Miracle-dz/UniFAR-FTUs huggingface dataset:
Risk Assessment and Gene Flow: Implication for Genetic Resource Conservation (A Review Article)

In this review the primary strategies employed in compiling a risk assessment for gene flow from a GM crop to a wild crop relative are outlined. A risk is defined as the likelihood of harm resulting from exposure to the hazard. The spread of new genes and genetic exchange between crops and their wild relatives by introgressive hybridization has been a reality ever since the birth of agriculture. The significance of such gene flow has received little interest, however, until the advent of molecular biotechnology and the emergence of genetically modified (GM) crops. In principle, the scope for the transfer of certain, completely novel transgenes from GM crops into wild relatives means that there is an increased capacity for rapid jumps in the adaptation profile of the recipient. This capacity carries risks for the genetic integrity and evolutionary survival of the wild species, and of the survival of other species with which it coexists. In evaluating such potential problems, one must first define the unwanted outcomes (hazards) as clearly as possible, and then measure the likelihood of their occurrence (exposure). The assessment of risk can be compiled (Risk = hazard × exposure). Risk is estimated as the product of the probability of exposure, P ( E ), and the conditional probability of harm given that exposure has occurred, P ( H|E ). That is, R = P ( E ) x P ( H|E ). In measuring risks in this way, it is important to consider the management of the crop, the ecology, demography and population genetics of the wild species, the number, nature and location of the transgene(s) and the extent of introgression within the natural setting. Crucially, these assessments should be made against comparable risks posed by non-GM cultivars of the same crop (i.e. baseline data) so that judgements can be made concerning the significance of any change envisaged. Keywords: Conservation, Gene flow, Genetic resources, Hazards, Risks DOI : 10.7176/ALST/73-02 Publication date : April 30 th 2019
Decision Making Under Risk on Independence Axiom: Lab Study of Traditional Merchant in Yogyakarta, Indonesia

This study presents basic analysis of individual preferences by experiment set and provides evidence that encounters expected utility theory (EUT). The main focus of this study is the independence axiom on decision making under risk which is required by EUT for rational behavior assumption. While people are difficult to follow the independence axiom, individual preferences cannot be predicted using EUT and alternative theory is required to predict individual preferences. The alternative theory of choice has been developed in many previous studies to give a different analysis instead of EUT. We also develop estimation analysis of factors affecting individual preferences according to independence axiom. In addition, this study provides an analysis of sex different by comparing both men and women preferences under risk. Allais paradox phenomena are performed for the design of systematically deviations proposed by prospect theory.
Relation between air-filled albumin microbubble and red blood cell rheology in the human myocardium. Influence of echocardiographic systems and chest wall attenuation.

BACKGROUND We have previously shown that the intravascular rheology of sonicated air-filled albumin microbubbles is similar to that of red blood cells (RBCs) and that their myocardial transit rate is also similar to that of RBCs in the beating canine heart. In the present study, we tested the hypothesis that the myocardial transit rates of these microbubbles reflect those of RBCs in humans at different coronary flow rates. METHODS AND RESULTS RBC and microbubble transit rates were measured in 17 patients undergoing coronary angiography: in 8, measurements were made only at rest, whereas in 9, they were performed both at rest and during a pacing-induced increase in coronary blood flow. A gamma-variate function was used to derive mean RBC and microbubble transit rates from the time-activity and time-intensity plots after the left main injection of RBCs and microbubbles, respectively. There was linear correlation between the myocardial transit rates with both tracers with the slope of the correlation determined by the specific echocardiographic system that was used. Microbubble transit rate consistently overestimated RBC transit rate due to artificial narrowing of the time-intensity curves caused by chest wall attenuation of the echocardiographic signal, which was confirmed through in vitro experiments. CONCLUSIONS There is close correlation between air-filled albumin microbubbles and RBC rheology in the human myocardium. The use of these microbubbles in the cardiac catheterization laboratory could, therefore, provide further insights into myocardial blood flow/myocardial blood volume relations in humans.
A controlled trial of intravaginal estriol in postmenopausal women with recurrent urinary tract infections.

BACKGROUND Recurrent urinary tract infections are a problem for many postmenopausal women. Estrogen replacement restores atrophic mucosa, lowers vaginal pH, and may prevent urinary tract infections. METHODS We enrolled 93 postmenopausal women with a history of recurrent urinary tract infections in a randomized, double-blind, placebo-controlled trial of a topically applied intravaginal estriol cream. Midstream urine cultures were obtained at enrollment, monthly for eight months, and whenever urinary symptoms occurred. Vaginal cultures and pH measurements were obtained at entry and after one and eight months. The women were assigned to receive either estriol (n = 50) or placebo (n = 43), both administered intravaginally; 36 and 24, respectively, completed the eight months of follow-up. RESULTS The incidence of urinary tract infection in the group given estriol was significantly reduced as compared with that in the group given placebo (0.5 vs. 5.9 episodes per patient-year, P < 0.001). Survival analysis showed that more of the women in the estriol group than in the placebo group remained free of urinary tract infection (P < 0.001). Lactobacilli were absent in all vaginal cultures before treatment and reappeared after one month in 22 of 36 estriol-treated women (61 percent) but in none of the 24 placebo recipients (P < 0.001). With estriol the mean vaginal pH declined from 5.5 to 3.8 (P < 0.001), whereas there was no significant change with placebo. The rate of vaginal colonization with Enterobacteriaceae fell from 67 percent to 31 percent in estriol recipients but was virtually unchanged (from 67 to 63 percent) in the placebo recipients (P < 0.005). Side effects were minor, but caused 10 estriol recipients (28 percent) and 4 placebo recipients (17 percent) to discontinue treatment. CONCLUSIONS The intravaginal administration of estriol prevents recurrent urinary tract infection in postmenopausal women, probably by modifying the vaginal flora.
Application of higher order spectral analysis to cubically nonlinear system identification

In this study, digital higher-order spectral analysis and frequency-domain Volterra system models are utilized to yield a practical methodology for the identification of weakly nonlinear time-invariant systems up to third order. The primary focus is on consideration of random excitation of nonlinear systems and, thus, the approach makes extensive use of higher-order spectral analysis to determine the frequency-domain Volterra kernels, which correspond to linear, quadratic, and cubic transfer functions. Although the Volterra model is nonlinear in terms of its input, it is linear in terms of its unknown transfer functions. Thus, a least squares approach is used to determine the optimal (in a least squares sense) set of linear, quadratic, and cubic transfer functions. Of particular practical note, is the fact that the approach of this paper is valid for non-Gaussian, as well as Gaussian, random excitation. It may also be utilized for multitone inputs. The complexity of the problem addressed in this paper arises from two principal causes: (1) the necessity to work in a 3D frequency space to describe cubically nonlinear systems, and (2) the necessity to characterize the non-Gaussian random excitation by computing higher-order spectral moments up to sixth order. A detailed description of the approach used to determine the nonlinear transfer functions, including considerations necessary for digital implementation, is presented. >
A software model for precision agriculture for small and marginal farmers

Precision Agriculture (PA) was originally developed to address variability in soil and crop parameters for large-scale agriculture in developed countries. The general concepts of PA can also be adapted for farm-based agriculture for small and marginal farmers in Developing Countries. This approach is characterized by a farmer-soil-crop database acquired from the field, crop calendars provided by agricultural experts, real-time acquisition of parameters such as temperature and rainfall through sensors, and an analytical model that simulates the crop calendar using static, semi-static and dynamic inputs, leading to farmer- and crop-level support advisories delivered through devices such as mobile phones and tablets.
Technology, trade, and prices

This thesis considers the structure of international production and trade. Chapter 2 uses direct information on factor input requirements to consider which elements best explain the patterns of actual technologies. If there is factor price equalization, all countries will share the same capital-labor ratios, regardless of endowments. I find that actual technologies are inconsistent with this view. Estimates of country productivities which ignore the patterns of factor substitution are incorrect. Once allowances are made for differences in capitallabor endowments, 90% of the variation in output per worker can be explained by countryspecific and industry-specific parameters. I also find that factor-augmenting productivities are negatively related to factor endowments. In Chapter 3, I consider the implications of these technological differences for measures of the factor content of trade. Typically, the factor content of trade is measured by applying one country's technology matrix to the output of all countries. Contrary to theory, this approach finds no relationship between factor endowments and the factor content of trade. Since countries use techniques which are biased towards their abundant factor, the factor content of trade flows in the correct direction when measured using actual technologies. However, the mystery of the missing trade remains: even when factor contents are measured correctly, they are a very small percentage of factor endowments. In Chapter 4, I use disaggregated price data from Canada and the United States to consider the propostion that the price of goods is equalized across countries. Using time-series cointegration methods, I find evidence in favour of the law of one price for some, mostly homogeneous traded goods. However, most goods, both traded and nontraded, provide little support for the law of one price. Moreover, deviations from the law of one price can persist for many years. Thesis Supervisor: Rudiger Dornbusch Title: Ford International Professor of Economics Thesis Supervisor: Daron Acemoglu Title: Associate Professor of Economics
Pityriasis versicolor‐A Study of 200 Cases in a Tropical Skin Clinic: Pityriasis versicolor — Eine Untersuchung an 200 Fällen in einer tropischen Hautklinik

Summary: A study of pityriasis versicolor was done in a total of 100 each of males and females. Incidence of the disease was equally high during summer (April) and winter (October). The adolescents were affected mainly. General hygiene showed no relevance to the disease. The lesions commonly occurred over the upper trunk and face. Hands, feet and ears were rarely involved. Achromic, chromic and a combination of both the varieties were equally common. Follicular and palpable lesions were not uncommon. Various other clinical varieties have been observed and described. Acne vulgaris and dermatophytoses were the common associated dermatoses. Striae distensae was seen frequently, especially in young girls. Wet mount in KOH was positive in all cases. A definite correlation of sebum and probably androgens to the disease has been observed and discussed.
Evaluation rapide du diamètre d'un graphe

Resume. Lors de l’analyse de graphes, il est important de connaitre leurs proprietes afin de pouvoir par exemple identifier leur structure et les comparer. Une des caracterisations importante de ces graphes repose sur le fait de determiner s’il s’agit ou non d’un "petit monde". Pour ce faire, la valeur du diametre du graphe est essentielle. Or la mesure du diametre est pour un tres grand graphe, une operation extremement longue. Nous proposons un algorithme en deux phases qui permet d’obtenir rapidement une estimation du diametre d’un graphe avec une proportion d’erreur faible. En reduisant cet algorithme a une seule phase et en acceptant une marge d’erreur plus elevee, nous obtenons une estimation tres rapide du diametre. Nous testons cet algorithme sur deux grands graphes de terrain (plus d’un million de nœuds) et comparons ses performances avec celles d’un algorithme de reference BFS (Breadth-First Search). Les resultats obtenus sont decrits et commentes.
Genetic association between 1425G/A SNP in PRKCH and hypertrophic cardiomyopathy in a Chinese population

Hypertrophic cardiomyopathy is a heterogeneous myocardial disorder with a broad spectrum of clinical presentation and morphologic features. Previous reports indicated that protein kinase C pathway as a major determinant of cardiac hypertrophy and heart failure. Population-based analyses of the association between PRKCH gene (encoded PKCη) and HCM has not been performed yet. The purpose of this study is to investigate the association of the nonsynonymous SNP (1425G/A) in PRKCH gene and hypertrophic cardiomyopathy in a Chinese population. 323 patients with HCM and 326 controls were examined using a case-control methodology. The 1425G/A SNP in PRKCH was genotyped by allele-specific real-time PCR assay. The 1425G/A SNP in PRKCH increased the risk of HOCM (hypertrophic obstructive cardiomyopathy) (OR=1.427, 95% confidence interval, 1.013 to 2.012, P=0.046) under a dominant model. After age- and sex-adjustment, the significant associations remained in HOCM (for GG +AG versus AA, OR= 2.497, 95% confidence interval, 1.01 to 6.17; P=0.047). The 1425G/A SNP in PRKCH increases the risk of hypertrophic obstructive cardiomyopathy in the Chinese population.
Rubisco Oligomers Composed of Linked Small and Large Subunits Assemble in Tobacco Plastids and Have Higher Affinities for CO2 and O21[C][W][OA]

Manipulation of Rubisco within higher plants is complicated by the different genomic locations of the large (L; rbcL) and small (S; RbcS) subunit genes. Although rbcL can be accurately modified by plastome transformation, directed genetic manipulation of the multiple nuclear-encoded RbcS genes is more challenging. Here we demonstrate the viability of linking the S and L subunits of tobacco (Nicotiana tabacum) Rubisco using a flexible 40-amino acid tether. By replacing the rbcL in tobacco plastids with an artificial gene coding for a S40L fusion peptide, we found that the fusions readily assemble into catalytic (S40L)8 and (S40L)16 oligomers that are devoid of unlinked S subunits. While there was little or no change in CO2/O2 specificity or carboxylation rate of the Rubisco oligomers, their Kms for CO2 and O2 were reduced 10% to 20% and 45%, respectively. In young maturing leaves of the plastome transformants (called ANtS40L), the S40L-Rubisco levels were approximately 20% that of wild-type controls despite turnover of the S40L-Rubisco oligomers being only slightly enhanced relative to wild type. The reduced Rubisco content in ANtS40L leaves is partly attributed to problems with folding and assembly of the S40L peptides in tobacco plastids that relegate approximately 30% to 50% of the S40L pool to the insoluble protein fraction. Leaf CO2-assimilation rates in ANtS40L at varying pCO2 corresponded with the kinetics and reduced content of the Rubisco oligomers. This fusion strategy provides a novel platform to begin simultaneously engineering Rubisco L and S subunits in tobacco plastids.
Prognostic factors for survival in adult patients with recurrent glioma enrolled onto the new approaches to brain tumor therapy CNS consortium phase I and II clinical trials.

PURPOSE Prognostic factor analyses have proven useful in predicting outcome in patients with newly diagnosed malignant glioma. Similar analyses in patients with recurrent glioma could affect the design and conduct of clinical trials substantially. PATIENTS AND METHODS Between 1995 and 2002, 333 adults with recurrent gliomas were enrolled onto 10 phase I or II trials of systemic or local therapy. The studies had similar inclusion criteria and were conducted within the New Approaches to Brain Tumor Therapy CNS Consortium. Ninety-three percent of the patients have died. Cox proportional hazards (PH) regression and recursive partitioning analysis (RPA) were performed to identify prognostic factors. RESULTS Factors associated with an increased risk of death were increased age, lower Karnofsky performance score (KPS), initial and on-study histologies of glioblastoma multiforme (GBM), corticosteroid use, shorter time from original diagnosis to recurrence, and tumor outside frontal lobe. The final PH model included initial histology of GBM (relative risk [RR] = 2.01), 10-year increase in age (RR = 1.23), KPS less than 80 (RR = 1.54), and corticosteroid use (RR = 1.49). RPA resulted in seven classes. Median survival time was poorest in non-GBM patients with KPS less than 80 or GBM patients, age 50 years, corticosteroid use (4.4 months; 95% CI, 3.6 to 5.4 months); median survival was best in patients with initial histology other than GBM with KPS 80 and tumor confined to the frontal lobe (25.7 months; 95% CI, 18.7 to 52.5), and was 7.0 months (95% CI, 6.2 to 8.0 months) for all patients. CONCLUSION Initial histology, age, KPS, and corticosteroid use are prognostic for survival in recurrent glioma patients. To allow comparisons across phase II trials, enrollment criteria may need to be restricted.
Urinary tract infection in old age: over-diagnosed and over-treated.

A careless and uncritical approach by some clinicians to the diagnosis of urinary tract infection in frail elderly people has resulted in the condition being overdiagnosed and over-treated. Symptoms of lower urinary tract infection are easily recognized and include dysuria, frequency and urgency. But even such typical symptoms require cautious interpretation, as they are common in elderly people without infection [1]. Is laboratory diagnosis by urine culture a more reliable diagnostic tool for urinary tract infection in old age? The isolation of >100 000 colony-forming units of a single species per ml in a mid-stream specimen of urine is regarded as ‘significant’ bacteriuria. This is based on criteria described by Kass [2], although Kass’s studies were performed in healthy young women. There are problems in using these criteria as the standard, since bacteriuria is common in old age, occurring for example in 25–40% of non-catheterized patients in long-stay units [3, 4]. Pyuria is also common in nursing-home residents—both in the presence and absence of bacteriuria—and should not be the sole determinant of the need for antimicrobial treatment [5]. The presence of bacteria in a urine sample does not help to distinguish between true infection and colonization or contamination. The chances of detecting coincidental asymptomatic bacteriuria in a frail elderly patient are high [6, 7]. A familiar scenario begins when a frail elderly patient is non-specifically unwell, and nurses ask if a urinary tract infection might be responsible. No other symptoms or signs of systemic infection are present but a urine specimen is sent for culture. The microbiology laboratory reports the presence of bacteria in the urine, and the ward doctor (perhaps without assessing the patient) prescribes an antibiotic. This leads to overuse of antimicrobials, provides opportunities for the colonizing organism to acquire antimicrobial resistance and exposes the patient to unnecessary antibiotic side-effects [8–11]. Awareness of this situation has led to the suggestion that urine culture in older patients be abandoned, but this remains one of the most commonly requested bacteriological investigations in elderly hospital patients [12]. Another common event is when ‘routine’ urinalysis is carried out for elderly patients in the absence of clinical symptoms suggestive of infection, and a positive stick test results in a urine sample being sent for culture. This misguided practice is perpetuated by the notion that urinary infection can occur in an asymptomatic older patient, and ignores the fact that asymptomatic bacteriuria is not an indication for treatment [13]. While dipstick testing and urine clarity can predict which urine specimens are likely to be culture-negative, the use of these procedures should be highly selective and confined to symptomatic patients [14].
On imperfect node protection in complex communication networks

Motivated by recent research on complex networks, we study enhancing complex communication networks against intentional attack which takes down network nodes in a decreasing order of their degrees. Specifically, we evaluate an effect which has been largely ignored in existing studies; many real-life systems, especially communication systems, have protection mechanisms for their important components. Due to the existence of such protection, it is generally quite difficult to totally crash a protected node, though partially paralyzing it may still be feasible. Our analytical and simulation results show that such ‘imperfect’ protections generally speaking still help significantly enhance network robustness. Such insight may be helpful for the future developments of efficient network attack and protection schemes.