-1 genes in UV-treated HaCaT cells. Elevated HYAL-1 and MMP-1 mRNA expression in H2O2-stimulated HaCaT cells was also decreased by Cs-ME, suggesting that Cs-ME exerts antiaging activity via the inhibition of ROS. Expression of skin barrier components including filaggrin and hyaluronic acid synthase-1 was increased by Cs-ME and was modulated by ERK/p38-AP-1 signaling. Collectively, our data show that Cs-ME has cytoprotective and antiaging activity based on antioxidant properties. Furthermore, Cs-ME exerts skin barrier protective ability by regulating the AP-1 signaling pathway. Therefore, Cs-ME has the potential for use as an ingredient in cosmetics to protect the skin from UV irradiation, prevent photoaging, and strengthen the skin barrier.
Chroesthes (Acanthaceae) in Peninsular Malaysia, including a new species from Kelantan and a new record from Terengganu

Abstract Chroesthes is a small genus that includes three species from Peninsular Malaysia: Chroesthes faizaltahiriana Siti-Munirah sp. nov., C. lanceolata (T. Anderson) B.Hansen and C. longifolia (Wight) B.Hansen. Chroesthes faizaltahiriana, recently discovered in the State of Kelantan, is described and illustrated. This species is similar to the common species C. longifolia, but is distinguished mainly by its inflorescence type, calyx shape and its flowers being bright orange instead of dark purple internally. Chroesthes lanceolata is a new record for Peninsular Malaysia and has only been collected once. Following the IUCN Red List Categories and Criteria, these three species are assessed (national scale assessment) as Critically Endangered (C. faizaltahiriana and C. lanceolata) and Least Concern (C. longifolia).
Covalent attachment of quaternary ammonium compounds to a polyethylene surface via a hydrolyzable ester linkage: Basis for a controlled‐release system of antiseptics from an inert surface

The colonization of medical devices such as catheters, topical wound dressings, and surgical implants by micro-organisms is an ongoing problem, particularly as many strains of bacteria are becoming resistant to antibiotics. Such a problem may be addressed by a material surface that is able to provide a slow release of a disinfectant during its period of usage. To achieve this objective, a novel material was prepared in which a quaternary ammonium salt was covalently bound onto a polyethylene backbone via a hydrolyzable ester linkage, which provided a slow release of the disinfecting agent. A low-density polyethylene film was treated with glow discharge followed by the graft polymerization of acrylic acid. A tertiary amine function was introduced onto the film by the esterification of the carboxylic acid groups, via an acid chloride intermediate, with 4-hydroxy-N-methyl piperidine. The tertiary amine on the piperidine was then quaternized with a series of alkyl bromides of various chain lengths. The quaternary ammonium salt was released slowly by the hydrolysis of the ester bond over a 4-h period. To test the efficacy of the quaternary ammonium function itself, soluble compounds were prepared as follows. 4-Hydroxy-N-methyl piperidine was esterified with acetic anhydride and a corresponding series of quaternary ammonium salts prepared again by a reaction with alkyl bromides of various chain lengths. A preliminary microbiological survey of the materials included an investigation of the effect of the chain length as well as the efficacy of the soluble quaternary salts themselves. As expected, only the longer alkyl chains provided quaternary ammonium salts with bactericidal properties, chain lengths of less than 10 carbon atoms proving ineffective. Both the polymer-bound and soluble long-chain quaternary ammonium salts were effective against suspensions of Staphylococcus aureus and Escherichia coli. The results therefore indicate that such a system may well be useful in the development of biomedical materials such as surgical implants or dressings in which a slow release of a disinfectant or other physiologically active agent such as an anti-inflammatory drug may be required.
Resonance Rayleigh Scattering Method for the Determination of Aminoglycoside Antibiotics with Trypan Blue

Abstract In weak acidic medium, some aminoglycoside antibiotics, such as kanamycin (KANA), gentamicin (GEN), tobramycin (TOB), and neomycin (NEO), or acid bisazo dye trypan blue (TB) can only produce very weak resonance Rayleigh scattering (RRS) signals. However, when the two agents react with each other to form the ion association complexes, the RRS intensity can be enhanced greatly and a new RRS spectrum and a significant enhancement of the RRS intensity in the wavelength range 350–600 nm can be observed. The maximum scattering peak was at 580 nm. There is a linear relationship between the RRS intensity and the antibiotic concentration in the range 0.01–6.0 µg mL−1 at 580 nm. This RRS method has therefore been developed for the determination of trace levels of aminoglycoside antibiotics. The detection limits (3σ) of the four antibiotics, whose order of sensitivity KANA>NEO>TOB> GEN, are 6.1–8.1 ng mL−1. This method has a good selectivity and has been successfully applied to the quick determination of antibiotics not only for injections and ear dips, but clinic serum samples as well. In addition, quantum chemistry-based analysis of the reaction mechanism, the factors influencing the RRS spectra, and the reasons for the enhancement of RRS are discussed.
Why are Women With Polycystic Ovary Syndrome at Increased Risk of Depression? Exploring the Etiological Maze

Polycystic ovary syndrome (PCOS) is a complex and common multisystemic disorder. Women with PCOS have up to eight times higher prevalence of depression than control groups. This paper aims to explore the underlying risk factors for developing depression in this high-risk group. Studies indicate an interplay of multiple mechanisms that place women with PCOS at an increased risk for depression. The pathophysiology thought to play a role includes disturbances in the endocrine axes and changes to the metabolic pathway. The risk of depression is independently linked to insulin resistance and obesity in this population. However, rates of depression were still higher than control groups when accounting for these variables, demonstrating that they are not the only mechanism causing depression. The clinical manifestations of hyperandrogenism and menstrual abnormalities may compound negative views and lower self-esteem and negatively impact mood. Many of these women also struggle with infertility, and due to the added external pressures like societal beliefs and culture, they may be further negatively impacted and worsen their depressive symptoms. The prevalence of depression in women with PCOS is high; thus, this paper highlights the essential understanding of the underlying mechanisms at play. This is to better aid in addressing the fundamental cause of depression in this high-risk group effectively.
Peptoid-based Positional Scanning Derivatives: Revealing the Optimum Residue Required for Ice Recrystallization Inhibition Activity for Every Position in the AFGPs

Department of Polar Sciences, University of Science and Technology, Incheon 406-840, KoreaReceived August 20, 2012, Accepted September 12, 2012Key Words : Glycopeptoid, Ice recrystallization inhibition, Positional scanningAntifreeze glycoproteins (AFGPs) bind to the ice crystals,thereby inhibit ice crystal growth. The discovery of AFGPsin the blood serum of fish by De Vries demonstrated thatAFGPs is an essential biomaterial for fish to survive at sub-zero temperature in the Antarctic Sea.
Comparative effectiveness of bisoprolol and carvedilol among patients receiving maintenance hemodialysis

Abstract Background Despite widespread use, there is no trial evidence to inform β-blocker’s (BB) relative safety and efficacy among patients undergoing hemodialysis (HD). We herein compare health outcomes associated with carvedilol or bisoprolol use, the most commonly prescribed BBs in these patients. Methods We created a cohort study of 9305 HD patients who initiated bisoprolol and 11 171 HD patients who initiated carvedilol treatment between 2004 and 2011. We compared the risk of all-cause mortality and major adverse cardiovascular events (MACEs) between carvedilol and bisoprolol users during a 2-year follow-up. Results Bisoprolol initiators were younger, had shorter dialysis vintage, were women, had common comorbidities of hypertension and hyperlipidemia and were receiving statins and antiplatelets, but they had less heart failure and digoxin prescriptions than carvedilol initiators. During our observations, 1555 deaths and 5167 MACEs were recorded. In the multivariable-adjusted Cox model, bisoprolol initiation was associated with a lower all-cause mortality {hazard ratio [HR] 0.66 [95% confidence interval (CI) 0.60–0.73]} compared with carvedilol initiation. After accounting for the competing risk of death, bisoprolol use (versus carvedilol) was associated with a lower risk of MACEs [HR 0.85 (95% CI 0.80–0.91)] and attributed to a lower risk of heart failure [HR 0.83 (95% CI 0.77–0.91)] and ischemic stroke [HR 0.84 (95% CI 0.72–0.97)], but not to differences in the risk of acute myocardial infarction [HR 1.03 (95% CI 0.93–1.15)]. Results were confirmed in propensity score matching analyses, stratified analyses and analyses that considered prescribed dosages or censored patients discontinuing or switching BBs. Conclusions Relative to carvedilol, bisoprolol initiation by HD patients was associated with a lower 2-year risk of death and MACEs, mainly attributed to lower heart failure and ischemic stroke risk.
Synergistic antitumor effect of the anti-ErbB2 antibodies trastuzumab and H2-18 on trastuzumab-resistant gastric cancer cells

Trastuzumab resistance is a severe problem in the treatment of ErbB2-amplified cancer. Although trastuzumab plus pertuzumab is able to partly overcome trastuzumab resistance in ErbB2-overexpressing cancer, its antitumor efficacy remains limited. The present study investigated the antitumor activity of the combination of trastuzumab with H2-18, which is an antibody targetinsg ErbB2 domain I. Cell proliferation and inhibition experiments indicated that H2-18 and trastuzumab synergistically inhibited the proliferation of both the trastuzumab-sensitive gastric cancer cell line, NCI-N87 and the trastuzumab-resistant gastric cancer cell line, NCI-N87-TraRT. Furthermore, H2-18 plus trastuzumab inhibited the growth of NCI-N87-TraRT cells more effectively than trastuzumab plus pertuzumab, both in vitro and in vivo. Compared with trastuzumab plus pertuzumab, H2-18 plus trastuzumab had a potent ability to inhibit NCI-N87-TraRT cells to form colonies. Notably, H2-18 plus trastuzumab was more effective in inducing cell death than trastuzumab plus pertuzumab. The in vivo studies demonstrated that H2-18 plus trastuzumab effectively inhibited the growth of both NCI-N87 and NCI-N87-TraRT xenograft tumors. Further experiments revealed that in NCI-N87-TraRT cells, H2-18 plus trastuzumab was comparable to trastuzumab plus pertuzumab in the inhibition of phosphorylated (p-)HER3, p-AKT and p-ERK. However, compared with trastuzumab plus pertuzumab, H2-18 plus trastuzumab effectively activated ROS production and the phosphorylation of JNK and c-jun in NCI-N87-TraRT cells. Therefore, the superior antitumor efficacy of H2-18 plus trastuzumab over trastuzumab plus pertuzumab may be mainly attributable to the potent cell death-inducing activity. In addition, the in vitro and in vivo antitumor effect of the combination of H2-18, trastuzumab and pertuzumab were further investigated. The results revealed that H2-18 plus trastuzumab plus pertuzumab exhibited a maximal antitumor effect among all the anti-ErbB2 monoclonal antibody combinations tested. In summary, H2-18 plus trastuzumab may have potential as an effective strategy to overcome the resistance to trastuzumab in ErbB2-amplified gastric cancer cell lines.
Análise do teor de cocaína em amostras apreendidas pela polícia utilizando-se a técnica de cromatografia liquida de alta eficiência com detector UV-Vis

A tecnica de CLAE com deteccao UV-Vis foi empregada na analise do teor de cocaina em amostras apreendidas de cocaina e crack. Uma fase movel de acetonitrila/agua (95:5v/v) possibilitou um sinal de pico para a cocaina em 3,5 minutos. O sinal espectrofotometrico otimizado foi obtido em um comprimento de onda de 224 nm. A curva analitica de 1,0 a 40,0 ppm para cocaina foi obtida, exibindo um coeficiente de correlacao linear de 0,9989, com limites de deteccao e quantificacao de 0,75 e 3,78 ppm, respectivamente. Esta metodologia foi aplicada na dosagem de amostras confiscadas de cocaina e crack no Laboratorio de Policia Cientifica de Ribeirao Preto-SP.
The “Parallel Pandemic” in the Context of China: The Spread of Rumors and Rumor-Corrections During COVID-19 in Chinese Social Media

Although studies have investigated cyber-rumoring previous to the pandemic, little research has been undertaken to study rumors and rumor-corrections during the COVID-19 (coronavirus disease 2019) pandemic. Drawing on prior studies about how online stories become viral, this study will fill that gap by investigating the retransmission of COVID-19 rumors and corrective messages on Sina Weibo, the largest and most popular microblogging site in China. This study examines the impact of rumor types, content attributes (including frames, emotion, and rationality), and source characteristics (including follower size and source identity) to show how they affect the likelihood of a COVID-19 rumor and its correction being shared. By exploring the retransmission of rumors and their corrections in Chinese social media, this study will not only advance scholarly understanding but also reveal how corrective messages can be crafted to debunk cyber-rumors in particular cultural contexts.
BMPR2 expression level is correlated with low immune infiltration and predicts metastasis and poor survival in osteosarcoma

Osteosarcoma is the most common malignant bone tumor in adolescents and young adults, and identifying biomarkers for prognosis and therapy is necessary. Bone morphogenetic protein receptor 2 (BMPR2) is involved in various cellular functions, including cell adhesion, proliferation and invasion, inflammation, apoptosis and metastatic spread. However, the correlation between BMPR2 expression levels and prognosis and tumor-infiltrating immune cells in osteosarcoma is not well understood. In the present study, the expression level of BMPR2 was investigated using the Oncomine and R2 databases. The association between the expression level of BMPR2 and the clinical prognosis of patients with cancer was analyzed using the R2 database. The relationship between the expression level of BMPR2 and immune cell infiltration in the stroma of osteosarcoma was assessed using the Tumor Immune Estimation Resource (TIMER) and CIBERSORT. The correlations between BMPR2 expression level and infiltrated immune cell gene marker sets in osteosarcoma were validated in the TIMER and R2 databases. Analysis of a cohort of patients with osteosarcoma revealed that BMPR2 expression was significantly higher in osteosarcoma compared with in normal tissue and was correlated with poor prognosis. M0 macrophages, M2 macrophages, resting mast, γ δ T and CD8+ T cells were the top five immune cells with the highest degrees of infiltration in osteosarcoma. In addition, BMPR2 expression level showed a significant negative correlation with the gene markers of CD8+ T cells, monocytes and M2 macrophages. Low levels of infiltrating CD8+ T cells, monocytes or M2 macrophages in osteosarcoma was significantly associated with poor survival. These data suggested that CD8+ T cells, monocytes and M2 macrophages play significant roles in the establishment of the immune microenvironment of osteosarcoma. High BMPR2 expression was associated with poor prognosis and low infiltration of CD8+ T cells, monocytes and M2 macrophages in osteosarcoma. Hence, BMPR2 can be considered a biomarker of the immune infiltration, metastasis and prognosis of osteosarcoma.
Nanocarbons-Induced Hardening of Ultrathin Polysiloxane Block Copolymer Films

Ultrathin films of polysiloxane block copolymers and their composites with a C60 modifying additive were studied by atomic force microscopy. Nanometer scale surface patterns independent of the additive concentration were revealed in the surface profiles of the films. These patterns were attributed to the spatial distribution of rigid block domains at the block copolymer surface. Reliable quantitative data on mechanical properties of the films were obtained in indentation tests with specially fabricated spherical probes with a calibrated submicrometer radius of curvature. It was found that the addition of C60 in an amount on the order of 0.01% significantly improves the elasticity of the block copolymer surface layers. At this concentration, several fullerene molecules can be introduced into each nanodomain of rigid blocks.
Surface species formed upon supporting molybdena on alumina by mechanically mixing both oxides

MoO[sub 3]/Al[sub 2]O[sub 3] mechanical mixtures have been prepared with MoO[sub 3] loadings ranging from 0.1 to 2 monolayers (S[sub BET] of the support 105 m[sup 2]/g), and calcination at 770K for 8 and 24 h, in the presence and in the absence of water vapour, in order to assess the nature and distribution of the surface species formed. The interaction between the supported phase and the support and the nature of the species formed thereby have been followed through changes in the zero-point-charge (ZPC) of the solids, X-ray diffractograms, and temperature-programmed reduction profiles. The ZPC of the samples changes from 8.8 (parent alumina) to a final value of 3.0 in all samples, but this value is reached at different molybdenum loadings depending on the preparation method. For samples prepared by calcining both oxides in air for 24 h, a monolayer distribution of polymolybdate species is found for molybdenum loadings up to 0.7-0.8 monolayer. With samples calcined for 8 h in air or in dry oxygen, a complete coverage of the alumina surface is achieved only for 2-monolayer loadings. 24 refs., 4 figs., 2 tabs.