Miracle-dz/UniFAR-FTUs huggingface dataset:
Ecosystem models for fisheries management: finding the sweet spot

The advent of an ecosystem-based approach dramatically expanded the scope of fisheries management, creating a critical need for new kinds of data and quantitative approaches that could be integrated into the management system. Ecosystem models are needed to codify the relationships among drivers, pressures and resulting states, and to quantify the trade-offs between conflicting objectives. Incorporating ecosystem considerations requires moving from the single-species models used in stock assessments, to more complex models that include species interactions, environmental drivers and human consequences. With this increasing model complexity, model fit can improve, but parameter uncertainty increases. At intermediate levels of complexity, there is a ‘sweet spot’ at which the uncertainty in policy indicators is at a minimum. Finding the sweet spot in models requires compromises: for example, to include additional component species, the models of each species have in some cases been simplified from age-structured to logistic or bioenergetic models. In this paper, we illuminate the characteristics, capabilities and short-comings of the various modelling approaches being proposed for ecosystem-based fisheries management. We identify key ecosystem needs in fisheries management and indicate which types of models can meet these needs. Ecosystem models have been playing strategic roles by providing an ecosystem context for single-species management decisions. However, conventional stock assessments are being increasingly challenged by changing natural mortality rates and environmentally driven changes in productivity that are observed in many fish stocks. Thus, there is a need for more tactical ecosystem models that can respond dynamically to changing ecological and environmental conditions.
SCENE BY SCENE SCRIPT

Today there is no “Google for video” that actually searches the content of the video. Content-based video search can be achieved by indexing video scene transcriptions much like a ﬁlm script. We propose to develop a tool that automatically processes video and produces a transcript representing its contents. This processing step may involve scene segmentation, object recognition, behavior recognition, face recognition, and speech transcription. We propose to address each one of these as time permits. In the ﬁrst semester we expect to have scene segmentation accomplished by implementing existing research. During the second semester we will apply techniques for object recognition, face recognition, speech transcription, and develop techniques for scene transcription.
Smart Corrosion Inhibition of Mild Steel Using Mesoporous Silica Nanocontainers Loaded with Molybdate

In this research, mesoporous silica was served as the host of molybdate (corrosion inhibitor). The loaded mesoporous silica was dispersed in a paint matrix. The composite was then coated on the carbon steel surface. Polarization and electrochemical impedance spectroscopy (EIS) tests showed that the corrosion resistance of the scratched paint containing molybdate loaded mesoporous silica was better than the one without it or neat paint at near neutral pH. Charge transfer resistance regarding inhibitor loaded mesoporous silica showed a higher value in comparison with unloaded one. This parameter for the coating with inhibitor loaded mesoporous silica at the higher pH recorded 589300 Ω. cm2, while it was 209100 Ω. cm2 for un-loaded mesoporous silica. On the other hand, scanning electron microscopy (SEM) studies showed the release of corrosion inhibitor in the scratch zone which was due to the pH-sensitive release of corrosion inhibitor in the corrosive media.
THE INHERITANCE OF ANTIBODY V REGIONS IN THE RABBIT: LINKAGE OF AN H-CHAIN-SPECIFIC IDIOTYPE TO I M M U N O G L O B U L I N ALLOTYPES*

Idiotypic inheritance was first demonstrated (1) in partially inbred rabbits immunized with streptococcal carbohydrate antigens. Several subsequent investigations in both the rabbit and the mouse have confirmed this finding and have suggested that idiotypes are linked to the H-chain allotypes (2, 3) and associated with specific L-chain subgroups (4). However, in studies on rabbit antiproteus, antisalmonella, and antipneumococcal antibodies, no evidence that idiotypic specificities are genetically transmitted could be obtained (5-8).
Biofilm Formation as a Pathogenicity Factor of Medically Important Fungi

To cause disease, the infectious agent makes use of both invasiveness factors—the patho‐ gen virulence factors—and the ability to resist and evade the host immune system. The success of the infection process is the result of a complex equation involving pathogen in‐ teraction with the host, wherein the expression of several virulence factors (and not just one or the other) will favor the establishment of the pathogen in the host. Fungal patho‐ gens are frequently associated with biofilm formation. Biofilms are communities of microbial cells adhered to a biotic or abiotic surface and sur‐ rounded by an extracellular matrix secreted by the biofilm cells. Pathogenic fungi are ca‐ pable of forming biofilms inside patients, which is often related to invasive and drug- resistant fungal infections. The most dangerous characteristic associated with biofilm development is the increased resistance of biofilm cells to antifungal drugs, which results from a multifactorial association of mechanisms. General properties of fungal biofilms, resistance behavior and its correlation with pathogenicity are discussed in this chapter.
Articulatory movements and coarticulation in Finnish vowels

Background: Vowel articulation has mostly been studied by using measurements of speech sound acoustics, which is in fact an indirect measure of articulation. The most important factors in vowel description are frequencies of the first and second formants (F1 and F2), and these values separate all vowels from each other (Ladefoged, 2001). By studying acoustics, it is possible to study the outcome of articulation and infer the gestures behind it. The description of vowel articulation has mostly been based on tactile and visual feedback of tongue and lips.
GWAS genetic variant data and their integration in the context of network biology

Regardless of the success of Genome Wide Association Studies (GWAS) to identify genetic variants associated with human diseases, investigating the molecular mechanisms and disease-associated genes linked to those genetic variants, is a very complex task. Specifically, where intergenic genetic variants are linked to the adjacent neighbouring genes. Consequently, the inference for the mechanistic connection between diseases and its susceptible genetic variants becomes more challenging. Functional genomics studies can support to reveal the significance of variants via intermediate molecular traits. Moreover, approaches like computational and bioinformatics predictions based on the variants location and its sequence attributes can assist to propose the candidate genes. As, the spectrum of potential functional consequences of variants is much broader; it still requires new methodologies to predict any molecular level perturbation. Thus, specialized algorithms and computable modelling approaches are essential, for the modelling and simulation of genetic regulatory networks. In this review, we are briefly summarizing all the existing methodologies for genome wide association studies, currently available algorithms and computable modelling approaches; moreover also emphasizing the required new approaches for modelling and simulations of genetic regulatory networks to predict the functional consequences of disease-associated genetic variants.
Rate and Accuracy of Bacterial Protein Synthesis with Natural and Unnatural Amino Acids

Translations with unnatural amino acids (AAs) are generally inefficient, and kinetic studies of their incorporations from transfer ribonucleic acids (tRNAs) are few. Here, the incorporations of small and large, non-N-alkylated, unnatural l-AAs into dipeptides were compared with those of natural AAs using quench-flow techniques. Surprisingly, all incorporations occurred in two phases: fast then slow, and the incorporations of unnatural AA-tRNAs proceeded with rates of fast and slow phases similar to those for natural Phe-tRNA Phe. The slow phases were much more pronounced with unnatural AA-tRNAs, correlating with their known inefficient incorporations. Importantly, even for unnatural AA-tRNAs the fast phases could be made dominant by using high EF-Tu concentrations and/or lower reaction temperature, which may be generally useful for improving incorporations. Also, our observed effects of EF-Tu concentration on the fraction of the fast phase of incorporation enabled direct assay of the affinities of the AA-tRNAs for EF-Tu during translation. Our unmodified tRNA Phe derivative adaptor charged with a large unnatural AA, biotinyl-lysine, had a very low affinity for EF-Tu:GTP, while the small unnatural AAs on the same tRNA body had essentially the same affinities to EF-Tu:GTP as natural AAs on this tRNA, but still 2-fold less than natural Phe-tRNA Phe. We conclude that the inefficiencies of unnatural AA-tRNA incorporations were caused by inefficient delivery to the ribosome by EF-Tu, not slow peptide bond formation on the ribosome.
Comparison of Radial and Femoral Approaches for Coronary Angiography with or without Percutaneous Coronary Intervention in Relation to Vascular Access Site Complications

Background A major population health objective in New Zealand is to reduce the incidence and impact of cardiovascular disease. Cardiovascular disease (CVD) remains New Zealand's leading cause of death (41%). This high demand on health services indicates the need for improved therapies and treatment. Significant advances in percutaneous coronary intervention (PCI) offers many patients who would not typically be eligible for treatment, the chance for a better quality of life living with coronary artery disease (CAD). At present femoral access is primarily used for coronary angiography and or PCI procedures, however more recently there has been a gradual shift to using the radial access approach. Study objective The study's objective was to look at comparing the different access sites used for coronary angiography (CA) and/or percutaneous coronary intervention (PCI) and the significance of the rates of vascular access site complications. The research question considered was; "Is there a significant difference in the vascular access site complication rates when comparing radial to femoral approaches for coronary angiography? " Methodology and design A cohort study design used observational prospective data on radial approaches and compared this with historical retrospective data on femoral approaches. The secondary (comparative) data was extracted from historical records, from earlier research I had completed. The collection of the secondary data involved strict criteria so that the observational study participants had similar baseline characteristics to ensure validity of this study. One hundred participants were recruited for each (prospective and retrospective) database and then compared and analysed. Findings The use of a radial approach for CA and PCI has a significant decrease in combined vascular access site complications (haematoma, vasovagal and arterial bleed), (p value 0.001), OR 0.28 (0.13-0.62). Haematoma is the main vascular complication (p value 0.009), OR 0.29 (0.11-0.74). Conclusion This study, although small, can be used as a pilot study for a more detailed and bigger national study within New Zealand. From the results it is clear there is a significant decrease in the vascular site complication rates when a radial approach is undertaken for CA and/or PCI. Through education and clinical practice, the radial approach would ensure better patient safety, satisfaction and comfort which would help reduce the patients length of stay and increase patients treated with timely discharges. It could also help decrease the nurses' workload caring for the patient with the radial approach due to the lesser complication rates. More extensive use of radial approaches for CA and or PCI would ensure the above benefits for the patients, staff and the organisation.
AN EFFECTIVE TOKENIZATION ALGORITHM FOR INFORMATION RETRIEVAL SYSTEMS

In the web, amount of operational data has been increasing exponentially from past few decades, the expectations of data-user is changing proportionally as well. The data-user expects more deep, exact, and detailed results. Retrieval of relevant results is always affected by the pattern, how they are stored/ indexed. There are various techniques are designed to indexed the documents, which is done on the token’s identified with in documents. Tokenization process, primarily effective is to identifying the token and their count. In this paper, we have proposed an effective tokenization approach which is based on training vector and result shows that efficiency/ effectiveness of proposed algorithm.Tokenization of a given documents helps to satisfy user’s information need more precisely and reduced search sharply, is believed to be a part of information retrieval. Tokenization involves pre-processing of documents and generates its respective tokens which is the basis of these tokens probabilistic IR generate its scoring and gives reduced search space. No of Token generated is the parameters used for result analysis.
Acoustic Neurinomas

Acoustic neuromas (AN) are schwann cell-derived tumors that commonly arise from the vestibular portion of the eighth cranial nerve also known as vestibular schwannoma(VS) causes unilateral hearing loss, tinnitus, vertigo and unsteadiness. In many cases, the tumor size may remain unchanged for many years following diagnosis, which is typically made by MRI. In the majority of cases the tumor is small, leaving the clinician and patient with the options of either serial scanning or active treatment by gamma knife radiosurgery (GKR) or microneurosurgery. Despite the vast number of published treatment reports, comparative studies are few. The predominant clinical endpoints of AN treatment include tumor control, facial nerve function and hearing preservation. Less focus has been put on symptom relief and health-related quality of life (QOL). It is uncertain if treating a small tumor leaves the patient with a better chance of obtaining relief from future hearing loss, vertigo or tinnitus than by observing it without treatment. In this paper we review the literature for the natural course, the treatment alternatives and the results of AN. Finally, we present our experience with a management strategy applied for more than 30 years.
Running Title: SF3B1 and non-MDS and mast cell disease

Citation: Visconte V, Tabarroki A, Rogers HJ, Hasrouni E, Traina F, Makishima H, Hamilton BK, Liu Y, O' Keefe C, Lichtin A, Horwitz L, Sekeres MA, Hsieh FH, and Tiu RV. SF3B1 mutations are infrequently found in non-Myelodysplastic bone marrow failure syndromes and mast cell diseases but, if present, are associated with the ring sideroblast phenotype. Haematologica. 2013; 98:xxx doi:10.3324/haematol.2013. 090506
Invited Article

We describe a general N -solitonic solution of the focusing nonlinear Schrödinger equation in the presence of a condensate by using the dressing method. We give the explicit form of oneand two-solitonic solutions and study them in detail as well as solitonic atoms and degenerate solutions. We distinguish a special class of solutions that we call regular solitonic solutions. Regular solitonic solutions do not disturb phases of the condensate at infinity by coordinate. All of them can be treated as localized perturbations of the condensate. We find a broad class of superregular solitonic solutions which are small perturbations at a certain moment of time. Superregular solitonic solutions are generated by pairs of poles located on opposite sides of the cut. They describe the nonlinear stage of the modulation instability of the condensate and play an important role in the theory of freak waves.
Hypercortisolaemia and Hyperinsulinaemia Interaction and their Impact upon Insulin Resistance/Sensitivity Markers at Birth

Information on insulin resistance/sensitivity in term-normoweight neonates is scarce. The hypothalamus-pituitary-adrenal cortex axis and pancreas are implicated in several aspects of foetal maturation and programming. This study aims to analyse the effects of a combination of hyperinsulinaemia plus hypercortisolaemia in such neonates together with their mothers ℉ gestational glucose tolerance on growth hormone (GH), insulin-like growth factor-1 (IGF)-1, glucose, and insulin resistance/sensitivity markers [homeostatic model assessment-insulin resistance (HOMA-IR)/quantitative insulin sensitivity check index (QUICKI)] at birth. Furthermore, the importance of pregnancy diet quality on these markers is discussed. In a selected group of 187 term-normoweight non-distressed neonates, about 9% had increased insulin and cortisol cord-blood concentrations. In spite of normality criteria applied, the combination of hypercortisolaemia and hyperinsulinaemia at birth was associated with higher body weight, body length, glucose, HOMA-IR, GH, IGF-1 and glucose/insulin ratio values than those of neonates presenting low/normal concentrations of insulin and cortisol. Hyperinsulinaemia preferentially to hypercortisolaemia affected the markers studied. Impaired glucose tolerance prevalence was higher in mothers whose neonates were hyperinsulinaemic at birth. The hyperinsulinaemic plus hypercortisolaemic status was more prevalent in neonates whose mothers had poor Mediterranean diet adherence. Results show the importance of analysing insulin and cortisol in cord-blood even in term-normoweight neonates.
Evaluating the Usefulness of the Diabetic Peripheral Neuropathy Screening Process

Summary Aims: To evaluate the clinical utility of the diabetic peripheral neuropathy (DPN) screening process in the diagnosis of DPN among diabetic patients. Methods: A total of 816 diabetic patients performed nerve conduction velocity (NCV), Somatosensory evoked potential (SEP), Toronto clinical scoring system (TCSS), and DPN screening process at baseline. The NCV and SEP were used as the ‘gold standard’ against which the sensitivity, specificity, positive predictive value, negative predictive value and Youden’s index of the TCSS and the DPN screening process determined by the Chinese Diabetes Society of the Chinese Medical Association in 2010. Results: According to the DPN screening process, 602 patients (73.77%) were positive while 458 patients (56.13%) were positive according to the TCSS score. The sensitivity, specificity, positive predictive value, negative predictive value, and Youden’s index of DPN screening process were 89.49%, 66.56%, 81.99%, 78.82%, and 0.5605, respectively. Patients with DPN exhibited numbness (46.02%), pain (15.71%), paresthesia (16.59%), pinprick sensation (12.17%), and others (10.62%). The sensitivity and specificity of the various DPN checks were as follows: pressure sensation (19.44% and 95.62%), vibration perception (77.78% and 60.87%), temperature sensation (35.19% and 89.13%), and pinprick (31.48% and 84.78%). The sensitivity, specificity, positive predictive value, negative predictive value, and Youden’s index of a TCSS score ≥ 6 were 78.21%, 84.11%, 89.33%, 69.40%, and 0.6232, respectively. DPN screening process took an average of 5.89 minutes, while TCSS spent an average of 10.32 minutes. Conclusion: DPN screening process is economical, simple, fast, accurate, and could be used for early clinical screening of DPN in patients with diabetes.
Deep Pyramidal Residual Networks with Stochastic Depth

In generic object recognition tasks, ResNet and its improvements have broken the lowest error rate records. ResNet enables us to make a network deeper by introducing residual learning. Some ResNet improvements achieve higher accuracy by focusing on channels. Thus, the network depth and channels are thought to be important for high accuracy. In this paper, in addition to them, we pay attention to use of multiple models in data-parallel learning. We refer to it as data-parallel multimodel learning. We observed that the accuracy increased as models concurrently used increased on some methods, particularly on the combination of PyramidNet and the stochastic depth proposed in the paper. As a result, we confirmed that the methods outperformed the conventional methods; on CIFAR-100, the proposed methods achieved error rates of 16.13% and 16.18% in contrast to PiramidNet achieving that of 18.29% and the current state-of-the-art DenseNet-BC 17.18%.
DNA barcoding in floral and faunal research

As I write this chapter in mid 2012, the context in which floral and faunal research is done is changing rapidly. Demand for biodiversity information, especially to understand global change, is increasing. The technologies that are available for carrying out biodiversity research and for disseminating the results are changing dramatically. The funding processes and organisational cultures of the institutions that have been the traditional homes of such research are evolving. This creates new challenges and opportunities for floral and faunal research. This chapter will focus on the intersection of DNA barcoding with floral and faunal research, the opportunities that DNA barcoding offers for increasing the quality and quantity of such work, and its connectivity with related activities. I will discuss the opportunities for DNA barcoding and then provide an example from my own research. The essay focuses on plants and animals, but will include some reference to other organisms. Because of the rapid evolution of the underlying technologies, and the related social changes, this essay represents a ‘slice of time’, and I expect some of the conclusions will be out of date before it is published. While challenges remain, I believe this is an exciting time of renaissance for taxonomy (Miller, 2007). A DNA barcode is a short gene sequence taken from standardised portions of the genome, used to identify species. Being DNA based, it can be used for specimens
STABILIZATION MECHANISM IN SWIMMING ODONTOCETE CETACEANS BY PHASED MOVEMENTS

Propulsive movements of the caudal oscillating flukes produce large forces chat could induce equally large recoil forces at the cranial end of the animal, and, thus, affect stability. To examine these vertical oscillations, video analysis was used to measure the motions of the rostrum, pectoral flipper, caudal peduncle, and fluke tip for seven odonrocere cetaceans: Delphinapterus leucas, Globicepbala melaena, Lagenvrhyncbus obliquidens, O~cinus orra, Pseudorca crassidens, Stenella plagiodon, and TarJiops truncatus. Animals swam over a range of speeds of 1.4-7.3 mlsec. For each species, oscillatory frequency of the fluke tip increased linearly with swimming speed. Peak-to-peak amplitude at each body position remained constanc with respect ro swimming speed for all species. Mean peak-to-peak amplitude ranged from 0.02 to 0.06 body length at the rostrum and from 0.17 to 0.25 body length at the fluke tip. The phase relationships between the various body components remain constant with respect to swimming speed. Oscillations of the rostrum were nearly in phase with the fluke tip with phase differences out of -9.4"-33.0" of a cycle period of 360". Pectoral flipper oscillations trailed fluke oscillations by 60.9°-123.40. The lower range in amplitude at the rostrum compared co rhe fluke rip reflects increased resistance to vertical oscillation at the cranial end, which enhances the animal's stability. This resistance is likely due to both active and passive increased body stiffness, resistance on the flippers, phased movements of body components, and use of a lift-based propulsion. Collectively, these mechanisms srabilize the body of cetaceans during active swimming, which can reduce locomotor energy expenditure and reduce excessive motions of the head affecting sensory capabilities.