Miracle-dz/UniFAR-FTUs huggingface dataset:
Mutation Detection Using Automated Fluorescence‐Based Sequencing

The development of high‐throughput DNA sequencing techniques has made direct DNA sequencing of PCR‐amplified genomic DNA a rapid and economical approach to the identification of polymorphisms that may play a role in disease. Point mutations as well as small insertions or deletions are readily identified by DNA sequencing. The mutations may be heterozygous (occurring in one allele while the other allele retains the normal sequence) or homozygous (occurring in both alleles). Sequencing alone cannot discriminate between true homozygosity and apparent homozygosity due to the loss of one allele due to a large deletion. In this unit, strategies are presented for using PCR amplification and automated fluorescence‐based sequencing to identify sequence variation. The size of the project and laboratory preference and experience will dictate how the data is managed and which software tools are used for analysis. A high‐throughput protocol is given that has been used to search for mutations in over 200 different genes at the Harvard Medical School – Partners Center for Genetics and Genomics (HPCGG, http://www.hpcgg.org/). Curr. Protoc. Hum. Genet. 57:7.9. 1‐7.9. 31. © 2008 by John Wiley & Sons, Inc.
Distributed output-based self-triggered control for general linear multi-agent systems

This paper addresses the consensus problem via output feedback for a multi-agent system under a distributed self-triggered control framework. A distributed observer-type protocol based on relative output measurements is proposed by incorporating the self-triggered control strategy, where each agent computes its next triggering time based on its local information at the last triggering time. Thus, there is no need to keep track of the measurement errors between two update instants. A simulation example is finally presented to verify the theoretical results.
ABCD1 mutations and the X‐linked adrenoleukodystrophy mutation database: Role in diagnosis and clinical correlations

X‐linked adrenoleukodystrophy (X‐ALD) is caused by mutations in the ABCD1 gene, which encodes a peroxisomal ABC half‐transporter (ALDP) involved in the import of very long‐chain fatty acids (VLCFA) into the peroxisome. The disease is characterized by a striking and unpredictable variation in phenotypic expression. Phenotypes include the rapidly progressive childhood cerebral form (CCALD), the milder adult form, adrenomyeloneuropathy (AMN), and variants without neurologic involvement. There is no apparent correlation between genotype and phenotype. In males, unambiguous diagnosis can be achieved by demonstration of elevated levels of VLCFA in plasma. In 15 to 20% of obligate heterozygotes, however, test results are false–negative. Therefore, mutation analysis is the only reliable method for the identification of heterozygotes. Since most X‐ALD kindreds have a unique mutation, a great number of mutations have been identified in the ABCD1 gene in the last seven years. In order to catalog and facilitate the analysis of these mutations, we have established a mutation database for X‐ALD ( http://www.x‐ald.nl). In this review we report a detailed analysis of all 406 X‐ALD mutations currently included in the database. Also, we present 47 novel mutations. In addition, we review the various X‐ALD phenotypes, the different diagnostic tools, and the need for extended family screening for the identification of new patients. Hum Mutat 18:499–515, 2001. © 2001 Wiley‐Liss, Inc.
Uniaxial-biaxial stress hybridization for super-critical strained-si directly on insulator (SC-SSOI) PMOS with different channel orientations.

This paper describes the novel stress engineering of SC-SSOI devices through the interactions between biaxial lattice strain, uniaxial relaxation, process-induced stressor and channel orientation. We have demonstrated a method of uniaxial stress relaxation with compressive capping layer (cESL) to achieve the desired stress configurations for enhanced short-channel SC-SSOIpMOS devices
Dissolution of Sexual Signal Complexes in a Hybrid Zone between the Swordtails Xiphophorus birchmanni and Xiphophorus malinche (Poeciliidae)

Abstract The evolution of sexual signaling systems is influenced by natural and sexual selection acting on complex interactions among traits. Natural hybrid zones are excellent systems for assessing fitness effects on sexual phenotypes. Most documented hybrid zones, however, show little variation in sexual signals. A hybrid zone between the swordtails Xiphophorus birchmanni and Xiphophorus malinche is characterized by numerous recombinants for male sexual traits. Analyses of geographic variation in morphological and isozyme traits in the Río Calnali, Hidalgo, Mexico, reveal an upstream-to-downstream gradient from X. malinche- to X. birchmanni-type traits. A second hybrid zone, likely isolated from the R. Calnali, occurs in the nearby Arroyo Pochutla. Although the presumed female preference for swords predicts the introgression of swords from X. malinche-like populations into hybrid populations, the opposite pattern was observed. Swords are reduced in populations otherwise characterized by X. malinche traits. Sexually dimorphic traits were poorly correlated within individuals, indicating that sexual selection does not act against recombinant phenotypes. Hybrid males also exhibit trait values outside the range of parental variation. These patterns are consistent with predictions that females are permissive, preferring generally conspicuous males without attending to specific features.
Programmed DNA Deletion As an RNA-Guided System of Genome Defense

Genomewide DNA rearrangements occur in many eukaryotes during development, but their functions and mechanisms are poorly understood. Previous studies have implicated a sequence-recognition mechanism based on RNA-mediated interactions between nuclei in ciliated protozoa. In this study, we found that the process recognized and deleted a foreign gene integrated in a Tetrahymena chromosome, suggesting an unusual mechanism of genome surveillance. We further found that injection of double-stranded RNA into the cell at specific developmental stages triggers efficient deletion of the targeted genomic regions. Together the results indicate an RNA-based mechanism that directs genomewide DNA rearrangements and serves to disable invading genetic agents.
Structure of polyadenylic acid in the ribonucleic acid of Saccharomyces cerevisiae

Investigations of the structure of polyadenylic acid [poly(A)] in yeast have shown that there are two classes of poly(A) distinguished by size and kinetics of synthesis. Each class is found directly on the 3' end of messenger RNA. One class contains poly(A) molecules ranging from 60 to less than 20 nucleotides long. The longest molecules in this poly(A) class are the first to become labeled when cells are exposed to [3H]adenine. Label then appears in progressively smaller molecules. The second class of poly(A) is about 20 nucleotides long. The length homogeneity of this class and the presence in nuclear DNA of many copies of a polythymidylate sequence which is the same length suggests that this poly(A) is synthesized by transcription from DNA.
Chromatin remodeling protein Chd1 interacts with transcription elongation factors and localizes to transcribed genes

Transcription in eukaryotes is influenced by the chromatin state of the template, and chromatin remodeling factors have well‐documented roles in regulating transcription initiation by RNA polymerase (pol) II. Chromatin also influences transcription elongation; however, little is known about the role of chromatin remodeling factors in this process. Here, we present evidence that the Saccharomyces cerevisiae chromatin remodeling factor Chd1 functions during transcription elongation. First, we identified Chd1 in a two‐hybrid screen for proteins that interact with Rtf1, a member of the Paf1 complex that associates with RNA pol II and regulates transcription elongation. Secondly, we show through co‐immunoprecipitation studies that Chd1 also interacts with components of two essential elongation factors, Spt4–Spt5 and Spt16–Pob3. Thirdly, we demonstrate that deletion of CHD1 suppresses a cold‐sensitive spt5 mutation that is also suppressed by defects in the Paf1 complex and RNA pol II. Finally, we demonstrate that Chd1, Rtf1 and Spt5 associate with actively transcribed regions of chromatin. Collectively, these findings suggest an important role for Chd1 and chromatin remodeling in the control of transcription elongation.
DNA rearrangements directed by non‐coding RNAs in ciliates

Extensive programmed rearrangement of DNA, including DNA elimination, chromosome fragmentation, and DNA unscrambling, takes place in the newly developed macronucleus during the sexual reproduction of ciliated protozoa. Recent studies have revealed that two distant classes of ciliates use distinct types of non‐coding RNAs to regulate such DNA rearrangement events. DNA elimination in Tetrahymena is regulated by small non‐coding RNAs that are produced and utilized in an RNA interference (RNAi)‐related process. It has been proposed that the small RNAs produced from the micronuclear genome are used to identify eliminated DNA sequences by whole‐genome comparison between the parental macronucleus and the micronucleus. In contrast, DNA unscrambling in Oxytricha is guided by long non‐coding RNAs that are produced from the parental macronuclear genome. These long RNAs are proposed to act as templates for the direct unscrambling events that occur in the developing macronucleus. Both cases provide useful examples to study epigenetic chromatin regulation by non‐coding RNAs. Copyright © 2010 John Wiley & Sons, Ltd.
Finding arguments for pseudo-resultative predicates

However, while resultative predicates modify the direct object of the verb, the predicate in (1) does not. That is, while the metal becomes flat as a result of Susan's hammering it, Mary's hair does not become tight as a result of her braiding it; nor is the event of braiding what is 'tight'. Rather, what becomes tight is the braid which is created by the braiding. Yet there is no overt 'braid' DP in the syntax for tight to modify. Thus, these sentences present a puzzle for the syntax/semantics interface what argument are these modifiers modifying? While resultatives are available with a variety of verbs in English, the problematic type of predicates as iri (l) seem to occur only with a relatively small number of verbs. In this paper, I argue that this is due to the fact that these 'pseudo-resultative' adjectives are dependent upon elements unique to the semantic decomposition of a particular class of verbs which I call 'creation inchoatives'. I also propose a parallel syntactic decomposition which provides for a compositional analysis of these predicates.
Odontogenic classification of craniopharyngiomas: a clinicopathological study of 54 cases

Based on the striking histological similarity of craniopharyngiomas and some odontogenic tumours, we reclassified a series of 54 craniopharyngiomas (52 adamantinomatous and two papillary variants) according to the WHO classification of odontogenic tumours. Twenty‐seven tumours (50%) corresponded histologically to calcifying odontogenic cyst, 13 tumours (24%) to ameloblastoma, and eight (15%) tumours showed features of both calcifying odontogenic cyst and ameloblastoma either within the same specimen or in specimens derived from different resections. Rare tumours included three cases resembling calcifying epithelial odontogenic tumour and one case resembling adenomatoid odontogenic tumour. No odontogenic counterpart could be established for papillary craniopharyngiomas. The two major subtypes, i.e. craniopharyngioma corresponding to calcifying odontogenic cyst and craniopharyngioma corresponding to ameloblastoma, did not differ in their basic clinical features. Our data confirm and extend the close histological resemblance between adamantinomatous craniopharyngioma and odontogenic tumours and cysts. Furthermore, although calcifying odontogenic cyst and ameloblastoma arising in the jaw differ in clinical presentation and outcome, our study did not reveal clinical differences for the corresponding subtypes of craniopharyngioma.
Effects of whole cottonseed, niacin, and niacinamide on in vitro rumen fermentation and on lactating Holstein cows.

In Experiment 1, effects of whole cottonseed (0, 5, 15, or 30% of the total ration DM) on in vitro ruminal fermentation showed increased ruminal pH and ammonia concentration but lowered microbial protein. Acetic acid concentration was greatest with diets of 15 and 30% whole cottonseed, but propionate and total VFA concentrations were reduced by increasing whole cottonseed from 0 to 30%. In Experiment 2, neither niacin nor niacinamide (0, 100, 200, or 400 ppm) altered substantially fermenter pH or ammonia concentration. Both niacin and niacinamide increased synthesis of microbial protein. Acetate and propionate concentrations were not altered by treatment. Total VFA concentration tended to be lower as concentration of niacin and niacinamide increased. In Experiment 3, 28 Holstein cows were used to determine the effects of supplemental niacin on feed intake, milk yield, and composition. Cows were fed individually complete mixed diets ad libitum containing either: 1) 0; 2) . 015; 3) . 03; or 4) . 06% niacin. There was a trend for lower milk fat test with niacin supplementation. Milk protein percentage was higher without niacin than with niacin at . 015 or . 03% in the diet, but daily milk and protein yields were higher with . 06% versus . 015% of niacin. Supplemental niacin did not affect casein nitrogen, lactose or minerals percentage, or concentrations of plasma glucose and insulin.
Presence and regulation of epithelial sodium channels in the marginal cells of stria vascularis

Conclusion. This study indicates that epithelial Na+-selective channels (ENaC) recycle Na+ via clathrin-mediated endocytosis in the marginal cells of the stria vascularis and that clathrin-independent endocytosis appeared to be modulated by the amount of Na+ transported. These results suggest the presence of ENaC in the luminal membrane of marginal cells and that ENaC are an efficient pathway for the uptake of Na+ from the endolymph. Objective. The ENaC found in many transporting epithelia play a key role in the regulation of salts and water homeostasis, cellular pH, cell volume, and cell function. Both biochemical and physiological approaches have been used to identify, characterize, and quantify this important channel, but its location in the marginal cells of the stria vascularis has not been fully clarified. The aim of this study was to determine the localization and regulation of ENaC. Materials and methods. Forty healthy female guinea pigs were used: 20 for the control experiment, 10 for the amiloride experiment, and 10 for the aldosterone experiment. We perfused cationized ferritin (CF) and microperoxidase (MPO) as tracers for clathrin-mediated and clathrin-independent endocytosis, respectively, into the cochlear duct. After 30 min of endolymphatic perfusion, the tissues were fixed and CF- and MPO-loaded endosomes within the marginal cell were observed by transmission electron microscopy. The numbers of CF- and MPO-loaded endosomes were compared between the three groups. Results. In the amiloride group, the numbers of CF- and MPO-loaded endosomes decreased in comparison with the control. In the aldosterone group, the numbers of CF- and MPO-loaded endosomes decreased and increased, respectively. Recently, it has been reported that ENaC are endocytosed via clathrin-mediated endosomes and aldosterone decreases the rate of endocytosis of ENaC. In this study, the results of the aldosterone experiment were consistent with those of recent studies.
OPTIMIZATION OF DRILL DESIGN AND COOLANT SYSTEMS DURING DENTAL IMPLANT SURGERY

OF THESIS OPTIMIZATION OF DRILL DESIGN AND COOLANT SYSTEMS DURING DENTAL IMPLANT SURGERY Dental implants are an effective alternative for the replacement of missing teeth. The success of the implant depends on how well a bone heals around the implant, a process known as osseointegration. However, excessive heat generated during the bone drilling will cause cell death and may prevent osseointegration of the implant, resulting in early failure. There are many factors which contribute to the heat generation during drilling. Experiments were carried out to investigate the affect of variable drilling factors on heat generation during drilling operation. Natural bone is not an ideal material for such research, as it varies widely in density and other parameters of interest. It would be desirable to have a more uniform and consistent material to use in such studies. However, such a material must be similar to bone to allow the results to be extrapolated to the clinical situation. The current study describes and validates a model for use in such studies. Polymethylmethacrylate (PMMA) is the material chosen for our studies. A theoretical model was developed to study the effect of different drilling parameters on temperature rise during drilling operations. Comparison of observed results obtained from experiments was made with the results from theoretical study. Comparison of results for PMMA and human bone are also shown explaining how PMMA material can be substituted for human bone. The results suggest that the PMMA model is an acceptable surrogate for bone in such studies.
Comparative study between two and three-level topologies of grid connected photovoltaic converters

The main objective of this paper is to achieve a comparative study between two and three-level converters used in transformerless grid connected two-stage photovoltaic systems. For this purpose, a numerical model of the conversion system has been implemented in Matlab/Simulink software. It consists of a PV array feeding a DC/DC converter as well as a three-phase voltage source converter that ensures the power transfer to the grid through a line inductor. The simulation results showed that the three-level voltage source converter has better performance than the two-level topology in terms of line current harmonic distortion (THD) as well as the line inductor's volume.
DOA Estimation Method for Two-Dimensional Wideband Signals by Sparse Recovery in Frequency Domain

The direction of arrival(DOA) estimation methods with sparse recovery need to separate the searching space into some angle meshes, which will cause some error to the result. Therefore, a novel approach for two-dimensional wideband signals by sparse recovery is used, the iterative functions are constructed and calculated by output signal, after that the support set is acquired according to the root finding and corresponding semidefinite programming, then the DOA is acquired by integrating the data of all frequency bins, meanwhile the signal can also be recovered in continuous frequency domain. It avoids the error brought by sparse recovery in discrete domain and particularly performs well when the number of snapshots is small.
Data from one GP to inform the debate whether patients should be able to email their general practitioner

To aid the debate on whether patients should be able to email their general practitioner,1 I analysed my email contacts with my patients from September 2013 to August 2014. Seventy of my 84 email contacts with patients were from me to my patients and 14 were from them to me. Most (43) of the 70 emails I sent to patients contained links to further …
Phototoxicity of TiO2 nanoparticles to zebrafish (Danio rerio) is dependent on life stage

Zebrafish embryos have been used increasingly to evaluate nanomaterial toxicity. The present study compared phototoxicity of TiO2 nanoparticles with zebrafish at 4 life stages (embryos, yolk‐sac larvae, free‐swimming larvae, and juvenile) under simulated sunlight using the 96‐h standard toxicity assay. Yolk‐sac larvae were found to be the most sensitive to TiO2 phototoxicity, suggesting that the widely used zebrafish embryo test may not fully or accurately predict hazard and risk of these nanoparticles to small fish. Environ Toxicol Chem 2013;32:2139–2143. © 2013 SETAC
Spatial Spectrum-Sharing Strategy in Cognitive Radio Networks

This paper presents a new spectrum-sharing strategy based on spatial information about mutual interference constraints, temporal spectrum usages and positions of devices. This strategy can solve the coexistence problem of Cognitive Radio (CR) networks and simplify the design of CR devices. In fact, it is a crosslayer design strategy that integrates useful information obtained from the physical, MAC and network layers, in order to fully exploit available spectrum resources without introducing interference to existing licensed incumbents.
The Role of Autophagy in Alpha-1-Antitrypsin Deficiency: A Specific Cellular Response in Genetic Diseases Associated with Aggregation-Prone Proteins

In the classical form of alpha-1-antitrypsin (AT) deficiency a point mutation renders aggregation-prone properties on a hepatic secretory protein. The mutant ATZ protein in retained in the endoplasmic reticulum (ER) of liver cells rather than secreted into the blood and body fluids where it ordinarily functions as an inhibitor of neutrophil proteases. A loss-of-function mechanism allows the neutrophil proteases to slowly destroy the connective tissue matrix of the lung, resulting in premature development of pulmonary emphysema as early as the third decade of life. A gain-of-toxic function mechanism is responsible for liver inflammation and carcinogenesis. Indeed this deficiency is the most common genetic cause of liver disease in children in the US. It also causes chronic liver inflammation and carcinoma that manifests itself later in life. However, the majority of affected homozygotes apparently escape liver disease. This last observation has led to the concept that genetic and/or environmental modifiers affect the disposal of mutant ATZ within the ER or affect the protective cellular responses activated by accumulation of ATZ in the ER and, in turn, these modifiers determine which homozygotes develop liver inflammation and carcinoma. In this article I review a series of studies published over the last 6 years showing that autophagy is specifically activated by ER accumulation of ATZ and that autophagy plays a critical role in the disposal of this mutant protein. Further, I review data suggesting that the autophagy is specifically designed for the cellular response to aggregated ATZ and aggregated proteins in general.