Miracle-dz/UniFAR-FTUs huggingface dataset:
Targeted Sequencing Reveals Large-Scale Sequence Polymorphism in Maize Candidate Genes for Biomass Production and Composition

A major goal of maize genomic research is to identify sequence polymorphisms responsible for phenotypic variation in traits of economic importance. Large-scale detection of sequence variation is critical for linking genes, or genomic regions, to phenotypes. However, due to its size and complexity, it remains expensive to generate whole genome sequences of sufficient coverage for divergent maize lines, even with access to next generation sequencing (NGS) technology. Because methods involving reduction of genome complexity, such as genotyping-by-sequencing (GBS), assess only a limited fraction of sequence variation, targeted sequencing of selected genomic loci offers an attractive alternative. We therefore designed a sequence capture assay to target 29 Mb genomic regions and surveyed a total of 4,648 genes possibly affecting biomass production in 21 diverse inbred maize lines (7 flints, 14 dents). Captured and enriched genomic DNA was sequenced using the 454 NGS platform to 19.6-fold average depth coverage, and a broad evaluation of read alignment and variant calling methods was performed to select optimal procedures for variant discovery. Sequence alignment with the B73 reference and de novo assembly identified 383,145 putative single nucleotide polymorphisms (SNPs), of which 42,685 were non-synonymous alterations and 7,139 caused frameshifts. Presence/absence variation (PAV) of genes was also detected. We found that substantial sequence variation exists among genomic regions targeted in this study, which was particularly evident within coding regions. This diversification has the potential to broaden functional diversity and generate phenotypic variation that may lead to new adaptations and the modification of important agronomic traits. Further, annotated SNPs identified here will serve as useful genetic tools and as candidates in searches for phenotype-altering DNA variation. In summary, we demonstrated that sequencing of captured DNA is a powerful approach for variant discovery in maize genes.
The Non-Linear Relationship between Agricultural Productivity and the Environment and its Effects on Human Health and the Economy

It has become increasingly clear that the relationship between agricultural productivity and the environment is highly non-linear. In this dissertation I evaluate yield measures commonly used to quantify agricultural productivity and demonstrate that the largest shocks, damages causing crops to become unharvestable, are omitted from the most commonly used productivity measure. I find that these losses are highly non-linear, and that infrequent but extreme damages account for substantial losses to global agriculture yet are often ignored. Accounting for these non-linearities, I examine the impact of climate (temperature, rainfall) and environmental condition (flood, drought) induced changes in agricultural productivity on human health (mortality rates) and the economy (farmer loans). I find that extreme climate conditions have significant impacts on agriculture and that losses in agricultural productivity, in turn, increase mortality rates and the amount of money borrowed by farmers in Southeast Asia. These findings have implications for our understanding of the broader importance of climate vulnerability in agriculture and how governments might value climate adaptation options for agriculture.
From Individual Wellbeing to Regional Priorities: Concepts and Measures to Assist Policy Makers

The understanding of subjective perceptions of wellbeing, that is, the perceived needs and current levels of satisfactions of people, could provide valuable information for policy and decision makers. It would allow for the mapping of the envisaged impacts of policy against things that people value and care about, thus providing information about the positive and negative potential of different policy options to impact upon human welfare. In this book, Dr Silva Larson takes us on a journey of explorations into the things that are important to people. She argues that an approach which takes into account both what people value most and how satisfied they are with the current state of affairs would assist decision makers with identifying perceived regional priorities. Further, she proposes and describes one such approach, that of using a quantitative composite value that combines both types of information, and demonstrates, using two shires in the Great Barrier Reef region of Australia as examples, how this can be done. The resulting “action lists” identify and quantify the unsatisfied needs of most importance to most people in the region, that is, factors that have high potential to improve the quality of life of residents, if restored.
A Comparison of Job Satisfaction among Filipino Nurses Employed in the Philippines and Overseas

Background and Objective: The shortage of nurses has led to increasing competition in the recruitment and retention of nurses globally. According to literature, retention of nurses is correlated with job satisfaction, making it an important topic for research. This study compared the level of general, intrinsic, and extrinsic job satisfaction of Filipino nurses employed locally and overseas. It identified the major motivators and problems that affect their job satisfaction. Methods and Research Participants: Eighty-four nurses were surveyed using the Minnesota Satisfaction Questionnaire. Fifty-five were locally-employed, while 29 were overseas Filipino nurses. The Mann-Whitney U Test was used to determine the significant difference in the level of satisfaction among the two groups. Answers on the open-ended questions were used to validate the quantitative data. Results: The results showed that Filipino nurses employed both locally and overseas have an average level of general satisfaction. Both groups also showed a high degree of intrinsic satisfaction and an average degree of extrinsic satisfaction. There is no significant difference found in the level of general, intrinsic, and extrinsic job satisfaction of locally and overseas employed Filipino nurses. Conclusion: The study found that social service, an intrinsic factor, is the major motivating force of job satisfaction. Workload, an extrinsic factor, is the most common problem encountered for both groups of nurses. Salary serves as one of the factors that keeps Filipino nurses overseas satisfied, while it is one of the factors that causes dissatisfaction among locally-employed nurses.
Demonstration and Electrical Performance Investigation of Wafer-Level Cu Oxide Hybrid Bonding Schemes

Wafer-level Cu oxide hybrid bonding owns a number of merits, including simultaneous formations of electrical and mechanical bonds, underfill free, high alignment accuracy, increasing bond strength, and excellent reliability performance in 3-D integration. This letter demonstrates the fabrication of wafer-level Cu oxide hybrid bonding. Investigations of experimental and electrical simulation data of Cu oxide hybrid bonding structures are reported. Their alignment accuracy, frequency responses, and passive elements are compared for 3-D integration applications.
Elucidation of the Molecular Interaction between miRNAs and the HOXA9 Gene, Involved in Acute Myeloid Leukemia, by the Assistance of Argonaute Protein through a Computational Approach

Acute myeloid leukemia is a well characterized blood cancer in which the unnatural growth of immature white blood cell takes place, where several genes transcription is regulated by the micro RNAs (miRNAs). Argonaute (AGO) protein is a protein family that binds to the miRNAs and mRNA complex where a strong binding affinity is crucial for its RNA silencing function. By understanding pattern recognition between the miRNAs-mRNA complex and its binding affinity with AGO protein, one can decipher the regulation of a particular gene and develop suitable siRNA for the same in disease condition. In the current work, HOXA9 gene has been selected from literature, whose deregulation is well-established in acute myeloid leukemia. Four miRNAs (mir-145, mir-126, let-7a, and mir-196b) have been selected to target mRNA of HOXA9 (NCBI accession No. NM_152739.3). The binding interaction between mRNAs and mRNA of HOXA9 gene was studied computationally. From result, it was observed mir-145 has highest affinity for HOXA9 gene. Furthermore, the interaction between miRNAs-mRNA duplex of all chosen miRNAs are docked with AGO protein (PDB ID: 3F73, chain A) to study their interaction at molecular level through an in silico approach. The residual interaction and hydrogen bonding are inspected in Discovery Studio 3.5 suites. The current investigation throws light on understanding of AGO-assisted miRNA based gene silencing mechanism in HOXA9 gene associated in acute myeloid leukemia computationally.
The long-run relationship between nominal interest rates and inflation of the Asian developing countries

Monetary aggregates movements and their influence on domestic economy are important and essential to policy makers and researchers. To the policy makers, the influence and the existence of special relationship between monetary aggregates and other macroeconomic variables are important in designing policies such as to curb inflation pressure, stimulating economic growth and reduce unemployment problem. On the other hand, the researchers may use these aggregates and their relations with macroeconomic variables to estimate a complex macro model of an economy. In Malaysia, traditionally, monetary aggregate has been the major monetary policy strategy. Targeting M1, M2 and M3 has been the main policy targets until the mid- I 990s. However, by the mid-1990s, the Central Bank of Malaysia (BNM) has shifted their policy strategy from monetary targeting to interest rate targeting. As a matter of fact, the de-emphasizing of monetary aggregates as intermediate target begins with the de-emphasizing of MI in 1987. One of the major reasons for de-emphasizing monetary aggregates as policy variables is the availability of alternative interest-bearing financial assets in the markets as a result of active financial liberalization in recent years. As a result of the shifting of money into interest- bearing financial assets, the relationship between money and income becomes unstable, consequently, monetary policy actions using monetary aggregates as targets become ineffective. Our question is: Does the move made by BNM to de-emphasis monetary aggregates point to the fact that money does not affect output in Malaysia? In other words, one can ask: Does changes in money bring about in the changes on real economic variables? If none of the real economic variables would change in response to the change in money, we say that money is neutral. The neutrality of money has important implications for the role of monetary policy. In monetary-business-cycle (MBC) models.
Emergency obstetric hysterectomy.

OBJECTIVE To assess the frequency of obstetric hysterectomy, its indications and associated maternal and perinatal morbidity and mortality. METHODS The retrospective observational analytical study was conducted at the Department of Obstetrics and Gynaecology, Unit-I, Jinnah Postgraduate Medical Centre, Karachi from January 2003 to December 2009. Records of all patients who had underone hysterectomy at the study centre during the study period were explored for age, parity, booking status indication and the type of operation performed. Maternal and foetal morbidity and mortality were also recorded. SPSS 13.0 was used for statistical analysis. RESULTS Against the total 44,612 deliveries during the period, 121 hysterectomies were performed for obstetric indications. The frequency of the procedure, as such, was 1 in 368 (0.27%) deliveries. The major indications were ruptured uterus in 57 (47.1%), and severe postpartum haemorrhage due to atony of uterus in 35 (28.9%). Other indications included severe haemorrhage due to placental abnormalities in 14 (11.6%); placenta previa in 3 (2.5%); abruptio placenta in 4 (3.3%); and severe infection following vaginal delivery in 3 (2.5%). Infection was the commonest complication seen in 14 (11.6%) patients. There were 11 (9.0%) maternal deaths and 65 (53.7%) perinatal deaths. CONCLUSION Emergency obstetric hysterectomy remains a necessary tool for consultant obstetricians. Acting at the optimal time with clear judgment, and professional surgical technique can reduce morbidity and mortality in such cases.
African regionalism and EU-African interregionalism

(The book:) Taking into account the expanded European Union (EU), this volume highlights external relations in the framework of the development of different forms of regional arrangements, within the globalized world of the 21st century. This volume offers: • A vigorous response to conventional wisdom on EU international identity • An exploration of key issues of regionalism versus globalization and the potential for world economic and political governance through regionalism • A key resource for postgraduate or undergraduate study and research of international relations, European studies, comparative politics and international political economy This distinctive collection is contributed to by the following established scholars: Catherine Borve Arnesen, Kjell A. Eliassen, Andrew Gamble, Bjorn Hettne, Richard Higgott, George Howard Joffe, Thomas Meyer, Pier Carlo Padoan, Sebastian Santander, Alberta M. Sbragia, Reimund Seidelmann, Fred Soderbaum, Mario Telo, Goran Therborn and Alvaro Vasconcelos providing the reader with a comparative analysis of regional arrangements.
Oracle Inequalities and Optimal Inference under Group Sparsity

We consider the problem of estimating a sparse linear regression vector s* under a gaussian noise model, for the purpose of both prediction and model selection. We assume that prior knowledge is available on the sparsity pattern, namely the set of variables is partitioned into prescribed groups, only few of which are relevant in the estimation process. This group sparsity assumption suggests us to consider the Group Lasso method as a means to estimate s*. We establish oracle inequalities for the prediction and l2 estimation errors of this estimator. These bounds hold under a restricted eigenvalue condition on the design matrix. Under a stronger coherence condition, we derive bounds for the estimation error for mixed (2,p)-norms with 1=p=8. When p=8, this result implies that a threshold version of the Group Lasso estimator selects the sparsity pattern of s* with high probability. Next, we prove that the rate of convergence of our upper bounds is optimal in a minimax sense, up to a logarithmic factor, for all estimators over a class of group sparse vectors. Furthermore, we establish lower bounds for the prediction and l2 estimation errors of the usual Lasso estimator. Using this result, we demonstrate that the Group Lasso can achieve an improvement in the prediction and estimation properties as compared to the Lasso.
Effects of Added Casein on Goitrogenic Action of Different Dietary Levels of Soybeans.∗

Summary The goitrogenic effect of raw soybeans was seen in significant increases of both fresh and dry weights of thyroid glands when a diet containing 60% of beans was fed to rats, and a significant increase in the dry weight only of the gland when a diet containing 35% of raw soybeans was fed. The goitrogenic effect of 35% or 60% of raw soybeans in rat diets was obliterated by adding casein to the diets. This result was not attributable to iodine in the casein.
Unsaid but not forgotten: patients' unvoiced desires in office visits.

OBJECTIVES To examine patient, physician, and health care system characteristics associated with unvoiced desires for action, as well as the consequences of these unspoken requests. PATIENTS AND METHODS Patient surveys were administered before, immediately after, and 2 weeks after outpatient visits in the practices of 45 family practice, internal medicine, and cardiology physicians working in a multispecialty group practice or group model health maintenance organization. Data were collected at the index visit from 909 patients, of whom 97.6% were surveyed 2 weeks after the outpatient visit. Before the visit, patients rated their trust in the physician, health concerns, and health status. After the visit, patients reported on various types of unexpressed desires and rated their visit satisfaction. At follow-up, patients rated their satisfaction, health concerns, and health status, and also described their postvisit health care use. Evaluations of the visit were also obtained from physicians. RESULTS Approximately 9% of the patients had 1 or more unvoiced desire(s). Desires for referrals (16.5% of desiring patients) and physical therapy (8.2%) were least likely to be communicated. Patients with unexpressed desires tended to be young, undereducated, and unmarried and were less likely to trust their physician. Patients with unvoiced desires evaluated the physician and visit less positively; these encounters were evaluated by physicians as requiring more effort. Holding an unvoiced desire was associated with less symptom improvement, but did not affect postvisit health care use. CONCLUSIONS Patients' unvoiced needs affect patients' and physicians' visit evaluations and patients' subjective perceptions of improvement. Implications of these findings for clinical practice are examined.
Role of the renin-angiotensin system in post-transplantation hypertension in patients with multiple kidneys.

To define the role of the renin-angiotensin system in post-transplantation hypertension we studied 12 hypertensive recipients of renal transplants. The patients received saralasin acetate, an angiotensin II antagonist, while on a normal sodium diet and again after seven days of sodium restriction. In six patients with only one kidney, saralasin did not lower blood pressure on either diet; salt depletion did not lower systolic or diastolic blood pressures. In six patients with more than one kidney, salt depletion also did not lower blood pressure; however, salt depletion plus saralasin lowered their systolic pressures from a mean (+/- S.E.M.) of 146 +/- 9 to 128 +/- 8 mm Hg, and mean diastolic pressures fell from 103 +/- 5 to 89 +/- 5 (P less than 0.001). In four of five patients renal-vein renin activity was greater in one or more host kidneys than in the transplant kidney (or kidneys). Although pre-transplant blood pressure was the same in both groups, post-transplantation hypertension is more likely to be angiotensin II-dependent in patients with more than one kidney.
High photosynthetic rate of a chlorophyll mutant of cotton.

In a chlorophyll mutant (virescent) and wild-type cotton (Gossypium hirsutum L.), a number of photosynthetic parameters have been measured and compared with those published for other chlorophyll mutants. (a) The photosynthetic rates at 230 w/m(2) (400-700 nm) from a tungsten lamp were 36.8 mg CO(2) fixed/dm(2). hr (virescent) and 39.5 mg CO(2) fixed/dm(2). hr (wild-type). On a chlorphyll basis, the photosynthetic rates were 36.8 and 12.1 mg CO(2) fixed/mg chl.hr, respectively. (b) The photosynthetic rates at 13 w/m(2) (400-700 nm) from a tungsten source were 7.1 mg CO(2) fixed/dm(2). hr (virescent) and 7.4 mg CO(2) fixed/dm(2). hr (wild-type). On a chlorophyll basis, the photosynthetic rates were 6.0 and 1.4 mg CO(2) fixed/mg chl.hr, respectively. (c) The chlorophyll a/b ratios of the virescent and wild-type leaves were 3.3 and 4.1 (d) The chlorophyll/carotenoid ratios for the virescent and wild-type leaves were 3.2 and 7.3, respectively. (e) The photosynthetic carbon metabolism of the chlorophyll mutant was through the reductive pentose phosphate cycle. (f) The CO(2) compensation points for the virescent and wild-type plants were similar. (g) The mutant and wild-type leaves have the same quantum yield in the red part of the visible spectrum, but the virescent leaves have a lower quantum yield in the blue part of the spectrum. (h) Virescent and wild-type leaves contain similar levels on a protein basis of several reductive pentose phosphate cycle enzymes.
Finite element analysis and experimental validation of eddy current losses in permanent magnet machines with fractional-slot concentrated windings

Permanent-magnet machines with fractional-slot concentrated windings are easy to manufacture. Their popularity therefore is steadily increasing. Without a proper design, however, the induced eddy-current losses in the solid rotor get rather high. The modeling and the prediction of eddy-current losses for these machines are thus very important during the design process. This paper focuses on the finite-element analysis and the experimental validation of eddy-current losses for this kind of machine with a small axial length. Two-dimensional and three-dimensional transient finite-element models are developed for computing the eddy-current losses. The rotor motion is taken into account using an Arbitrary Lagrangian-Eulerian formulation. The total iron losses are measured experimentally and a method to separate the rotor iron losses from the total iron losses is presented. The validation results show that the two-dimensional finite-element model overestimates the losses due to the end-effects being neglected. The three-dimensional model agrees much better with the measurements in both no-load and on-load operations.
In-vitro effects of polyphenols from cocoa and &bgr;-sitosterol on the growth of human prostate cancer and normal cells

Cocoa contains many different types of physiologically active components. It was shown that cocoa beans are rich in specific antioxidants such as flavonoids, catechins, epicatechins and proanthocyanidins. Additionally, &bgr;-sitosterol, the most common phytosterol, may play a protective role in the development of cancer. The aim of this in-vitro study was to evaluate the inhibitory effect of different cocoa polyphenols extracts, alone or combined with &bgr;-sitosterol, on two human prostate cancer cell lines (nonmetastatic 22Rv1 cells and metastatic DU145 cells) and a normal human prostate cell line (RWEP-1). A synergy between &bgr;-sitosterol and cocoa polyphenols extract was also researched. Cells were treated independently with five products from 1 to 72 h: (1/) synthetic &bgr;-sitosterol, (2/) a cocoa polyphenols extract supplemented with &bgr;-sitosterol, (3/) three different cocoa polyphenols extracts naturally containing &bgr;-sitosterol. In the experiment, &bgr;-sitosterol was tested from 10−6 to 10−3%; cocoa polyphenols extract supplementation was with 0.72% &bgr;-sitosterol; finally cocoa polyphenols extracts were added to the cells at very low concentrations ranging from 0.001 to 0.2%. The growth and viability of cells were measured using colorimetric assay at 1, 3, 6, 24, 48 and 72 h of treatment. IC50 and IC100 corresponding to the concentration leading to a decrease of 50% and 100% of cell growth were determined. At the highest tested concentration, cocoa polyphenols extracts induced a complete inhibition of growth of metastatic and nonmetastatic cancer cell lines. In addition, cocoa polyphenols extracts were more active against local cancer cells than against metastatic cells. Moreover, at the highest tested concentration, cocoa polyphenols extracts are not effective on a normal prostate cell lines. &bgr;-Sitosterol induced low growth inhibition of both cancer cell line. Cocoa polyphenols extracts, however, were significantly more active and showed a strong and fast inhibition of cell growth than &bgr;-sitosterol alone. No synergy or addition was observed when &bgr;-sitosterol was tested together with the cocoa polyphenols extract. Our results show that cocoa polyphenols extracts have an antiproliferative effect on prostate cancer cell growth but not on normal cells, at the highest tested concentration.