Miracle-dz/UniFAR-FTUs huggingface dataset:
Using Invalid Instruments on Purpose: Focused Moment Selection and Averaging for GMM, Second Version

In finite samples, the use of a slightly endogenous but highly relevant instrument can reduce mean-squared error (MSE). Building on this observation, I propose a novel moment selection procedure for GMM–the Focused Moment Selection Criterion (FMSC)–in which moment conditions are chosen not based on their validity but on the MSE of their associated estimator of a user-specified target parameter. The FMSC mimics the situation faced by an applied researcher who begins with a set of relatively mild “baseline” assumptions and must decide whether to impose any of a collection of stronger but more controversial “suspect” assumptions. When the (correctly specified) baseline moment conditions identify the model, the FMSC provides an asymptotically unbiased estimator of asymptotic MSE, allowing us to select over the suspect moment conditions. I go on to show how the framework used to derive the FMSC can address the problem of inference post-moment selection. Treating post-selection estimators as a special case of moment-averaging, in which estimators based on different moment sets are given data-dependent weights, I propose simulation-based procedures for inference that can be applied to a variety of formal and informal moment-selection and averaging procedures. Both the FMSC and confidence interval procedures perform well in simulations. I conclude with an empirical example examining the effect of instrument selection on the estimated relationship between malaria and income per capita.
Syntenic gene analysis between Brassica rapa and other Brassicaceae species

Chromosomal synteny analysis is important in genome comparison to reveal genomic evolution of related species. Shared synteny describes genomic fragments from different species that originated from an identical ancestor. Syntenic genes are orthologs located in these syntenic fragments, so they often share similar functions. Syntenic gene analysis is very important in Brassicaceae species to share gene annotations and investigate genome evolution. Here we designed and developed a direct and efficient tool, SynOrths, to identify pairwise syntenic genes between genomes of Brassicaceae species. SynOrths determines whether two genes are a conserved syntenic pair based not only on their sequence similarity, but also by the support of homologous flanking genes. Syntenic genes between Arabidopsis thaliana and Brassica rapa, Arabidopsis lyrata and B. rapa, and Thellungiella parvula and B. rapa were then identified using SynOrths. The occurrence of genome triplication in B. rapa was clearly observed, many genes that were evenly distributed in the genomes of A. thaliana, A. lyrata, and T. parvula had three syntenic copies in B. rapa. Additionally, there were many B. rapa genes that had no syntenic orthologs in A. thaliana, but some of these had syntenic orthologs in A. lyrata or T. parvula. Only 5,851 genes in B. rapa had no syntenic counterparts in any of the other three species. These 5,851 genes could have originated after B. rapa diverged from these species. A tool for syntenic gene analysis between species of Brassicaceae was developed, SynOrths, which could be used to accurately identify syntenic genes in differentiated but closely-related genomes. With this tool, we identified syntenic gene sets between B. rapa and each of A. thaliana, A. lyrata, T. parvula. Syntenic gene analysis is important for not only the gene annotation of newly sequenced Brassicaceae genomes by bridging them to model plant A. thaliana, but also the study of genome evolution in these species.
Heterogeneous microarchitectures trump voltage scaling for low-power cores

Heterogeneous architectures offer many potential avenues for improving energy efficiency in today's low-power cores. Two common approaches are dynamic voltage/frequency scaling (DVFS) and heterogeneous microarchitectures (HMs). Traditionally both approaches have incurred large switching overheads, which limit their applicability to coarse-grain program phases. However, recent research has demonstrated low-overhead mechanisms that enable switching at granularities as low as 1K instructions. The question remains, in this fine-grained switching regime, which form of heterogeneity offers better energy efficiency for a given level of performance? The effectiveness of these techniques depend critically on both efficient architectural implementation and accurate scheduling to maximize energy efficiency for a given level of performance. Therefore, we develop PaTH, an offline analysis tool, to compute (near-)optimal schedules, allowing us to determine Pareto-optimal energy savings for a given architecture. We leverage PaTH to study the potential energy efficiency of fine-grained DVFS and HMs, as well as a hybrid approach. We show that HMs achieve higher energy savings than DVFS for a given level of performance. While at a coarse granularity the combination of DVFS and HMs still proves beneficial, for fine-grained scheduling their combination makes little sense as HMs alone provide the bulk of the energy efficiency.
Early clinical exposure program in learning renal physiology

Introduction: Teaching renal physiology for undergraduate medical students in an understandable way using methods which improve their deep learning has always been a problem. In this study, Early Clinical Exposure (ECE) was used in teaching renal physiology for the second year medical students in Shiraz Medical School. This article aims to introduce and develop this program and also measure the attitude of medical students toward ECE in learning renal physiology. Methods: This is a mixed method study conducted on 120 second year undergraduate students. After performing the course, both qualitative and quantitative methods were used for measuring the viewpoints of the students. In the qualitative part, 10 high rank medical students were selected. These students participated in brain storming sessions to express their opinion about the program based on the strengths and weaknesses. For trustworthiness of the qualitative part, member check and peer check were done. In the quantitative part, a researcher-made questionnaire was used based on the objectives of the program in a 4 point Likert scale. The validity of questionnaire was determined by medical education experts and reliability was determined after a pilot study. Results: Based on the results of the quantitative part of the study, 98 percent of the students stated that the ECE program was generally a useful program. In the qualitative part, the students’ comments were obtained. The benefits of the program were summarized in 4 main themes. These themes are “understanding of renal physiology”, ”Integration of basic and clinical knowledge”, ”Improvement of attitude toward importance of physiology”, and “encouragement to study”. In response to the questions about negetive aspects of this program in qualitative part, the two main themes were insufficient time and large grup size. Conclusion: Students reported that ECE was useful, but they stated that they needed to have more encounter with patients and more hospital teaching. The results also reveal that this ECE program is an excellent approach to strengthen learning in a difficult subject like renal physiology. This approach is adjustable to other basic science topics and subjects as well.
Performance Analysis of Sorting of FHE Data: Integer-Wise Comparison vs Bit-Wise Comparison

In this paper, we present the exact method foran integer-wise comparison technique in FHE domain usingpolynomial interpolaion and analyze the performance againstbit-wise comparison techniques. We observe that even thoughthe integer-wise comparison requires only one ciphertext unit forinteger in contrast to l ciphertext units for an l-bit integer forbit-wise comparison, bit-wise comparison schemes have betterperformance due to less multiplicative depth of the comparisoncircuit. Our analysis shows that bit-wise comparison based ondepth optimized circuits have O(log(l)) multiplicative depth, where as the integer-wise comparison has O(l) multiplicativedepth and bit-wise comparison based on two's complementarithmetic techniques has O(l) multiplicative depth. We haveevaluated the performance of odd-even merge sort and direct sortby considering all the three above stated comparison techniqueson FHE data using HElib library and analyzed their complexities.
Role of CCN2 in Amino Acid Metabolism of Chondrocytes

CCN2/connective tissue growth factor (CTGF) is a multi‐functional molecule that promotes harmonized development and regeneration of cartilage through its matricellular interaction with a variety of extracellular biomolecules. Thus, deficiency in CCN2 supply profoundly affects a variety of cellular activities including basic metabolism. A previous study showed that the expression of a number of ribosomal protein genes was markedly enhanced in Ccn2‐null chondrocytes. Therefore, in this study, we analyzed the impact of CCN2 on amino acid and protein metabolism in chondrocytes. Comparative metabolome analysis of the amino acids in Ccn2‐null and wild‐type mouse chondrocytes revealed stable decreases in the cellular levels of all of the essential amino acids. Unexpectedly, uptake of such amino acids was rather enhanced in Ccn2‐null chondrocytes, and the addition of exogenous CCN2 to human chondrocytic cells resulted in decreased amino acid uptake. However, as expected, amino acid consumption by protein synthesis was also accelerated in Ccn2‐null chondrocytes. Furthermore, we newly found that expression of two genes encoding two glycolytic enzymes, as well as the previously reported Eno1 gene, was repressed in those cells. Considering the impaired glycolysis and retained mitochondrial membrane potential in Ccn2‐null chondrocytes, these findings suggest that Ccn2 deficiency induces amino acid shortage in chondrocytes by accelerated amino acid consumption through protein synthesis and acquisition of aerobic energy. Interestingly, CCN2 was found to capture such free amino acids in vitro. Under physiological conditions, CCN2 may be regulating the levels of free amino acids in the extracellular matrix of cartilage. J. Cell. Biochem. 117: 927–937, 2016. © 2015 Wiley Periodicals, Inc.
Resource-Bounded Information Gathering for Correlation Clustering

We present a new class of problems, called resource-bounded information gathering for correlation clustering. Our goal is to perform correlation clustering under circumstances in which accuracy may be improved by augmenting the given graph with additional information. This information is obtained by querying an external source under resource constraints. The problem is to develop the most effective query selection strategy to minimize some loss function on the resulting partitioning. We motivate the problem using an entity resolution task.
Multinational Banks, Credit Risk, and Financial Crises : A Qualitative Response Analysis

The global financial unrest over the last decade has shifted the attention of banking regulators (Basel II, 2001) in estimating default probabilities for a variety of borrowers. Within a binary choice panel data framework, the current study analyzes various models and cross-examines their performance in identifying financial crises in emerging markets. Using financial ratios, macroeconomic variables, and international factors, the paper identifies a set of warning indicators and discriminates among the three estimators employed. The most important determinants of commercial/official arrears and reschedulings are the debt-to-GDP ratio, inflation, trade liberalization, and the variability of GNP per capita growth. In addition to that, changes in financial flows from foreign investors do affect default frequencies, while external developments are found to be insignificant. Cross-modeling comparison indicates the presence of different exogenous risk factors, depending on the approach employed. Further analysis indicates the presence of heterogeneity, but pertinent estimators fail to perform well. Unlike the fixed- and random-effects estimators, the pooled-logit model yields the minimum number of misclassifications. When past credit performance is taken into account, the significance of some signals is reduced, but the model's misclassification performance is markedly enhanced.
Novel perspectives for hepatitis A virus therapy revealed by comparative analysis of hepatitis C virus and hepatitis A virus RNA replication

Hepatitis A virus (HAV) and hepatitis C virus (HCV) are two positive‐strand RNA viruses sharing a similar biology, but causing opposing infection outcomes, with HAV always being cleared and HCV establishing persistence in the majority of infections. To gain deeper insight into determinants of replication, persistence, and treatment, we established a homogenous cell‐culture model allowing a thorough comparison of RNA replication of both viruses. By screening different human liver‐derived cell lines with subgenomic reporter replicons of HAV as well as of different HCV genotypes, we found that Huh7‐Lunet cells supported HAV‐ and HCV‐RNA replication with similar efficiency and limited interference between both replicases. HAV and HCV replicons were similarly sensitive to interferon (IFN), but differed in their ability to establish persistent replication in cell culture. In contrast to HCV, HAV replicated independently from microRNA‐122 and phosphatidylinositol 4‐kinase IIIα and β (PI4KIII). Both viruses were efficiently inhibited by cyclosporin A and NIM811, a nonimmunosuppressive analog thereof, suggesting an overlapping dependency on cyclophilins for replication. However, analysis of a broader set of inhibitors revealed that, in contrast to HCV, HAV does not depend on cyclophilin A, but rather on adenosine‐triphosphate–binding cassette transporters and FK506‐binding proteins. Finally, silibinin, but not its modified intravenous formulation, efficiently inhibited HAV genome replication in vitro, suggesting oral silibinin as a potential therapeutic option for HAV infections. Conclusion: We established a cell‐culture model enabling comparative studies on RNA replication of HAV and HCV in a homogenous cellular background with comparable replication efficiency. We thereby identified new host cell targets and potential treatment options for HAV and set the ground for future studies to unravel determinants of clearance and persistence. (Hepatology 2015;62:397–408
Energy efficient multiple target tracking in sensor networks

Classical tracking methods are not concerned with energy efficiency and require precise localisation. We addressed these in our previous work through HMTT (hierarchical Markov decision process for target tracking) that tracks single targets at location granularity. HMTT conserves energy by reducing the rate of sensing but preserves acceptable tracking accuracy through trajectory prediction. In this paper, HMTT is extended for the multiple targets case where the state of clusters could be affected by multiple incoming targets and where multiple updates are required at the lower level. The theoretical performance of HMTT in the multiple targets case is derived and simulations demonstrate its effectiveness against 2 other predictive tracking algorithms with up to 200% improvement.
Psychological trait and state characteristics, social support and attitudes to the surrogate pregnancy and baby.

BACKGROUND Personality differences between surrogate mothers (SMs) who gestate and relinquish and intended mothers (IMs) who commission a genetically related or unrelated baby have been unexplored in the UK. Furthermore, the psychological effects of the arrangement have not been determined in a prospective longitudinal study, making this the first quantitative report of psychological functioning in SMs and IMs. METHODS SMs and IMs (n = 81: 61 surrogate, 20 intended) undergoing genetic or gestational surrogacy (4 groups) were assessed by postal questionnaire during the first, second and third trimesters of pregnancy. Those with a positive outcome were assessed again in the first week, at 6 weeks and 6 months post-delivery of the surrogate baby. RESULTS There were no significant differences between or within SM and IM groups on personality characteristics. Social support, marital harmony and state anxiety differed significantly (to P < 0.01) between SMs and IMs at different stages of the arrangement. Differences in attitudes towards the pregnancy and the baby were also observed between groups during pregnancy (to P < 0.001), but there was no evidence of post-natal depression amongst the groups studied. CONCLUSIONS These results are important because they demonstrate psychological effects of the surrogate arrangement are notable and occur over an extended period of time. It also shows that psychological screening and support prior to, during and following surrogacy is indicated.
Concomitant Effects of Ramadan Fasting and Time-Of-Day on Apolipoprotein AI, B, Lp-a and Homocysteine Responses during Aerobic Exercise in Tunisian Soccer Players

Objective To examine the time-of-day and Ramadan fasting (RF) effects on serum apolipoprotein-AI (Apo-AI) and B (Apo-B), lipoprotein particles-a (Lp-a), high-sensitive C-reactive-protein (hs-CRP), and homocysteine (Hcy) during the Yo-Yo intermittent recovery test (YYIRT). Design Performance and biochemical measures were completed at two times-of-day (07:00 and 17:00 h), 1-week before RF (BR), the second week of RF (SWR), and the fourth week of RF (ER). Setting For each session, subjects performed the YYIRT, and blood samples were taken before and 3-min after the test for biochemical measures. Participants Fifteen soccer players. Main Outcome Measures Total distance during the YYIRT, core temperature, body composition, dietary intakes, lipid (HDL-C, LDL-C, Apo-AI, B and Lp-a) and inflammatory (hs-CRP and Hcy) profiles. Results Performances during the YYIRT were higher in the evening than the morning BR (P < 0.05), but this fluctuation was not observed during RF. Moreover, LDL-C, ApoB, and Lp-a were stable throughout the daytime BR. However, during RF, they decreased at 17:00 h (P < 0.05). Likewise, HDL-C and Apo-AI increased after the exercise and were higher at 17:00 h BR (P < 0.001). Moreover, these parameters increased during RF (P < 0.01). Furthermore, Hcy and hs-CRP increased during the exercise (P < 0.01) with higher evening levels BR. During ER, the diurnal pattern of Hcy was inversed (P < 0.001). Conclusions This study concluded that caloric restriction induced by RF seems to ameliorate lipid and inflammatory markers of cardiovascular health during intermittent exercise performed in the evening.
Quadrocopter Trajectory Generation and Control

Abstract An algorithm is presented that allows the calculation of flight trajectories for quadrocopters. Trajectory feasibility constraints regarding the vehicle dynamics and input constraints are derived. They are then used in the planning algorithm to guarantee the feasibility of generated trajectories. The translational degrees of freedom of the quadrotor are decoupled, and time-optimal trajectories are found for each degree of freedom separately. The trajectory generation is fast enough to be performed online. Control inputs are calculated from the generated trajectory, and used to achieve closed-loop control similar to model predictive control. The trajectory generation and tracking performance is demonstrated in the ETH Zurich Flying Machine Arena testbed. Experimental results show good performance, with unmodeled aerodynamic effects causing trajectory deviations when decelerating from high speeds. Development potential for the future is highlighted, focusing on improving the performance and correcting for aerodynamic effects.
Eclipsing binary statistics – Theory and observation

The expected distributions of eclipse-depth versus period for eclipsing binaries of different luminosities are derived from large-scale population synthesis experiments. Using the rapid Hurley et al. BSE binary evolution code, we have evolved several hundred million binaries, starting from various simple input distributions of masses and orbit-sizes. Eclipse probabilities and predicted distributions over period and eclipse-depth (P/Delta m) are given in a number of main-sequence intervals, from O-stars to brown dwarfs. The comparison between theory and Hipparcos observations shows that a standard (Duquennoy & Mayor) input distribution of orbit-sizes ( a) gives reasonable numbers and P/Delta m-distributions, as long as the mass-ratio distribution is also close to the observed flat ones. A random pairing model, where the primary and secondary are drawn independently from the same IMF, gives more than an order of magnitude too few eclipsing binaries on the upper main sequence. For a set of eclipsing OB-systems in the LMC, the observed period-distribution is different from the theoretical one, and the input orbit distributions and/or the evolutionary environment in LMC has to be different compared with the Galaxy. A natural application of these methods are estimates of the numbers and properties of eclipsing binaries observed by large-scale surveys like Gaia.
The twilight zone: ambient light levels trigger activity in primitive ants

Many animals become active during twilight, a narrow time window where the properties of the visual environment are dramatically different from both day and night. Despite the fact that many animals including mammals, reptiles, birds and insects become active in this specific temporal niche, we do not know what cues trigger this activity. To identify the onset of specific temporal niches, animals could anticipate the timing of regular events or directly measure environmental variables. We show that the Australian bull ant, Myrmecia pyriformis, starts foraging only during evening twilight throughout the year. The onset occurs neither at a specific temperature nor at a specific time relative to sunset, but at a specific ambient light intensity. Foraging onset occurs later when light intensities at sunset are brighter than normal or earlier when light intensities at sunset are darker than normal. By modifying ambient light intensity experimentally, we provide clear evidence that ants indeed measure light levels and do not rely on an internal rhythm to begin foraging. We suggest that the reason for restricting the foraging onset to twilight and measuring light intensity to trigger activity is to optimize the trade-off between predation risk and ease of navigation.