Miracle-dz/UniFAR-FTUs huggingface dataset:
The million mutation project: A new approach to genetics in Caenorhabditis elegans

We have created a library of 2007 mutagenized Caenorhabditis elegans strains, each sequenced to a target depth of 15-fold coverage, to provide the research community with mutant alleles for each of the worm's more than 20,000 genes. The library contains over 800,000 unique single nucleotide variants (SNVs) with an average of eight nonsynonymous changes per gene and more than 16,000 insertion/deletion (indel) and copy number changes, providing an unprecedented genetic resource for this multicellular organism. To supplement this collection, we also sequenced 40 wild isolates, identifying more than 630,000 unique SNVs and 220,000 indels. Comparison of the two sets demonstrates that the mutant collection has a much richer array of both nonsense and missense mutations than the wild isolate set. We also find a wide range of rDNA and telomere repeat copy number in both sets. Scanning the mutant collection for molecular phenotypes reveals a nonsense suppressor as well as strains with higher levels of indels that harbor mutations in DNA repair genes and strains with abundant males associated with him mutations. All the strains are available through the Caenorhabditis Genetics Center and all the sequence changes have been deposited in WormBase and are available through an interactive website.
inhibits tRNA degradation via RTD pathway Maf 1-mediated repression of RNA polymerase III transcription Material Supplemental

tRNA precursors, which are transcribed by RNA polymerase III, undergo end-maturation, splicing, and base modifications. Hypomodified tRNAs, such as tRNA, lacking 7-methylguanosine and 5-methylcytidine modifications, are subject to degradation by a rapid tRNA decay pathway. Here we searched for genes which, when overexpressed, restored stability of tRNA molecules in a modification-deficient trm4Dtrm8D mutant. We identified TEF1 and VAS1, encoding elongation factor eEF1A and valyl-tRNA synthetase respectively, which likely protect hypomodified tRNA by direct interactions. We also identified MAF1 whose product is a general negative regulator of RNA polymerase III. Expression of a Maf1-7A mutant that constitutively repressed RNA polymerase III transcription resulted in increased stability of hypomodified tRNA. Strikingly, inhibition of tRNA transcription in a Maf1-independent manner, either by point mutation in RNA polymerase III subunit Rpc128 or decreased expression of Rpc17 subunit, also suppressed the turnover of the hypomodified tRNA. These results support a model where inhibition of tRNA transcription leads to stabilization of hypomodified tRNA due to more efficient protection by tRNA-interacting proteins.
An Adaptive Minimum-BER Approach for Multi-User Detection in STBC-MIMO MC-CDMA Systems

In the recent years, MIMO MC-CDMA techniques have been proposed in order to increase system capacity over frequency-selective wireless channels. The key feature of MIMO MC-CDMA is the capability of exploiting diversity jointly in time, frequency and in the space domains. Very promising results have been achieved by STBC-MIMO MC-CDMA using receiver schemes targeted to maximize the signal-to-noise plus interference ratio (SINR) at the output of the diversity combiner. Such a concept turns on the minimum mean squared error (MMSE) combining criterion. Nevertheless, it is known by literature that MSE cost function is not always optimal in digital communications. In this work, we are proposing an adaptive multi-user detection approach based on a minimum-BER (M- BER) concept for a synchronous STBC-MIMO MC-CDMA system transmitting data over time-varying multipath fading channels. The practical implementation of the M-BER receiver relies on an adaptive least-mean-square (LMS)-like algorithm, periodically aided by a training sequence and working in decision-directed modality during a coherence time window. Experimental results have shown a performance improvement yielded by the proposed adaptive M-BER MUD with respect to MMSE adaptive MUD achieved by spending an affordable computational effort.
The Dubious Link: Civic Engagement and Democratization

Table of Contents List of Tables and Figures Preface Introduction Chapter 1: Conceptual Issues Chapter 2: The "Serpent's Egg": Civil Society's Dark Side Chapter 3: Association and Context in a Third Wave Democracy Chapter 4: Civic Engagement and Social Dysfunction Chapter 5: A Cross-National Analysis Chapter 6: Conclusion Notes References Index Library of Congress Subject Headings for this publication: Civil society, Political participation
Serum insulin‐like growth factor II levels in normal adolescents and those with insulin dependent diabetes mellitus

OBJECTIVE Unlike IGF‐I and its principal binding proteins, data regarding IGF‐II levels have not been well defined in normal subjects and those with insulin‐dependent diabetes mellitus (IDDM). We have therefore measured IGF‐II, as well as IGF‐I, and IGFBP‐3, levels In a large cohort of subjects with IDDM and in age/sex matched controls.
Microevolutionary support for a developmental hourglass: gene expression patterns shape sequence variation and divergence in Drosophila

SUMMARY A central goal of evolutionary developmental biology (Evo‐Devo) is to synthesize comparative molecular developmental genetics and its description of the dynamic relationship between genotype and phenotype with the microevolutionary processes (mutation, random drift, and selection) of population genetics. To this end, we analyzed sequence variation of five gene classes that act sequentially to shape early embryo development in Drosophila: maternal, gap, pair‐rule, segment polarity, and segment identity genes. We found two related patterns: (1) a microevolutionary pattern, wherein relative sequence variation within species is 2‐ to 3‐fold higher for maternal‐effect genes than for any other gene class; and, (2) a macroevolutionary pattern, wherein the relative sequence divergence among species for maternal‐effect genes is 2‐ to 4‐fold greater than for any other gene class. Both patterns are qualitatively and quantitatively consistent with the predictions of microevolutionary theory. Our findings connect within‐species genetic variation to between‐species divergence and shed light on the controversy over the existence of a “developmental hourglass,” where mid‐embryonic stages are more evolutionarily constrained than either earlier or later stages. Because maternal‐effect genes experience relaxed selective constraint relative to zygotic‐effect genes, they explore a wider mutational and phenotypic space. As a result, early acting maternal‐effect genes diverge more widely across taxa and thereby broaden the base of the developmental hourglass. In contrast, later acting zygotic genes are relatively more constrained and limited in their diversification across taxa, narrowing the waist of the developmental hourglass. This pattern is obscured by genes with both maternal and zygotic expression, which experience the strongest evolutionary constraint.
Interactions of AChE with Aβ Aggregates in Alzheimer’s Brain: Therapeutic Relevance of IDN 5706

Acetylcholinesterase (AChE; EC 3.1.1.7) plays a crucial role in the rapid hydrolysis of the neurotransmitter acetylcholine, in the central and peripheral nervous system and might also participate in non-cholinergic mechanism related to neurodegenerative diseases. Alzheimer’s disease (AD) is a neurodegenerative disorder characterized by a progressive deterioration of cognitive abilities, amyloid-β (Aβ) peptide accumulation and synaptic alterations. We have previously shown that AChE is able to accelerate the Aβ peptide assembly into Alzheimer-type aggregates increasing its neurotoxicity. Furthermore, AChE activity is altered in brain and blood of Alzheimer’s patients. The enzyme associated to amyloid plaques changes its enzymatic and pharmacological properties, as well as, increases its resistant to low pH, inhibitors and excess of substrate. Here, we reviewed the effects of IDN 5706, a hyperforin derivative that has potential preventive effects on the development of AD. Our results show that treatment with IDN 5706 for 10 weeks increases brain AChE activity in 7-month-old double transgenic mice (APPSWE–PS1) and decreases the content of AChE associated with different types of amyloid plaques in this Alzheimer’s model. We concluded that early treatment with IDN 5706 decreases AChE–Aβ interaction and this effect might be of therapeutic interest in the treatment of AD.
Associations of Variants in CHRNA5/A3/B4 Gene Cluster with Smoking Behaviors in a Korean Population

Multiple genome-wide and targeted association studies reveal a significant association of variants in the CHRNA5-CHRNA3-CHRNB4 (CHRNA5/A3/B4) gene cluster on chromosome 15 with nicotine dependence. The subjects examined in most of these studies had a European origin. However, considering the distinct linkage disequilibrium patterns in European and other ethnic populations, it would be of tremendous interest to determine whether such associations could be replicated in populations of other ethnicities, such as Asians. In this study, we performed comprehensive association and interaction analyses for 32 single-nucleotide polymorphisms (SNPs) in CHRNA5/A3/B4 with smoking initiation (SI), smoking quantity (SQ), and smoking cessation (SC) in a Korean sample (N = 8,842). We found nominally significant associations of 7 SNPs with at least one smoking-related phenotype in the total sample (SI: P = 0.015∼0.023; SQ: P = 0.008∼0.028; SC: P = 0.018∼0.047) and the male sample (SI: P = 0.001∼0.023; SQ: P = 0.001∼0.046; SC: P = 0.01). A spectrum of haplotypes formed by three consecutive SNPs located between rs16969948 in CHRNA5 and rs6495316 in the intergenic region downstream from the 5′ end of CHRNB4 was associated with these three smoking-related phenotypes in both the total and the male sample. Notably, associations of these variants and haplotypes with SC appear to be much weaker than those with SI and SQ. In addition, we performed an interaction analysis of SNPs within the cluster using the generalized multifactor dimensionality reduction method and found a significant interaction of SNPs rs7163730 in LOC123688, rs6495308 in CHRNA3, and rs7166158, rs8043123, and rs11072793 in the intergenic region downstream from the 5′ end of CHRNB4 to be influencing SI in the male sample. Considering that fewer than 5% of the female participants were smokers, we did not perform any analysis on female subjects specifically. Together, our detected associations of variants in the CHRNA5/A3/B4 cluster with SI, SQ, and SC in the Korean smoker samples provide strong evidence for the contribution of this cluster to the etiology of SI, ND, and SC in this Asian population.
Harnessing Wisdom of the Crowds Dynamics for Time-Dependent Reputation and Ranking

The “wisdom of the crowds” is a concept used to describe the utility of harnessing group behaviour, where user opinion evolves over time and the opinion of the masses collectively demonstrates wisdom. Web 2.0 is a new medium where users are not just consumers, but are also contributors.By contributing content to the system, users become part of the network and relationships between users and content can be derived. Example applications are collaborative bookmarking networks such as del.icio. us and file sharing applications such as YouTube and Flickr. These networks rely on user contributed content, described and classified using tags. The wealth of user generated content can be hard to navigate and search due to difficulties in comparing documents with similar tags and the application of traditional information retrieval scoring techniques are limited. Evaluating the time evolving interests of users maybe used to derive quality of content. In this paper, we propose a technique to rank documents based on reputation. The reputation is a combination of the number of bookmarkers, the reputation of the bookmarking user and the time dynamics of the document.Experimental results and analysis are presented on a large collaborative IBM bookmarking network called Dogear.
Investigation of Helicobacter pullorum Occurence in Chicken in the Marmara Region of Turkey

The present study was to investigate the incidence of Helicobacter pullorum in caecum and colon of 96 broiler chickens. A l l samples were obtained from different commercial broiler slaughtering facilities in Marmara region of Turkey. The presence of H. pullorum was assessed by conventional culture method and specific polymerase chain reaction (PCR) test. H. pullorum were not isolated from any of the samples. In contrast, H. pullorum DNA was detected by PCR in 55.21% (53/96) of the samples. Also, it was indicated that caecum was commonly infected than colon. The results showed that H. pullorum is present in Marmara region of Turkey. Further studies are needed to identify the risk factors for the presence of H. pullorum for human health
The Mauna Kea Observatories Near‐Infrared Filter Set. I. Defining Optimal 1–5 Micron Bandpasses

A new Mauna Kea Observatories near‐infrared (MKO‐NIR) filter set is described, including techniques and considerations given to designing a new set of bandpasses that are useful at both mid‐ and high‐altitude sites. These filters offer improved photometric linearity and in many cases reduced background, as well as preserving good throughput within the JHKLM atmospheric windows. MKO‐NIR filters have already been deployed within a number of instruments around the world as part of a filter consortium purchase to reduce the unit cost of filters. Through this effort we hope to establish, for the first time, a single standard set of infrared filters at as many observatories as possible.
Reconstitution of protein translocation from solubilized yeast membranes reveals topologically distinct roles for BiP and cytosolic Hsc70

We reconstituted prepro-alpha-factor translocation and signal peptide processing using a yeast microsomal detergent soluble fraction formed into vesicles with soybean phospholipids. Reconstituted translocation required ATP, and was deficient when sec63 and kar2 (BiP) mutant cells were used as a source of membranes. Normal translocation was observed with vesicles reconstituted from a mixture of pure wild-type yeast BiP and a soluble fraction of kar2 mutant membranes. Two other heat-shock cognate (hsc) 70 homologs, yeast cytosolic hsc70 (Ssalp) and E. coli dnaK protein did not replace BiP. Conversely, BiP was not active under conditions where translocation into native ER vesicles required cytosolic hsc70. We conclude that cytosolic hsc70 and BiP serve noninterchangeable roles in polypeptide translocation, possibly because distinct, asymmetrically oriented membrane proteins are required to recruit each protein to opposing surfaces of the ER membrane.
Preserving Privacy in MapReduce Based Clouds: Insight into Frameworks and Approaches

The massive increase in computational power and data storage capacity provided by Cloud Computing as well as the vast amount of data generated each day have provided many organizations, businesses and authorities with more opportunities due to the advancement in data analysis and mining techniques. A serious problem is that Big Data includes sensitive user information that cannot be released to the cloud without proper protection because of multi-tenancy issues and threats. Privacy preservation of big data has been under intensive investigation with many different approaches proposed. In this paper, we focus on the research challenges of the privacy-preserving problem in the context of cloud computing and we survey existing solution approaches. Furthermore, a review of different existing MapReduce based frameworks will be presented and investigated against the research challenges identified in this paper.
Performance metrics study for repeater-insertion strategies

Parallel and serial repeater-insertion strategies use, respectively, parallel and serial repeaters to minimize the propagation delay over global SoC interconnects. General performance trade-offs refer to any combination of silicon area (Area), delay (T), power (P), energy (E) and reliability. In this paper we address the VLSI designs performance metrics within the repeater-insertion strategies. We study the effect of modeling the power, reliability, as well performance trade-offs on the area-delay optimum found using the repeater-insertion strategies. Simulation results using a 0.25 mum TSMC technology show that the parallel repeater-insertion strategy starts achieving a better speed than the non-regenerated interconnect at wire lengths smaller than that achieved when the interconnect is serially regenerated. It also features a 47% time delay saving and a 96% Area-Delay product saving over the serial repeater-insertion strategy.
The puzzling afterglow of GRB 050721: a rebrightening seen in the optical but not in the X-ray

We present here the analysis of the early and late multiwavelength afterglow emission, as observed by Swift a small robotic telescope and very large telescope (VLT). We compare early observations with late afterglow observations obtained with Swift and the VLT and we observe an intense rebrightening in the optical band at about 1 day after the burst, which is not present in the X-ray band. The lack of detection in X-ray of such a strong rebrightening at lower energies may be described with a variable external density profile. In such a scenario, the combined X-ray and optical observations allow us to derive that the matter density located at ∼1017 cm from the burst is approximately a factor of 10 higher than in the inner region. This is the first time in which a rebrightening has been observed in the optical afterglow of a gamma-ray burst that is clearly absent in the X-ray afterglow.
IBM Research Report Evaluating the E(cid:11)ectiveness of Pointer Alias Analyses

This paper describes an empirical comparison of the e(cid:11)ectiveness of six context-insensitive pointer analysis algorithms that use varying degrees of (cid:13)ow-sensitivity. Four of the algorithms are (cid:13)ow-insensitive, one is (cid:13)ow-sensitive, and another is (cid:13)ow-insensitive, but uses precomputed (cid:13)ow-sensitive information. The e(cid:11)ectiveness of each analysis is quanti(cid:12)ed in terms of compile-time e(cid:14)ciency and precision. E(cid:14)ciency is reported by measuring CPU time and memory consumption of each analysis. Precision is reported by measuring the computed solutions at the program points where a pointer is dereferenced. The results of this paper will help implementors determine which pointer analysis is appropriate for their application.
Optimal size, freshness and time-frame for voice search vocabulary

In this paper, we investigate how to optimize the vocabulary for a voice search language model. The metric we optimize over is the out-of-vocabulary (OoV) rate since it is a strong indicator of user experience. In a departure from the usual way of measuring OoV rates, web search logs allow us to compute the per-session OoV rate and thus estimate the percentage of users that experience a given OoV rate. Under very conservative text normalization, we find that a voice search vocabulary consisting of 2 to 2.5 million words extracted from 1 week of search query data will result in an aggregate OoV rate of 1%; at that size, the same OoV rate will also be experienced by 90% of users. The number of words included in the vocabulary is a stable indicator of the OoV rate. Altering the freshness of the vocabulary or the duration of the time window over which the training data is gathered does not significantly change the OoV rate. Surprisingly, a significantly larger vocabulary (approximately 10 million words) is required to guarantee OoV rates below 1% for 95% of the users.
Racial Inequality in the Distribution of Hazardous Waste: A National-Level Reassessment

National-level studies examining racial disparities around hazardous waste treatment, storage, and disposal facilities have been very influential in defining the academic and political debates about the existence and importance of “environmental injustice. ” However, these studies tend to employ methods that fail to adequately control for proximity between environmentally hazardous sites and nearby residential populations. By using GIS and applying methods increasingly used in environmental inequality research that better control for proximity, we conduct a comprehensive reassessment of racial inequality in the distribution of the nation's hazardous waste facilities. We compare the magnitude of racial disparities found with those of prior studies and test competing racial, economic, and sociopolitical explanations for why such disparities exist. We find that the magnitude of racial disparities around hazardous waste facilities is much greater than what previous national studies have reported. We also find these disparities persist even when controlling for economic and sociopolitical variables, suggesting that factors uniquely associated with race, such as racial targeting, housing discrimination, or other race-related factors are associated with the location of the nation's hazardous waste facilities. We further conclude that the more recent methods for controlling for proximity yield more consistent and definitive results than those used previously, and therefore argue for their wider utilization in environmental inequality research.
A Systematic In Silico Search for Target Similarity Identifies Several Approved Drugs with Potential Activity against the Plasmodium falciparum Apicoplast

Most of the drugs in use against Plasmodium falciparum share similar modes of action and, consequently, there is a need to identify alternative potential drug targets. Here, we focus on the apicoplast, a malarial plastid-like organelle of algal source which evolved through secondary endosymbiosis. We undertake a systematic in silico target-based identification approach for detecting drugs already approved for clinical use in humans that may be able to interfere with the P. falciparum apicoplast. The P. falciparum genome database GeneDB was used to compile a list of ≈600 proteins containing apicoplast signal peptides. Each of these proteins was treated as a potential drug target and its predicted sequence was used to interrogate three different freely available databases (Therapeutic Target Database, DrugBank and STITCH3.1) that provide synoptic data on drugs and their primary or putative drug targets. We were able to identify several drugs that are expected to interact with forty-seven (47) peptides predicted to be involved in the biology of the P. falciparum apicoplast. Fifteen (15) of these putative targets are predicted to have affinity to drugs that are already approved for clinical use but have never been evaluated against malaria parasites. We suggest that some of these drugs should be experimentally tested and/or serve as leads for engineering new antimalarials.
Failure Mechanism of Rock Bridge Based on Acoustic Emission Technique

Acoustic emission (AE) technique is widely used in various fields as a reliable nondestructive examination technology. Two experimental tests were carried out in a rock mechanics laboratory, which include (1) small scale direct shear tests of rock bridge with different lengths and (2) large scale landslide model with locked section. The relationship of AE event count and record time was analyzed during the tests. The AE source location technology and comparative analysis with its actual failure model were done. It can be found that whether it is small scale test or large scale landslide model test, AE technique accurately located the AE source point, which reflected the failure generation and expansion of internal cracks in rock samples. Large scale landslide model with locked section test showed that rock bridge in rocky slope has typical brittle failure behavior. The two tests based on AE technique well revealed the rock failure mechanism in rocky slope and clarified the cause of high speed and long distance sliding of rocky slope.