Miracle-dz/UniFAR-FTUs huggingface dataset:
Reply to RM Ortega and AM López-Sobaler

REFERENCES 1. Luscombe-Marsh ND, Noakes M, Wittert GA, Keogh JB, Foster P, Clifton PM. Carbohydrate-restricted diets high in either monounsaturated fat or protein are equally effective at promoting fat loss and improving blood lipids. Am J Clin Nutr 2005;81:762–72. 2. World Health Organization. Diet, nutrition and the prevention of chronic diseases. Report of a Joint WHO/FAO Expert Consultation. World Health Organ Tech Rep Ser 2003;916. 3. Ortega RM, López-Sobaler AM, Requejo AM, Andrés P. Nutritional objectives for the Spanish population. Recommended steps for improving the health of the population. In: Department of Nutrition, ed. Food composition. A basic tool for assessing nutritional status. Madrid, Spain: Complutense, 2004:86. 4. Ortega RM, Requejo AM, Quintas ME, Redondo MR, López-Sobaler AM, Andrés P. Concern regarding bodyweight and energy balance in a group of female university students from Madrid: differences with respect to body mass index. J Am Coll Nutr 1997;16:244–51. 5. Ortega RM, Redondo MR, Zamora MJ, López-Sobaler AM, Andrés P, Encinas-Sotillos A. Energy balance and caloric profile in the elderly obese or in those with overweight compared to those of normal weight. Med Clin (Barc) 1995;104:526–9. 6. Ortega RM, Requejo AM, Andrés P, López-Sobaler A, Redondo MR, González-Fernández M. Relationship between diet composition and body mass index in a group of Spanish adolescents. Br J Nutr 1995;74: 765–73. 7. Ortega RM, Andrés P. Carbohydrates and obesity. Med Clin (Barc) 1998;110:797–801. 8. Astrup A, Toubro S, Raben A, Skov AR. The role of low-fat diets and fat substitutes in body weight management: what have we learned from clinical studies? J Am Diet Assoc 1997;97:S82–7. 9. Anderson GH, Moore SE. Dietary proteins in the regulation of food intake and body weight in humans. J Nutr 2004;134:S974–9.
General inverse solution of six-degrees-of-freedom serial robots based on the product of exponentials model

Purpose Developing general closed-form solutions for six-degrees-of-freedom (DOF) serial robots is a significant challenge. This paper thus aims to present a general solution for six-DOF robots based on the product of exponentials model, which adapts to a class of robots satisfying the Pieper criterion with two parallel or intersecting axes among its first three axes. Design/methodology/approach The proposed solution can be represented as uniform expressions by using geometrical properties and a modified Paden–Kahan sub-problem, which mainly adopts the screw theory. Findings A simulation and experiments validated the correctness and effectiveness of the proposed method (general resolution for six-DOF robots based on the product of exponentials model). Originality/value The Rodrigues rotation formula is additionally used to turn the complex problem into a solvable trigonometric function and uniformly express six solutions using two formulas.
Methylglyoxal enhances the proliferation of vascular smooth muscle cells via Akt phosphorylation

Abstract Methylglyoxal (MGO) is predominantly produced as a by-product of the glycolysis pathway. The glyoxalase system effectively removes it in a healthy organism. However, this process is impaired, and MGO level is elevated in people with diabetes. MGO’s effects on proliferation were mostly studied in cancer cells, and the data in other cell types are limited. This study inspected the proliferative capacity of MGO in vascular smooth muscle cells (VSMCs), which have a crucial role in atherosclerosis and restenosis. The roles of ERK1/2 MAPK and Akt phosphorylations in proliferation were determined. Telmisartan, irbesartan, and NF-κB inhibitor JSH-23’s roles in protecting the cells from MGO-induced proliferation were also investigated. Primary VSMCs were isolated from the rat aorta. The proliferation was spectrophotometrically measured by using a tetrazolium salt (Wst-1). The cells were cultured in standard media (SM, glucose conc. 5.5 mM) or high glucose media (HGM, glucose conc. 25 mM; an in vitro model of hyperglycemia). ERK1/2 MAPK and Akt phosphorylations were determined by the western blot method. MGO triggered the proliferation at 24, 48, and 72 hrs in SM and 48 and 72 hrs in HGM. Low doses of MGO such as 1–10 µM can induce proliferation. The phosphorylated ERK1/2 MAPK and Akt participated in MGO-induced proliferation. Telmisartan, irbesartan, and JSH-23 effectively alleviated the proliferation and Akt phosphorylation. MGO could proliferate VSMCs even at low doses. Moreover, hypertensive diabetic patients might benefit from a sartan family drug to protect VSMCs from MGO-induced proliferation.
De novo assembly of human genome at single-cell levels

Abstract Genome assembly has been benefited from long-read sequencing technologies with higher accuracy and higher continuity. However, most human genome assembly require large amount of DNAs from homogeneous cell lines without keeping cell heterogeneities, since cell heterogeneity could profoundly affect haplotype assembly results. Herein, using single-cell genome long-read sequencing technology (SMOOTH-seq), we have sequenced K562 and HG002 cells on PacBio HiFi and Oxford Nanopore Technologies (ONT) platforms and conducted de novo genome assembly. For the first time, we have completed the human genome assembly with high continuity (with NG50 of ∼2 Mb using 95 individual K562 cells) at single-cell levels, and explored the impact of different assemblers and sequencing strategies on genome assembly. With sequencing data from 30 diploid individual HG002 cells of relatively high genome coverage (average coverage ∼41.7%) on ONT platform, the NG50 can reach over 1.3 Mb. Furthermore, with the assembled genome from K562 single-cell dataset, more complete and accurate set of insertion events and complex structural variations could be identified. This study opened a new chapter on the practice of single-cell genome de novo assembly.
What Do Sub-second Price Data Tell Us about the Arrowhead Stock Market?

—In this paper, we study ultrafast stock time series of the newly developed arrowhead trading system in Tokyo Market, in order to investigate the statistical nature of the stock time series under sub-second time scales. We also compare the current result to the past study on longer time scale up to a few minutes. It is shown that the empirical distributions obtained in this study follow the scaling law of the Lévy stable distribution of index α ranging from 1.4 to 2.0.
Altered carbon status in Glycine max hairy roots induced by Agrobacterium rhizogenes

ABSTRACT Plants fix CO2 into carbohydrates through photosynthesis, and various organisms interact with plants to obtain carbohydrates. Agrobacterium rhizogenes is a soil bacterium known as a plant pathogen that induces hairy root disease. Through A. rhizogenes-plant interactions, transfer-DNA (T-DNA) of the Ri plasmid is inserted into the host plant genome, leading to excessive formation of hairy roots and the synthesis of opines that are carbon and nitrogen sources for A. rhizogenes. In this study, we analyzed the carbohydrate contents in soybean (Glycine max) hairy roots. We found that the starch content was strongly increased in hairy roots, whereas the glucose was significantly decreased. On the other hand, no significant differences were observed in sucrose levels between the main roots and hairy roots of A. rhizogenes-inoculated plants. This result suggests that A. rhizogenes infection caused a change in primary carbon metabolism in the host plant cells.
Factors Limiting the Translatability of Rodent Model–Based Intranasal Vaccine Research to Humans

The intranasal route of vaccination presents an attractive alternative to parenteral routes and offers numerous advantages, such as the induction of both mucosal and systemic immunity, needle-free delivery, and increased patient compliance. Despite demonstrating promising results in preclinical studies, however, few intranasal vaccine candidates progress beyond early clinical trials. This discrepancy likely stems in part from the limited predictive value of rodent models, which are used frequently in intranasal vaccine research. In this review, we explored the factors that limit the translatability of rodent-based intranasal vaccine research to humans, focusing on the differences in anatomy, immunology, and disease pathology between rodents and humans. We also discussed approaches that minimize these differences and examined alternative animal models that would produce more clinically relevant research.
Optimal Management of Energy Consumption and Comfort for Smart Buildings Operating in a Microgrid

This paper presents a mixed integer non-linear programming model to optimize, in a centralized fashion, the operation of multiple buildings in a microgrid. The proposed model aims to minimize the total cost of the energy imported from the main grid at the interconnection point, managing the power demand and generation of buildings, while operational constraints of the electrical grid are guaranteed. This approach considers the management of heating, ventilation, and air conditioning units, lighting appliances, photovoltaic generation and energy storage system of each building. Comfortable indoor conditions for the occupants are kept by a set of mathematical constraints. Additionally, a strategy that simplifies the original model is presented, based on a set of linearization techniques and equivalent representations, obtained through a pre-processing stage executed in EnergyPlus software. This strategy allows approximating the proposed model into a mixed integer linear programming formulation that can be solved using commercial solvers. The proposed model was tested in a 13-bus microgrid for different deterministic cases of study with non-manageable loads and smart buildings. A large-size test case is also considered. Finally, a rolling horizon strategy is proposed with the aim of addressing the uncertainty of the data, as well as reducing the amount of forecasting data required.
University of Birmingham The Role of Atmospheric Gases in Global Warming

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Co-Inheritance of Variation in All-Cause Mortality and Biochemical Risk Factors

Abstract Biomarkers may be useful endophenotypes for genetic studies if they share genetic sources of variation with the outcome, for example, with all-cause mortality. Australian adult study participants who had reported their parental survival information were included in the study: 14,169 participants had polygenic risk scores (PRS) from genotyping and up to 13,365 had biomarker results. We assessed associations between participants’ biomarker results and parental survival, and between biomarker results and eight parental survival PRS at varying p-value cut-offs. Survival in parents was associated with participants’ serum bilirubin, C-reactive protein, HDL cholesterol, triglycerides and uric acid, and with LDL cholesterol for participants’ fathers but not for their mothers. PRS for all-cause mortality were associated with liver function tests (alkaline phosphatase, butyrylcholinesterase, gamma-glutamyl transferase), metabolic tests (LDL and HDL cholesterol, triglycerides, uric acid), and acute-phase reactants (C-reactive protein, globulins). Association between offspring biomarker results and parental survival demonstrates the existence of familial effects common to both, while associations between biomarker results and PRS for mortality favor at least a partial genetic cause of this covariation. Identification of genetic loci affecting mortality-associated biomarkers offers a route to the identification of additional loci affecting mortality.
Explaining Black Box Drug Target Prediction Through Model Agnostic Counterfactual Samples

Many high-performance DTA deep learning models have been proposed, but they are mostly black-box and thus lack human interpretability. Explainable AI (XAI) can make DTA models more trustworthy, and allows to distill biological knowledge from the models. Counterfactual explanation is one popular approach to explaining the behaviour of a deep neural network, which works by systematically answering the question “How would the model output change if the inputs were changed in this way? ”. We propose a multi-agent reinforcement learning framework, Multi-Agent Counterfactual Drug-target binding Affinity (MACDA), to generate counterfactual explanations for the drug-protein complex. Our proposed framework provides human-interpretable counterfactual instances while optimizing both the input drug and target for counterfactual generation at the same time. We benchmark the proposed MACDA framework using the Davis and PDBBind dataset and find that our framework produces more parsimonious explanations with no loss in explanation validity, as measured by encoding similarity. We then present a case study involving ABL1 and Nilotinib to demonstrate how MACDA can explain the behaviour of a DTA model in the underlying substructure interaction between inputs in its prediction, revealing mechanisms that align with prior domain knowledge.
Historic masonry monitoring by motion magnification analysis

Vibration monitoring of historic structures in urban environment is a relevant issue for health survey and early damaging detection in sustainable and enhanced resilient cities. This study explores the potentialities of vibration monitoring by Motion Magnification Analysis. Motion magnification acts like a microscope for motion in video sequences, but affecting only some groups of pixels. The motion magnification uses the spatial resolution of the video-camera to extract physical properties from images to make inferences about the dynamical behaviour of the object, e.g. to visualize at least the first mode shape, no matter its dimensions, since any point on the surface of the object can be considered a virtual sensor. Recently, a number of experiments conducted on simple geometries like rods and other small objects, as well as on bridges, showed the reliability of this methodology compared to accelerometers and lasers. Researchers have been also very interested in assessing the method’s feasibility, since conventional devices are surely more precise, but more expensive and much less practical. In this paper, we give an introduction to MMA and describe its application to the analysis of two full-scale historic masonry walls tested on shaking tables. This is an interesting point, because the size of tested walls is larger than usual small experimental set-ups implemented in MMA testbed until now. Results showed that MMA allowed a visual identification of fractures in advance. Moreover, we performed some conventional calculation for modal analysis of the walls, such as FRF and PSD, on MMA output data. Though the used equipment (camera, tripod and lighting) was of low quality, in order to test the methodology in an unfavourable environment with very high data noise, the estimate of the first modal frequency showed a good agreement with modal analysis by a more conventional optical system used as reference.
On verbal subgroups of ﬁnitely generated nilpotent groups

The paper concerns the problem of characterization of verbal subgroups in ﬁnitely generated nilpotent groups. We introduce the notion of verbal poverty and show that every verbally poor ﬁnitely generated nilpotent group is a ﬁnite 𝑝 -group with the lower 𝑝 -central series for certain prime 𝑝 . We conclude with few examples of verbally poor groups.
Marine bacteria and omic approaches: A novel and potential repository for bioremediation assessment

Marine environments accommodating diverse assortments of life constitute a great pool of differentiated natural resources. The cumulative need to remedy unpropitious effects of anthropogenic activities on estuaries and coastal marine ecosystems has propelled the development of effective bioremediation strategies. Marine bacteria producing biosurfactants are promising agents for bio‐remediating oil pollution in marine environments, making them prospective candidates for enhancing oil recovery. Molecular omics technologies are considered an emerging field of research in ecological and diversity assessment owing to their utility in environmental surveillance and bioremediation of polluted sites. A thorough literature review was undertaken to understand the applicability of different omic techniques used for bioremediation assessment using marine bacteria. This review further establishes that for bioremediation of environmental pollutants (i.e. heavy metals, hydrocarbons, xenobiotic and numerous recalcitrant compounds), organisms isolated from marine environments can be better used for their removal. The literature survey shows that omics approaches can provide exemplary knowledge about microbial communities and their role in the bioremediation of environmental pollutants. This review centres on applications of marine bacteria in enhanced bioremediation, using the omics approaches that can be a vital biological contrivance in environmental monitoring to tackle environmental degradation. The paper aims to identify the gaps in investigations involving marine bacteria to help researchers, ecologists and decision‐makers to develop a holistic understanding regarding their utility in bioremediation assessment.
Synergy effect of microwave annealing and high-pressure hydrogen annealing on Poly-Si thin-film transistor

Grain boundary (GB) is a significant factor that deteriorates the transfer characteristics of poly-Si thin-film transistors (TFTs). In this study, we utilized the synergistic effect of microwave annealing (MWA) and high-pressure hydrogen annealing (HPHA) to effectively reduce grain boundary trap (GBT) density, resulting in improved field-effect mobility (μ) and subthreshold swing (SS). To investigate the synergistic effect of MWA and HPHA, the transfer characteristics of rapid thermal annealing and forming gas annealing devices were compared and analyzed as control devices. Furthermore, the mechanism of SS and mobility enhancement can be quantitatively understood by lowering the GB barrier height. In addition, Raman spectroscopy proved that poly-Si crystallinity was improved during MWA. Our results showed that MWA and HPHA play a vital role in reducing GBT density and improving poly-Si TFT characteristics.
Enriching Proteolysis Targeting Chimeras with a Second Modality: When Two Are Better Than One

Proteolysis targeting chimera (PROTAC)-mediated protein degradation has prompted a radical rethink and is at a crucial stage in driving a drug discovery transition. To fully harness the potential of this technology, a growing paradigm toward enriching PROTACs with other therapeutic modalities has been proposed. Could researchers successfully combine two modalities to yield multifunctional PROTACs with an expanded profile? In this Perspective, we try to answer this question. We discuss how this possibility encompasses different approaches, leading to multitarget PROTACs, light-controllable PROTACs, PROTAC conjugates, and macrocycle- and oligonucleotide-based PROTACs. This possibility promises to further enhance PROTAC efficacy and selectivity, minimize side effects, and hit undruggable targets. While PROTACs have reached the clinical investigation stage, additional steps must be taken toward the translational development of multifunctional PROTACs. A deeper and detailed understanding of the most critical challenges is required to fully exploit these opportunities and decisively enrich the PROTAC toolbox.
A 73-Year-Old Woman Treated for Rheumatoid Arthritis with Lower Rectal Carcinoma Who Underwent Abdominoperineal Resection, Lateral Regional Lymph Node Resection, and Partial Hepatectomy by Hand-Assisted Laparoscopic Surgery (HALS): A Case Report

Patient: Female, 73-year-old Final Diagnosis: Lateral lymph node metastases • liver metastases • rectum carcinoma Symptoms: Hematochezia Medication: — Clinical Procedure: Hand-assisted laparoscopic surgery Specialty: Gastroenterology and Hepatology • Rheumatology • Surgery Objective: Unusual clinical course Background: This report describes the case of a 73-year-old woman treated for rheumatoid arthritis with lower rectal carcinoma who underwent abdominoperineal resection, lateral regional lymph node resection, and partial hepatectomy by hand-assisted laparoscopic surgery (HALS). More recently, HALS has proven to be useful in multiple organ resections. Case Report: A 73-year-old woman who presented with hematochezia was diagnosed with lower rectal cancer and referred to our hospital. The patient had a history of rheumatoid arthritis and was taking oral nonsteroidal anti-inflammatory drugs. After further evaluation, the patient was diagnosed with stage IV rectal cancer with a metastatic liver lesion and a right lateral lymph node metastasis. All lesions were resected using HALS. A 50-mm longitudinal umbilical incision was created for use as a hand access site, and 3 ports with a diameter of 5 mm each were inserted into the lower abdomen to perform right lateral lymph node dissection and abdominoperineal resection. HALS was performed in the upper abdomen, where the liver was used to partially resect segment S6. The patient was discharged without complications 13 days after the operation. Conclusions: In this complex case of advanced rectal carcinoma with liver metastases, use of the HALS surgical method was shown to be possible. Immunomodulatory treatment for rheumatoid arthritis may have influenced the outcome for this patient.
Computationally Relaxed Unscented Kalman Filter

Advanced robotics and autonomous vehicles rely on filtering and sensor fusion techniques to a large extent. These mobile applications need to handle the computations onboard at high rates while the computing capacities are limited. Therefore, any improvement that lowers the CPU time of the filtering leads to more accurate control or longer battery operation. This article introduces a generic computational relaxation for the unscented transformation (UT) that is the key operation of the Unscented Kalman filter-based applications. The central idea behind the relaxation is to pull out the linear part of the filtering model and avoid the calculations for the kernel of the nonlinear part. The practical merit of the proposed relaxation is demonstrated through a simultaneous localization and mapping (SLAM) implementation that underpins the superior performance of the algorithm in the practically relevant cases, where the nonlinear dependencies influence only an affine subspace of the image space. The numerical examples show that the computational demand can be mitigated below 50% without decreasing the accuracy of the approximation. The method described in this article is implemented and published as an open-source C++ library RelaxedUnscentedTransformation on GitHub.