Miracle-dz/UniFAR-FTUs huggingface dataset:
Novel glycopolypeptide synthesis induced by gametic cell fusion in Chlamydomonas reinhardtii

Within the first hour of zygote maturation, Chlamydomonas reinhardtii cells stop synthesizing certain polypeptides that characterize the vegetative and gametic stages of the life cycle and initiate the synthesis of novel, zygote-specific polypeptides. At least six of these polypeptides are secreted into the medium, and fine-structural studies indicate that they represent components of the cell wall that is synthesized and secreted early in zygote development. We conclude that a new program of protein synthesis, and possibly also gene transcription, is initiated shortly after gametic cells fuse, a program that appears highly suited to cell-differentiation studies.
Molecular Characterization and Functions of Fatty Acid and Retinoid Binding Protein Gene (Ab-far-1) in Aphelenchoides besseyi

Rice white tip nematode, Aphelenchoides besseyi, is a kind of plant parasitic nematodes that cause serious losses in rice and many other crops. Fatty acid and retinoid binding protein (FAR) is a specific protein in nematodes and is related to development, reproduction, infection to the host, and disruption of plant defense reactions, so the inhibition of FAR function is the potential approach to control A. besseyi. The full-length of Ab-far-1 cDNA is 805 bp, including 546 bp of ORF that encodes 181 amino acids. Software analysis revealed that the Ab-FAR-1 was rich in α-helix structure, contained a predicted consensus casein kinase II phosphorylation site and a hydrophobic secretory signal peptide, but did not have glycosylation sites. The Ab-FAR-1 had 52% homology to Gp-FAR-1 protein. The Ab-FAR-1 and Gp-FAR-1 were grouped in the same branch according to the phylogenetic tree. Fluorescence-based ligand binding analysis confirmed that the recombinant Ab-FAR-1 (rAb-FAR-1) bound with the fluorescent analogues 11-((5-dimethylaminonaphthalene-1-sulfonyl) amino) undecannoic acid (DAUDA), cis-parinaric acid and retinol, but the oleic acid would compete with the binding site. Quantitative PCR (qPCR) was used to assess the expression level of Ab-far-1 at different development stages of A. besseyi, the highest expression was found in the females, followed by eggs, juveniles and males. Using in situ hybridization technique, Ab-far-1 mRNA was present in the hypodermis of juveniles and adults, the ovaries of females and the testes of males. When A. besseyi was treated with Ab-far-1 dsRNA for 48 h, the silencing efficiency of Ab-far-1 was the best and the number of nematodes on the carrot was the least. Thus FAR plays important roles in the development and reproduction of nematodes. This study is useful and helpful to figure out a new way to control the plant parasitic nematodes.
Temporal Dynamics of Abundance and Composition of Nitrogen-Fixing Communities across Agricultural Soils

Background Despite the fact that the fixation of nitrogen is one of the most significant nutrient processes in the terrestrial ecosystem, a thorough study of the spatial and temporal patterns in the abundance and distribution of N-fixing communities has been missing so far. Methodology/Principal Findings In order to understand the dynamics of diazotrophic communities and their resilience to external changes, we quantified the abundance and characterized the bacterial community structures based on the nifH gene, using real-time PCR, PCR-DGGE and 454-pyrosequencing, across four representative Dutch soils during one growing season. In general, higher nifH gene copy numbers were observed in soils with higher pH than in those with lower pH, but lower numbers were related to increased nitrate and ammonium levels. Results from nifH gene pyrosequencing confirmed the observed PCR-DGGE patterns, which indicated that the N fixers are highly dynamic across time, shifting around 60%. Forward selection on CCA analysis identified N availability as the main driver of these variations, as well as of the evenness of the communities, leading to very unequal communities. Moreover, deep sequencing of the nifH gene revealed that sandy soils (B and D) had the lowest percentage of shared OTUs across time, compared with clayey soils (G and K), indicating the presence of a community under constant change. Cosmopolitan nifH species (present throughout the season) were affiliated with Bradyrhizobium , Azospirillum and Methylocistis, whereas other species increased their abundances progressively over time, when appropriate conditions were met, as was notably the case for Paenibacilus and Burkholderia. Conclusions Our study provides the first in-depth pyrosequencing analysis of the N-fixing community at both spatial and temporal scales, providing insights into the cosmopolitan and specific portions of the nitrogen fixing bacterial communities in soil.
Social Interactions and Geographical Variation in Medical Care ∗

This paper shows how social influences on individual decisions help resolve a public health puzzle—the inordinate effect of geography on treatment. To explain geographical variations, we construct a theoretical model in which physician choices are subject to either local increasing returns or a desire to conform. Small regional differences in the patient mix give rise to divergent treatment patterns—the treatment a patient receives depends on where she lives. The patterns of practice depend, in predictable ways, upon regional demographics. The empirical analysis uses data from Florida on coronary patients and their doctors. The data reveal significant geographic variation in treatment rates along lines predicted by our model. We also find empirical support for the claim that local peer behavior influences a physician’s treatment choices. We wish to thank Peyton Young for bringing the geographical variation puzzle to our attention, and for several subsequent discussions. We are grateful to Dennis Epple for comments on an earlier draft of the paper. We also wish to acknowledge participants of the 13th Annual Conference on Health Economics (2002), and seminars at the Brookings Institution, the Santa Fe Institute, the Universities of Iowa, Bergen (Norway) and South Florida. Support from the Brookings Institution and University of Bergen is greatly appreciated. Please address correspondence to: Gary M. Fournier, Department of Economics, Florida State University, Tallahassee, FL 32306-2180, U.S.A. Tel. (850)644-7080 Email: gfournie@coss.fsu. edu.
Regional Calibration of Watershed Models

1. INTRODUCTION As watershed models become increasingly sophisticated and useful, there is a need to extend their applicability to locations where they cannot be calibrated or validated. It is only natural that as watershed models, computer technology and hydrometeorologic data sources continue to evolve, there will be an ever increasing need to apply watershed models where streamflow data is unavailable for calibration. Without streamflow data, a watershed model cannot be calibrated or validated, hence regional methods are needed which relate easily measured watershed characteristics to watershed model parameters. The focus of this chapter is on a review of the various approaches which have been taken for estimating watershed model parameters in situations when streamflow data is unavailable for model calibration and validation. In the past decade, there has been a significant increase in research relating to the regional calibration of watershed models to enable their use at ungauged sites. The increased importance of regional methods for estimating watershed model parameters is influenced by and related to the following emerging themes:
A Cost-Based Approach to Adaptive Resource Management in Data Stream Systems

Data stream management systems need to adaptively control their resources, since stream characteristics and query workload may vary over time. In this paper, we investigate an approach to adaptive resource management for continuous sliding-window queries that adjusts window sizes and time granularities to keep resource usage within bounds. These two novel techniques differ from standard load shedding approaches based on sampling, as they ensure exact query answers for given user-defined quality of service specifications, even under query reoptimization. In order to quantify the effects of both techniques on the various operations in a query plan, we develop an appropriate cost model for estimating operator resource allocation in terms of memory usage and processing costs. A thorough experimental study not only validates the accuracy of our cost model but also demonstrates the efficacy and scalability of the proposed techniques.
Video gender recognition using temporal coherent face descriptor

In this paper, we propose a new temporal coherent face descriptor for video gender recognition. The proposed face descriptor is constructed from detected faces of continuous video frames. Because it describes detected faces under variant changes in continuous video frames and provides a unified feature description, face normalization and alignment processes can be avoided during gender recognition. Based on the face descriptor, a support vector machine classifier is applied to identify the gender of the subject in the videos. As shown in the experiments, our method not only achieves better results compared to the state-of-the-art methods but also the real-time performance for video processing.
Association of Fas -1377 G/A Polymorphism with Susceptibility to Cancer

Background The relationship between Fas -1377 G/A polymorphism and cancer susceptibility has been implicated in accumulating data. However, the data presented inconsistent results. This study was devised to investigate the association of Fas -1377 G/A polymorphism and cancer susceptibility in a large number of participants. Methods The databases of PubMed, Embase, and Web of Science were searched and a total of 27 case-control studies including 13,355 cases and 16,078 controls were included in this meta-analysis. Pooled odds ratios (ORs) with 95% confidence intervals (CIs) were calculated using the fixed-effects model. Statistical analyses were performed by using Stata software. Results The results suggested that Fas -1377 G/A polymorphism was overall associated with cancer susceptibility (additive model: OR, 1.16, 95%CI = 1.06–1.27, P heterogeneity = 0.381; recessive model: OR, 1.19, 95%CI = 1.10–1.29, P heterogeneity = 0.137). In the subgroup analysis by cancer type, significantly increased risk was observed in breast cancer (additive model: OR, 1.24, 95%CI = 1.04–1.58, P heterogeneity = 0.614; recessive model: OR, 1.24, 95%CI = 1.02–1.51, P heterogeneity = 0.349) and lung cancer (recessive model: OR, 1.25, 95%CI = 1.04–1.49, P heterogeneity = 0.090). Similarly, elevated cancer risk associated with Fas -1377 G/A polymorphism was revealed in Asians. Conclusions The combined results suggest that Fas -1377 G/A polymorphism might modulate cancer susceptibility in an Asian-specific manner.
A Modified SRP-PHAT Functional for Robust Real-Time Sound Source Localization With Scalable Spatial Sampling

The Steered Response Power - Phase Transform (SRP-PHAT) algorithm has been shown to be one of the most robust sound source localization approaches operating in noisy and reverberant environments. However, its practical implementation is usually based on a costly fine grid-search procedure, making the computational cost of the method a real issue. In this letter, we introduce an effective strategy that extends the conventional SRP-PHAT functional with the aim of considering the volume surrounding the discrete locations of the spatial grid. As a result, the modified functional performs a full exploration of the sampled space rather than computing the SRP at discrete spatial positions, increasing its robustness and allowing for a coarser spatial grid. To this end, the Generalized Cross-Correlation (GCC) function corresponding to each microphone pair must be properly accumulated according to the defined microphone setup. Experiments carried out under different acoustic conditions confirm the validity of the proposed approach.
Hybrid genetic algorithm PID control for a five-fingered smart prosthetic hand

A hybrid of soft control technique of adaptive neuro-fuzzy inference system (ANFIS) and genetic algorithm (GA) and hard control technique of proportional-integral-derivative (PID) for a five-fingered, smart prosthetic hand is presented. The ANFIS is used for inverse kinematics and GA is used for tuning the PID parameters with the objective of minimizing the error squared between desired and actual angles of the links of the fingers of the prosthetic hand. Simulation results for all the five fingers with GA-tuned PID controller exhibit superior performance compared to the PID control without GA.
Glottal Marking of Vowel-initial Words in German

Glottal marking of vowel-initial German words by glottalization and glottal stop insertion were investigated in dependence on speech rate, word type (content vs. function words), word accent, phrasal position and the following vowel. The analysed material consisted of speeches of Konrad Adenauer, Thomas Mann and Richard von Weizsacker. The investigation shows that not only the left boundary of accented syllables (including phrasal stress boundary) and lexical words favour glottal stops/glottalization, but also that the segmental level appears to have a strong impact on these insertion processes. Specifically, the results show that low vowels in contrast to non-low ones favour glottal stops/glottalization even before non-accented syllables and functional words.
Plasma exosomes can deliver exogenous short interfering RNA to monocytes and lymphocytes

Despite the promise of RNA interference (RNAi) and its potential, e.g. for use in cancer therapy, several technical obstacles must first be overcome. The major hurdle of RNAi-based therapeutics is to deliver nucleic acids across the cell’s plasma membrane. This study demonstrates that exosome vesicles derived from humans can deliver short interfering RNA (siRNA) to human mononuclear blood cells. Exosomes are nano-sized vesicles of endocytic origin that are involved in cell-to-cell communication, i.e. antigen presentation, tolerance development and shuttle RNA (mainly mRNA and microRNA). Having tested different strategies, an optimized method (electroporation) was used to introduce siRNA into human exosomes of various origins. Plasma exosomes (exosomes from peripheral blood) were used as gene delivery vector (GDV) to transport exogenous siRNA to human blood cells. The vesicles effectively delivered the administered siRNA into monocytes and lymphocytes, causing selective gene silencing of mitogen-activated protein kinase 1. These data suggest that human exosomes can be used as a GDV to provide cells with heterologous nucleic acids such as therapeutic siRNAs.
EXPLICIT SOLUTION OF THE PROBLEM OF EQUIVALENCE FOR SOME PAINLEVE EQUATIONS

Abstact. For an arbitrary ordinary second order differential equation a test is constructed that checks if this equation is equivalent to Painleve I, II or Painleve III with three zero parameters equations under the substitutions of variables. If it is true then in case the Painleve equations I and II an explicite change of variables is given that is written using the differential invariants of the equation.
Comparing the efficacy of efavirenz and boosted lopinavir using viremia copy-years

HIV‐1 plasma viral load during treatment can be highly variable. Thus, there is the need to find a measure of cumulative viremia that can be used to assess both the short‐ and long‐term efficacy of highly active antiretroviral therapy (HAART). Here, we validate a measure of cumulative viremia to evaluate HAART efficacy.
Increased Young’s Modulus and Hardness of Col1a2oim Dentin

Mice harboring the Col1a2 oim mutation (oim) express dentinogenesis imperfecta. To determine the effect of Col1a2 genotype on tissue mechanical properties, we compared Young’s modulus and hardness of dentin in the 3 Col1a2 genotypes. Upper incisors were tested by nanoindentation. Genotype had a significant effect on Young’s modulus, but there was not a simple mutant allele dosage relationship. The effect of genotype on hardness did not reach significance. Hardness and Young’s modulus were greater near the dento-enamel junction than near the pulp chamber. Greater hardness and Young’s modulus values near the dento-enamel junction reflected continued mineralization of the dentin following its initial synthesis. Analysis showed the mechanical data to be consistent with Fourier transform infrared and backscattered electron microscopy studies that revealed increased mineralization in oim bone. Analysis of the data suggests that clinical fragility of teeth in oim mice is not due to deficiencies of hardness or Young’s modulus, but may be due to defects in post-yield behavior or resistance to fatigue damage.
Data Debugging

Testing and static analysis can help root out bugs in programs, but not in data. This paper introduces data debugging, an approach that combines program analysis and statistical analysis to find potential data errors. Since it is impossible to know a priori whether data are erroneous or not, data debugging locates data that has an unusual impact on the computation. Such data is either very important, or wrong. Data debugging is especially useful in the context of data-intensive programming environments that intertwine data with programs in the form of queries or formulas. We present the first data debugging tool, CHECKCELL, an add-in for Microsoft Excel. CHECKCELL colors cells red when they have an unusually high impact on the spreadsheet’s computations. We show that CHECKCELL is both analytically and empirically fast and effective; in a case study, it automatically identifies a key flaw in the infamous Reinhart and Rogoff spreadsheet.
A Distributed Representation Based Query Expansion Approach for Image Captioning

In this paper, we propose a novel query expansion approach for improving transferbased automatic image captioning. The core idea of our method is to translate the given visual query into a distributional semantics based form, which is generated by the average of the sentence vectors extracted from the captions of images visually similar to the input image. Using three image captioning benchmark datasets, we show that our approach provides more accurate results compared to the state-of-theart data-driven methods in terms of both automatic metrics and subjective evaluation.
The Effects of Ratings-Contingent Regulation on International Bank Lending Behavior: Evidence from the Basel 2 Accord

We investigate the effects of credit ratings-contingent financial regulation on foreign bank lending behavior. We examine the sensitivity of international bank flows to debtor countries’ sovereign credit rating changes before and after the implementation of the Basel 2 risk-based capital regulatory rules. We study the quarterly bilateral flows from G-10 creditor banking systems to 77 recipient countries over the period Q4:1999 to Q2:2013. We find direct evidence that sovereign credit re-ratings that lead to changes in risk-weights for capital adequacy requirements have become more significant since the implementation of Basel 2 rules for assessing banks’ credit risk under the standardized approach. This evidence is consistent with global banks acting via their international lending decisions to minimize required capital charges associated with the use of ratings-contingent regulation. We find no evidence to suggest that banking regulation induced foreign lending has heightened the perceived sovereign credit risks of recipient countries.
Particle Swarm Optimization and Other Metaheuristic Methods in Hybrid Flow Shop Scheduling Problem

Multiprocessor task scheduling is a generalized form of classical machine scheduling where a task is processed by more than one processor. It is a challenging problem encountered in wide range of applications and it is vastly studied in the scheduling literature (see for instance (Chan & Lee, 1999 and Drozdowski, 1996) for a comprehensive introduction on this topic). However, Drozdowski (1996) shows that multiprocessor task scheduling is difficult to solve even in its simplest form. Hence, many heuristic algorithms are presented in literature to tackle multiprocessor task scheduling problem. Jin et al. (2008) present a performance study of such algorithms. However, most of these studies primarily concerned with a single stage setting of the processor environment. There are many practical problems where multiprocessor environment is a flow-shop that is it is made of multiple stages and tasks have to go through one stage to another. Flow-shop scheduling problem is also vastly studied in scheduling context though most of these studies concerned with single processor at each stage (see for instance Linn & Zhang, 1999, Dauzere-Peres & Paulli, 1997). With the advances made in technology, in many practical applications, we encounter parallel processors at each stage instead of single processors such as parallel computing, power system simulations, operating system design for parallel computers, traffic control in restricted areas, manufacturing and many others (see for instance (Krawczyk & Kubale, 1985, Lee & Cai, 1999, Ercan & Fung, 2000, Caraffa et. al.,2001)). This particular problem is defined as hybrid flow-show with multiprocessor tasks in scheduling terminology and minimizing the schedule length (makespan) is the typical scheduling problem addressed. However, Brucker & Kramer (1995) show that multiprocessor flow-shop problem to minimize makespan is also NP-hard. Gupta (1988) showed that hybrid flow-shop even with two stages is NP-hard. Furthermore, the complexity of the problem increases with the increasing number of stages. Multiprocessor task scheduling in a hybrid flow-shop environment has recently gained the attention of the research community. To the best of our knowledge, one of the earliest papers that deal with this problem in the scheduling literature is by Oguz and Ercan, 1997. However, due to the complexity of the problem, in the early studies (such as (Lee & Cai, 1999, Oguz et. al., 2003)) researchers targeted two layer flow-shops with multiprocessors. Simple list based heuristics as well as meta-heuristics were introduced for the solution
Online Product Opinions: Incidence, Evaluation, and Evolution

Whereas recent research has demonstrated the impact of online product ratings and reviews on product sales, we still have a limited understanding of the individual's decision to contribute these opinions. In this research, we empirically model the individual's decision to provide a product rating and investigate factors that influence this decision. Specifically, we consider how previously posted ratings may affect an individual's posting behavior in terms of whether to contribute (incidence) and what to contribute (evaluation), and we identify selection effects that influence the incidence decision and adjustment effects that influence the evaluation decision. Across individuals, our results show that positive ratings environments increase posting incidence, whereas negative ratings environments discourage posting. Our results also indicate important differences across individuals in how they respond to previously posted ratings, with less frequent posters exhibiting bandwagon behavior and more active customers revealing differentiation behavior. These dynamics affect the evolution of online product opinions. Through simulations, we illustrate how the evolution of posted product opinions is shaped by the underlying customer base and show that customer bases with the same median opinion may evolve in substantially different ways because of the presence of a core group of “activists” posting increasingly negative opinions.