jimnoneill/paper-to-field-training huggingface dataset:
Quantifying uncertainty of molecular mismatch introduced by mislabeled ancestry using haplotype-based HLA genotype imputation

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

Modern histocompatibility algorithms depend on the comparison and analysis of high-resolution HLA protein sequences and structures, especially when considering epitope-based algorithms, which aim to model the interactions involved in antibody or T cell binding. HLA genotype imputation can be performed in the cases where only low/intermediate-resolution HLA genotype is available or if specific loci are missing, and by providing an individuals’ race/ethnicity/ancestry information, imputation results can be more accurate. This study assesses the effect of imputing high-resolution genotypes on molecular mismatch scores under a variety of ancestry assumptions. We compared molecular matching scores from “ground-truth” high-resolution genotypes against scores from genotypes which are imputed from low-resolution genotypes. Analysis was focused on a simulated patient-donor dataset and confirmed using two real-world datasets, and deviations were aggregated based on various ancestry assumptions. We observed that using multiple imputation generally results in lower error in molecular matching scores compared to single imputation, and that using the correct ancestry assumptions can reduce error introduced during imputation. We conclude that for epitope analysis, imputation is a valuable and low-risk strategy, as long as care is taken regarding epitope analysis context, ancestry assumptions, and (multiple) imputation strategy.
Site-Directed Mutagenesis of Proline 52 To Glycine in Amicyanin Converts a True Electron Transfer Reaction into One that Is Conformationally Gated,

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

Amicyanin is a type I copper protein that is the natural electron acceptor for the quinoprotein methylamine dehydrogenase (MADH). The conversion of Proline52 of amicyanin to a glycine does not alter the physical and spectroscopic properties of the copper binding site, but it does alter the rate of electron transfer (ET) from MADH. The values of electronic coupling (H(AB)) and reorganization energy (lambda) that are associated with the true ET reaction from the reduced O-quinol tryptophan tryptophylquinone (TTQ) of MADH to oxidized amicyanin are significantly altered as a consequence of the P52G mutation. The experimentally determined H(AB) increases from 12 to 78 cm(-1), and lambda increases from 2.3 to 2.8 eV. The rate and salt-dependence of the proton transfer-gated ET reaction from N-quinol MADH to amicyanin are also changed by the P52G mutation. Kinetic data suggests that a new common reaction step has become rate-limiting for both the true and gated ET reactions that occur from different redox forms of MADH. A comparison of the crystal structures of P52G amicyanin with those of native amicyanin free and in complex with MADH provided clues as to the basis for the change in ET parameters. The mutation results in the loss of three carbons from Pro52 and the movement of the neighboring residue Met51. This reduces the number of hydrophobic interactions with MADH in the complex and perturbs the protein-protein interface. A model is proposed for the ET reaction with P52G amicyanin in which the most stable conformation of the protein-protein complex with MADH is not optimal for ET. A new preceding kinetic step is introduced prior to true ET that requires P52G amicyanin to switch from this redox-inactive stable complex to a redox-active unstable complex. Thus, the ET reaction of P52G amicyanin is no longer a true ET but one that is conformationally gated by the reorientation of the proteins within the ET protein complex. This same reaction step now also gates the ET from N-quinol MADH, which is normally rate-limited by a proton transfer.
The C-Terminal Repeat Domains of nsP3 from the Old World Alphaviruses Bind Directly to G3BP

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

ABSTRACT The Old World alphaviruses block stress granule assembly by sequestration of RasGAP SH3-domain binding protein (G3BP). Here, we show that the proline-rich sequences in the hypervariable domain of nonstructural protein 3 (nsP3) of both Semliki Forest virus and Chikungunya virus were dispensable for binding to G3BP. nsP3 variants with or without this domain colocalized with G3BP. Furthermore, we show that the C-terminal repeat motifs of nsP3 were sufficient for G3BP binding.
The bipolar behavior of the Richtmyer–Meshkov instability

Field: Physics and Astronomy (Physical Sciences)

A numerical study of the evolution of the multimode planar Richtmyer-Meshkov instability (RMI) in a light-heavy (air-SF6, Atwood number A = 0.67) configuration involving a Mach number Ma = 1.5 shock is carried out. Our results demonstrate that the initial material interface morphology controls the evolution characteristics of RMI (for fixed A, Ma), and provide a significant basis to develop metrics for transition to turbulence. Depending on initial rms slope of the interface, RMI evolves into linear or nonlinear regimes, with distinctly different flow features and growth rates, turbulence statistics, and material mixing rates. We have called this the bipolar behavior of RMI. Some of our findings are not consistent with heuristic notions of mixing in equilibrium turbulence: more turbulent flow—as measured by spectral bandwidth, can be associated with higher material mixing but, paradoxically, to lower integral measures of turbulent kinetic energy and mixing layer width.
Eco‐evolutionary contributions to community trait change in floating aquatic plants

Field: Agricultural and Biological Sciences (Life Sciences)

Abstract An entire community of organisms may become modified when its environment changes. These modifications can happen through physiological processes (plasticity), evolutionary processes (adaptation) or shifts in species composition (sorting). The outcome of these three sources of change constitutes the community's phenotypic response, but how they combine to drive community trait dynamics is not currently well understood. We have conducted a community selection experiment in which communities of short‐lived floating aquatic plants were grown in a range of stressful conditions, and measured changes in their body size. Determinants of phenotypic change were assessed with a full community reciprocal transplant which led to estimates of the contributions of plasticity, adaptation, and sorting. Species were modified during the experiment by both plasticity and adaptation, but in either case the magnitude and direction of change differed among species. Sorting and adaptation were of equal magnitude but tended to act in opposite directions: in conditions where species with large fronds prevailed, each species evolved smaller fronds, and vice versa. We conclude that community trait dynamics cannot be understood simply by extrapolating the adaptive response of any single species to the whole community.
LanePro: A new approach towards Lane assistance

Field: Computer Science (Physical Sciences)

Lane detection is a critical component of autonomous driving systems, enabling vehicles to identify and navigate within lanes accurately. This paper presents a novel approach to enhancing lane detection ac curacy using the Mask R-CNN algorithm. By leveraging the capabilities of Mask R-CNN, the proposed algorithm demonstrates efficient and precise detection of road lanes, including the classification of lane types and angle evaluation for steer ing purposes. The algorithm's functionality encompasses determining bounding boxes of lanes, angle evaluation through image cropping, classification, and lane data configuration for schematic environ mental surveillance. Through extensive testing, the algorithm has shown superior performance in scenarios with challenging conditions such as insufficient lighting and lane line degradation. The results indicate a significant improvement in lane detection accuracy, making it a promising solution for advancing the capabilities of autonomous driving systems.
A New Perspective on Visualising EEG Signal of Post-Stroke Patients

Field: Computer Science (Physical Sciences)

Abstract To date, numerous methods have been developed in response to the EEG signal classification of post-stroke patients, among which feature extraction methods are of particular interest. This paper presents a new perspective on the visualisation of the EEG signal of different post-stroke patients in the image representation that can be used to assist in the classification phase. The new perspective for extracting and visualising EEG sub-band features considers the sequential application of power spectral density (PSD) represented in the kernel distribution estimation (KDE) of the PSD manifold. Experiments conducted on 45 post-stroke patients; 14 early, 17 intermediate and 14 advanced patients demonstrated the potential of the proposed perspective to estimate significant parameters under spectral pattern image representation. Visual representation of this new approach shows that the pattern and relationship of post-stroke patients can be clearly visualised. Significant performance can be achieved by classifying post-stroke patients into early-advanced or early intermediate classes as they reach a perfect dissimilarity score, r = 1.00. In the meantime, the absence of beta or theta in pairs has relatively consistent performance in classifying post-stroke patients using sub-bands, and the combination of the two has shown the worst results among other pairs. This paradigm should be included in the future context of the EEG signal classification of post-stroke classes, which could better explain the importance of image representation while improving the accuracy of the specified network.
Illuminating Long-lived Cycas Cotyledons Reduces Sink Demands on Megagametophytes during Initial Seedling Growth

Field: Agricultural and Biological Sciences (Life Sciences)

Cycas megagametophyte resources are translocated to developing seedlings through the persistent green cotyledons. The source activities of cotyledons and megagametophytes following germination are not adequately understood. The decline in megagametophyte weight during seedling development was quantified until ultimate tissue desiccation for two Cycas species. In addition, the influence of illuminating the green cotyledons during germination and initial radicle growth on megagametophyte, root, and cotyledon dry weight (DW) was determined to evaluate the role of cotyledon photosynthesis on growth and megagametophyte source activity. Cycas micronesica megagametophytes declined 64% in DW during initial growth of the radicle and maturation of the first true leaf. The rate of DW decline slowed after this stage but continued for ≈18 months when the seedlings were supported by six leaves. Cycas edentata megagametophytes exhibited similar patterns with a 72% decline in DW when the first true leaf reached full expansion, and the resources were depleted by ≈14 months when the seedlings had five leaves. Illuminating cotyledons during initial seedling growth reduced the rate of megagametophyte DW decline by up to 20% and increased total seedling DW above that of dark-grown seedlings by up to 21%. The results provide direct evidence for the long-term source activity of the Cycas megagametophyte and provide indirect evidence that photosynthetic contributions of illuminated cotyledons reduce the reliance on gametophytes as a source of resources for initial Cycas seedling growth. Improved design of Cycas nursery germination microenvironments may be enabled by this new knowledge.
Building family connectedness—A new practice tool for social workers

Field: Social Sciences (Social Sciences)

Abstract Family connectedness is important for youth mental health and well-being. Social workers can help families build and maintain connections during adolescence. Evidence-based practice tools which approach youth well-being through a whole-of-family lens help legitimise social work’s person-in-environment approach to mental health. In this study, fifteen Australian social workers piloted a new practice tool to support family connectedness. The tool outlines key elements of family connectedness from the perspectives of young people and provides detailed examples to help understand and strengthen family connections. The social workers trialled the Family Connectedness Practice Tool for two months. Before the trial, participants were surveyed on which skills, theories and practice approaches they used to support family connectedness. After the trial, participants were surveyed on how they used the tool and how useful it was in their practice. The findings highlight the range of knowledge informing practice with children, youth and families. The tool was considered very useful by participants and helped with family connectedness education, assessment and intervention. The findings raise questions about how much young people’s perspectives are valued in practice and the challenges social workers face when using a whole-of-family approach.
Analysis of Constitutional Court Decision Number 46/PUU-XIV/2016 Related to LGBT and Community Attitude

Field: Social Sciences (Social Sciences)

The Constitutional Court in Decision Number 46 / PUU-XIV / 2016 had pros and cons in the community. One of the materials that became the pros and cons of the decision was regarding the existence of LGBT. This study discusses the Constitutional Court's Decision Number 46 / PUU-XIV / 2016, especially concerning LGBT. There are two important topics contained in this study, namely (1) normative juridical analysis of the Constitutional Court Decision Number 46 / PUU-XIV / 2016 related to LGBT and (2) community attitudes towards LGBT after the Constitutional Court Decision Number 46 / PUU-XIV / 2016 This study concludes that Constitutional Court Decision Number 46 / PUU-XIV / 2016 is legally normative and does not conflict with statutory regulations. Decision of the Constitutional Court Number 46 / PUU-XIV / 2016 actually refers to the laws and regulations that govern the provisions of the ruling for the Constitutional Court. The attitude of the community related to LGBT after the Constitutional Court Decision Number 46 / PUU-XIV / 2016 was in fact influenced by various factors
Intrusion Detection System (DBN-IDS) for IoT using Optimization Enabled Deep Belief Neural Network

Field: Computer Science (Physical Sciences)

In the era of Internet of Things (IoT), the connection links are established from devices easily, which is vulnerable to insecure attacks from intruders, hence intrusion detection system in IoT is the need of an hour. One of the important thing for any organization is securing the confidential information and data from outside attacks as well as unauthorized access. There are many attempts made by the researchers to develop the strong intrusion detection system having high accuracy. These systems suffer from many disadvantages like unacceptable accuracy rates including high False Positive Rate (FPR) and high False Negative Rate (FNR), more execution time and failure rate. More of these system models are developed by using traditional machine learning techniques, which have performance limitations in terms of accuracy and timeliness both. These limitations can be overcome by using the deep learning techniques. Deep learning techniques have the capability to generate highly accurate results and are fault tolerant. Here, the intrusion detection model for IoT is designed by using the Taylor-Spider Monkey optimization (Taylor-SMO) which will be developed to train the Deep belief neural network (DBN) towards achieving an accurate intrusion detection model. The deep learning accuracy gets increased with increasing number of training data samples and testing data samples. The optimization based algorithm for training DBN helps to reduce the FPR and FNR in intrusion detection. The system will be implemented by using the NSL KDD dataset. Also, this model will be trained by using the samples from this dataset, before which feature extraction will be applied and only relevant set of attributes will be selected for model development. This approach can lead to better and satisfactory results in intrusion detection.
Designing Optimized Organic Rankine Cycles Systems for Waste Heat-to-Power Conversion of Gas Turbine Flue Gases

Field: Energy (Physical Sciences)

Abstract The focus of this work is to develop a flexible ORC design procedure that compares thermo-economic performances of simple and recuperative ORCs for both subcritical and supercritical cycles through a multi-objective optimization that relates the economic parameters to the network output for waste heat-to-power conversion of exhaust gases. Few researches have proposed rather simpler methods by modifications to the Jacob number (Ja) but these are insufficient to make technical and economic decisions on the subject matter as Ja is only appropriate for comparing performances of different working fluids at the same operating condition. Coupled with the barrier on the minimum temperature the exhaust gases from power plants may attain, the use of Ja as the only criteria is not sufficient for varying operating condition presented by Gas Turbine power plants. Hence, this review presents follow-through numerical methodology for designing adapted ORC for waste heat-to-power energy conversion.
[Specific cell-mediated cytotoxicity in patients with cerebral infarct].

Field: Medicine (Health Sciences)

The purpose of the work was to assess changes in the activity of cytotoxic lymphocates in patients with cerebral infarction. The material comprised 27 patients with the diagnosis of cerebral infarction and 18 controls. The authors analyzed the activity of cytotoxic lymphocytes, against the cerebral antigen-encephalitogenic peptide (EP). As target cells they used syngenic lymphocytes coated with EP and labelled with 51Cr, the activity of which released during reaction with supernatan is proportional to the amount of cells disrupted by cytotoxic lymphocytes. The reaction is specific for the encephalitogenic peptide. The activity of specific cytotoxic lymphocytes was in patients with cerebral infarction almost four times higher than in controls. The percentage activity was higher in "seriously affected patients" and two weeks after the onset of the disease. Then the activity declined. Investigation of the activity of cytotoxic lymphocytes could prove important in patients with cerebral infarction with symptoms of sensitization against cerebral antigen.
The Leadership of Headmaster in Improving the Quality of Madrasa Education

Field: Social Sciences (Social Sciences)

The Quality of madrasa education depends on many factors like the leadership of headmaster which is crucial and influential to other supporting factors in maintaining and securing quality education of madrasa. This paper was aimed at investigating the leadership of madrasa headmasters in improving the quality of madrasa education in Maluku Province. It also investigated the contribution of headmaster leadership toward the teachersâ€™ characteristic that contribute immensely to educational service. This study applied descriptive qualitative using a naturalistic approach. To achieve the objectives of the study, observations, interviews, and documentation were used in data collection techniques. The data collected were analyzed using Miles and Huberman model. The study found that the leadership of headmaster has contributed to the improvement quality of madrasa education. The leaderships included many aspects like the ability to create, plan, organize and communicate within organization of madrasa. The headmaster leadership also played significant role in building the characteristics of teacher like theological trait, physical, intelligence and personal charcteristics. Those characteristics are pivotal in improving teachersâ€™ quality of educational service.
Causes and Risk Factors of Vitamin B12 Deficiency at the Bookends of Life, From Infancy to Old Age

Field: Medicine (Health Sciences)

The causes and risk factors of vitamin B12 deficiency are many and varied. Importantly, they vary considerably across the lifespan, from infancy to old age. The complexity of the physiology of vitamin B12 bespeaks the myriad of possible causes of deficiency and possible disruptions of its functional integrity. These lead ultimately to the pathobiological effects witnessed in deficiency of this fascinating micronutrient. This brief overview of the multiplicity of mechanisms that can result in vitamin B12 deficiency, and the panoply of its manifestations explores the underlying reasons for the protean presentations of the disease. As the human organism progresses through the chronology and milestones of age, various susceptibility factors arise resulting from the interplay of environmental and genetic factors. Acting independently and in concert, these factors produce the common denominator of vitamin B12 deficiency. However, the rate at which such deficiency develops and the way in which it presents clinically vary widely, subject to such influences as genetic variability, end-organ susceptibility, and concomitant micronutrient status. Some examples of unusual cases of vitamin B12 deficiency are described. Much has been learned about the last of the numbered vitamins in almost a century. Much yet remains to be discovered.
Pharmacological Activities of Andrographis serpyllifolia

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

The traditional use of medicinal plants played a vital role in treating disease free human existence on this planet and can be traced back over five millennia. Although we have drugs of mineral and animal origin form nature and synthetic substances, plants are almost the exclusive source of drugs for the majority of the world’s population. Inspite of overwhelming influence of modern medicine and tremendous advances made in the production of synthetic drugs, traditional medicaments referred to now-a-days as herbal drugs in different places in literature, have retained their place in therapy. Their effectiveness, low cost and comparative freedom from serious toxic effects make these medicaments not only popular but also an accepted mode of treating diseases even in developed countries.In view of the potential use of the medicinal plants as a source of active constituents in eliciting novel drug molecules, We have selected the medicinal plant Andrographis serpyllifolia to examine chemical and biological properties.