ethicalabs/Research-Intent-Collab huggingface dataset:
Topological links in predicted protein complex structures reveal limitations of AlphaFold

Abstract                   AlphaFold is making great progress in protein structure prediction, not only for single-chain proteins but also for multi-chain protein complexes. When using AlphaFold-Multimer to predict protein‒protein complexes, we observed some unusual structures in which chains are looped around each other to form topologically intertwining links at the interface. Based on physical principles, such topological links should generally not exist in native protein complex structures unless covalent modifications of residues are involved. Although it is well known and has been well studied that protein structures may have topologically complex shapes such as knots and links, existing methods are hampered by the chain closure problem and show poor performance in identifying topologically linked structures in protein‒protein complexes. Therefore, we address the chain closure problem by using sliding windows from a local perspective and propose an algorithm to measure the topological–geometric features that can be used to identify topologically linked structures. An application of the method to AlphaFold-Multimer-predicted protein complex structures finds that approximately 1.72% of the predicted structures contain topological links. The method presented in this work will facilitate the computational study of protein‒protein interactions and help further improve the structural prediction of multi-chain protein complexes.
Mesenchymal stem cell-based therapies in regenerative medicine: applications in rheumatology

Growing knowledge on the biology of mesenchymal stem cells (MSCs) has provided new insights into their potential clinical applications, particularly for rheumatologic disorders. Historically, their potential to differentiate into cells of the bone and cartilage lineages has led to a variety of experimental strategies to investigate whether MSCs can be used for tissue engineering approaches. Beyond this potential, MSCs also display immunosuppressive properties, which have prompted research on their capacity to suppress local inflammation and tissue damage in a variety of inflammatory autoimmune diseases and, in particular, in rheumatoid arthritis. Currently, an emerging field of research comes from the possibility that these cells, through their trophic/regenerative potential, may also influence the course of chronic degenerative disorders and prevent cartilage degradation in osteoarthritis. This review focuses on these advances, specifically on the biological properties of MSCs, including their immunoregulatory characteristics, differentiation capacity and trophic potential, as well as the relevance of MSC-based therapies for rheumatic diseases.
Solar modulation of galactic cosmic rays in the three-dimensional heliosphere according to meteorite data

Cosmogenic radionuclides with distinctive half-lives from chondritic falls were used as natural detectors of galactic cosmic rays (GCR). A unique series of uniform data was obtained for variations in the integral gradients of GCR with a rigidity of R > 0.5 GV in 1955–2000 on heliocentric distances of 1.5–3.3 AU and heliographic latitudes between 23° S and 16° N. Correlation analysis was performed for the variations in GCR gradients and variations in solar activity (number of sunspots, SS, and intensity of the green coronal line, GCL), the intensity of the interplanetary magnetic field (IMF), and the inclination of the heliospheric current sheet (HCS). Distribution and variations of GCR were analyzed in 11-year solar cycles and during a change in 22-year magnetic cycles. The detected dependencies of GCR gradients on the intensity of IMF and HCS inclination provided insight into the differences in the processes of structural transformation of IMF during changes between various phases of solar and magnetic cycles. The investigated relationships lead to the conclusion that a change of secular solar cycles occurred during solar cycle 20; moreover, there is probably still an increase in the 600-year solar cycle, which can be among the major reasons for the observed global warming.
Digital Phenotyping of Mental Health using multimodal sensing of multiple situations of interest: A Systematic Literature Review

Many studies have used Digital Phenotyping of Mental Health (DPMH) to complement classic methods of mental health assessment and monitoring. This research area proposes innovative methods that perform multimodal sensing of multiple situations of interest (e.g., sleep, physical activity, mobility) to health professionals. In this paper, we present a Systematic Literature Review (SLR) to recognize, characterize and analyze the state of the art on DPMH using multimodal sensing of multiple situations of interest to professionals. We searched for studies in six digital libraries, which resulted in 1865 retrieved published papers. Next, we performed a systematic process of selecting studies based on inclusion and exclusion criteria, which selected 59 studies for the data extraction phase. First, based on the analysis of the extracted data, we describe an overview of this field, then presenting characteristics of the selected studies, the main mental health topics targeted, the physical and virtual sensors used, and the identified situations of interest. Next, we outline answers to research questions, describing the context data sources used to detect situations, the DPMH workflow used for multimodal sensing of situations, and the application of DPMH solutions in the mental health assessment and monitoring process. In addition, we recognize trends presented by DPMH studies, such as the design of solutions for high-level information recognition, association of features with mental states/disorders, classification of mental states/disorders, and prediction of mental states/disorders. We also recognize the main open issues in this research area. Based on the results of this SLR, we conclude that despite the potential and continuous evolution for using these solutions as medical decision support tools, this research area needs more work to overcome technology and methodological rigor issues to adopt proposed solutions in real clinical settings.
A Cluster-Based Similarity Fusion Approach for Scaling-Up Collaborative Filtering Recommender System

Collaborative Filtering (CF) recommenders work by collecting user ratings for items in a given domain and computing similarities between users or items to produce recommendations. The user-item rating database is extremely sparse. This means the number of ratings obtained is very small compared with the number of ratings that need to be predicted. CF suffers from the sparsity problem, resulting in poor quality recommendations and reduced coverage. Further, a CF algorithm needs calculations that are very expensive and grow non-linearly with the number of users and items in a database. Incited by these challenges, we present Cluster-Based Similarity Fusion (CBSF), a new hybrid collaborative filtering algorithm which can deal with the sparsity and scalability issues simultaneously. By the use of carefully selected clusters of users and items, CBSF reduces the computational cost of traditional CF, while retaining high accuracy. Experimental results demonstrate that apart from being scalable, CBSF leads to a better precision and coverage for the recommendation engine.
Transport in two-dimensional topological materials: recent developments in experiment and theory

We review theoretical and experimental highlights in transport in two-dimensional materials focussing on key developments over the last five years. Topological insulators are finding applications in magnetic devices, while Hall transport in doped samples and the general issue of topological protection remain controversial. In transition metal dichalcogenides valley-dependent electrical and optical phenomena continue to stimulate state-of-the-art experiments. In Weyl semimetals the properties of Fermi arcs are being actively investigated. A new field, expected to grow in the near future, focuses on the non-linear electrical and optical responses of topological materials, where fundamental questions are once more being asked about the intertwining roles of the Berry curvature and disorder scattering. In topological superconductors the quest for chiral superconductivity, Majorana fermions and topological quantum computing is continuing apace.
Dual-attention bidirectional LSTM with feature genomic analysis improves prognostic survival prediction in colorectal cancer patients

Abstract                   The increasing incidence and mortality rates of colorectal cancer necessitate accurate prediction of patients’ prognostic survival time for better management, early screening, and extended lifespan. This study uses the TCGA public dataset to conduct differential analysis on lncRNAs in 39 diseased tissues and their normal counterparts from 413 colorectal cancer patient samples, identifying 458 differentially expressed lncRNAs (DELncRNAs). Univariate Cox regression analysis revealed 23 DELncRNAs significantly associated with overall survival (OS). These 23 DELncRNAs were further refined using the LASSO algorithm to determine their feature coefficients. An adaptive mining approach with dual-attention mechanisms was employed to explore the correlative properties between various factors and survival time. A bidirectional long short-term memory (BiLSTM) neural network was established for survival prediction. The model was validated using the Jiangnan University colorectal cancer dataset, demonstrating reliable predictions for patient survival and valuable support for clinical decision-making. The AUC values for patient survival prediction during the 3-year, 3-6 year, and 6-year periods were nearly 1.00, significantly outperforming other comparative trials.
Controls on Devonian–Carboniferous magmatism in Tasmania, based on inherited zircon age patterns, Sr, Nd and Pb isotopes, and major and trace element geochemistry

Devonian-Carboniferous granites are widespread in Tasmania. In eastern Tasmania, Devonian granites intrude Ordovician-Early Devonian quartz-rich turbidites of the Mathinna Supergroup. The earliest (*400 Ma) I-type granodiorites may be arc-related. Following the Tabberabberan Orogeny (*389 Ma), more felsic and, finally, strongly fractionated I- and S-type granites were emplaced until *373 Ma. In contrast, western Tasmania granites intrude a more diverse terrane of predominantly marine shelf successions, with depositional ages as old as Late Mesoproterozoic. They are mostly felsic and fractionated I- and S-types emplaced from *374-351 Ma, possibly in response to post-collisional crustal extension following juxtaposition of the eastern and western Tasmanian terranes. Granites from the two terranes are readily distinguishable by the age spectra of their inherited zircon, which are noticeably similar to those of the detrital zircon from sedimentary successions in their respective terranes. Furthermore, within each terrane, both I and S-types yield similar inheritance patterns. This suggests a pivotal role for the sedimentary successions in the petrogenesis of both types. Western Tasmanian granites are also enriched in *1600 Ma zircon, which is essentially unrepresented in the exposed supracrustal succession. Subtle differences between the inheritance and detrital age spectra in eastern Tasmania probably relate to unrepresentative sampling of the supracrustal rocks. Nd, Sr and Pb isotopic characteristics of the granites are consistent with their derivation by mixing of magmas derived from the mantle, possibly the lower crust, and from supracrustal rocks. Systematic isotopic trends in some eastern Tasmanian I-types, particularly in the Scottsdale Batholith, correlate well with major and trace element geochemistry and age. The isotopes are inconsistent with simple restite unmixing or crystal fractionation in a closed magma chamber, and indicate progressive contamination by the Mathinna Supergroup, or similar rocks. The isotopic characteristics of late, strongly fractionated granites, although sometimes obscured by hydrothermal alteration, are also consistent with concurrent assimilation-fractional crystallisation processes. Together with the close association of some strongly fractionated I- and S-types, this suggests that such granites were generated directly in the lower crust, and were not derived from unfractionated parental granite magmas.
A Machine Learning Methodology for Cache Recommendation

Cache memories are an important component of modern processors and consume a large percentage of the processor’s power consumption. The quality of service of this cache memories relies heavily on the memory demands of the software, what means that a certain program might benefit more from a certain cache configuration which is highly inefficient for another program. Moreover, finding the optimal cache configuration for a certain program is not a trivial task and usually, involves exhaustive simulation. In this paper, we propose a machine learning-based methodology that, given an unknown application as input, it outputs a prediction of the optimal cache reconfiguration for that application, regarding energy consumption and performance. We evaluated our methodology using a large benchmark suite, and our results show a 99.8% precision at predicting the optimal cache configuration for a program. Furthermore, further analysis of the results indicates that 85% of the mispredictions produce only up to a 10% increase in energy consumption in comparison to the optimal energy consumption.
Simulation and Analysis of the Complex Behavior of Supply Chain Inventory System Based on Third‐Party Logistics Management Inventory Model with No Accumulating of Unsatisfied Demand

Under the third‐party logistics management inventory model, the system dynamics method is used to establish a nonlinear supply chain system model with supply capacity limitation and nonpermissible return, which is based on unsatisfied demand nonaccumulation. The theory of singular value and the Jury Test are used to derive the stable interval of the model which is simplified. The Largest Lyapunov Exponent (LLE) of the system is calculated by the Wolf reconstruction method and used to analyze the influence of different parameters of system’s stability. Then, the most reasonable and unreasonable combination of decision parameters under different demand environment is found out. Next, this paper compared and analyzed the change of inventory or transportation volume of system members under the combination of rational and irrational decision parameters. All of these provided guidance for decision making, which shows an important practical significance.
Practical scheme for long distance side-channel-free quantum key distribution with weak coherent states only

We show that a side-channel-free (SCF) source does not have to be an ideal source by introducing the idea of mapping from ideal source.   We propose a 3-state no-touch protocol for quantum key distribution (QKD) where Alice and Bob does not modulate any light sent out, the only thing the do is to send (or not send, in sending-or-not protocol). The reference light are from independent Lasers. We show that, the protocol is side-channel-free (i.e., both source side channel free and measurement device independent) and there is no modulation to the weak beams for QKD coding, except for sending or not sending. Calculation shows that one can reach a side-channel-free secure distance over 300 km using only coherent-state source. We use worst-case analysis which takes no limitation to the channel or detection loss for security. Our protocol is immune to all adverse due to side channels such as the photon frequency spectrum, emission time, propagation direction, spatial angular moment, and so on. Numerical simulations show that our scheme can reach a side-channel-free result for quantum key distribution over a distance longer than 200 km given the single-photon-interference misalignment error rate of 30%, and a distance longer than 300 km given the single-photon-interference misalignment error rate of 10%. Our no-touch idea can also apply to phase-coding twin-field QKD protocols. The no-touch idea also applies to twin-field QKD with phase coding.
Separate but not Equal: The Supreme Court's First Decision on Racial Discrimination in Schools

Research for this paper was partially supported by the Arnold L. and Lois S. Graves Award and by research funds from the Division of Humanities and Social Sciences at Caltech. I owe a great deal of thanks to several people who provided me with information and leads to further information: Professor Edward J. Cashin of Augusta College, Mr. Joseph B. Cumming, Mrs. Virginia de Treville of the Augusta College Library, and especially Mrs. Mary Harper Ingram.   Published as Kousser, J. Morgan. "Separate but not equal: The Supreme Court's first decision on racial discrimination in schools." The Journal of Southern History 46.1 (1980): 17-44.
Violations of Common Article 3 of the Geneva Conventions as Violations of the Laws or Customs of War under Article 3 of the Statute of the International Criminal Tribunal for the Former Yugoslavia

A controversial issue in international humanitarian law is whether violations of norms applicable in internal armed conflicts constitute criminal offences under international law and can be adjudicated as such. The International Criminal Tribunal for the former Yugoslavia (ICTY) recently faced this question in the context of a preliminary motion lodged by the Defence alleging lack of jurisdiction in the Tadic case. The indictment against Dusko Tadic charges the accused, inter alia, with violating the laws or customs of war, ‘recognised by Article 3 of the Statute of the Tribunal and Article 3(1 )(a) of the Geneva Conventions of 1949’ (Article 3 common to the Geneva Conventions enumerates prohibitions applicable in conflicts not of an international character).
Attitudes of Lecturers Regarding Integration of Food and Nutrition Security and Right to Food into Njala University Curriculum

This study was a descriptive, quantitative research design that was built from a phenomenological, qualitative study. The SWOT analysis methodology was used to describe the curriculum integration of food and nutrition security and right to food into Njala University. A sample size of 215 lecturers was selected using the random sampling technique. Data were collected using structured research questionnaires. Findings of the study revealed that i) Lecturers perceived the integration of FNS and RtF into the NU’s curriculum as a positive idea to integrate FNS and RtF in its curriculum. ii) Lecturers acknowledged that home economics and agriculture students should take compulsory FNS and RtF courses and it should be included in science and teacher training programmes. iii)  Most lecturers agreed that NU has the strengths to integrate FNS and RtF, they indicated that opportunities exist in the global market. FNS and RtF courses and programmes should be integrated into various NU curricula, and to be enhanced by supporting science education and collaborations with other organizations and government institutions. NU and its supporting partners should be prepared to address potential undesirable consequences, such as resistance to change, etc. Recommendations made were i) more female lecturers should be recruited.
A statistical mechanical model of the lipid bilayer above its phase transition

A statistical mechanical model of a bilayer of dipalmitoyl-3-sn-phosphatidylcholine molecules above their phase transition is presented. A molecular field approximation developed in previous work by Marcelja is extended by setting the molecular field at each depth in the bilayer in proportion to the average chain order at that depth. The free energy of the hydrocarbon/water interface and that due to the interaction of the polar headgroups is included in the evaluation of the statistical weights of the chain conformations. The model gives good agreement with several independent experimental results. It resolves the dilemma posed by the experimental evidence that there is (i) a considerable variation in order parameter along the lipid chain, but (ii) no collective tilt in the more ordered region of the chain. The model gives an explanation of how the lipid chains pack under these two constraints. The order parameter profile down the chain does not correspond to the profile across the bilayer.
Interactive open access publishing and public peer review: The effectiveness of transparency and self-regulation in scientific quality assurance

The traditional forms of scientific publishing and peer review do not live up to the demands of efficient communication and quality assurance in today’s highly diverse and rapidly evolving world of science. They need to be complemented by interactive and transparent forms of review, publication, and discussion that are open to the scientific community and to the public. The advantages of open access, public peer review and interactive discussion can be efficiently and flexibly combined with the strengths of traditional publishing and peer review. Since 2001 the benefits and viability of this approach are clearly demonstrated by the highly successful interactive open access journal Atmospheric Chemistry and Physics (ACP, www.atmoschem-phys.net) and a growing number of sister journals launched by the publisher Copernicus (www.copernicus.org) and the European Geosciences Union (EGU, www.egu.eu). These journals are practicing a two-stage process of publication and peer review combined with interactive public discussion, which effectively resolves the dilemma between rapid scientific exchange and thorough quality assurance. The same or similar concepts have recently also been adopted in other disciplines, including the life sciences and economics. Note, however, that alternative approaches where interactive commenting and public discussion are not fully integrated with formal peer review by designated referees tend to be less successful. The principles, key aspects and achievements of interactive open access publishing (top quality and impact, efficient self-regulation and low rejection rates, little waste and low cost) are outlined and discussed. Further information is available on the internet: www.atmospheric-chemistry-and-physics.net/general_information/ public_relations.html
A cross-model comparison of global long-term technology diffusion under a 2 degrees C climate change control target. Special Issue on Implementing Climate Policies in the Major Economies: An Assessment of Durban Platform Architectures — Results from the LIMITS Project

We investigate the long-term global energy technology diffusion patterns required to reach a stringent climate change target with a maximum average atmospheric temperature increase of 2 degrees C. If the anthropogenic temperature increase is to be limited to 2 degrees C, total CO2 emissions have to be reduced massively, so as to reach substantial negative values during the second half of the century. Particularly power sector CO2 emissions should become negative from around 2050 onwards according to most models used for this analysis in order to compensate for GHG emissions in other sectors where abatement is more costly. The annual additional capacity deployment intensity (expressed in GW/yr) for solar and wind energy until 2030 needs to be around that recently observed for coal-based power plants, and will have to be several times higher in the period 2030.2050. Relatively high agreement exists across models in terms of the aggregated low-carbon energy system cost requirements on the supply side until 2050, which amount to about 50 trillion US$.