Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Cloning and Structural Characterization of the Arg-gingipain Proteinase of Porphyromonas gingivalis

The identification of proteinases of Porphyromonas gingivalis that act as virulence factors in periodontal disease has important implications in the study of host-pathogen interactions as well as in the discovery of potential therapeutic and immunoprophylactic agents. We have cloned and characterized a gene that encodes the 50-kDa cysteine proteinase gingipain or Arg-gingipain-1 (RGP-1) described previously (Chen, Z., Potempa, J., Polanowski, A., Wikstrom, M., and Travis, J. (1992) J. Biol. Chem. 267, 18896-18901). Analysis of the amino acid sequence of RGP-1 deduced from the cloned DNA sequence showed that the biosynthesis of this proteinase involves processing of a polyprotein that contains multiple adhesin molecules located at its carboxyl terminus. This finding corroborates previous evidence (Pike R., McGraw, W., Potempa, J., and Travis, J.(1994) J. Biol. Chem. 269, 406-411) that RGP-1 is closely associated with adhesin molecules, and that high molecular weight forms of the proteinase are involved in the binding of erythrocytes.
A generalized uncertainty principle and sparse representation in pairs of bases

An elementary proof of a basic uncertainty principle concerning pairs of representations of R/sup N/ vectors in different orthonormal bases is provided. The result, slightly stronger than stated before, has a direct impact on the uniqueness property of the sparse representation of such vectors using pairs of orthonormal bases as overcomplete dictionaries. The main contribution in this paper is the improvement of an important result due to Donoho and Huo (2001) concerning the replacement of the l/sub 0/ optimization problem by a linear programming (LP) minimization when searching for the unique sparse representation.
Central Tolerance to Tissue-specific Antigens Mediated by Direct and Indirect Antigen Presentation

Intrathymic expression of tissue-specific antigens (TSAs) by medullary thymic epithelial cells (Mtecs) leads to deletion of autoreactive T cells. However, because Mtecs are known to be poor antigen-presenting cells (APCs) for tolerance to ubiquitous antigens, and very few Mtecs express a given TSA, it was unclear if central tolerance to TSA was induced directly by Mtec antigen presentation or indirectly by thymic bone marrow (BM)-derived cells via cross-presentation. We show that professional BM-derived APCs acquire TSAs from Mtecs and delete autoreactive CD8 and CD4 T cells. Although direct antigen presentation by Mtecs did not delete the CD4 T cell population tested in this study, Mtec presentation efficiently deleted both monoclonal and polyclonal populations of CD8 T cells. For developing CD8 T cells, deletion by BM-derived APC and by Mtec presentation occurred abruptly at the transitional, CD4high CD8low TCRintermediate stage, presumably as the cells transit from the cortex to the medulla. These studies reveal a cooperative relationship between Mtecs and BM-derived cells in thymic elimination of autoreactive T cells. Although Mtecs synthesize TSAs and delete a subset of autoreactive T cells, BM-derived cells extend the range of clonal deletion by cross-presenting antigen captured from Mtecs.
Ballooning dispersal in arthropod taxa: conditions at take-off

We have solved a long-standing and seemingly paradoxical set of questions that relate to the conditions which govern spider ballooning. We show that observations of spider ballooning excursions are best explained by meteorological conditions which maximize dispersal. Dispersal is predicted to be most effective in terms of distance when the stability of the atmosphere is non-ideally convective and is less effective during purely convective or neutrally stable conditions. Ballooners are most likely to travel a few hundred metres, but dispersal distances of several hundred kilometres are possible.
ITEAMS - An Intelligent Teaching Environment with Assessment Modules for Self-Study

We propose a system that provides a framework for an intelligent teaching environment. The strengths of the system are that it is domain independent, it is adaptive to the subjects level of difficulty and has an expendable set of metrics that evaluate students’ assignments performance in external systems, (e.g., neural network simulators). The evaluation of students d the system’s adaptability are accomplished through belief networks. We demonstrate the use of the system by applying it to an agent design course in which it evaluates student programs.
Classification of mechanisms, climatic context, areal scaling, and synchronization of floods: the hydroclimatology of floods in the Upper Paraná River basin, Brazil

Abstract. Floods are the main natural disaster in Brazil, causing substantial economic damage and loss of life. Studies suggest that some extreme floods result from a causal climate chain. Exceptional rain and floods are determined by large-scale anomalies and persistent patterns in the atmospheric and oceanic circulations, which influence the magnitude, extent, and duration of these extremes. Moreover, floods can result from different generating mechanisms. These factors contradict the assumptions of homogeneity, and often stationarity, in flood frequency analysis. Here we outline a methodological framework based on clustering using self-organizing maps (SOMs) that allows the linkage of large-scale processes to local-scale observations. The methodology is applied to flood data from several sites in the flood-prone Upper Parana River basin (UPRB) in southern Brazil. The SOM clustering approach is employed to classify the 6-day rainfall field over the UPRB into four categories, which are then used to classify floods into four types based on the spatiotemporal dynamics of the rainfall field prior to the observed flood events. An analysis of the vertically integrated moisture fluxes, vorticity, and high-level atmospheric circulation revealed that these four clusters are related to known tropical and extratropical processes, including the South American low-level jet (SALLJ); extratropical cyclones; and the South Atlantic Convergence Zone (SACZ). Persistent anomalies in the sea surface temperature fields in the Pacific and Atlantic oceans are also found to be associated with these processes. Floods associated with each cluster present different patterns in terms of frequency, magnitude, spatial variability, scaling, and synchronization of events across the sites and subbasins. These insights suggest new directions for flood risk assessment, forecasting, and management.
Polyculture and fish yield in rice-cum-fish culture system in Dadin Kowa, Gombe, Nigeria

Rice-cum-fish culture was carried out in Dadin Kowa rice fields, Gombe State, Nigeria with a view to determining the effect of different combination of Clarias gariepinus, Oreochromis niloticus and Cyprinus carpio on fish yield. Six rice paddy fields labeled A – C were used for the study. Raised rice seedlings (FARO 27) were transplanted in the paddies before flooding of water. The fish species were stocked at 200 fish / pond in three replicates in different combinations as treatments I, II and III. The fish were fed with wheat bran and rice bran at 5 % body weight. The lowest rice yield (2560 kg/ha) was obtained in the paddy where rice was grown without fish. The fish production recorded in treatment I (534 kg) is significantly higher (P < 0.05) than in other two treatments. It is therefore recommended that rice farmers using irrigation facilities of the river Basin Development Authorities should adopt the rice-cum-fish system for increased rice and fish production in Nigeria
Novel methods for expression of foreign antigens in live vector vaccines

Bacterial live vector vaccines represent a vaccine development strategy that offers exceptional flexibility. In this approach, genes encoding protective antigens of unrelated bacterial, viral or parasitic pathogens are expressed in an attenuated bacterial vaccine strain that delivers these foreign antigens to the immune system, thereby eliciting relevant immune responses. Rather than expressing these antigens using low copy expression plasmids, here we pursue expression of foreign proteins from the live vector chromosome. Our strategy is designed to compensate for the inherent disadvantage of loss of gene dosage (vs. plasmid-based expression) by integrating antigen-encoding gene cassettes into multiple chromosomal sites already inactivated in an attenuated Salmonella enterica serovar Typhi vaccine candidate. We tested expression of a cassette encoding the green fluorescent protein (GFPuv) integrated separately into native guaBA, htrA or clyA chromosomal loci. Using single integrations, we show that expression levels of GFPuv are significantly affected by the site of integration, regardless of the inclusion of additional strong promoters within the incoming cassette. Using cassettes integrated into both guaBA and htrA, we observe cumulative synthesis levels from two integration sites superior to single integrations. Most importantly, we observe that GFPuv expression increases in a growth phase-dependent manner, suggesting that foreign antigen synthesis may be “tuned” to the physiology of the live vaccine. We expect this novel platform expression technology to prove invaluable in the development of a wide variety of multivalent live vector vaccines, capable of expressing multiple antigens from both chromosomal and plasmid-based expression systems within a single strain.
Behavioral measures of auditory streaming in ferrets (Mustela putorius).

An important aspect of the analysis of auditory "scenes" relates to the perceptual organization of sound sequences into auditory "streams. " In this study, we adapted two auditory perception tasks, used in recent human psychophysical studies, to obtain behavioral measures of auditory streaming in ferrets (Mustela putorius). One task involved the detection of shifts in the frequency of tones within an alternating tone sequence. The other task involved the detection of a stream of regularly repeating target tones embedded within a randomly varying multitone background. In both tasks, performance was measured as a function of various stimulus parameters, which previous psychophysical studies in humans have shown to influence auditory streaming. Ferret performance in the two tasks was found to vary as a function of these parameters in a way that is qualitatively consistent with the human data. These results suggest that auditory streaming occurs in ferrets, and that the two tasks described here may provide a valuable tool in future behavioral and neurophysiological studies of the phenomenon.
The web centipede: understanding how web communities influence each other through the lens of mainstream and alternative news sources

As the number and the diversity of news outlets on the Web grows, so does the opportunity for "alternative" sources of information to emerge. Using large social networks like Twitter and Facebook, misleading, false, or agenda-driven information can quickly and seamlessly spread online, deceiving people or influencing their opinions. Also, the increased engagement of tightly knit communities, such as Reddit and 4chan, further compounds the problem, as their users initiate and propagate alternative information, not only within their own communities, but also to different ones as well as various social media. In fact, these platforms have become an important piece of the modern information ecosystem, which, thus far, has not been studied as a whole. In this paper, we begin to fill this gap by studying mainstream and alternative news shared on Twitter, Reddit, and 4chan. By analyzing millions of posts around several axes, we measure how mainstream and alternative news flows between these platforms. Our results indicate that alt-right communities within 4chan and Reddit can have a surprising level of influence on Twitter, providing evidence that "fringe" communities often succeed in spreading alternative news to mainstream social networks and the greater Web.
Effect of ketorolac in pediatric sickle cell vaso-occlusive pain crisis.

BACKGROUND Ketorolac is a parenteral, nonsteroidal analgesic that does not have a narcotic's risks of respiratory depression, hypotension, or dependence. Its usefulness in providing pain relief in pediatric patients with acute vaso-occlusive crisis of sickle cell disease has not been studied to date. METHODS Twenty-nine patients with sickle cell disease between the ages of 5 and 18 years who presented to The Children's Hospital of Alabama emergency department (ED) with 41 distinct episodes of acute vaso-occlusive pain crisis were enrolled prospectively and randomized to receive either 0.9 mg/kg intravenous (IV) ketorolac or placebo in a double-blind fashion. All patients also received IV fluids and an initial 0.1 mg/kg of IV morphine. Subsequent standardized doses of morphine were given every 2 hours over a 6-hour observation period based upon severity of pain as scored by a 10-cm linear visual analog scale (VAS). Vital signs and pain severity were recorded initially and assessed hourly. Disposition was made at the end of the observation period. RESULTS Patients receiving ketorolac and those receiving placebo were of similar age, weight, gender, number of prior ED visits, number of prior hospital admissions, duration of pain prior to presentation, and initial pain score. The total dose of morphine received, reduction in severity of pain as measured by VAS, rate of hospital admission, and rate of return to the ED for discharged patients did not differ significantly between the two groups. CONCLUSION We were unable to demonstrate a synergistic analgesic effect for ketorolac in the treatment of pain from acute vaso-occlusive crisis in pediatric sickle cell disease. Further investigations involving larger samples of sickle cell patients may be needed to further define a role for ketorolac in the acute management of sickle cell vaso-occlusive pain.
SUB1 Plays a Negative Role during Starvation Induced Sporulation Program in Saccharomyces cerevisiae

Saccharomyces cerevisiae Sub1 is involved in several cellular processes such as, transcription initiation, elongation, mRNA processing and DNA repair. It has also been reported to provide cellular resistance during conditions of oxidative DNA damage and osmotic stress. Here, we report a novel role of SUB1 during starvation stress-induced sporulation, which leads to meiosis and spore formation in diploid yeast cells. Deletion of SUB1 gene significantly increased sporulation efficiency as compared to the wild-type cells in S288c genetic background. Whereas, the sporulation functions of the sub1(Y66A) missense mutant were similar to Sub1. SUB1 transcript and protein levels are downregulated during sporulation, in highly synchronized and sporulation proficient wild-type SK1 cells. The changes in Sub1 levels during sporulation cascade correlate with the induction of middle sporulation gene expression. Deletion of SUB1 increased middle sporulation gene transcript levels with no effect on their induction kinetics. In wild-type cells, Sub1 associates with chromatin at these loci in a temporal pattern that correlates with their enhanced gene expression seen in sub1Δ cells. We show that SUB1 genetically interacts with HOS2, which led us to speculate that Sub1 might function with Set3 repressor complex during sporulation. Positive Cofactor 4, human homolog of Sub1, complemented the sub1Δ sporulation phenotype, suggesting conservation of function. Taken together, our results suggest that SUB1 acts as a negative regulator of sporulation.
Combined state and parameter estimation for adaptive control and feedback applications for a gait rehabilitation robot

Unsupervised gait training of patients using a robotic trainer requires an individual adaption of the modelbased control for each patient as well as a feedback of the patient's performance. For these adaption and feedback tasks, estimation of the kinematic states, the friction states, and the patient-dependent parameters of the model is necessary. In this contribution, a combined estimation approach is proposed for a new gait training robot using a central difference Kalman filter, which is based on a simplified gait trainer model extended by a dynamic friction model. In the resulting overall model, the three dominating mass parameters, which depend on the patient's mass and activity, are redefined as states with integrating character. The observer approach is applied on a prototype of the gait trainer and its accuracy is evaluated with measured data using reference weights.
Hierarchically Distributed Dynamic Mean Shift

A fast and memory-efficient method is presented for dynamic mean shift (DMS) algorithm, which is an iterative mode-seeking algorithm. The DMS algorithm requires a large amount of memory to run because it dynamically updates all samples during the iterations. Therefore, it is difficult to use the DMS for clustering a large set of samples. The difficulty of the DMS is solved by partitioning a set of samples into subsets hierarchically, and the resultant procedure is called the hierarchically distributed DMS (HDDMS). Experimental results on image segmentation show that the HDDMS requires less memory than that of the DMS.
BDNF splice variants from the second promoter cluster support cell survival of differentiated neuroblastoma upon cytotoxic stress

The neurotrophin brain-derived neurotrophic factor (BDNF) is a key survival factor for neural cells. In particular, in neuroblastoma tumour cells, expression of the BDNF/TrkB autocrine signalling system promotes a more malignant phenotype and resistance to chemotherapy. The human BDNF gene contains two clusters of upstream exons encoding the 5′UTR (exon 1 to exon 3 and exon 4 to exon 9a), these are alternatively spliced to a common exon 9, which contains the coding region and the 3′UTR. At least 34 different BDNF mRNA transcripts can be generated, although their physiological role is still unknown. The purpose of this study is to determine which BDNF transcript is involved in cell survival of the human neuroblastoma cell lines SH-SY-5Y (single-copy MYCN) and SK-N-BE (amplified MYCN). Expression of human BDNF mRNAs encoding all possible isoforms was characterised in the two neuroblastoma cell lines. We then investigated whether selective silencing of the different BDNF mRNAs using specific siRNAs could reduce cell survival in response to serum deprivation or the anticancer drugs cisplatin, doxorubicin and etoposide. We found that three isoforms located in the second exon cluster are essential for neuroblastoma cell survival under cytotoxic stress. Notably, promoters of the second exon cluster, but not the first, are controlled by Ca2+-sensitive elements.
Performance Comparison of Different Multilayer Perceptron Network Activation Functions in Automated Weather Classification

Multilayer perceptron network (MLP) has been recognized as a powerful tool for many applications including classification. Selection of the activation functions in the multilayer perceptron (MLP) network plays an essential role on the network performance. This paper presents a comparison study of two commonly used MLP activation function, sigmoid and hyperbolic tangent for weather classification. Meteorological data such as solar radiation, ambient temperature, current, surface temperature, voltage, wind direction and wind speed data are acquired from a photovoltaic (PV) system. Then, the meteorological data are input to the MLP network to classify the weather condition. In this study, weather conditions are classified into four types, rain, cloudy, dry day and storm. Levenberg-Marquardt algorithm is used to train the MLP network since it is the fastest training and ensure the best converges towards a minimum error. Experimental results show that hyperbolic tangent activation function is more efficient compared to sigmoid activation function. The MLP network using hyperbolic tangent function has achieved higher classification accuracy with less number of hidden nodes compared to sigmoid activation function.
Motor cortical function and the precision grip

While task‐dependent changes in motor cortical outputs have been previously reported, the issue of whether such changes are specific for complex hand tasks remains unresolved. The aim of the present study was to determine whether cortical inhibitory tone and cortical output were greater during precision grip and power grip. Motor cortex excitability was undertaken by using the transcranial magnetic stimulation threshold tracking technique in 15 healthy subjects. The motor‐evoked potential (MEP) responses were recorded over the abductor pollicis brevis (APB), with the hand in the following positions: (1) rest, (2) precision grip and (3) power grip. The MEP amplitude (MEP amplitude REST 23.6 ± 3.3%; MEP amplitude PRECISION GRIP 35.2 ± 5.6%; MEP amplitude POWER GRIP 19.6 ± 3.4%, F = 2.4, P < 0.001) and stimulus‐response gradient (SLOPEREST 0.06 ± 0.01; SLOPEPRCISION GRIP 0.15 ± 0.04; SLOPE POWER GRIP 0.07 ± 0.01, P < 0.05) were significantly increased during precision grip. Short interval intracortical inhibition (SICI) was significantly reduced during the precision grip (SICI REST 15.0 ± 2.3%; SICI PRECISION GRIP 9.7 ± 1.5%, SICI POWER GRIP 15.9 ± 2.7%, F = 2.6, P < 0.05). The present study suggests that changes in motor cortex excitability are specific for precision grip, with functional coupling of descending corticospinal pathways controlling thumb and finger movements potentially forming the basis of these cortical changes.
The Gene Frequency of Acute Werdnig-Hoffmann Disease (SMA Type 1). A Total Population Survey in North-East England

A retrospective total population study of acute Werdnig-Hoffmann disease (spinal muscular atrophy type 1) has been undertaken in three counties of North-East England (Northumberland, Newcastle upon Tyne, and Durham). The gene frequency for the disease is q=0·00625 with a carrier frequency for this part of the English population of 1 in 80. The data suggest that there may be differences in gene frequency within the region sampled, a finding in keeping with other investigations of variations in gene frequency in this region. The suggestion that this disease is the second most common fatal autosomal recessive disease of childhood in Britain is confirmed. An hypothesis of heterozygote advantage due to relative resistance to epidemic poliomyelitis is presented to account for the high gene frequency observed.
Experimental Bacillus cereus post-traumatic endophthalmitis and treatment with ciprofloxacin.

BACKGROUND: Bacillus species remain an important cause of post-traumatic endophthalmitis, often causing permanent visual loss. METHODS: Twenty two rabbits were used to evaluate the clinical and histological findings of Bacillus cereus experimental post-traumatic endophthalmitis. Eyes that had received a scleral laceration and surgical repair were inoculated with Bacillus cereus. Thirty four other rabbits were used to evaluate the efficacy of intravitreal ciprofloxacin in treating experimental disease. RESULTS: Animals developed a post-traumatic endophthalmitis that closely mimicked human disease, characterised by a rapidly progressive and destructive endophthalmitis. Histological evaluation revealed retinal detachment, retinal necrosis, and the infiltration of inflammatory cells into the subretinal space. Intravitreal ciprofloxacin (100 micrograms) prevented the development of disease when given 1 hour and 6 hours after trauma and inoculation. CONCLUSIONS: Clinical and histological examination of experimental Bacillus cereus post-traumatic endophthalmitis suggests that retinal detachment and retinal necrosis play important roles in visual loss. Ciprofloxacin may be of benefit in the management of certain intraocular infections following penetrating injury.