Miracle-dz/UniFAR-FTUs huggingface dataset:
Orchidectomized (orx) marmoset (Callithrix jacchus) as a model to study the development of osteopenia/osteoporosis

The common marmoset serves as a primate model for many human diseases. Hypogonadal and particularly aged men develop osteopenia or osteoporosis. Whether marmosets develop osteoporosis after orchidectomy is not known. This was tested in seven young and two older adult male orchidectomy animals using quantitative computer tomography, which allowed quantification of total surface and density of the cortex and of the cancellous structures of the metaphysis of the tibia and of the fifth or sixth lumbal vertebra (L5/L6) before or after orchidectomy (orx), and 1, 6 and 12 months later. Surrogate parameters of whole skeletal bone metabolism (osteocalcin, OC) and C‐terminal breakdown products (telopeptides) of collagen‐α1 (CrossLaps) were also measured. Male marmosets lost between 5 and 20% of their initial cancellous density in the metaphysis of the tibia and this was statistically significant 6 months after castration. No loss of cancellous density was observed in L5/L6 of young marmosets and OC and the CrossLaps in the serum were decreased at this time point while a reduction was observed in bone mineral density of L5/L6 in two aged animals. It is concluded that castration of young male marmoset for 1 year results in a significant loss of bone mineral density in the metaphysis of the tibia resulting in osteopenia but not in the vertebra. The results indicate that male orx marmosets become osteopenic within 12 months after castration and may be a more human‐like experimental model for bone research. Am. J. Primatol. 70:294–300, 2008. © 2007 Wiley‐Liss, Inc.
The Carboxyl-terminal End of Cox1 Is Required for Feedback Assembly Regulation of Cox1 Synthesis in Saccharomyces cerevisiae Mitochondria*

Synthesis of the largest cytochrome c oxidase (CcO) subunit, Cox1, on yeast mitochondrial ribosomes is coupled to assembly of CcO. The translational activator Mss51 is sequestered in early assembly intermediate complexes by an interaction with Cox14 that depends on the presence of newly synthesized Cox1. If CcO assembly is prevented, the level of Mss51 available for translational activation is reduced. We deleted the C-terminal 11 or 15 residues of Cox1 by site-directed mutagenesis of mtDNA. Although these deletions did not prevent respiratory growth of yeast, they eliminated the assembly-feedback control of Cox1 synthesis. Furthermore, these deletions reduced the strength of the Mss51-Cox14 interaction as detected by co-immunoprecipitation, confirming the importance of the Cox1 C-terminal residues for Mss51 sequestration. We surveyed a panel of mutations that block CcO assembly for the strength of their effect on Cox1 synthesis, both by pulse labeling and expression of the ARG8m reporter fused to COX1. Deletion of the nuclear gene encoding Cox6, one of the first subunits to be added to assembling CcO, caused the most severe reduction in Cox1 synthesis. Deletion of the C-terminal 15 amino acids of Cox1 increased Cox1 synthesis in the presence of each of these mutations, except pet54. Our data suggest a novel activity of Pet54 required for normal synthesis of Cox1 that is independent of the Cox1 C-terminal end.
Driver Reaction Time Before and After Treatment for Lumbar Radiculopathy

Study Design. Prospective observational pilot study. Objective. To investigate the effect of right and left radiculopathy on driver reaction time (DRT), and the effect of selective nerve root block (SNRB) on DRT. Summary of Background Data. The effect of many orthopedic procedures on DRT has already been assessed. To date the effect of radiculopathy and SNRB on DRT has not been studied. Methods. DRTs of 20 radiculopathic patients (10 right, 10 left) were measured using a custom-built car simulator. Each patient was tested pre-SNRB, immediately post-SNRB, and 2 and 6 weeks post-SNRB. As controls 20 age- and sex-matched normal subjects were tested once. Full departmental, institutional, and ethical committee approval were obtained. Results. Mean DRT of the control group was 452 milliseconds. Mean DRT of patients with right or left radiculopathy pre-SNRB was 521 milliseconds (P < 0.045) and 535 milliseconds (P < 0.018), respectively. In the right radiculopathic group, the measurements immediately post-SNRB, 2 weeks, and 6 weeks were 656 milliseconds (P < 0.005), 589 milliseconds (P < 0.019), and 564 milliseconds (P < 0.10), respectively. The delay immediately and at 2 weeks post-SNRB translates into an increase in stopping distance of 3.8 and 1.9 m, respectively at the speed of 100 km/h. In the left radiculopathic group, the measurements immediately post-SNRB, 2 weeks, and 6 weeks were 585 milliseconds (P < 0.037), 534 milliseconds, and 530 milliseconds, respectively. The delay immediately post-SNRB translates into an increase in stopping distance of 1.4 m at the speed of 100 km/h. Conclusion. The study identified significant DRTs’ changes both in radiculopathy and after SNRB. Right and left radiculopathic patients should be advised about the possible changes in their DRTs post-SNRB. Future research with regard to the suitability for radiculopathic patients to drive and the best time to resume driving post-SNRB is needed.
LiveS Cube: An Experiment for Mobile Social Network

Contacts Address Book (CAB)'s maintenance is a big problem because each user has to deal with hundreds of contact information in his or her address book. Data Lock-in also hurdle their desire to change mobile platform for new applications. In this paper, we solve this problem by exploiting the online social network (OSN), making mobile users maintain their own contacts information and still get every friend's most recent information by sharing the information through the social network. We transform the existing contacts address books function with social network aware function and build a social network since a huge network with enormous number of nodes (users) and edges (relations) could be built very quickly as there are billions of mobile users and almost every mobile user has an contacts address book inside the mobile phone and that address book is the real relationships (contacts). This social network is named LiveS Cube because its design objective is making mobile devices simple, secured and shared (LiveS3). We deploy the LiveS Cube in the real campus environment for about a half year and collect interesting data and problems. The implementation of this social network is also presented and some unexpected problems came out and it turned out to be quite difficult to be built from scratch. Keywords-Mobile Social Network, Contacts address book,
Properties of a Ribonucleoprotein Particle Isolated from Nonidet P-40-Treated Rous Sarcoma Virus

A ribonucleoprotein particle containing about 20% ribonucleic acid (RNA), and containing little if any phospholipid or glucosamine, was recovered in high yield after treatment of Schmidt-Ruppin strain of Rous sarcoma virus and B77 virus with the nonionic detergent Nonidet P-40. This structure, which probably derives from the internal ribonucleoprotein filament described in electron microscopy studies, contained 80 to 90% of the viral 60 to 70S RNA and only about 10% of the protein present in intact virions. It sedimented in glycerol density gradients at approximately 130S and had a buoyant density in sucrose of about 1.34 g/ml. Studies with 32P-labeled virus indicated that the ribonucleoprotein particle contained approximately 30 4S RNA molecules per 107 daltons of high-molecular-weight viral RNA. Intact virions contained about 70 4S RNA molecules per 107 daltons of high-molecular-weight RNA. Electrophoretic studies in dodecyl sulfate-containing polyacrylamide gels showed that the ribonucleoprotein particle contained only 5 of the 11 polypeptides found in the virion; of these the major component was a polypeptide weighing 14,000 daltons.
Cystatin C and incident peripheral arterial disease events in the elderly: results from the Cardiovascular Health Study.

BACKGROUND The association of cystatin C, a novel marker of renal function, with risk for developing complications related to peripheral arterial disease (PAD) has not been examined. METHODS We evaluated the hypothesis that a high cystatin C concentration is independently associated with future PAD events among 4025 participants in the Cardiovascular Health Study who underwent serum cystatin C measurement at the 1992-1993 visit and who did not have PAD at baseline. The association of cystatin C quintiles with time to first lower-extremity PAD procedure (bypass surgery, angioplasty, or amputation) was evaluated using multivariable proportional hazards models. Secondary analyses were conducted using quintiles of serum creatinine level and estimated glomerular filtration rate (eGFR). RESULTS The annualized risk of undergoing a procedure for PAD was 0.43% per year among participants in the highest cystatin C quintile (>1.27 mg/L) compared with 0.21% per year or less in all other quintiles. After multivariable adjustment for known risk factors for PAD, elevated cystatin C levels remained associated with the outcome (hazard ratio, 2.5 for highest vs lowest quintile of cystatin C, 95% confidence interval, 1.2-5.1). The highest quintiles of serum creatinine level and eGFR were not associated with future PAD events in either unadjusted or adjusted analyses. CONCLUSION Elevated concentrations of cystatin C were independently predictive of incident PAD events among community-dwelling elderly patients.
Who benefits from CBT for insomnia in primary care? Important patient selection and trial design lessons from longitudinal results of the Lifestyles trial.

STUDY OBJECTIVES Evaluate long-term effects of group interventions on sleep and pain outcomes in a primary care population of older adults with osteoarthritis pain and sleep disturbance. DESIGN Double-blind, cluster-randomized controlled trial with 18-mo follow-up. SETTING Group Health and University of Washington, Seattle, WA, from 2009 to 2011. PARTICIPANTS Three hundred sixty-seven adults age 60 y and older, with osteoarthritis pain and insomnia symptoms. INTERVENTIONS Six weekly sessions of group cognitive behavioral therapy for insomnia and pain (CBT-PI), pain alone (CBT-P), and education-only control (EOC) delivered in patients' primary care clinics. MEASUREMENTS AND RESULTS There were no significant differences between treatment groups in sleep outcomes at 18 mo. This is a change from published significant 9-mo follow-up results for insomnia severity (Insomnia Severity Index) and sleep efficiency. There were no significant treatment differences in pain at either follow-up. Post hoc analyses of participants with greater insomnia and pain severity at baseline (n = 98) showed significant (P = 0.01) 18-mo reductions in pain comparing CBT-PI versus CBT-P (adjusted mean difference [AMD] = -1.29 [95% confidence interval (CI): -2.24,-0.33]). Moderate, albeit nonsignificant, CBT-PI versus EOC treatment effects for insomnia severity (AMD = -1.43 [95% CI: -4.71, 1.86]) and sleep efficiency (AMD = 2.50 [95% CI: -5.04, 10.05]) were also observed. Possible trial design and methodological considerations that may have affected results are discussed. CONCLUSIONS Results suggest patients with higher levels of comorbid pain and insomnia may be most likely to experience sustained benefit from cognitive behavioral therapy interventions over time, and inclusion of insomnia treatment may yield more clinically meaningful improvements than cognitive behavioral therapy for pain alone. TRIAL REGISTRATION clinicaltrials.gov identifier: NCT01142349.
Associative Learning of Visual and Vestibular Stimuli inLymnaea


A conditioned withdrawal response was characterized in the pond snail Lymnaea stagnalis. Using light as the conditioned stimulus and high-speed orbital rotation as the unconditioned stimulus, experimental animals were trained with 30 paired presentations of light and orbital rotation per day for 3 days. After training, all experimental animals responded to light with a withdrawal response, the conditioned response. Control animals exposed to the same number of explicitly unpaired presentations of light and orbital rotation, light alone, or no stimulation did not respond to light. Thirty paired presentations per day for 2 days produced less than optimal acquisition of the conditioned withdrawal response. Neither 45 paired presentations per day for 2 days nor 90 paired presentations for 1 day resulted in complete acquisition of the conditioned withdrawal response. The conditioned withdrawal response observed following 30 paired presentations per day for 3 to 5 days persisted to Day 10, regardless of the number of training days. As a measure of savings, reacquisition of the conditioned response after extinction was investigated. After the conditioned withdrawal response was extinguished, only 2 to 5 paired presentations of light and orbital rotation were required for reacquisition of the conditioned response for most animals. This study further establishes Lymnaea as an animal model of basic associative learning.
A new robust LPCCS for speech recogniton in channel distortion environments

Linear Prediction (LP) analysis plays an important role in speech processing. Linear Prediction Cepstral Coefficients (LPCCs) are proved to be better features for speech recognition. In LP analysis, the generation of speech is modeled with an autoregressive (AR) random process. In fact, speech from vocal cord goes through vocal tract first, and then goes through channel. However, general LP analysis does not consider the effect of channel and the LPCCs show little robustness in speech recognition under channel distortion. In this paper, distorted speech is modeled by two different AR models which denote vocal tract and channel, respectively. After the poles are computed, K-means is used to cluster all poles and a new method is proposed to choose Channel poles. For each frame of test utterances, instead of designing a filter using channel poles, robust LPCCs are computed directly by removing channel poles from all poles. Experiment shows that this approach can obtain a better performance than general methods.
UvA-DARE ( Digital Academic Repository ) Adhesion-induced DNA

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The power of species sorting: Local factors drive bacterial community composition over a wide range of spatial scales

There is a vivid debate on the relative importance of local and regional factors in shaping microbial communities, and on whether microbial organisms show a biogeographic signature in their distribution. Taking a metacommunity approach, spatial factors can become important either through dispersal limitation (compare large spatial scales) or mass effects (in case of strongly connected systems). We here analyze two datasets on bacterial communities [characterized by community fingerprinting through denaturing gradient gel electrophoresis (DGGE)] in meso- to eutrophic shallow lakes to investigate the importance of spatial factors at three contrasting scales. Variation partitioning on datasets of both the bacterial communities of 11 shallow lakes that are part of a strongly interconnected and densely packed pond system <1 km apart, three groups of shallow lakes ≈100 km apart, as well as these three groups of shallow lakes combined that span a large part of a North-South gradient in Europe (>2,500 km) shows a strong impact of local environmental factors on bacterial community composition, with a marginal impact of spatial distance. Our results indicate that dispersal is not strongly limiting even at large spatial scales, and that mass effects do not have a strong impact on bacterial communities even in physically connected systems. We suggest that the fast population growth rates of bacteria facilitate efficient species sorting along environmental gradients in bacterial communities over a very broad range of dispersal rates.
quaddRAD: a new high‐multiplexing and PCR duplicate removal ddRAD protocol produces novel evolutionary insights in a nonradiating cichlid lineage

The identification of thousands of variants across the genomes and their accurate genotyping are crucial for estimating the genetic parameters needed to address a host of molecular ecological and evolutionary questions. With rapid advances of massively parallel high‐throughput sequencing technologies, several methods have recently been developed to access genomewide data on population variation. One of the most successful and widely used techniques relies on the combination of restriction enzymes and sequencing‐by‐synthesis: restriction‐site‐associated DNA sequencing (RADSeq). We developed a new, more time‐ and cost‐efficient double‐digest RAD paired‐end protocol (quaddRAD) that simplifies and speeds up the identification of PCR duplicates and permits large‐scale multiplexing. Assessing its performance on a technical data set, we also applied the quaddRAD method on population samples of a Neotropical cichlid fish lineage (Archocentrus centrarchus) to assess its genetic structure and demographic history. While we identified allopatric interlake genetic divergence, most likely driven by drift, no signature of sympatric divergence was detected. This differs from what has been observed in the clade of Midas cichlids (Amphilophus citrinellus spp.), another cichlid lineage that inhabits the same lakes and shares a similar demographic history, but has evolved into small‐scale adaptive radiations via sympatric speciation. We demonstrate that quaddRAD is a robust and efficient method for genotyping a massive number and widely overlapping set of loci with high accuracy. Furthermore, the results on A. centrarchus open new research avenues providing an ideal system to investigate genome‐level mechanisms that could alter the speciation potential of different but closely related cichlid lineages.
Blunt circulatory response to exercise in coronary high-risk subjects among apparently healthy Japanese.

BACKGROUND Endothelial dysfunction leads to atherosclerosis and the hypothesis of the present study was that the systemic circulatory response during exercise would be a manifestation of endothelial dysfunction. METHODS AND RESULTS The circulatory response to exercise of 1,214 apparently healthy people (946 men, mean age 51.2 +/- 10.3; 268 women, mean age 52.7 +/- 10.1) was investigated, as well as the number of coronary risk factors. Systemic vascular resistance (SVR) was calculated from heart rate, blood pressure and oxygen uptake at rest and at maximal exercise during a ramp protocol using a bicycle ergometer. SVRs at rest (1,751-2,001 (dynes.s.cm(-5)) in women and 1,528-1,564 in men) did not significantly differ among the groups by number of coronary risk factors. At maximal exercise, however, they were lower in the group with fewer risk factors; that is, among women 929 (dynes.s.cm (-5)) with no risk factor to 1,305 with 5 risk factors; among men 793 with 1 risk factor to 1,170 with 6 risk factors. CONCLUSIONS Those with more coronary risk factors showed a lower but lengthier reduction in SVR during exercise. This weak circulatory response to exercise is a manifestation of deteriorated circulatory function in coronary high-risk subjects.
Data compression and transmission aspects of panoramic videos

Panoramic videos are effective means for representing static or dynamic scenes along predefined paths. They allow users to change their viewpoints interactively at points in time or space defined by the paths. High-resolution panoramic videos, while desirable, consume a significant amount of storage and bandwidth for transmission. They also make real-time decoding computationally very intensive. This paper proposes efficient data compression and transmission techniques for panoramic videos. A high-performance MPEG-2-like compression algorithm, which takes into account the random access requirements and the redundancies of panoramic videos, is proposed. The transmission aspects of panoramic videos over cable networks, local area networks (LANs), and the Internet are also discussed. In particular, an efficient advanced delivery sharing scheme (ADSS) for reducing repeated transmission and retrieval of frequently requested video segments is introduced. This protocol was verified by constructing an experimental VOD system consisting of a video server and eight Pentium 4 computers. Using the synthetic panoramic video Village at a rate of 197 kb/s and 7 f/s, nearly two-thirds of the memory access and transmission bandwidth of the video server were saved under normal network traffic.
Military expenditure and economic growth in Middle Eastern countries and Turkey: a non-linear panel data approach

The economic growth effects of military expenditure have been the subject of a large literature in defence economics. Theories on the economic impacts of military expenditure greatly differ and include arguments that they either enhance economic growth or crowd out productive investments. Empirical literature on defence expenditure and economic growth nexus generally employs linear specifications to investigate the impact of defence expenditures on economic growth. Although it is now well established that many economic variables may have a non-linear data-generating mechanism, it seems that this reality has long been neglected in empirical work on defence–growth nexus. This paper attempts to fill this gap by employing non-linear panel data models to examine the effects of military expenditures on economic growth for Middle Eastern countries and Turkey, for the time period 1988–2012. Results show that the effect of military expenditure on economic growth is nonlinear such that the state of the economy actually determines the effect of the former on the latter. This is important not only in showing asymmetric relationship between these variables but also in revealing the reasons of mixed results of earlier literature.
Methicillin-resistant Staphylococcus aureus isolates recovered from a New York City hospital: analysis by molecular fingerprinting techniques

Fifty-five methicillin-resistant Staphylococcus aureus (MRSA) isolates collected at New York Hospital Medical Center of Queens in 1989 were analyzed by molecular fingerprinting techniques. Close to 70% of these isolates (38 of 55) shared a common pulsed-field gel electrophoretic pattern, carried the same mecA gene polymorph type II, were free of the transposon Tn554, and would not react with a mecI-specific gene probe. An additional five isolates shared all properties of the major MRSA clone except that they carried mecA gene polymorph type III. All these isolates had an extremely heterogeneous methicillin resistance phenotype that belonged to population analysis profile class 1 or 2. The rest of the 12 MRSA isolates showed a variety of chromosomal pulsed-field gel electrophoretic patterns that carried different mecA polymorphs and that also gave positive reactions with DNA probes for Tn554 and for the mecI gene. The molecular features of the majority MRSA clone suggest that it is an archaic MRSA isolate similar in features to early MRSA isolates recovered in the 1960s.