Miracle-dz/UniFAR-FTUs huggingface dataset:
The transition state for peptide bond formation reveals the ribosome as a water trap

Recent progress in elucidating the peptide bond formation process on the ribosome has led to notion of a proton shuttle mechanism where the 2'-hydroxyl group of the P-site tRNA plays a key role in mediating proton transfer between the nucleophile and leaving group, whereas ribosomal groups do not actively participate in the reaction. Despite these advances, the detailed nature of the transition state for peptidyl transfer and the role of several trapped water molecules in the peptidyl transferase center remain major open questions. Here, we employ high-level quantum chemical ab initio calculations to locate and characterize global transition states for the reaction, described by a molecular model encompassing all the key elements of the reaction center. The calculated activation enthalpy as well as structures are in excellent agreement with experimental data and point to feasibility of an eight-membered “double proton shuttle” mechanism in which an auxiliary water molecule, observed both in computer simulations and crystal structures, actively participates. A second conserved water molecule is found to be of key importance for stabilizing developing negative charge on the substrate oxyanion and its presence is catalytically favorable both in terms of activation enthalpy and entropy. Transition states calculated both for six- and eight-membered mechanisms are invariably late and do not involve significant charge development on the attacking amino group. Predicted kinetic isotope effects consistent with this picture are similar to those observed for uncatalyzed ester aminolysis reactions in solution.
C4 Cycles: Past, Present, and Future Research on C4 Photosynthesis

In the late 1960s, a vibrant new research field was ignited by the discovery that instead of fixing CO2 into a C3 compound, some plants initially fix CO2 into a four-carbon (C4) compound. The term C4 photosynthesis was born. In the 20 years that followed, physiologists, biochemists, and molecular and developmental biologists grappled to understand how the C4 photosynthetic pathway was partitioned between two morphologically distinct cell types in the leaf. By the early 1990s, much was known about C4 biochemistry, the types of leaf anatomy that facilitated the pathway, and the patterns of gene expression that underpinned the biochemistry. However, virtually nothing was known about how the pathway was regulated. It should have been an exciting time, but many of the original researchers were approaching retirement, C4 plants were proving recalcitrant to genetic manipulation, and whole-genome sequences were not even a dream. In combination, these factors led to reduced funding and the failure to attract young people into the field; the endgame seemed to be underway. But over the last 5 years, there has been a resurgence of interest and funding, not least because of ambitious multinational projects that aim to increase crop yields by introducing C4 traits into C3 plants. Combined with new technologies, this renewed interest has resulted in the development of more sophisticated approaches toward understanding how the C4 pathway evolved, how it is regulated, and how it might be manipulated. The extent of this resurgence is manifest by the publication in 2011 of more than 650 pages of reviews on different aspects of C4. Here, I provide an overview of our current understanding, the questions that are being addressed, and the issues that lie ahead.
Title Circulating CD 133 + VEGFR 2 + and CD 34 + VEGFR 2 + cells andarterial function in patients with beta-thalassaemia major

Arterial dysfunction has been documented in patients with beta-thalassaemia major. This study aimed to determine the quantity and proliferative capacity of circulating CD133VEGFR2 and CD34VEGFR2 cells in patients with beta-thalassaemia major and those after haematopoietic stem cell transplantation (HSCT), and their relationships with arterial function. Brachial arterial flow-mediated dilation (FMD), carotid arterial stiffness, the quantity of these circulating cells and their number of colony-forming units (CFUs) were determined in 17 transfusion-dependent thalassaemia patients, 14 patients after HSCT and 11 controls. Compared with controls, both patient groups had significantly lower FMD and greater arterial stiffness. Despite having increased CD133VEGFR2 and CD34VEGFR2 cells, transfusion-dependent patients had significantly reduced CFUs compared with controls (p=0.002). There was a trend of increasing CFUs across the three groups with decreasing iron load (p=0.011). The CFUs correlated with brachial FMD (p=0.029) and arterial stiffness (p=0.02), but not with serum ferritin level. Multiple linear regression showed that CFU was a significant determinant of FMD (p= 0.043) and arterial stiffness (p=0.02) after adjustment of age, sex, body mass index, blood pressure and serum ferritin level. In conclusion, arterial dysfunction found in patients with beta-thalassaemia major before and after HSCT may be related to impaired proliferation of CD133VEGFR2 and CD34VEGFR2 cells.
Grasping strategy of two robot arms based on tactile and slippage sensation of optical three-axis tactile sensor system

This paper presents a new grasping strategy of two robot arms based on active tactile and slippage sensation using a novel optical three-axis tactile sensor system. The tactile sensors are mounted on the tip of robotic hands of two robot arms. In the robot motion control, a recurrent mechanism was implemented in which the next behavior is induced by the tactile data to make the robot accept intention embedded in the environment. Since this mechanism is based on the tactile data, it is possible to apply it to communication between the hand-arms to obtain the best timing for cooperative work. A slippage distribution analysis was conducted which result shows that slippage occurred according to direction of force applied to the sensing elements. In experiments, the two-hand-arm robot performed object grasping, twisting, transferring and assembling tasks. Experimental results show that the proposed strategy has great potential to improve grasping performance of robot hand because appropriate behavior is induced according to tactile and slippage direction.
Aboodh Homotopy Perturbation Method of solving Burgers Equation.

In this paper, we present a reliable combination of Aboodh Transform and Homotopy perturbation method to determine the exact solution of one dimensional Burgers equation which is a nonlinear partial differential equation. Some cases of one dimensional nonlinear partial differential equations are considered to illustrate the capability and reliability of Aboodh Homotopy perturbation method. We have compared the analytical solution obtained with the available Laplace decomposition method. The solution which is found to be exactly the same. The result revealed that the combination of the Aboodh Transform and homotopy perturbation method is quite capable, practically well appropriate for use in such problems. The method is tested on three examples and results show that the new method is more effective and convenient to use and high accuracy of it is evident.
Initial Public Offering Disclosure Rules and Information Production Incentives

We show that, in an environment where information regarding firm quality is endogenously produced, mandatory disclosure can reduce the incentives of an issuer contemplating an initial public offering of common stock to produce information regarding the issuer's expected return. We consider the effect of three disclosure regimes (no disclosure, voluntary disclosure, and mandatory disclosure) on information production incentives. We find that the value of information may be positive, zero, or negative, depending on the disclosure regime, the cost of information, and issuer preferences. With endogenous issuer information production, a more rigorous disclosure standard may create a more opaque informational environment. We find that, regardless of the level of information costs, unless the amount of external financing required destroys signaling opportunities or information affects the investment decision, mandatory disclosure Pareto dominates the other disclosure environments. JEL Codes: G32, D82, G18
Relation of Campylobacter pyloridis to gastritis and peptic ulcer.

Biopsy specimens from the gastric antral mucosa of 50 patients with upper gastrointestinal complaints were studied by light and electron microscopy and culture. Of 46 assessable specimens, seven were histologically normal, and 39 showed evidence of gastritis. Twenty-seven of the specimens with evidence of gastritis (69%) contained spiral bacteria, whereas only one of the normal specimens (14%) contained these bacteria (P = .02). Of 17 patients found to have gastric ulcers, 10 (59% [P greater than .10] ) also had spiral bacteria. The bacteria could be seen scattered over the surface of the epithelial cells and just under the layer of mucus but were rarely found inside the epithelial cells. Curved or spiral gramnegative bacilli were isolated from 10 of the specimens on chocolate agar incubated at 37 C under microaerophilic conditions. The bacteria resembled the organism recently named Campylobacter pyloridis by other investigators.
Modeling Food Retail Format Choice and Shopping Frequency Decision in Urban Ghana: A Multivariate Ordered Probit Regression Application

The goal of this study is to investigate consumer food shopping behavior in terms of food shopping frequencies at open-air markets, from hawkers, and in supermarkets. The study uses primary data collected in urban Ghana in 2011. The present paper contributes to the development of methods for analysis of consumer food shopping behavior by considering the correlation between different food retail formats in an emerging African economy. Results of multivariate ordered probit model indicate that open-air markets still dominate the food supply system in urban households of Ghana, and the food shopping frequency in open-air markets is not significantly related to other food retail stores. While the food shopping frequency in supermarkets and from hawkers are found to be significantly positive. The study also provides insights about the joint distribution and conditional distribution of food shopping frequency in these retail outlets, providing valuable practical knowledge to both public sectors and private organizations.
EFFECTS OF DEVELOPMENTAL ENVIRONMENT ON SIGNAL‐PREFERENCE COUPLING IN A HAWAIIAN CRICKET

Abstract Previous work has suggested that developmental temperature influences expression of the adult male calling song of the cricket, a sexually selected mate recognition signal. The role of developmental temperature in shaping female preference functions, and thus its influence on signal‐preference coupling has not been investigated. In this study, the effects of developmental temperature are examined in both males and females of the Hawaiian cricket, Laupala cerasina, to determine the degree of signal‐preference matching between male song and female preference due to developmental environment. We found that rearing females in different temperature environments affected adult female acoustic preference functions in the same direction as male calling song, thereby influencing variation in adult reproductive behavior in such a way that male and female components remain coordinated. However, we further demonstrate that for male song, the effect of the rearing environment is not permanent but appears only to exert influence for a period of days. This mid‐term temperature effect is distinct from the effect of short‐term ambient temperature, which influences song in a matter of minutes and has been well documented. Signal‐preference coordination, and sexual selection pressures due to mismatching within natural populations, likely will be influenced by nymphal developmental environments of males and females, as well as by adult singing and preference environments.
CircHIPK3 overexpression accelerates the proliferation and invasion of prostate cancer cells through regulating miRNA-338-3p

Objective: Circular RNA is a type of endogenous RNA molecule with a stable closed-loop structure which is ubiquitous in mammals. Circular RNA HIPK3 (circHIPK3) is highly expressed in hepatocellular carcinoma and promotes the growth of hepatoma cells. However, its role in prostate cancer (PCa) has not been reported. This study aims to explore whether circHIPK3 could affect the proliferative and invasive potentials of PCa cells by regulating miRNA-338-3p. Methods: Expression levels of circHIPK3 and miRNA-338-3p in PCa tissues and cells were determined by RT-qPCR. The regulatory effects of circHIPK3 and miRNA-338-3p on proliferative and invasive potentials of PCa cells were evaluated by CCK-8 and transwell assay, respectively. We verified the binding between miRNA-338-3p and ADAM17, as well as miRNA-338-3p and circHIPK3 through dual-luciferase reporter gene assay. Rescue experiments were conducted to clarify whether circHIPK3 affected the proliferative and invasive potentials of PCa cells by regulating miRNA-338-3p. Results: Expression level of circHIPK3 in PCa tissues was remarkably higher than that of paracancerous tissues. Knockdown of circHIPK3 inhibited the proliferative and invasive rates of PC-3 and DU145 cells. Dual-luciferase reporter gene assay indicated that circHIPK3 could bind to miRNA-338-3p. Moreover, miRNA-338-3p expression was downregulated in PCa tissues. miRNA-338-3p expression was negatively correlated with lymph node metastasis and distant metastasis. miRNA-338-3p overexpression markedly reduced proliferative and invasive abilities of PC-3 and DU145 cells. Furthermore, ADAM17 was confirmed to be the target gene of miRNA-338-3p. Overexpression of ADAM17 enhanced proliferative and invasive abilities of PC-3 and DU145 cells. Finally, rescue experiments indicated that miRNA-338-3p knockdown in PC-3 and DU145 cells partially reversed the regulatory effects of circHIPK3 on proliferative and invasive potentials. Conclusion: Overexpression of circHIPK3 promotes the proliferative and invasive potentials of PCa cells through sponging miRNA-338-3p to regulate ADAM17 expression, thus accelerating the malignant progression of PCa.
A Review on Acidifying Treatments for Vegetable Canned Food

As is well known, pasteurization treatments are not sufficient for destroying heat resistance of spore forming microorganisms, which are prevented from germination and growing by pH reducing. So, the acidification process becomes one of the most important pre-treatments for the canning industry. It is commonly applied before pasteurization treatment with the purpose of inhibiting spore germination and for reducing heat resistance of the microorganism, thereby allowing to reduce the time or temperature values of the heat treatment. With the aim to reduce the pH of vegetables several techniques are available but their application is not easy to plan. Often, industries define operative conditions only on the basis of empirical experience, thus increasing the risk of microbial growth or imparting an unpleasant sour taste. With the aim of highlighting the correct plan and management of acidification treatments to reach safety without degrading quality of canned fruit and vegetables, the topics that are reviewed and discussed are the effects of low pH on heat resistance of the most important microorganisms, acidification techniques and significant process variables, the effect of low pH on sensorial properties, and future trends.
Prevalence of smoking and its association with the use of other drugs among students in the Federal District of Brasília, Brazil.

OBJECTIVE To estimate the prevalence of smoking, as well as to determine the association between smoking and the use of other drugs, among middle and high school students in the Federal District of Brasília, Brazil. METHODS Epidemiological study involving a reference population of students in the District. Our sample comprised 2,661 students from 9 to 19 years of age, in all middle and high school grades. All participating students completed a standard questionnaire. Results were analyzed by gender and type of school (public or private). RESULTS The prevalence of smoking among students in the District was 10.5%. Smoking was found to be associated with the use of alcohol and other drugs. CONCLUSIONS Smoking is a gateway to the use of other drugs.
Randomized controlled trials investigating the relationship between dietary pattern and high-sensitivity C-reactive protein: a systematic review

CONTEXT Elevated serum concentration of high-sensitivity C-reactive protein (hsCRP), a biomarker of systemic inflammation, is associated with increased risk for coronary heart disease (CHD) and cardiovascular events (CVEs). Because elevations in hsCRP often occur in parallel with elevations in low-density lipoproteins (LDLs) and both biomarkers are reduced by hydroxymethylglutaryl-CoA reductase inhibitors (ie, statin drugs), efforts to determine nonpharmacological treatments to lower hsCRP remain limited. Dietary modifications in particular are rarely discussed as viable clinical interventions yet merit investigation. OBJECTIVE This systematic review was performed to assess the relationship between dietary patterns and hsCRP among individuals enrolled in randomized controlled trials. DATA SOURCES National Library of Medicine (ie, MEDLINE) and Google Scholar searches were performed using the search terms "C-reactive protein," "CRP," "dietary pattern," and/or "diet" to identify articles published between January 2000 and October 2017. DATA EXTRACTION Data were extracted and analyzed according to PRISMA guidelines. Identified abstracts were reviewed and cross-referenced for relevance to dietary pattern. Full-text manuscripts were then abstracted for their principal findings. Fifty-six manuscripts met inclusion criteria for detailed review. RESULTS Clinical trials of dietary interventions to reduce hsCRP are mixed in quality and findings. Several specific dietary patterns may reduce hsCRP, including low-fat, low-carbohydrate, Mediterranean, Portfolio, Paleolithic, and the Dietary Approaches to Stop Hypertension (DASH) diets. However, results were mixed for the majority of dietary patterns (eg, low-glycemic load diets). CONCLUSION Information available to date suggests that a wide variety of dietary patterns may impact serum hsCRP, although studies are mixed in quality. The efficacy of dietary patterns for the treatment of elevated hsCRP as a strategy for primary prevention of CHD may be best elucidated in randomized clinical trials in healthy participants with elevated hsCRP but low or normal traditional risk factors, or by using more aggressive dietary modifications in high-risk patients. Given current incidence and prevalence of CHD risk factors, additional randomized controlled trials of this type are justified and needed.
Leaving sex work: Barriers, facilitating factors and consequences for female sex workers in northern Thailand

Factors facilitating or inhibiting women's ability to leave sex work are still poorly characterized, and little is known about women's lives after they leave the profession. This paper presents findings from a qualitative study about factors affecting women's ability to leave sex work and influencing their lives after leaving. We interviewed 42 current and former female sex workers (FSWs) drawn from a cohort study of 500 FSWs in northern Thailand. All but one of the participants had quit sex work at least once. The majority experienced one or more quit-re-entry-quit cycles. Women's ability and decisions to leave sex work were determined primarily by four factors: economic situation, relationship with a steady partner, attitudes towards sex work and HIV/AIDS experience. Economic concerns, ranging from survival needs to materialistic desires, had the strongest influence. Most women perceived their risk for HIV infection to be lower after leaving sex work, but three of the 17 HIV-infected women acquired infection after having left, presumably from their steady partners. Prevention efforts should guide women as they transition out of commercial sex work. Interventions aimed at assisting women wanting to leave sex work need to address the role of economic factors.
Women living alone have an increased risk to develop diabetes, which is explained mainly by lifestyle factors.

OBJECTIVE The purpose of this study was to assess the role of household conditions for the progression to diabetes in women with impaired glucose tolerance (IGT). RESEARCH DESIGN AND METHODS A total of 461 women, aged 50-64 years, with IGT defined by an oral glucose tolerance test, had baseline advice on physical exercise, diet, smoking, and alcohol habits. Physical examination, blood tests, and questionnaires were completed at baseline and after 2.5 years. Household status was categorized into living alone or with a partner, other adults, or children. RESULTS Women living alone had a 2.68-fold increased risk (95% CI 1.02-7.05) of developing diabetes after adjustments for biological risk factors. Further stepwise adjustments for education, occupation, subjective mental health, exercise, diet, and alcohol showed remaining significant odds ratios (ORs), decreasing from 3.26 (1.19-8.96) to 3.03 (1.02-8.99). However, when smoking status was added, the OR became nonsignificant, 2.07 (0.62-6.88). More women who lived alone smoked and did not reduce their daily cigarette consumption compared with women in other household conditions. At follow-up, women living alone had reduced their alcohol consumption and were more often abstainers and fewer had healthy dietary habits or had improved their diet. Physical exercise did not differ among the groups. Separate analyses of any other household status did not show any excess risk for development of diabetes. CONCLUSIONS Women living alone had a higher risk to progress from IGT to diabetes, mostly explained by smoking, alcohol, and dietary habits. Household conditions should be accounted for when assessing future risk for diabetes.
Expression and regulation of CReMM, a chromodomain helicase‐DNA‐binding (CHD), in marrow stroma derived osteoprogenitors

This study follows the expression of CReMM, a new CHD family member, in osteoprogenitors. CReMM expression was analyzed in primary cultured mesnchymal cells from rat and human. Analysis in ex vivo cultured marrow stromal cells (MSC) from rats revealed higher level of CReMM in cells from young (3 months), when compared to cells from old (15 months) rats. CReMM level was higher in human MSC then in mature trabecular bone cells (TBC). Within the MSC population, osteogenic clones showed higher levels of CReMM then non‐osteogenic ones. We used bone marrow derived osteogenic cell line (MBA‐15) to elaborate on the regulation of CReMM expression in correlation with cell proliferation and co‐expression with alkaline phosphatase (ALK). CReMM is highly expressed in proliferating cells and is inversely related to expression of ALK. MBA‐15 cells were challenged with dexamethasone (Dex) or 17β‐estradiol and quantification of CReMM at the protein (ELISA) and mRNA (RT‐PCR) levels had shown that Dex upregulated CReMM levels. Since CReMM is regulated by Dex, we analyzed the interaction of CReMM with the glucocorticoid receptor (GR), which mediates Dex action. Co‐immunopercipitation (Co‐IP) demonstrated an association between CReMM and GR. In summary, CReMM is a CHD protein expressed by osteoprogenitors, and we suggest it plays a role in mediating transcriptional response to hormones that coordinate osteoblast function. J. Cell. Physiol. © 2006 Wiley‐Liss, Inc.