Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessing the value of clean air in Jakarta-Indonesia: A spatial hedonic price analysis of housing values

It is commonly argued that clean air is a luxury good and most people in developing countries would hardly know what it means to consume it. Therefore, they do not consider an air pollution policy to be a priority. In Jakarta-Indonesia, there has recently been a new initiative to implement a program to improve air quality. However, it remains to be seen whether the people in Jakarta value this program enough to provide strong political support for its implementation. This paper applies a spatial hedonic property value analysis, using the combination of data on house values and their characteristics from the Indonesian Family Life Survey, and spatial data of the ambient level of six different pollutants to investigate the value of clean air for the people in Jakarta. The study finds a typical household in Jakarta is willing to pay roughly 9.7 per cent of its expenditure to halve the level of lead concentration. JEL Classification: R22; H40; Q21; C14
Assessment of colorectal cancer molecular features along bowel subsites challenges the conception of distinct dichotomy of proximal versus distal colorectum

Objective Colorectal cancer is typically classified into proximal colon, distal colon and rectal cancer. Tumour genetic and epigenetic features differ by tumour location. Considering a possible role of bowel contents (including microbiome) in carcinogenesis, this study hypothesised that tumour molecular features might gradually change along bowel subsites, rather than change abruptly at splenic flexure. Design Utilising 1443 colorectal cancers in two US nationwide prospective cohort studies, the frequencies of molecular features (CpG island methylator phenotype (CIMP), microsatellite instability (MSI), LINE-1 methylation and BRAF, KRAS and PIK3CA mutations) were examined along bowel subsites (rectum, rectosigmoid junction, sigmoid, descending colon, splenic flexure, transverse colon, hepatic flexure, ascending colon and caecum). The linearity and non-linearity of molecular relations along subsites were statistically tested by multivariate logistic or linear regression analysis. Results The frequencies of CIMP-high, MSI-high and BRAF mutations gradually increased from the rectum (<2.3%) to ascending colon (36–40%), followed by falls in the caecum (12–22%). By linearity tests, these molecular relations were significantly linear from rectum to ascending colon (p<0.0001), and there was little evidence of non-linearity (p>0.09). Caecal cancers exhibited the highest frequency of KRAS mutations (52% vs 27–35% in other sites; p<0.0001). Conclusions The frequencies of CIMP-high, MSI-high and BRAF mutations in cancer increased gradually along colorectum subsites from the rectum to ascending colon. These novel data challenge the common conception of discrete molecular features of proximal versus distal colorectal cancers, and have a substantial impact on clinical, translational and epidemiology research, which has typically been performed with the dichotomous classification of proximal versus distal tumours.
Comparison of methods for determining the effectiveness of antibacterial functionalized textiles

Antimicrobial functionalization of textiles is important for various applications, such as protection of textile materials from decomposition, generation of more effective wound dressings, and the prevention of infections or malodors resulting from bacterial growth. In order to test the efficacy of new products, their antibacterial activity needs to be evaluated. At present, several different procedures are being used for this purpose, hindering comparisons among different studies. The present paper compares five of these assays using a sample panel of different textiles functionalized with copper (Cu) and silver (Ag) as antibacterial agents, and discusses the suitability of these methods for different analytical requirements. Bacterial viability was determined by measuring the optical density at 600 nm, a colorimetric assay based on MTT (3-[4, 5-dimethylthiazol-2-yl]-2, 5 diphenyl tetrazolium bromide) conversion, an agar diffusion assay, and colony formation, either after culturing in media containing textile samples, or after recovery from textiles soaked with bacterial suspension. All experiments were performed with a Gram-negative (Escherichia coli) and a Gram-positive (Staphylococcus warneri) model organism. In general, the results yielded by the different methods were of good comparability. To identify the most suitable test system for the particular type of antibacterial coating, several factors need to be taken into account, such as choosing appropriate endpoints for analyzing passive or active antibacterial effects, selection of relevant microorganisms, correcting for potential interference by leaching of colored textile coatings, required hands on time, and the necessary sensitivity.
Analysis of a key regulatory region upstream of the Myf5 gene reveals multiple phases of myogenesis, orchestrated at each site by a combination of elements dispersed throughout the locus

Myf5 is the first myogenic regulatory factor to be expressed in the mouse embryo and it determines the entry of cells into the skeletal muscle programme. A region situated between -58 kb and -48 kb from the gene directs Myf5 transcription at sites where muscles will form. We now show that this region consists of a number of distinct regulatory elements that specifically target sites of myogenesis in the somite, limbs and hypoglossal cord, and also sites of Myf5 transcription in the central nervous system. Deletion of these sequences in the context of the locus shows that elements within the region are essential, and also reveals the combinatorial complexity of the transcriptional regulation of Myf5. Both within the -58 kb to -48 kb region and elsewhere in the locus, multiple sequences are present that direct transcription in subdomains of a single site during development, thus revealing distinct phases of myogenesis when subpopulations of progenitor cells enter the programme of skeletal muscle differentiation.
Structural insights and membrane binding properties of MGD1, the major galactolipid synthase in plants.

Monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG) are the major lipid components of photosynthetic membranes, and hence the most abundant lipids in the biosphere. They are essential for assembly and function of the photosynthetic apparatus. In Arabidopsis, the first step of galactolipid synthesis is catalyzed by MGDG synthase 1 (MGD1), which transfers a galactosyl residue from UDP-galactose to diacylglycerol (DAG). MGD1 is a monotopic protein that is embedded in the inner envelope membrane of chloroplasts. Once produced, MGDG is transferred to the outer envelope membrane, where DGDG synthesis occurs, and to thylakoids. Here we present two crystal structures of MGD1: one unliganded and one complexed with UDP. MGD1 has a long and flexible region (approximately 50 amino acids) that is required for DAG binding. The structures reveal critical features of the MGD1 catalytic mechanism and its membrane binding mode, tested on biomimetic Langmuir monolayers, giving insights into chloroplast membrane biogenesis. The structural plasticity of MGD1, ensuring very rapid capture and utilization of DAG, and its interaction with anionic lipids, possibly driving the construction of lipoproteic clusters, are consistent with the role of this enzyme, not only in expansion of the inner envelope membrane, but also in supplying MGDG to the outer envelope and nascent thylakoid membranes.
The PPH1 phosphatase is specifically involved in LHCII dephosphorylation and state transitions in Arabidopsis

The ability of plants to adapt to changing light conditions depends on a protein kinase network in the chloroplast that leads to the reversible phosphorylation of key proteins in the photosynthetic membrane. Phosphorylation regulates, in a process called state transition, a profound reorganization of the electron transfer chain and remodeling of the thylakoid membranes. Phosphorylation governs the association of the mobile part of the light-harvesting antenna LHCII with either photosystem I or photosystem II. Recent work has identified the redox-regulated protein kinase STN7 as a major actor in state transitions, but the nature of the corresponding phosphatases remained unknown. Here we identify a phosphatase of Arabidopsis thaliana, called PPH1, which is specifically required for the dephosphorylation of light-harvesting complex II (LHCII). We show that this single phosphatase is largely responsible for the dephosphorylation of Lhcb1 and Lhcb2 but not of the photosystem II core proteins. PPH1, which belongs to the family of monomeric PP2C type phosphatases, is a chloroplast protein and is mainly associated with the stroma lamellae of the thylakoid membranes. We demonstrate that loss of PPH1 leads to an increase in the antenna size of photosystem I and to a strong impairment of state transitions. Thus phosphorylation and dephosphorylation of LHCII appear to be specifically mediated by the kinase/phosphatase pair STN7 and PPH1. These two proteins emerge as key players in the adaptation of the photosynthetic apparatus to changes in light quality and quantity.
The Interactive Effect of Major Depression and Nonsuicidal Self-Injury on Current Suicide Risk and Lifetime Suicide Attempts

This study examined the main and interactive effects of MDD and lifetime nonsuicidal self-injury (NSSI) on current suicide risk and past suicide attempts. We predicted that individuals with a history of NSSI and current MDD would be at greater suicide risk than those with either risk factor alone. An interaction between lifetime MDD and NSSI was hypothesized for past suicide attempts. 204 substance dependent inpatients completed self-report measures and a diagnostic interview. Patients with both a history of NSSI and current MDD, relative to all other groups, had the greatest suicide risk. No support was found for the lifetime MDD by NSSI interaction. Conclusion: Findings suggest the relevance of both NSSI and MDD in suicide risk.
Translocation of long peptides by transporters associated with antigen processing (TAP)

The major histocompatibility complex (MHC)‐encoded transporters associated with antigen processing (TAP) translocate peptides from the cytosol into the lumen of the endoplasmic reticulum (ER) where they associate with MHC class I molecules. The length of class I‐binding peptides is usually 8–11 amino acids, but examples of significantly longer peptides have been described. The preferred lengths and upper and lower size limits for peptides translocated by TAP have not been determined in detail because in the currently used test systems, peptides are subject to proteolytic degradation. In the present study, three sets of individual peptides or partially randomized peptide libraries ranging between 6 and 40 residues were used that contained a radiolabeled tyrosine and a consensus sequence for ER‐specific N‐glycosylation at opposite ends, thus ensuring that only nondegraded peptides were monitored in the transport/glycosylation assay. For three different transporters, rat TAP1/2a, rat TAP1/2u and hTAP, the most efficient ATP‐dependent transport was observed for peptides with 8–12 amino acids. Hexamers and longer peptides of up to 40 amino acids were also translocated, albeit less efficiently. For two of the three sets of peptides analyzed, rat TAP1/2a showed a less stringent length selection than rat TAP1/2u and human TAP. The superior transport of the decamer of the TNKT. Y series was not due to faster degradation or less efficient glycosylation of shorter or longer length variants. A binding assay with TAP‐containing microsomes revealed a high affinity for the radiolabeled decamer (KD = 580 nM), while other length variants were clearly inferior in their binding affinities. Thus, TAP binds and preferentially translocates peptides with a length suitable for binding to MHC class I molecules, but peptides that are considerably longer may also be substrates. About 105 peptide binding sites per cell equivalent of microsomes were determined, providing an estimate for the number of TAP complexes in the ER membrane.
A Wi-Fi based passive technique for speed estimation in indoor environments

The conventional positioning systems require the users to carry an electronic device, which helps in the localization process. Device-free Passive Localization (DfPL) techniques are used to position the users in a passive manner such that they do not engage in the process. A typical DfPL setup comprises of Wi-Fi Access Points (APs) that transmit periodic signals to Monitoring Points (MPs). Any intrusion within the area of interest is detected by constantly examining the strength of Wi- Fi signals received at MPs. In this paper, we examine DfPL using 1 AP and 1 MP to estimate the speed of motion in a given indoor area. The proposed method is shown to achieve high accuracy.
An intrinsic Cramér-Rao bound on SO(3) for (dynamic) attitude filtering

In this note an intrinsic version of the Cramér-Rao bound on estimation accuracy is established on the Special Orthogonal group SO(3). It is intrinsic in the sense that it does not rely on a specific choice of coordinates on SO(3): the result is derived using rotation matrices, but remains valid when using other parameterizations, such as quaternions. For any estimator R̂ of R ∈ SO(3) we give indeed a lower bound on the covariance matrix of log (RR̂T), that is, the estimation error expressed in terms of group multiplication, whereas the usual estimation error (R̂-R) is meaningless on SO(3). The result is first applied to Whaba's problem. Then, we consider the problem of a continuous-time nonlinear deterministic system on SO(3) with discrete measurements subject to additive isotropic Gaussian noise, and we derive a lower bound to the estimation error covariance matrix. We prove the intrinsic Cramér-Rao bound coincides with the covariance matrix returned by the Invariant EKF, and thus can be computed online. This is in sharp contrast with the general case, where the bound can only be computed if the true trajectory of the system is known.
Plasma Cortisol Concentrations Before and After Social Stress in Rainbow Trout and Brown Trout

Two related experiments examined the relationship between plasma cortisol concentrations and the development of social hierarchies in fish. In the first, rainbow trout, Oncorhynchus mykiss, and brown trout, Salmo trutta, were observed for dominance interactions when confined within single‐species pairs for 4, 48, or 168 h. Subordinate members of a pair exhibited significantly higher cortisol concentrations than dominant and single fish, but the pattern of cortisol elevation differed between the two species, being quicker to rise and increasing to a higher level in rainbow trout. Cortisol concentrations were correlated with behavioural measurements; the more subordinate the behaviour exhibited by a fish, the higher its cortisol concentration. Social stress was a chronic stressor, and no acclimation to social status occurred during the week. In the second experiment, measurements of plasma cortisol were made before pairing of rainbow trout and then after 48 h of confinement in pairs. Subordinate fish demonstrated significantly higher concentrations of plasma cortisol both before and after social stress. It therefore appears that in addition to cortisol being elevated during periods of social stress, an association may exist between initial cortisol levels and the likelihood of a fish becoming subordinate.
Stevioside induces antihyperglycaemic, insulinotropic and glucagonostatic effects in vivo: studies in the diabetic Goto-Kakizaki (GK) rats.

Extracts of leaves from the plant Stevia rebaudiana Bertoni have been used in the traditional treatment of diabetes in Paraguay and Brazil. Recently, we demonstrated a direct insulinotropic effect in isolated mouse islets and the clonal beta cell line INS-1 of the glycoside stevioside that is present in large quantity in these leaves. Type 2 diabetes is a chronic metabolic disorder that results from defects in both insulin and glucagon secretion as well as insulin action. In the present study we wanted to unravel if stevioside in vivo exerts an antihyperglycaemic effect in a nonobese animal model of type 2 diabetes. An i.v. glucose tolerance test (IVGT) was carried out with and without stevioside in the type 2 diabetic Goto-Kakizaki (GK) rat, as well as in the normal Wistar rat. Stevioside (0.2 g/kg BW) and D-glucose (2.0 g/kg BW) were administered as i.v. bolus injections in anaesthetized rats. Stevioside significantly suppressed the glucose response to the IVGT in GK rats (incremental area under the curve (IAUC): 648 +/- 50 (stevioside) vs 958 +/- 85 mM x 120 min (control); P < 0.05) and concomitantly increased the insulin response (IAUC: 51116 +/- 10967 (stevioside) vs 21548 +/- 3101 microU x 120 min (control); P < 0.05). Interestingly, the glucagon level was suppressed by stevioside during the IVGT, (total area under the curve (TAUC): 5720 +/- 922 (stevioside) vs 8713 +/- 901 pg/ml x 120 min (control); P < 0.05). In the normal Wistar rat stevioside enhanced insulin levels above basal during the IVGT (IAUC: 79913 +/- 3107 (stevioside) vs 17347 +/- 2882 microU x 120 min (control); P < 0.001), however, without altering the blood glucose response (IAUC: 416 +/- 43 (stevioside) vs 417 +/- 47 mM x 120 min (control)) or the glucagon levels (TAUC: 5493 +/- 527 (stevioside) vs 5033 +/- 264 pg/ml x 120 min (control)). In conclusion, stevioside exerts antihyperglycaemic, insulinotropic, and glucagonostatic actions in the type 2 diabetic GK rat, and may have the potential of becoming a new antidiabetic drug for use in type 2 diabetes.
The role of antigen-specific and non-specific immunotherapy in the treatment of cancer

Immunotherapy in the treatment of cancer is increasing, particularly with the recent FDA approval of sipuleucel-T and ipilimumab. The efficacy of anti-tumor immunotherapies has been modest compared to their theoretical and pre-clinical promise. This review evaluates the promise and pitfalls of immunotherapy and highlight some of the obstacles to improving anti-tumor immunotherapy: the need for technical refinement of therapies, the need for an increased understanding of how best to combine therapies with traditional cytotoxic therapies, the inability of patients to mount an effective immune response either due to disease burden or tumor induced immune suppression, the significant toxicities associated with many immunotherapies, and the lack of strongly immunogenic antigens required by many therapies. Further, antigen-non-specific immunotherapies, including cytokines such as interleukins and interferons, immuno-stimulatory agents such as CpG oligonucleotides, or BCG, antibodies targeted against receptors such as the agonistic CD40 or inhibitory CTLA-4 antibodies, and enzyme inhibitors such as those targeting cyclo-oxygenase or indolamine-2,3-dioxygenase are discussed. In addition, potential mechanisms of these therapies such as direct anti-tumor effects, reversal of immune suppression, activation of innate immunity, and antigen-non-specific T-cell activation are reviewed. We also appraise the potential of these antigen-non-specific therapies to overcome some of the previously described pitfalls of immunotherapy. Lastly, we discuss a recent series of studies from our laboratory demonstrating the importance of antigen-non-specific ‘bystander activation’ of memory T-lymphocytes by immunomodulatory therapies such as interleukin-2 and the antigen-non-specific anti-tumor effects of these cells.
Preference for Insuring against Probable Small Losses: Insurance Implications

A series of laboratory studies of insurance decision making shows that people buy more insurance against events having a moderately high probability of inflicting a relatively small loss than against low-probability, high-loss events. Two explanations are discussed, both contrary to traditional utility theory. One postulates a utility function convex over losses. The second asserts that people refuse to protect themselves against losses whose probability is below some threshold. This research provides insight into other, often puzzling, facts about people's insurance behavior. Relevance for public policy is discussed. What determines whether people will act to protect themselves from the severe consequences arising from a low probability event? The answer to this question is vital for understanding how people cope with the risks from accidents, diseases, and natural hazards and for helping them to manage their lives more effectively in the face of such risks. The importance of this question has motivated a major research project concerned with one class of risks, those from natural hazards (floods and earthquakes), and one class of protective mechanisms, insurance. ' The project staff, under the direction of Howard Kunreuther, interviewed 2,000 homeowners residing in flood-prone areas, half of whom were insured and half uninsured. In addition, 1,000 homeowners residing in earthquakePaul Slovic, Ph.D., Baruch Fischhoff, Ph.D., and Sarah Lichtenstein, Ph.D., are Research Associates; Bernard G. Corrigan, M.A., is Research Programmer/Analyst; and Barbara J. Combs, M.A., is Research Assistant, all with Decision Research in Eugene, Oregon. Slovic, Fischhoff, and Lichtenstein have worked together for a number of years on psychological studies of judgment, risk taking, and decision processes. They have recently reviewed this field for the Annual Review of Psychology. Slovic and Fischhoff are consultants to the National Research Council's Committee on SocioEconomic Effects of Earthquake Predictions. Slovic is a member of the socio-political resource group of the National Academy of Sciences Study of Nuclear and Alternative Energy Systems and is Adjunct Professor, Department of Psychology, University of Oregon. 1 This research was supported by NSF-RANN Grant ATA 73-03064-A03 to the Wharton School of the University of Pennsylvania under subcontract to the Oregon Research Institute. We thank Howard Kunreuther, Daniel Kahneman, and Amos Tversky for their invaluable contributions to this project. Frank Conklin supplied us with a prototype for the farm game. Comments and reprint requests may be addressed to the authors at Decision Research, 1201 Oak Street, Eugene, Oregon 97401.
Mad enough to see the other side: Anger and the search for disconfirming information

The current research explored the effect of anger on hypothesis confirmation—the propensity to seek information that confirms rather than disconfirms one's opinion. We argued that the moving against action tendency associated with anger leads angry individuals to seek out more disconfirming information than sad individuals, attenuating the confirmation bias. We tested this hypothesis in two studies of experimentally primed anger and sadness on the selective exposure to hypothesis confirming and disconfirming information. In Study 1, participants in the angry condition were more likely to choose disconfirming information than those in the sad or neutral condition when given the opportunity to read more about a social debate, and reading the disconfirming information affected their subsequent attitude. Study 2 measured participants' opinions and information selection about the 2008 US Presidential Election and their desire to “move against” a person or object. Participants in the angry condition reported a greater tendency to oppose a person or object, which resulted in the attenuation of the confirmation bias.