ethicalabs/Research-Intent-Collab huggingface dataset:
Emerging frontiers in protein structure prediction following the AlphaFold revolution

Models of protein structures enable molecular understanding of biological processes. Current protein structure prediction tools lie at the interface of biology, chemistry and computer science. Millions of protein structure models have been generated in a very short space of time through a revolution in protein structure prediction driven by deep learning, led by AlphaFold. This has provided a wealth of new structural information. Interpreting these predictions is critical to determining where and when this information is useful. But proteins are not static nor do they act alone, and structures of proteins interacting with other proteins and other biomolecules are critical to a complete understanding of their biological function at the molecular level. This review focuses on the application of state-of-the-art protein structure prediction to these advanced applications. We also suggest a set of guidelines for reporting AlphaFold predictions.
3335 Retrieval Number: D8118118419/2019©BEIESP DOI:10.35940/ijrte.D8118.118419 Journal Website: www.ijrte.org Published By: Blue Eyes Intelligence Engineering &amp; Sciences Publication A Model for Accurate Prediction of Child Immunization Data for Knowledge Discovery using Bayesian TAN and Naive Bayes Classifiers

Knowledge Discovery in Databases (KDD) is a splendid methodology of discovering knowledge from gigantic databases by using its various stages viz. Data Selection, Data Preprocessing, Data Transformation, Data Mining and Interpretation/Evaluation. Data Mining is a vital sub-process of KDD methodology that is particularly used to apply the various mining algorithms on the data. In the present research paper, the authors have made an attempt to discover new knowledge by classifying the child immunization data of Jammu and Kashmir State of India. The data for the present work was collected from a web portal named as Health Management Information System (HMIS) facilitated by Ministry of Health and Family Welfare (MoHFW), Government of India. The data consists of diverse health parameters pertaining to the immunization of children and for the present study, the child immunization data of all districts of Jammu and Kashmir State was considered. Two classifiers viz. Bayesian TAN and Naïve Bayes were employed for classifying the districts of Jammu and Kashmir State into High IMR and Low IMR districts based on the available past data from 2014 to 2018. Additionally, various measurement methods have been used to evaluate the performance of the models developed by Bayesian TAN and Naïve Bayes.
ReaxFF Reactive Force Field for Molecular Dynamics Simulations of Hydrocarbon Oxidation

To investigate the initial chemical events associated with high-temperature gas-phase oxidation of hydrocarbons, we have expanded the ReaxFF reactive force field training set to include additional transition states and chemical reactivity of systems relevant to these reactions and optimized the force field parameters against a quantum mechanics (QM)-based training set. To validate the ReaxFF potential obtained after parameter optimization, we performed a range of NVT-MD simulations on various hydrocarbon/O2 systems. From simulations on methane/O2, o-xylene/O2, propene/O2, and benzene/O2 mixtures, we found that ReaxFF obtains the correct reactivity trend (propene > o-xylene > methane > benzene), following the trend in the C-H bond strength in these hydrocarbons. We also tracked in detail the reactions during a complete oxidation of isolated methane, propene, and o-xylene to a CO/CO2/H2O mixture and found that the pathways predicted by ReaxFF are in agreement with chemical intuition and our QM results. We observed that the predominant initiation reaction for oxidation of methane, propene, and o-xylene under fuel lean conditions involved hydrogen abstraction of the methyl hydrogen by molecular oxygen forming hydroperoxyl and hydrocarbon radical species. While under fuel rich conditions with a mixture of these hydrocarbons, we observed different chemistry compared with the oxidation of isolated hydrocarbons including a change in the type of initiation reactions, which involved both decomposition of the hydrocarbon or attack by other radicals in the system. Since ReaxFF is capable of simulating complicated reaction pathways without any preconditioning, we believe that atomistic modeling with ReaxFF provides a useful method for determining the initial events of oxidation of hydrocarbons under extreme conditions and can enhance existing combustion models.
Integration of genomic classification and clinical characteristics predicts survival in metastatic prostate cancer

Abstract                                    Purpose                   Tumor comprehensive genomic profiling (CGP) has revolutionized cancer care and identifies patients for biomarker-specific therapy. In metastatic hormone-sensitive prostate cancer (mHSPC), CGP is not currently prognostic and no DNA-based genomic classification exists that accounts for combinations of alterations. We developed a DNA-based CGP classification that is prognostic for overall survival (OS) and could inform treatment.                                                     Methods                   Retrospective cross-sectional study using multivariable models to develop a clinico-genomic prognostic risk classification in U.S. Veterans diagnosed with synchronous mHSPC. Primary outcome was overall survival (OS) from time of metastatic diagnosis.                                                     Results                   7201 Veterans with metastatic prostate cancer who underwent CGP were identified. There were 2484 Veterans (median [IQR] age 72 [67-77] years) with synchronous mHSPC and tissue CGP, which were divided into training and testing datasets. 16 genes associated with survival were identified and favorable, intermediate, and unfavorable genomic prognostication groups were created based upon mortality risk to generate the STRATOS-P classification. In a multivariable model, classification into intermediate and unfavorable groups was associated with increased mortality relative to the favorable group (aHR 1.54 [95% CI 1.33-1.78]; aHR 2.37 [95% CI 1.97-2.485], respectively), demonstrating an average AUC of 0.83. In an external validation cohort of non-Veterans, intermediate and unfavorable classifications were associated with increased mortality (aHR 2.45 [95% CI 1.87-3.21]; aHR 4.37 [95% CI 3.06-6.22], respectively) with an AUC of 0.79. The intermediate and unfavorable genomic prognostication groups were also associated with increased mortality across multiple disease states including synchronous and metachronous diagnoses, castration-resistance, and analyte type.                                                     Conclusions                   In metastatic prostate cancer, tumor DNA genomic alterations are prognostic for OS. The STRATOS-P classification is a validated prognostic tool that has the potential to guide decision-making in mHSPC.
Cyclic variations of the heliospheric tilt angle and cosmic ray modulation

Abstract   Using data on cosmic ray modulation parameter since 1951, we have estimated the evolution of the heliospheric current sheet tilt angle for the period 1951–1975, i.e., 25 years before regular observations of the tilt angle. This estimate is based on our recent empirical model relating cosmic ray intensity with global heliospheric parameters. We propose a simple model to describe the cyclic evolution of the tilt angle with the solar cycle. This model agrees with available observational data. Using this model, we have estimated the cosmic ray intensity since 1710. This estimate is consistent with the results based on cosmogenic isotopes ( 14 C and  10 Be).
Clarity, surprises, and further questions in the Article 29 Working Party draft guidance on automated decision-making and profiling

Cite as: Michael Veale and Lilian Edwards, 'Clarity, Surprises, and Further Questions in the Article 29 Working Party Draft Guidance on Automated Decision-Making and Profiling' (forthcoming) Computer Law and Security ReviewThe new Article 29 Data Protection Working Party’s draft guidance on automated decision-making and profiling seeks to clarify the European data protection (DP) law’s little-used right to prevent automated decision-making, as well as the provisions around profiling more broadly, in the run-up to the General Data Protection Regulation. In this paper, we analyse these new guidelines in the context of recent scholarly debates and technological concerns. They foray into the less-trodden areas of bias and non-discrimination, the significance of advertising, the nature of “solely” automated decisions, impacts upon groups and the inference of special categories of data — at times, appearing more to be making or extending rules than to be interpreting them. At the same time, they provide only partial clarity — and perhaps even some extra confusion — around both the much discussed “right to an explanation” and the apparent prohibition on significant automated decisions concerning children. The Working Party appear to feel less mandated to adjudicate in these conflicts between the recitals and the enacting articles than to explore altogether new avenues. Nevertheless, the directions they choose to explore are particularly important ones for the future governance of machine learning and artificial intelligence in Europe and beyond.
Genesis of the Gangcha gold deposit, West Qinling Orogen, China: Constraints from Rb-Sr geochronology, in-situ sulfur isotopes and trace element geochemistry of pyrite

Abstract   The Gangcha gold deposit, in the western zone of the Xiahe-Hezuo region within the West Qinling orogen of Central China, is a newly discovered medium-scale epithermal gold deposit with 19 tons of identified gold reserves. Mainly hosted in the Permian metasedimentary rocks and Triassic altered volcaniclastic rocks, and gold mineralization is closely associated with pyrite. Here we present results from field observation and geochemical studies of pyrite using electron probe microanalysis (EPMA), in-situ laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) and femtosecond laser ablation coupled multi-collector inductively coupled plasma mass spectrometry (fsLA-MC-ICP-MS) analyses. Based on the results, we identified five types of pyrite in the ores and wall rocks (namely Py1, Py2, Py3, Py4 and Py5). Among these, the pre-ore Py1, which is enriched in As, shows markedly negative δ34S values of −30.99 to −17.70‰ that are assumed to be the reflection of abiotic thermochemical reduction of sulfate (TSR) related to extremely oxidized magmas that have assimilated carbonaceous sedimentary rocks. Py2, occurring in the pyrite veins, displays internal rhythmic As- and Au-enriched growth zoning, and the δ34S values of Py2 progressively increase from the cores to the outer rims that are interpreted to result from mixing between the pyrite-forming fluid and magmatic vapor that invaded the main hydrothermal system episodically. The intermediate ore stage pyrite (Py3), represented by the quartz-pyrite (±arsenopyrite) veins, is enriched in As, Sb and Au. The comparable δ34S values of Py3 (−4.59 to + 7.05‰, average + 4.46‰) and Py4 (−5.66 to + 6.50‰, average + 1.80‰) could indicate magmatic sulfur. Compared with pyrites of the earlier stages, the late ore stage pyrite (Py5) is distinctly more enriched in δ34S, and is interpreted to have formed by mixing between a magmatic fluid and meteoric water. Additionally, some of the pyrites (Py5) from Stage V, occurring as the rim of pyrite grain, are interpreted to have formed by replacement via a dissolution-reprecipitation process of the earlier-formed Py4. The Rb-Sr data of pyrites from veins of different mineralization stages yield a mean isochron age of 225.3 ± 2.6 Ma, interpreted as the age of gold mineralization. Based on a combination of geochronological and geochemical date of pyrite, we propose that the ore-forming fluids of the Gangcha gold deposit are closely associated with coeval magmatic activity during the region collisional orogenic event.
THE RELATIONSHIP BETWEEN THE DSU ARTICLES 21(5) AND 22  AND THE ISSUE OF THE LITIGATION DEADLOCKS  IN THE DISPUTE SETTLEMENT SYSTEM OF THE WORLD TRADE ORGANIZATION

In December 2019, the World Trade Organization (WTO) litigation system was deadlocked. One of the important concerns which arose then was how the blockage of the litigation system could affect Dispute Settlement Understanding (DSU) procedural provisions governing the suspension of concession and other obligations. In the light of this these circumstances, we need to discuss the “sequencing” issues regarding the claimant’s procedural right to seek authorization for suspension in accordance with Article 22 of the DSU and implementation procedure envisaged in Article 21(5). Thus far, the WTO judicial bodies have been inclined to the position that there is no “sequencing condition” for exercising procedural rights provided in Article 22. Contrary to the position of the WTO jurisprudence, academics mostly advocate that the relationship between Articles 21(5) and 22 of the DSU exists through sequencing prerequisite. However, this problem needs to be redefined in the light of the irregular circumstances that may be created by the blockage of the litigation system. Therefore, exclusively in situation where litigation is in blockage, the claimant should be entitled to commence the Article 22 procedure, without prior employment of the implementation procedure in accordance with Article 21(5) of the DSU. In normal circumstances, the claimant must respect a sequencing prerequisite.
Optimizing Logistic Processes and Transport Challenges in the Dynamic Landscape of Online Commerce

The article discusses modern challenges and trends in logistics associated with dynamic online commerce. It explores the optimization of logistical processes and solutions to transport problems in the context of evolving needs in the contemporary market. The article presents key innovative approaches, such as using Internet of Things technologies, artificial intelligence, and big data analytics to enhance route management, reduce excess inventory, and ensure precise delivery to endpoints. It also highlights the importance of environmental sustainability in logistics and adaptability of logistical networks to quickly respond to changes in demand. Overall, the article presents modern logistics management strategies necessary for effective operation in the online commerce sphere. The article provides a detailed analysis of the challenges faced by logistics in the dynamic online market and offers efficient solutions for optimizing transport tasks. Principles like Just-in-Time and Lean Logistics are considered pivotal methods for reducing excess inventory and improving inventory management, contributing to a more efficient supply chain. Additionally, it covers modern approaches to last-mile logistics, including the use of drones, robots, and other innovations for delivering goods to endpoints. This revolutionizes delivery methods and enhances speed and efficiency in customer service. In conclusion, it emphasizes the importance of sustainability and environmental responsibility in logistical schemes, encouraging the use of eco-friendly transportation and packaging to reduce adverse effects on the environment. The strategies discussed in the article represent vital directions for the development of contemporary logistics, aimed at efficiency, sustainability, and adaptability in the dynamic landscape of online commerce.
Countering Terrorist Content Online: Removal = Success? : A Critical Discourse Analysis of the EU Regulation 2021/784

This thesis critically interrogates the underlying assumptions which legitimise the hard regulation of online platforms regarding terrorist content, by turning to the case of the EU Regulation 2021/784. Utilising qualitative critical discourse analysis, the study analyses how the EU's strategy against terrorist content online is discursively legitimised through the lens of Theo van Leeuwen's framework for discursive legitimisation strategies, focusing on moral and rational justifications. The study's empirical contribution demonstrates how the EU's strategy is legitimised primarily through public security, fundamental rights, digital economy and efficiency discourses. It contributes theoretically by highlighting how counter-terrorism measures regarding online spaces function through rationalisation and moralisation strategies which legitimise policies as reasonable and morally justifiable, when in fact they rest upon a series of contested assumptions and narratives about the threat from terrorist content. Furthermore, the study puts forward that the regulation contributes to the institutionalisation of online platforms role in countering terrorist content online and reproduces unequal power relations between large and small hosting service companies, public authorities, and individuals.
Communicating sexual reproductive health and rights to Zambian youth : A case study of the non-governmental organization Youth Vision Zambia

HIV/AIDS is widely spread in Zambia. Numerous organizations work to disseminate information about how individuals can prevent themselves and others from infection. Youth Vision Zambia (YVZ) is a non- governmental organization that works from Lusaka, Zambia to increase knowledge about sexual reproductive health and rights among young people aged 10-24. This qualitative case study explores which means of communication strategies YVZ uses to reach and inform their target group about Sexual Reproductive Health and Rights (SRHR) by interviewing staff working for the organization. A qualitative survey was also conducted where 29 respondents belonging to the target group answered questions regarding the information about SRHR they have received from YVZ, how they were reached and if they find the work of YVZ of importance. In order to also get a perception about the interpersonal communication channels YVZ use I attended four meetings arranged for young people where the purpose was to discuss sexual health related issues conducting participant observations. In addition, YVZ put an extensive effort on providing an SMS-short code system which allows people to send questions related to SRHR and in turn get answers from a YVZ councilor. The aim was to seek answers to whether the users had found the SMS service useful or not. The results show a variety of different communication tools that YVZ uses in their daily work and in the light of previous research on communication for development and social change and health communication an analysis was carried out.
Uncertainty in environmental risk assessment and management: case studies of the application of the precautionary principle in Portugal

The application of the precautionary principle in the assessment and management of uncertain and serious potential risks to human health and the environment at the national and international levels has shown some ambiguity in the interpretation of the concept of precaution, insufficient knowledge of the potential impacts and lack of operational frameworks to support decisions. This has hindered the functioning of administrative justice and generated discretion and unpredictability in the decision process. This study intends to contribute to the debate on when and how to apply precautionary measures towards sustainability and to improve their implementation conditions. To this end it aims at clarifying how the precautionary principle has been interpreted and applied in the analysis of conflicts associated with the above-mentioned uncertain risks in a recent set of relevant court cases in Portugal in the areas of waste incineration, high voltage power lines, dam and wind farm construction. The degree of consistency of the courts’ decisions and of their reasons in the different judicial bodies was analyzed with the support of a theoretical framework based on three attributes: level of seriousness of potential hazards, level of evidence required and severity of precautionary actions taken. Different positions among courts were observed, with contradictory arguments in the same case or in similar cases. In order to counteract this situation, more explicit legal requirements and criteria for the analysis of uncertain risks and for the weighting of interests by area of activity are proposed.
Urban Active Transportation Behaviour is Sensitive to the Fresh Start Effect: Triangulating observational evidence from real world data

Abstract         Objective: This study was designed to determine if active transportation (AT) was sensitive to the behavioural economics heuristic “The Fresh Start Effect”, with a temporal peak in traffic at the beginning of a work week, that declined by the end of the week. Design and Methods: We triangulated data from five data sources to test the study hypothesis. First, we categorized 5 urban trails as “AT” or “leisure” based on hourly traffic patterns collected from May to September between 2014 to 2019 using electromagnetic counters (EcoCounter Inc, Montreal Qc.). Daily trends in cycling traffic were then compared with daily trends bicycle parking (n=56,307 counts), vehicular traffic (n=6.2M counts), fitness centre attendance (n=563,290 counts) and sales from a local coffee shop (n=166,753 counts). Results: We found a significant ~22% decline in cycling traffic on both AT (-147 cyclists/day; 95% CI: -199.0 to -95 cyclists/day) and leisure trails (-22 cyclists/day; 95% CI: -59 to +15 cyclists/day) over the course of a work week. The relative decline in AT-based cycling traffic was similar to the decline in bicycle parking (~14%; -12 cyclists/day; 95% CI: -17 to -7 cyclists/day). The relative effect size of this trend was nearly identical to the weekly decline in fitness centre attendance (~21%; -592 visits/day; 95% CI: -759 visits/day to -425 visits/day), replicating the original Fresh Start Effect. In contrast, to the decline in AT-based cycling traffic, daily vehicular traffic (+2248 cars/day; 95% CI: 2022 to +3674 cars/day) and coffee sales (+31 units/day; 95% CI: +22 to +42 units/day) increased ~7% from the beginning to the end of a work week. Conclusions: Weekly patterns of leisure and AT-based cycling are sensitive to the Fresh Start Effect and could be used to inform policies for increasing cycling rates in urban centres.