Miracle-dz/UniFAR-FTUs huggingface dataset:
New insights into the molecular and cellular workings of the cardiac Na / Ca 2 exchanger

Hilgemann, Donald W. New insights into the molecular and cellular workings of the cardiac Na /Ca exchanger. Am J Physiol Cell Physiol 287: C1167–C1172, 2004; doi:10.1152/ajpcell.00288. 2004. —The cardiac Na /C 2 exchanger (NCX1) is almost certainly the major Ca 2 extrusion mechanism in cardiac myocytes, although the driving force for Ca 2 extrusion is quite small. To explain multiple recent results, it is useful to think of the exchanger as a slow Ca 2 buffer that can reverse its function multiple times during the excitation-contraction cycle (ECC). An article by the group of John Reeves brings new insights to this function by analyzing the role of regulatory domains of NCX1 that mediate its activation by a rise of cytoplasmic Ca 2 . It was demonstrated that the gating reactions are operative just in the physiological range of Ca 2 changes, a few fold above resting Ca level, and that they prevent the exchanger from damping out the influence of mechanisms that transiently increase Ca 2 levels. Furthermore, exchangers with deleted regulatory domains are shown to reduce resting Ca 2 to lower levels than achieved by wild-type exchangers. A study by the group of Kenneth Philipson demonstrated that the NCX1 regulatory domain can bind and respond to Ca 2
Theta-specific susceptibility in a model of adaptive synaptic plasticity

Learning and memory formation are processes which are still not fully understood. It is widely believed that synaptic plasticity is the most important neural substrate for both. However, it has been observed that large-scale theta band oscillations in the mammalian brain are beneficial for learning, and it is not clear if and how this is linked to synaptic plasticity. Also, the underlying dynamics of synaptic plasticity itself have not been completely uncovered yet, especially for non-linear interactions between multiple spikes. Here, we present a new and simple dynamical model of synaptic plasticity. It incorporates novel contributions to synaptic plasticity including adaptation processes. We test its ability to reproduce non-linear effects on four different data sets of complex spike patterns, and show that the model can be tuned to reproduce the observed synaptic changes in great detail. When subjected to periodically varying firing rates, already linear pair based spike timing dependent plasticity (STDP) predicts a specific susceptibility of synaptic plasticity to pre- and postsynaptic firing rate oscillations in the theta-band. Our model retains this band-pass property, while for high firing rates in the non-linear regime it modifies the specific phase relation required for depression and potentiation. For realistic parameters, maximal synaptic potentiation occurs when the postsynaptic is trailing the presynaptic activity slightly. Anti-phase oscillations tend to depress it. Our results are well in line with experimental findings, providing a straightforward and mechanistic explanation for the importance of theta oscillations for learning.
Optimal streaming of layered video

This paper presents a model and theory for streaming layered video. We model the bandwidth available to the streaming application as a stochastic process whose statistical characteristics are unknown a priori. The random bandwidth models short-term variations due to congestion control (such as TCP-friendly conformance). We suppose that the video has been encoded into a base and an enhancement layer, and that to decode the enhancement layer the base layer has to be available to the client. We make the natural assumption that the client has abundant local storage and attempts to prefetch as much of the video as possible during playback. At any instant of time, starvation or partial starvation can occur at the client in either of the two layers. During periods of starvation, the client applies video error concealment to hide the loss. We study the dynamic allocation of the available bandwidth to the two layers in order to minimize the impact pact of client starvation. For the case of an infinitely-long video, we find that the optimal policy takes on a surprisingly simple and static form. For finite-length videos, the optimal policy is a simple static policy when the enhancement layer is deemed at least as important as the base layer. When the base layer is more important, we design a threshold policy heuristic which switches between two static policies. We provide numerical results that compare the performance of no-prefetching, static and threshold policies.
Schistosome Satellite DNA Encodes Active Hammerhead Ribozymes

ABSTRACT Using a computer program designed to search for RNA structural motifs in sequence databases, we have found a hammerhead ribozyme domain encoded in the Smα repetitive DNA of Schistosoma mansoni. Transcripts of these repeats are expressed as long multimeric precursor RNAs that cleave in vitro and in vivo into unit-length fragments. This RNA domain is able to engage in bothcis and trans cleavage typical of the hammerhead ribozyme. Further computer analysis of S. mansoni DNA identified a potential trans cleavage site in the gene coding for a synaptobrevin-like protein, and RNA transcribed from this gene was efficiently cleaved by the Smα ribozyme in vitro. Similar families of repeats containing the hammerhead domain were found in the closely related Schistosoma haematobium and Schistosomatium douthitti species but were not present in Schistosoma japonicum orHeterobilharzia americana, suggesting that the hammerhead domain was not acquired from a common schistosome ancestor.
Joint morphology and cartilage composition in people following anterior cruciate ligament reconstruction

iii CHAPTER 1: THESIS OVERVIEW AND INTRODUCTION . 1 1.1 Thesis overview . 1 1.2 Introduction . 2 1.2.1 Prevalence and impact of knee OA . 2 1.2.2 Post-traumatic phenotype of knee OA and clinical relevance . 3 1.2.3 Clinical importance of post-traumatic OA . 4 1.3 Why is investigating ACLR patients important? 5 CHAPTER 2: LITERATURE REVIEW . 7 2.1 ACL injury, ACLR and post-traumatic OA . 7 2.1.1 ACL injury and ACLR . 7 2.1.2 Post-traumatic OA following ACLR and concomitant meniscal pathology . 8 2.1.3 Potential mechanism of post-traumatic OA following ACL injury . 10 2.2 Understanding OA from an imaging perspective . 14 2.2.1 MRI is important to detect early joint changes . 14 2.2.2 Cartilage volume . 15 2.2.3 Cartilage defects . 16 2.2.4 Bone marrow lesions (BMLs) . 17 2.2. 5 T2 mapping . 19 2.3 MRI findings following ACLR . 21 2.3. 1 Cartilage volume and cartilage thickness following ACLR . 21 2.3. 2 Cartilage defects following ACLR . 26 2.3. 3 BMLs in patients following ACL injury and ACLR . 31 2.3. 4 Association between BMLs and cartilage morphology change . 42 2.3. 5 T2 mapping following ACLR . 45 2.4 Summary and aims . 50
Sleep duration and body mass index in 0–7-year olds

Objectives To determine in children aged 0–7 years (1) cross-sectional relationships between body mass index (BMI) and sleep duration, and whether (2) sleep duration predicts later BMI and/or (3) BMI predicts later sleep duration. Design Longitudinal Study of Australian Children, Waves 1 and 2. Participants Infants aged 0–1 years (Wave 1), followed at age 2–3 years (Wave 2); children aged 4–5 years (Wave 1), followed at age 6–7 years (Wave 2). Main outcome measures BMI, sleep duration by time-use diary, parent-reported sleep problems (none/mild vs moderate/severe). Analyses: Cross-sectional, ANOVA (sleep duration) and χ2 (sleep problems); longitudinal, linear regression. Results 3857 (76%) infants and 3844 (77%) children had BMI and sleep data. At every wave, approximately 15% and 5% of children were overweight and obese, respectively. Obesity was not associated with sleep duration at 0–1, 2–3 or 4–5 years, though obese 6–7-year olds slept approximately 30 min less (p<0.001). Sleep problems were similar across BMI categories at all ages. Wave 1 sleep duration did not predict Wave 2 BMI, nor did Wave 1 BMI predict Wave 2 sleep duration. Conclusions In these large child population cohorts, sleep duration did not predict obesity up to age 6–7 years. Current trials of sleep interventions to prevent or manage obesity in young children may be premature.
HOST GALAXY IDENTIFICATION FOR SUPERNOVA SURVEYS

Host galaxy identification is a crucial step for modern supernova (SN) surveys such as the Dark Energy Survey and the Large Synoptic Survey Telescope, which will discover SNe by the thousands. Spectroscopic resources are limited, and so in the absence of real-time SN spectra these surveys must rely on host galaxy spectra to obtain accurate redshifts for the Hubble diagram and to improve photometric classification of SNe. In addition, SN luminosities are known to correlate with host-galaxy properties. Therefore, reliable identification of host galaxies is essential for cosmology and SN science. We simulate SN events and their locations within their host galaxies to develop and test methods for matching SNe to their hosts. We use both real and simulated galaxy catalog data from the Advanced Camera for Surveys General Catalog and MICECATv2.0, respectively. We also incorporate “hostless” SNe residing in undetected faint hosts into our analysis, with an assumed hostless rate of 5%. Our fully automated algorithm is run on catalog data and matches SNe to their hosts with 91% accuracy. We find that including a machine learning component, run after the initial matching algorithm, improves the accuracy (purity) of the matching to 97% with a 2% cost in efficiency (true positive rate). Although the exact results are dependent on the details of the survey and the galaxy catalogs used, the method of identifying host galaxies we outline here can be applied to any transient survey.
Graph partitioning using single commodity flows

We show that the sparsest cut in graphs can be approximated within O(log2 n) factor in Õ(n3/2) time using polylogarithmic single commodity max-flow computations. Previous algorithms are based on multicommodity flows which take time Õ(n2). Our algorithm iteratively employs max-flow computations to embed an expander flow, thus providing a certificate of expansion. Our technique can also be extended to yield an O(log2 n) (pseudo) approximation algorithm for the edge-separator problem with a similar running time.
Towards an Autonomous System Monitor for Mitigating Correlation Attacks in the Tor Network

After carefully considering the scalability problem in Tor and exhaustively evaluating related works on AS-level adversaries, the author proposes ASmoniTor, which is an autonomous system monitor for mitigating correlation attacks in the Tor network. In contrast to prior works, which often released offline packets, including the source code of a modified Tor client and a snapshot of the Internet topology, ASmoniTor is an online system that assists end users with mitigating the threat of AS-level adversaries in a near real-time fashion. For Tor clients proposed in previous works, users need to compile the source code on their machine and continually update the snapshot of the Internet topology in order to obtain accurate AS-path inferences. On the contrary, ASmoniTor is an online platform that can be utilized easily by not only technical users, but also by users without a technical background, because they only need to access it via Tor and input two parameters to execute an AS-aware path selection algorithm. With ASmoniTor, the author makes three key technical contributions to the research against AS-level adversaries in the Tor network. First, ASmoniTor does not require the users to initiate complicated source code compilations. Second, it helps to reduce errors in AS-path inferences by letting users input a set of suspected ASes obtained directly from their own traceroute measurements. Third, the Internet topology database at the back-end of ASmoniTor is periodically updated to assure near real-time AS-path inferences between Tor exit nodes and the most likely visited websites. Finally, in addition to its convenience, ASmoniTor gives users full control over the information they want to input, thus preserving their privacy.
Depression Following Thrombotic Cardiovascular Events in Elderly Medicare Beneficiaries: Risk of Morbidity and Mortality

Purpose. Depression and antidepressant use may independently increase the risk of acute myocardial infarction and mortality in adults. However, no studies have looked at the effect of depression on a broader thrombotic event outcome, assessed antidepressant use, or evaluated elderly adults. Methods. A cohort of 7,051 community-dwelling elderly beneficiaries who experienced a thrombotic cardiovascular event (TCE) were pooled from the 1997 to 2002 Medicare Current Beneficiary Survey and followed for 12 months. Baseline characteristics, antidepressant utilization, and death were ascertained from the survey, while indexed TCE, recurrent TCE, and depression (within 6 months of indexed TCE) were taken from ICD-9 codes on Medicare claims. Time to death and first recurrent TCE were assessed using descriptive and multivariate statistics. Results. Of the elders with a depression claim, 71.6% had a recurrent TCE and 4.7% died within 12 months of their indexed TCE, compared to 67.6% and 3.9% of those elders without a depression claim. Of the antidepressant users, 72.6% experienced a recurrent TCE and 3.9% died, compared to 73.7% and 4.6% in the subset of selective serotonin reuptake inhibitor (SSRI) users. Depression was associated with a shorter time to death (P = .008) in the unadjusted analysis. However, all adjusted comparisons revealed no effect by depression, antidepressant use, or SSRI use. Conclusions. Depression was not associated with time to death or recurrent TCEs in this study. Antidepressant use, including measures of any antidepressant use and SSRI use, was not associated with shorter time to death or recurrent TCE.
Localization and globalization in conscious vision.

The primate visual brain consists of many separate, functionally specialized processing systems, each consisting of several apparently hierarchical stages or nodes. The evidence reviewed here leads me to speculate (a) that the processing systems are autonomous with respect to one another, (b) that activity at each node reaches a perceptual end point at a different time, resulting in a perceptual asynchrony in vision, and (c) that, consequently, activity at each node generates a microconsciousness. Visual consciousness is therefore distributed in space and time, with the universal organizing principle of abstraction applied separately within each processing system. The consequence of spatially and temporally distributed microconsciousnesses is that their integration is a multistage, nonhierarchical process that may involve a neural "glue. "
Investigation into the optimal surgical conditions for coronary artery ligation for establishing a myocardial infarction model in mice

In the present study, the left anterior descending coronary arteries of mice under anesthesia were ligated, and the optimal surgical conditions for coronary artery ligation (CAL) in the establishment of a myocardial infarction (MI) mouse model were investigated. All mice that survived were sacrificed seven days subsequent to the successful surgery. Body weight, blood serum and heart tissues were obtained for further analysis or biochemical and histopathological examinations. The survival rate of the mice following the CAL procedure was 70%. The aspartate aminotransferase (AST), creatine kinase (CK) and lactate dehydrogenase (LDH) concentrations in the serum of the experimental mice were significantly increased compared with those of the control mice, which reflected the enzyme release from the infarcted myocardial cells. Histopathological examination showed different degrees of MI in the heart tissues of the experimental mice. The results indicate that an MI model in mice may be successfully established using CAL under the surgical conditions utilized in the present study. These conditions were cost effective and the results may be replicated by laboratories that are less well-equipped.
Mechanisms Underlying Ectopic Persistent Tooth-Pulp Pain following Pulpal Inflammation

In order to clarify the peripheral mechanisms of ectopic persistent pain in a tooth pulp following pulpal inflammation of an adjacent tooth, masseter muscle activity, phosphorylated extracellular signal-regulated protein kinase (pERK) and TRPV1 immunohistochemistries and satellite cell activation using glial fibrillary acidic protein (GFAP) immunohistochemistry in the trigeminal ganglion (TG) were studied in the rats with molar tooth-pulp inflammation. And, Fluorogold (FG) and DiI were also used in a neuronal tracing study to analyze if some TG neurons innervate more than one tooth pulp. Complete Freund’s adjuvant (CFA) or saline was applied into the upper first molar tooth pulp (M1) in pentobarbital-anesthetized rats, and capsaicin was applied into the upper second molar tooth pulp (M2) on day 3 after the CFA or saline application. Mean EMG activity elicited in the masseter muscle by capsaicin application to M2 was significantly larger in M1 CFA-applied rats compared with M1 vehicle-applied rats. The mean number of pERK-immunoreactive (IR) TG cells was significantly larger in M1 CFA-applied rats compared with M1 vehicle-applied rats. Application of the satellite cell inhibitor fluorocitrate (FC) into TG caused a significant depression of capsaicin-induced masseter muscle activity and a significant reduction of satellite cell activation. The number of TRPV1-IR TG cells innervating M2 was significantly larger in M1 CFA-applied rats compared with M1 vehicle-applied rats, and that was decreased following FC injection into TG. Furthermore, 6% of TG neurons innervating M1 and/or M2 innervated both M1 and M2. These findings suggest that satellite cell activation following tooth pulp inflammation and innervation of multiple tooth pulps by single TG neurons may be involved in the enhancement of the activity of TG neurons innervating adjacent non-inflamed teeth that also show enhancement of TRPV1 expression in TG neurons, resulting in the ectopic persistent tooth-pulp pain following pulpal inflammation of adjacent teeth.
Endonuclease Associations with Three Distinct Editosomes in Trypanosoma brucei*

Three distinct editosomes, typified by mutually exclusive KREN1, KREN2, or KREN3 endonucleases, are essential for mitochondrial RNA editing in Trypanosoma brucei. The three editosomes differ in substrate endoribonucleolytic cleavage specificity, which may reflect the vast number of editing sites that need insertion or deletion of uridine nucleotides (Us). Each editosome requires the single RNase III domain in each endonuclease for catalysis. Studies reported here show that the editing endonucleases do not form homodimeric domains, and may therefore function as intermolecular heterodimers, perhaps with KREPB4 and/or KREPB5. Editosomes isolated via TAP tag fused to KREPB6, KREPB7, or KREPB8 have a common set of 12 proteins. In addition, KREN3 is only found in KREPB6 editosomes, KREN2 is only found in KREPB7 editosomes, and KREN1 is only found in KREPB8 editosomes. These are the same associations previously found in editosomes isolated via the TAP-tagged endonucleases KREN1, KREN2, or KREN3. Furthermore, TAP-tagged KREPB6, KREPB7, and KREPB8 complexes isolated from cells in which expression of their respective endonuclease were knocked down were disrupted and lacked the heterotrimeric insertion subcomplex (KRET2, KREPA1, and KREL2). These results and published data suggest that KREPB6, KREPB7, and KREPB8 associate with the deletion subcomplex, whereas the KREN1, KREN2, and KREN3 endonucleases associate with the insertion subcomplex.
Traumatic brain injuries in children: A hospital-based study in Nigeria

Background: Traumatic Brain Injury (TBI) is a significant cause of morbidity and mortality worldwide. Our previous studies showed a high frequency of motor vehicle accidents among neurosurgical patients. However, there is a dearth of data on head injuries in children in Nigeria. Aims: To determine the epidemiology of paediatric traumatic brain injuries. Setting and Design: This is a prospective analysis of paediatric head trauma at the University of Benin Teaching Hospital, a major referral centre for all traumatic brain injuries in Nigeria between October 2006 and September 2011. Materials and Methods: We studied the demographic, clinical and radiological data and treatment outcomes. Data was analysed using statistical package for the social sciences (SPSS) 16.0. Results: We managed 127 cases of paediatric head injuries, 65 boys and 62 girls representing 13% of all head injuries managed over the 5-year period. They were aged 3 months to 17 years. The mean age was 7.4 years (median 7 years) with peak incidence occurring at 6-8 years i.e. 31 (24.4%) cases. Motor vehicle accidents resulted in 67.7%, falls 14% and violence 7%. The most frequent computed tomography finding was intracerebral haemorrhage. Mean duration of hospitalization was 18 days (median 11 days). Eleven patients died, mortality correlating well with severity and the presence of intracerebral haematoma. Conclusion: Head injuries in children are due to motor vehicle and motor vehicle-related accidents. Hence, rational priorities for prevention of head injuries in children should include prevention of vehicular, especially pedestrian, accidents in developing countries.
Randomized clinical trial evaluating metformin versus oral contraceptive pills in the treatment of adolescents with polycystic ovarian syndrome

Abstract Background: Polycystic ovarian syndrome (PCOS) is characterized by irregular menses, elevated androgens, and insulin resistance. Little information is published about the treatment of adolescent PCOS. Objectives: The aim of this study was to evaluate metformin versus oral contraceptive pills (OCP) in treating adolescent PCOS. Twenty-two girls were randomized to either treatment for 6 months. The outcomes variables included body mass index (BMI) and free testosterone (FT). Results: BMI decreased in all patients (metformin p=0.004, OCP p=0.045). FT decreased significantly only with OCP. Insulin resistance measures decreased in all patients but did not reach significance. The only significant difference in any of the variables between the two groups was number of menses. BMI and FT remained less than baseline for 3 months off treatment. Conclusions: Metformin and OCP have a positive effect on BMI, which persists after treatment is discontinued. FT decreased with both treatments, but only reached significance with OCP.