Miracle-dz/UniFAR-FTUs huggingface dataset:
Diversity and spatial distribution of epiphytic flora associated with four tree species of partially disturbed ecosystem in tropical rainforest zone

As components of forest communities, epiphytes influence litter and nutrient cycling while providing shelter, nesting materials and food for arboreal animals, thereby promoting diversity. Their preference for certain tree species (phorophytes) influences biodiversity and distribution, but this association is poorly understood in the tropics. We assessed the diversity and spatial distribution of epiphytes associated with four phorophytes ( Alstonia booneii , Peltophorum pterocarpum , Mangifera indica and Terminalia catappa ) in southern Nigeria, with number of trees sampled as 4, 29, 32 and 44, respectively. The epiphytes were delineated, sampled and identified. Soil samples were collected from tree pockets for textural and pH analyses. On the four phorophytes, 265 epiphytes under seven species ( Platycerium elephantotis , Microgamma owariensis , Nephrolepis biserrata , Funaria hygrometrica , Axonopus compressus , Commelina benghalensis and Ficus spp.) and five families ( Polypoidaceae , Funariaceae , Poaceae , Commelinaceae and Moraceae ) were recorded. The three most abundant were Funaria hygrometrica (109), Platycerium elephantotis (102) and Microgamma owariensis (44), being present on all four phorophytes. Funaria hygrometrica and Platycerium elephantotis were the most abundant on M. indica (32 each) and T. catappa (44 and 39, respectively). Nephrolepis biserrata appeared only once on T. catappa ; so too did Axonopus compressus and Commelina benghalensis on P. pterocarpum . Altogether, A. booneii , P. pterocarpum , M. indica and T. catappa had 11, 62, 89 and 103 epiphytes, respectively. Funaria hygrometrica traversed three tree strata, while others were restricted to two or even one stratum. Canopy layer, middle stratum and lower portion hosted four, five and three epiphytic species, respectively out of the seven recorded, pointing to the relative importance of light, spaciousness and moisture, respectively in epiphyte abundance on trees. Epiphytes distribution on phorophytes was not influenced by texture of the arboreal soils, but was inversely related to their pH. This study has provided useful information on epiphyte-phorophyte association in tropical environments and deserves repetition with more tree species in more natural forests. Keywords: forest tree species, tree spatial strata, epiphyte distribution, species abundance, Nigeria
Anti-inflammatory profile of circulating immune cells after surgery for seizure.

AIM The central nervous system has been described as the coordinator of the inflammatory response to infection through the hypothalamo-pituitary axis and the autonomic nervous system. Brain lesions have been associated with impaired immunity and postoperative infections. We studied alterations of the inflammatory response in relation to neurohormonal patterns after neurosurgery for seizure. METHODS Nine patients were studied before, during and immediately after operation, and then on days 1, 2 and 4 post-operatively. Monocyte HLA-DR (mHLA-DR) expression and plasma interleukin (IL)-10, IL-12 and MIF were measured ex vivo and after an in vitro 6-h our lipopolysaccharide (LPS) stimulation of whole blood. Corticotropin (ACTH), cortisol, arginine vasopressin, prolactin, epinephrine and norepinephrine were quantified in plasma. The effect of plasma mediators on LPS stimulation was studied by replacing plasma with standard culture medium. RESULTS Surgery resulted in decreased ex vivo mHLA-DR expression, but no change in IL-10 or IL-12 plasma levels. mHLA-DR was low in LPS culture over the 4 postoperative days, whereas IL-10 release was increased and not counterbalanced by IL-12p40 production. The hormonal plasma pattern showed increased prolactin during anesthesia and peaks of cortisol, ACTH and arginine vasopressin during waking, but no alteration in catecholamine levels. mHLA-DR expression in LPS culture was not modified by plasma replacement, except immediately after surgery. CONCLUSION Postoperatively, mHLA-DR expression was associated with an anti-inflammatory phenotype of whole blood. The anti-inflammatory profile was not related to the plasma mediators measured, suggesting that neural control might take place upstream in the circulation, at the level of progenitors in bone marrow.
Stem cells in inflammatory demyelinating disorders: a dual role for immunosuppression and neuroprotection

In recent years much excitement has been generated over the possibility that adult stem cells may attempt repair of the injured central nervous system (CNS), thus setting the stage for their utilisation in the treatment of neurodegenerative disorders. Recent studies have shown that some subsets of stem cells can also modulate the (auto)immune response, thus providing a rationale for their use as therapy for experimental autoimmune encephalomyelitis (EAE), an animal model for multiple sclerosis (MS). This article reviews the scientific evidence supporting the possible use of neural stem cells (NSCs) and mesenchymal stem cells (MSCs) for the treatment of MS. In addition, possible mechanisms sustaining the beneficial mode of action of haematopoietic stem cells (HSCs) following transplantation in MS individuals are discussed. Overall, it is proposed that limited subsets of adult stem cells may have a dual function that may be effective for the treatment of MS, an autoimmune disease of the CNS where degeneration of neural cells follows inflammation.
Final results of the Balloon vs Optimal Atherectomy Trial (BOAT)

BACKGROUND Previous directional coronary atherectomy (DCA) trials have shown no significant reduction in angiographic restenosis, more in-hospital complications, and higher 1-year mortality than conventional balloon angioplasty (percutaneous transluminal coronary angioplasty [PTCA]). DCA, however, has subsequently evolved toward a more "optimal" technique (larger devices, more extensive tissue removal, and routine postdilation to obtain diameter stenosis <20%). METHODS AND RESULTS The Balloon vs Optimal Atherectomy Trial (BOAT) was conducted to evaluate whether optimal DCA provides short- and long-term benefits compared with balloon angioplasty. One thousand patients with single de novo, native vessel lesions were randomized to either DCA or PTCA at 37 participating centers. Lesion success was obtained in 99% versus 97% (P=.02) of patients to a final residual diameter stenosis of 15% versus 28% (P<.0001) for DCA and PTCA, respectively, the latter including stents in 9.3% of the patients. There was no increase in major complications (death, Q-wave myocardial infarction, or emergent coronary artery bypass graft surgery [2.8% versus 3.3%]), although creatine kinase-MB >3X normal was more common with DCA (16% versus 6%; P<.0001). Angiographic restudy (in 79.6% of eligible patients at 7.2+/-2.6 [median, 6.9] months) showed a significant reduction in the prespecified primary end point of angiographic restenosis by DCA (31.4% versus 39.8%; P=.016). Clinical follow-up to 1 year showed nonsignificant 13% to 17% reductions in the DCA arm of the study for mortality rate (0.6% versus 1.6%; P=.14), target-vessel revascularization (17.1% versus 19.7%; P=.33), target-site revascularization (15.3% versus 18.3%; P=.23), and target-vessel failure (death, Q-wave myocardial infarction, or target-vessel revascularization, 21.1% versus 24.8%; P=.17). CONCLUSIONS Optimal DCA provides significantly higher short-term success, lower residual stenosis, and lower angiographic restenosis than conventional PTCA, despite failing to reach statistical significance for reducing late clinical events compared with PTCA with stent backup.
Combining Transcranial Direct Current Stimulation and Tailor-Made Notched Music Training to Decrease Tinnitus-Related Distress – A Pilot Study

The central auditory system has a crucial role in tinnitus generation and maintenance. Curative treatments for tinnitus do not yet exist. However, recent attempts in the therapeutic application of both acoustic stimulation/training procedures and electric/magnetic brain stimulation techniques have yielded promising results. Here, for the first time we combined tailor-made notched music training (TMNMT) with transcranial direct current stimulation (tDCS) in an effort to modulate TMNMT efficacy in the treatment of 32 patients with tonal tinnitus and without severe hearing loss. TMNMT is characterized by regular listening to so-called notched music, which is generated by digitally removing the frequency band of one octave width centered at the individual tinnitus frequency. TMNMT was applied for 10 subsequent days (2.5 hours of daily treatment). During the initial 5 days of treatment and the initial 30 minutes of TMNMT sessions, tDCS (current strength: 2 mA; anodal (N = 10) vs. cathodal (N = 11) vs. sham (N = 11) groups) was applied simultaneously. The active electrode was placed on the head surface over left auditory cortex; the reference electrode was put over right supra-orbital cortex. To evaluate treatment outcome, tinnitus-related distress and perceived tinnitus loudness were assessed using standardized tinnitus questionnaires and a visual analogue scale. The results showed a significant treatment effect reflected in the Tinnitus Handicap Questionnaire that was largest after 5 days of treatment. This effect remained significant at the end of follow-up 31 days after treatment cessation. Crucially, tDCS did not significantly modulate treatment efficacy - it did not make a difference whether anodal, cathodal, or sham tDCS was applied. Possible explanations for the findings and functional modifications of the experimental design for future studies (e.g. the selection of control conditions) are discussed.
Topographic change and numerically modelled near surface wind flow in a bowl blowout

A number of studies have measured and numerically modelled near surface wind velocity over a range of aeolian landforms and made suppositions about topographic change and landform evolution. However, the precise measurement and correlation of flow dynamics and resulting topographic change have not yet been fully realized. Here, using repeated high‐resolution terrestrial laser scanning and numerical flow modelling within a bowl blowout, we statistically analyse the relationship between wind speed, vertical wind velocity, turbulent kinetic energy and topographic change over a 33‐day period.
Tree-level unitarity constraints on the gravitational couplings of higher-spin massive fields.

We analyse the high-energy behavior of tree-level graviton Compton amplitudes for particles of mass m and arbitrary spin, concentrating on a combination of forward amplitudes that will be unaffected by eventual cross-couplings to other, higher spins. We first show that for any spin > 2, tree-level unitarity is already violated at energies ∼ √ mMPl, rather than at the Planck scale MPl, even for m ≪ MPl. We then restore unitarity to this amplitude up to MPl by adding non-minimal couplings that depend on the curvature and its derivatives, and modify the minimal description – including particle gravitational quadrupole moments – at ∼ m −1 scales.
A dual gradient projection quadratic programming algorithm tailored for model predictive control

The objective of this work is to derive a QP algorithm tailored for MPC. More specifically, the primary target application is MPC for discrete-time hybrid systems. A desired property of the algorithm is that warm starts should be possible to perform efficiently. This property is very important for on-line linear MPC, and it is crucial in branch and bound for hybrid MPC. In this paper, a dual active set-like QP method was chosen because of its warm start properties. A drawback with classical active set methods is that they often require many iterations in order to find the active set in optimum. Gradient projection methods are methods known to be able to identify this active set very fast and such a method was therefore chosen in this work. The gradient projection method was applied to the dual QP problem and it was tailored for the MPC application. Results from numerical experiments indicate that the performance of the new algorithm is very good, both for linear MPC as well as for hybrid MPC. It is also noticed that the number of QP iterations is significantly reduced compared to classical active set methods.
Reducing the Variability of Neural Responses: A Computational Theory of Spike-Timing-Dependent Plasticity

Experimental studies have observed synaptic potentiation when a presynaptic neuron fires shortly before a postsynaptic neuron and synaptic depression when the presynaptic neuron fires shortly after. The dependence of synaptic modulation on the precise timing of the two action potentials is known as spike-timing dependent plasticity (STDP). We derive STDP from a simple computational principle: synapses adapt so as to minimize the postsynaptic neuron's response variability to a given presynaptic input, causing the neuron's output to become more reliable in the face of noise. Using an objective function that minimizes response variability and the biophysically realistic spike-response model of Gerstner (2001), we simulate neurophysiological experiments and obtain the characteristic STDP curve along with other phenomena, including the reduction in synaptic plasticity as synaptic efficacy increases. We compare our account to other efforts to derive STDP from computational principles and argue that our account provides the most comprehensive coverage of the phenomena. Thus, reliability of neural response in the face of noise may be a key goal of unsupervised cortical adaptation.
myomiR-dependent switching of BAF60 variant incorporation into Brg1 chromatin remodeling complexes during embryo myogenesis

Myogenesis involves the stable commitment of progenitor cells followed by the execution of myogenic differentiation, processes that are coordinated by myogenic regulatory factors, microRNAs and BAF chromatin remodeling complexes. BAF60a, BAF60b and BAF60c are structural subunits of the BAF complex that bind to the core ATPase Brg1 to provide functional specificity. BAF60c is essential for myogenesis; however, the mechanisms regulating the subunit composition of BAF/Brg1 complexes, in particular the incorporation of different BAF60 variants, are not understood. Here we reveal their dynamic expression during embryo myogenesis and uncover the concerted negative regulation of BAF60a and BAF60b by the muscle-specific microRNAs (myomiRs) miR-133 and miR-1/206 during somite differentiation. MicroRNA inhibition in chick embryos leads to increased BAF60a or BAF60b levels, a concomitant switch in BAF/Brg1 subunit composition and delayed myogenesis. The phenotypes are mimicked by sustained BAF60a or BAF60b expression and are rescued by morpholino knockdown of BAF60a or BAF60b. This suggests that myomiRs contribute to select BAF60c for incorporation into the Brg1 complex by specifically targeting the alternative variants BAF60a and BAF60b during embryo myogenesis, and reveals that interactions between tissue-specific non-coding RNAs and chromatin remodeling factors confer robustness to mesodermal lineage determination.
Expression profiling of metalloproteinases and tissue inhibitors of metalloproteinases in normal and degenerate human achilles tendon.

OBJECTIVE To profile the messenger RNA (mRNA) expression for the 23 known genes of matrix metalloproteinases (MMPs), 19 genes of ADAMTS, 4 genes of tissue inhibitors of metalloproteinases (TIMPs), and ADAM genes 8, 10, 12, and 17 in normal, painful, and ruptured Achilles tendons. METHODS Tendon samples were obtained from cadavers or from patients undergoing surgical procedures to treat chronic painful tendinopathy or ruptured tendon. Total RNA was extracted and mRNA expression was analyzed by quantitative real-time reverse transcription-polymerase chain reaction, normalized to 18S ribosomal RNA. RESULTS In comparing expression of all genes, the normal, painful, and ruptured Achilles tendon groups each had a distinct mRNA expression signature. Three mRNA were not detected and 14 showed no significant difference in expression levels between the groups. Statistically significant (P < 0.05) differences in mRNA expression, when adjusted for age, included lower levels of MMPs 3 and 10 and TIMP-3 and higher levels of ADAM-12 and MMP-23 in painful compared with normal tendons, and lower levels of MMPs 3 and 7 and TIMPs 2, 3, and 4 and higher levels of ADAMs 8 and 12, MMPs 1, 9, 19, and 25, and TIMP-1 in ruptured compared with normal tendons. CONCLUSION The distinct mRNA profile of each tendon group suggests differences in extracellular proteolytic activity, which would affect the production and remodeling of the tendon extracellular matrix. Some proteolytic activities are implicated in the maintenance of normal tendon, while chronically painful tendons and ruptured tendons are shown to be distinct groups. These data will provide a foundation for further study of the role and activity of many of these enzymes that underlie the pathologic processes in the tendon.
Urdu Qaeda: Recognition System for Isolated Urdu Characters

This paper presents an online system for recognizing isolated, hand-sketched Urdu characters drawn on a Tablet PC. Attributes of Urdu characters are analyzed to define a set of features which are then trained and classified using a weighted, linear classifier. As a proof of concept, we have integrated our recognition algorithm into an application used to help people learn the Urdu language. Preliminary results obtained from our studies showed an accuracy of 92.8% for native Urdu writers. Author Keywords
Finding Candidate Drugs for Hepatitis C Based on Chemical-Chemical and Chemical-Protein Interactions

Hepatitis C virus (HCV) is an infectious virus that can cause serious illnesses. Only a few drugs have been reported to effectively treat hepatitis C. To have greater diversity in drug choice and better treatment options, it is necessary to develop more drugs to treat the infection. However, it is time-consuming and expensive to discover candidate drugs using experimental methods, and computational methods may complement experimental approaches as a preliminary filtering process. This type of approach was proposed by using known chemical-chemical interactions to extract interactive compounds with three known drug compounds of HCV, and the probabilities of these drug compounds being able to treat hepatitis C were calculated using chemical-protein interactions between the interactive compounds and HCV target genes. Moreover, the randomization test and expectation-maximization (EM) algorithm were both employed to exclude false discoveries. Analysis of the selected compounds, including acyclovir and ganciclovir, indicated that some of these compounds had potential to treat the HCV. Hopefully, this proposed method could provide new insights into the discovery of candidate drugs for the treatment of HCV and other diseases.
Cardiovascular Risk in Systemic Autoimmune Diseases: Epigenetic Mechanisms of Immune Regulatory Functions

Autoimmune diseases (AIDs) have been associated with accelerated atherosclerosis (AT) leading to increased cardio- and cerebrovascular disease risk. Traditional risk factors, as well as systemic inflammation mediators, including cytokines, chemokines, proteases, autoantibodies, adhesion receptors, and others, have been implicated in the development of these vascular pathologies. Yet, the characteristics of vasculopathies may significantly differ depending on the underlying disease. In recent years, many new genes and signalling pathways involved in autoimmunity with often overlapping patterns between different disease entities have been further detected. Epigenetics, the control of gene packaging and expression independent of alterations in the DNA sequence, is providing new directions linking genetics and environmental factors. Epigenetic regulatory mechanisms comprise DNA methylation, histone modifications, and microRNA activity, all of which act upon gene and protein expression levels. Recent findings have contributed to our understanding of how epigenetic modifications could influence AID development, not only showing differences between AID patients and healthy controls, but also showing how one disease differs from another and even how the expression of key proteins involved in the development of each disease is regulated.
Performance Prediction for Large-Scale Parallel Applications Using Representative Replay

Automatically predicting performance of parallel applications has been a long-standing goal in the area of high performance computing. However, accurate performance prediction is challenging, since the execution time of parallel applications is determined by several factors, such as sequential computation time, communication time and their complex interactions. Despite previous efforts, accurately estimating the sequential computation time in each process for large-scale parallel applications remains an open problem. In this paper, we propose a novel approach to acquiring accurate sequential computation time using a parallel debugging technique called deterministic replay. The main advantage of our approach is that we only need a single node of a target platform but the whole target platform does not need to be available. Therefore, with this approach we can simply measure the real sequential computation time on a target node for each process on by one. Moreover, we observe that there is great computation similarity in parallel applications, not only within each process but also among different processes. Based on this observation, we further propose representative replay that can significantly reduce replay overhead, because we only need to replay partial iterations for representative processes instead of all of them. Finally, we implement a complete performance prediction system, called Phantom, which combines the above computation-time acquisition approach and a trace-driven simulator. We validate our approach on both traditional HPC platforms and the latest Amazon EC2 cloud platform. On both types of platforms, prediction error of our approach is less than 7 percent on average up to 2,500 processes.