Miracle-dz/UniFAR-FTUs huggingface dataset:
Plant dehydrins — Tissue location, structure and function

Dehydrins (DHNs) are part of a large group of highly hydrophilic proteins known as LEA (Late Embryogenesis Abundant). They were originally identified as group II of the LEA proteins. The distinctive feature of all DHNs is a conserved, lysine-rich 15-amino acid domain, EKKGIMDKIKEKLPG, named the K-segment. It is usually present near the C-terminus. Other typical dehydrin features are: a track of Ser residues (the S-segment); a consensus motif, T/VDEYGNP (the Y-segment), located near the N-terminus; and less conserved regions, usually rich in polar amino acids (the Φ-segments). They do not display a well-defined secondary structure. The number and order of the Y-, S-and K-segments define different DHN sub-classes: YnSKn, YnKn, SKn, Kn and KnS. Dehydrins are distributed in a wide range of organisms including the higher plants, algae, yeast and cyanobacteria. They accumulate late in embryogenesis, and in nearly all the vegetative tissues during normal growth conditions and in response to stress leading to cellular dehydration (e.g. drought, low temperature and salinity). DHNs are localized in different cell compartments, such as the cytosol, nucleus, mitochondria, vacuole, and the vicinity of the plasma membrane; however, they are primarily localized to the cytoplasm and nucleus. The precise function of dehydrins has not been established yet, but in vitro experiments revealed that some DHNs (YSKn-type) bind to lipid vesicles that contain acidic phospholipids, and others (KnS) were shown to bind metals and have the ability to scavenge hydroxyl radicals [Asghar, R. et al. Protoplasma 177 (1994) 87–94], protect lipid membranes against peroxidation or display cryoprotective activity towards freezing-sensitive enzymes. The SKn-and K-type seem to be directly involved in cold acclimation processes. The main question arising from the in vitro findings is whether each DHN structural type could possess a specific function and tissue distribution. Much recent in vitro data clearly indicates that dehydrins belonging to different subclasses exhibit distinct functions.
Results of Genome-Wide Analyses on Neurodevelopmental Phenotypes at Four-Year Follow-Up following Cardiac Surgery in Infancy

Background Adverse neurodevelopmental sequelae are reported among children who undergo early cardiac surgery to repair congenital heart defects (CHD). APOE genotype has previously been determined to contribute to the prediction of these outcomes. Understanding further genetic causes for the development of poor neurobehavioral outcomes should enhance patient risk stratification and improve both prevention and treatment strategies. Methods We performed a prospective observational study of children who underwent cardiac surgery before six months of age; this included a neurodevelopmental evaluation between their fourth and fifth birthdays. Attention and behavioral skills were assessed through parental report utilizing the Attention Deficit-Hyperactivity Disorder-IV scale preschool edition (ADHD-IV), and Child Behavior Checklist (CBCL/1.5-5), respectively. Of the seven investigated, three neurodevelopmental phenotypes met genomic quality control criteria. Linear regression was performed to determine the effect of genome-wide genetic variation on these three neurodevelopmental measures in 316 subjects. Results This genome-wide association study identified single nucleotide polymorphisms (SNPs) associated with three neurobehavioral phenotypes in the postoperative children ADHD-IV Impulsivity/Hyperactivity, CBCL/1.5-5 PDPs, and CBCL/1.5-5 Total Problems. The most predictive SNPs for each phenotype were: a LGALS8 intronic SNP, rs4659682, associated with ADHD-IV Impulsivity (P = 1.03×10−6); a PCSK5 intronic SNP, rs2261722, associated with CBCL/1.5-5 PDPs (P = 1.11×10−6); and an intergenic SNP, rs11617488, 50 kb from FGF9, associated with CBCL/1.5-5 Total Problems (P = 3.47×10−7). 10 SNPs (3 for ADHD-IV Impulsivity, 5 for CBCL/1.5-5 PDPs, and 2 for CBCL/1.5-5 Total Problems) had p<10−5. Conclusions No SNPs met genome-wide significance for our three neurobehavioral phenotypes; however, 10 SNPs reached a threshold for suggestive significance (p<10−5). Given the unique nature of this cohort, larger studies and/or replication are not possible. Studies to further investigate the mechanisms through which these newly identified genes may influence neurodevelopment dysfunction are warranted.
New 2-D filter architectures with quadrantal symmetry and octagonal symmetry and their error analysis

In this paper, two new two-dimensional (2-D) IIR and FIR filter architectures possessing quadrantal and octagonal symmetries are proposed. Furthermore, the theoretical error analysis for the proposed filters is also presented. Utilizing the presented error analysis, user can decide the bit width of the filters with satisfactory error tolerance.
Large-Scale Transcriptome Analysis of Retroelements in the Migratory Locust, Locusta migratoria

Background Retroelements can successfully colonize eukaryotic genome through RNA-mediated transposition, and are considered to be some of the major mediators of genome size. The migratory locust Locusta migratoria is an insect with a large genome size, and its genome is probably subject to the proliferation of retroelements. An analysis of deep-sequencing transcriptome data will elucidate the structure, diversity and expression characteristics of retroelements. Results We performed a de novo assembly from deep sequencing RNA-seq data and identified 105 retroelements in the locust transcriptome. Phylogenetic analysis of reverse transcriptase sequences revealed 1 copia, 1 BEL, 8 gypsy and 23 non-long terminal repeat (LTR) retroelements in the locust transcriptome. A novel approach was developed to identify full-length LTR retroelements. A total of 5 full-length LTR retroelements and 2 full-length non-LTR retroelements that contained complete structures for retrotransposition were identified. Structural analysis indicated that all these retroelements may have been activated or deprived of retrotransposition activities very recently. Expression profiling analysis revealed that the retroelements exhibited a unique expression pattern at the egg stage and showed differential expression profiles between the solitarious and gregarious phases at the fifth instar and adult stage. Conclusion We hereby present the first de novo transcriptome analysis of retroelements in a species whose genome is not available. This work contributes to a comprehensive understanding of the landscape of retroelements in the locust transcriptome. More importantly, the results reveal that non-LTR retroelements are abundant and diverse in the locust transcriptome.
Natural Language Processing: What’s Really Involved?

The question before us is whether or not NLP has gone anywhere since the last TINLAP. The answer depends strongly on what we take NLP to be. If we accept the common assumption that language processing can be isolated from the rest of cognition, and that the goal of NLP research to study language as a formal system independent of such (admittedly difficult) issues as memory, learning, and explanation, then our conclusion is grim. Not only has this approach failed to make significant progress in the eight years since TINLAP2, it is permanently doomed to failure because it misses the point of what language is all about. It is only possible for research on understanding natural language to make progress when the researchers realize that the heart of NLU is the understanding process, not language per se.
An Ecosystem Evaluation Framework for Global Seamount Conservation and Management

In the last twenty years, several global targets for protection of marine biodiversity have been adopted but have failed. The Convention on Biological Diversity (CBD) aims at preserving 10% of all the marine biomes by 2020. For achieving this goal, ecologically or biologically significant areas (EBSA) have to be identified in all biogeographic regions. However, the methodologies for identifying the best suitable areas are still to be agreed. Here, we propose a framework for applying the CBD criteria to locate potential ecologically or biologically significant seamount areas based on the best information currently available. The framework combines the likelihood of a seamount constituting an EBSA and its level of human impact and can be used at global, regional and local scales. This methodology allows the classification of individual seamounts into four major portfolio conservation categories which can help optimize management efforts toward the protection of the most suitable areas. The framework was tested against 1000 dummy seamounts and satisfactorily assigned seamounts to proper EBSA and threats categories. Additionally, the framework was applied to eight case study seamounts that were included in three out of four portfolio categories: areas highly likely to be identified as EBSA with high degree of threat; areas highly likely to be EBSA with low degree of threat; and areas with a low likelihood of being EBSA with high degree of threat. This framework will allow managers to identify seamount EBSAs and to prioritize their policies in terms of protecting undisturbed areas, disturbed areas for recovery of habitats and species, or both based on their management objectives. It also identifies seamount EBSAs and threats considering different ecological groups in both pelagic and benthic communities. Therefore, this framework may represent an important tool to mitigate seamount biodiversity loss and to achieve the 2020 CBD goals.
Object tracking based on adaptive updating of a spatial-temporal context model

Recently, a tracking algorithm called the spatial-temporal context model has been proposed to locate a target by using the contextual information around the target. This model has achieved excellent results when the target undergoes slight occlusion and appearance changes. However, the target location in the current frame is based on the location in the previous frame, which will lead to failure in the presence of fast motion because of the lack of a prediction mechanism. In addition, the spatial context model is updated frame by frame, which will undoubtedly result in drift once the target is occluded continuously. This paper proposes two improvements to solve the above two problems: First, four possible positions of the target in the current frame are predicted based on the displacement between the previous two frames, and then, we calculate four confidence maps at these four positions; the target position is located at the position that corresponds to the maximum value. Second, we propose a target reliability criterion and design an adaptive threshold to regulate the updating speed of the model. Specifically, we stop updating the model when the reliability is lower than the threshold. Experimental results show that the proposed algorithm achieves better tracking results than traditional STC and other algorithms.
A New Body Shape Index Predicts Mortality Hazard Independently of Body Mass Index

Background Obesity, typically quantified in terms of Body Mass Index (BMI) exceeding threshold values, is considered a leading cause of premature death worldwide. For given body size (BMI), it is recognized that risk is also affected by body shape, particularly as a marker of abdominal fat deposits. Waist circumference (WC) is used as a risk indicator supplementary to BMI, but the high correlation of WC with BMI makes it hard to isolate the added value of WC. Methods and Findings We considered a USA population sample of 14,105 non-pregnant adults () from the National Health and Nutrition Examination Survey (NHANES) 1999–2004 with follow-up for mortality averaging 5 yr (828 deaths). We developed A Body Shape Index (ABSI) based on WC adjusted for height and weight: ABSI had little correlation with height, weight, or BMI. Death rates increased approximately exponentially with above average baseline ABSI (overall regression coefficient of per standard deviation of ABSI [95% confidence interval: –]), whereas elevated death rates were found for both high and low values of BMI and WC. (–) of the population mortality hazard was attributable to high ABSI, compared to (–) for BMI and (–) for WC. The association of death rate with ABSI held even when adjusted for other known risk factors including smoking, diabetes, blood pressure, and serum cholesterol. ABSI correlation with mortality hazard held across the range of age, sex, and BMI, and for both white and black ethnicities (but not for Mexican ethnicity), and was not weakened by excluding deaths from the first 3 yr of follow-up. Conclusions Body shape, as measured by ABSI, appears to be a substantial risk factor for premature mortality in the general population derivable from basic clinical measurements. ABSI expresses the excess risk from high WC in a convenient form that is complementary to BMI and to other known risk factors.
Overstating the Effects of Loving-Kindness Meditation: Comment on Kok et al. (2013)

Kok et al. (2013) examined the relations among change in positive emotions, change in perceived social connections, and change in vagal tone in a longitudinal field experiment in which participants were randomly assigned to either a control condition or an intervention condition. Participants in the intervention condition “self-generated” positive emotions by practicing lovingkindness meditation (LKM). Kok et al. claimed to have demonstrated support for their three hypotheses. First, as predicted by Hypothesis 1, the practice of LKM increased positive emotions; vagal tone moderated this effect such that LKM participants who entered the study with higher vagal tone showed greater increases in positive emotions over 9 weeks’ time (b = 0.043, z = 2.63, p = .009). Second, as predicted by Hypothesis 2, increased positive emotions predicted increased perceived social connections over the same 9 weeks’ time (b = 1.04, z = 4.12, p < .001). Finally, as predicted by Hypothesis 3, increased perceived social connections predicted an increase in vagal tone from the start to the end of the study (b = 4.90, z = 2.14, p = .03). 1 Kok et al. described this sequence of changes as an “upward spiral. ” On the basis of these findings, they recommended that the practice of LKM be added to the armamentarium of advice for improving physical health, for which they asserted that vagal tone is an objective marker. I believe that Kok et al. have overstated their findings and that those findings do not justify their recommendation. This overstatement can be demonstrated from two different vantage points. First, Kok et al.’s findings depended on the inclusion in their sample of a small number of unusual participants. Second, few participants had a pattern of change in positive emotions, perceived social connections, and vagal tone that conformed to the upward spiral. I elaborate on each of these points in turn.
Acoustic behavior associated with cooperative task success in bottlenose dolphins ( Tursiops truncatus )

Although many species have proven capable of cooperating to achieve common goals, the role of communication in cooperation has received relatively little attention. Analysis of communication between partners is vital in determining whether actions are truly cooperative rather than serendipitous or learned via trial and error (Chalmeau and Gallo in Behav Process 35:101–111, 1996a. doi:10.1016/0376-6357(95)00049-6, Primates 37:39–47, 1996b. doi:10.1007/BF02382918). Wild cetaceans often produce sounds during cooperative foraging, playing, and mating, but the role of these sounds in cooperative events is largely unknown. Here, we investigated acoustic communication between two male bottlenose dolphins while they cooperatively opened a container (Kuczaj et al. in Anim Cogn 18:543–550, 2015b. doi:10.1007/s10071-014-08224). Analyses of whistles, burst pulses, and bi-phonations that occurred during four contexts (i.e., no container, no animals interacting with container, one animal interacting with container, and two animals interacting with container) revealed that overall sound production rate significantly increased during container interactions. Sound production rates were also significantly higher during cooperative successes than solo successes, suggesting that the coordination of efforts rather than the apparatus itself was responsible for the phonation increase. The most common sound type during cooperative successes was burst pulse signals, similar to past recordings of cooperative events in bottlenose dolphins (Bastian in Animal sonar systems. Laboratoire de Physiologie Acoustique, Jouy-en Josas, pp 803–873, 1967; Connor and Smolker 1996).
Investigation of structural, crystallochemical and surface electrical properties of synthetic nano-sized calcium-deficient carbonated hydroxyapatite

CHAP (carbonated hydroxyapatite) with various degrees of calcium-deficiency were synthesized. Characterization of the samples using X-ray diffraction, Fourier transform infrared spectroscopy (FT-IR) and Brunauer–Emmett–Teller (BET) methods showed that the synthesized samples are single phase, nano-sized carbonated hydroxyapatites, possessing high specific surface areas (up to 184 m 2 /g). The sign and magnitude of zeta potential of HAP (hydroxyapatite) nanoparticles are influenced by the molar ratio Ca/(P+CO3 2). The results suggest that synthetic CHAP (carbonated hydroxyapatite) can become a promising biomaterial as
Timing of postexercise protein intake is important for muscle hypertrophy with resistance training in elderly humans

1 Age‐associated loss of skeletal muscle mass and strength can partly be counteracted by resistance training, causing a net synthesis of muscular proteins. Protein synthesis is influenced synergistically by postexercise amino acid supplementation, but the importance of the timing of protein intake remains unresolved. 2 The study investigated the importance of immediate (P0) or delayed (P2) intake of an oral protein supplement upon muscle hypertrophy and strength over a period of resistance training in elderly males. 3 Thirteen men (age, 74 ± 1 years; body mass index (BMI), 25 ± 1 kg m−2 (means ± S.E.M.)) completed a 12 week resistance training programme (3 times per week) receiving oral protein in liquid form (10 g protein, 7 g carbohydrate, 3 g fat) immediately after (P0) or 2 h after (P2) each training session. Muscle hypertrophy was evaluated by magnetic resonance imaging (MRI) and from muscle biopsies and muscle strength was determined using dynamic and isokinetic strength measurements. Body composition was determined from dual‐energy X‐ray absorptiometry (DEXA) and food records were obtained over 4 days. The plasma insulin response to protein supplementation was also determined. 4 In response to training, the cross‐sectional area of m. quadriceps femoris (54.6 ± 0.5 to 58.3 ± 0.5 cm2) and mean fibre area (4047 ± 320 to 5019 ± 615 μm2) increased in the P0 group, whereas no significant increase was observed in P2. For P0 both dynamic and isokinetic strength increased, by 46 and 15 %, respectively (P < 0.05), whereas P2 only improved in dynamic strength, by 36 % (P < 0.05). No differences in glucose or insulin response were observed between protein intake at 0 and 2 h postexercise. 5 We conclude that early intake of an oral protein supplement after resistance training is important for the development of hypertrophy in skeletal muscle of elderly men in response to resistance training.
Traffic responsive intersection control algorithm using GPS data

This paper reports on the performance of signalised intersection control using vehicle GPS information compared to fixed-time and inductive loop based control. Traffic congestion forecasts estimate an increase of about 60% in 2030. At present, poor choice of signal timings by isolated intersection controllers cause traffic delays that have enormous negative impacts on the economy and environment. Signal timings can be improved by using vehicles' GPS information to overcome the control action deficit at isolated intersections. This new signal control algorithm is beneficial for traffic engineers and governmental agencies, as traffic flow can be optimised and, hence, fuel consumption and emissions decreased. Under the open European Telecommunication Standards Institute (ETSI) Cooperative Awareness Message (CAM) framework, a traffic responsive GPS based vehicle actuation algorithm (GPS-VA) is proposed. GPS-VA uses position and heading data from vehicle status broadcasts, and inferred velocity information to determine vehicle queue lengths and detect vehicles passing through the intersection. The gathered information is then used to actuate intersection signal timings. Microscopic simulations comparing GPS-VA to fixed-time control and inductive loop based vehicle actuation (Loop-VA) on four urban road networks were performed to see how the proposed GPS-VA algorithm performs compared to existing control strategies. The results show that GPS-VA is an effective alternative to traditional intersection control strategies, offering delay reductions of up to 50% for connected vehicle fleet penetrations above 30%.
A Scalable Architecture for Network Traffic Monitoring and Analysis Using Free Open Source Software

The lack of current network dynamics studies that evaluate the effects of new application and protocol deployment or long-term studies that observe the effect of incremental changes on the Internet, and the change in the overall stability of the Internet under various conditions and threats has made network monitoring challenging. A good understanding of the nature and type of network traffic is the key to solving congestion problems. In this paper we describe the architecture and implementation of a scalable network traffic moni-toring and analysis system. The gigabit interface on the monitoring system was configured to capture network traffic and the Multi Router Traffic Grapher (MRTG) and Webalizer produces graphical and detailed traffic analysis. This system is in use at the Obafemi Awolowo University, IleIfe, Nigeria; we describe how this system can be replicated in another environment.
Regional Integration in Africa

This paper examines the history of regional integration in Africa, what has motivated it, the different initiatives that African governments have pursued, the nature of the integration process, and the current challenges. Regional integration is seen as a rational response to the difficulties faced by a continent with many small national markets and landlocked countries. As a result, African governments have concluded a very large number of regional integration arrangements, several of which have significant membership overlap. While characterized by ambitious targets, they have a dismally poor implementation record. Part of the problem may lie in the paradigm of linear market integration, marked by stepwise integration of goods, labour and capital markets, and eventually monetary and fiscal integration. This tends to focus on border measures such as the import tariff. However, supply-side constraints may be more important. A deeper integration agenda that includes services, investment, competition policy and other behind-the-border issues can address the national-level supply-side constraints far more effectively than an agenda which focuses almost exclusively on border measures.