Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterisation of amyloid oligomers by electrospray ionisation- ion mobility spectrometry-mass spectrometry

Soluble oligomers formed during the self-assembly of amyloidogenic peptide and protein species are generally thought to be highly toxic. Consequently, thorough characterisation of these species is of much interest in the quest for effective therapeutics and for an enhanced understanding of amyloid fibrillation pathways. The structural characterisation of oligomeric species, however, is challenging as they are often transiently and lowly-populated, and highly heterogeneous. Electrospray ionisation-ion mobility spectrometry-mass spectrometry (ESI-IMS-MS) is a powerful technique which is able to detect individual ion species populated within a complex heterogeneous mixture and characterise them in terms of shape, stoichiometry, ligand binding capability and relative stability. Herein, we describe the use of ESI-IMS-MS to characterise the size and shape of oligomers of beta-2-microglobulin through use of data calibration and the derivation of models. This enables information about the range of oligomeric species populated en route to amyloid formation and the mode of oligomer growth to be obtained.
Bias and Type I error Control in Correcting Treatment Effect for Treatment Switching Using Marginal Structural Models in Phase III Oncology Trials

ABSTRACT This research focuses on the bias and type I error control issues when the marginal structural models (MSMs) are applied to evaluate the causal survival benefits of active intervention versus control in randomized clinical trials (RCTs) with treatment switching after disease progression. When MSMs are applied in the RCT setting, the question of interest, model specifications, strategies for type I error control, bias reduction, etc. differ somewhat from those for observational studies. This manuscript discusses the approaches used to accommodate these differences. Through Monte Carlo simulations and a case study, our research demonstrates that, with sufficient attention paid to issues applicable to RCTs in particular, MSMs may perform better than the inverse probability of censoring weighting (IPCW) method in analyzing the survival endpoint in RCTs with treatment switching because more information is used by the MSM.
A simple control algorithm for controlling biped dynamic walking with stopping ability based on the footed inverted pendulum model

In biped walking, dynamic balance ability is an important evaluation index. Zero-moment-point-based trajectory control is a common method for biped dynamic walking, but it requires complex control mechanisms that limit its applications. With the help of passive dynamics, the biped walking based on the inverted pendulum model can achieve dynamic walking in a simple way; however, it has no stopping ability, which is necessary for practical use. To solve this problem, this article proposes a footed inverted pendulum model and develops a simple three-part decomposition control algorithm for controlling biped dynamic walking based on the model. In the control algorithm, the biped walking is decomposed into three separate control parts: body posture, body height, and body velocity. Body posture is controlled by the stance hip, body height is controlled by the stance knee, and body velocity is controlled by the stance ankle and swing foot placement simultaneously. A simulation is presented to analyze the foot’s effect on the inverted pendulum model. Two hardware experiments exploring velocity control and balance are described, with the results showing that the biped can achieve dynamic walking with stopping ability by using the simple control algorithm based on the footed inverted pendulum model.
On‐Surface Synthesis of Unsaturated Hydrocarbon Chains through C−S Activation

Abstract We use an on‐surface synthesis approach to drive the homocoupling reaction of a simple dithiophenyl‐functionalized precursor on Cu(111). The C−S activation reaction is initiated at low annealing temperature and yields unsaturated hydrocarbon chains interconnected in a fully conjugated reticulated network. High‐resolution atomic force microscopy imaging reveals the opening of the thiophenyl rings and the presence of trans‐ and cis‐oligoacetylene chains as well as pentalene units. The chemical transformations were studied by C 1s and S 2p core level photoemission spectroscopy and supported by theoretical calculations. At higher annealing temperature, additional cyclization reactions take place, leading to the formation of small graphene flakes.
Radiation hard analog circuits for ALICE ITS upgrade

The ALICE experiment is planning to upgrade the ITS (Inner Tracking System) [1] detector during the LS2 shutdown. The present ITS will be fully replaced with a new one entirely based on CMOS monolithic pixel sensor chips fabricated in TowerJazz CMOS 0.18 μ m imaging technology. The large (3 cm × 1.5 cm = 4.5 cm2) ALPIDE (ALICE PIxel DEtector) sensor chip contains about 500 Kpixels, and will be used to cover a 10 m2 area with 12.5 Gpixels distributed over seven cylindrical layers. The ALPOSE chip was designed as a test chip for the various building blocks foreseen in the ALPIDE [2] pixel chip from CERN. The building blocks include: bandgap and Temperature sensor in four different flavours, and LDOs for powering schemes. One flavour of bandgap and temperature sensor will be included in the ALPIDE chip. Power consumption numbers have dropped very significantly making the use of LDOs less interesting, but in this paper all blocks are presented including measurement results before and after irradiation with neutrons to characterize robustness against displacement damage.
Virtual source aperture image processing methodsfor non-destructive testing

Until recently, the processing of ultrasonic array data has been based on parallel transmission strategies enabling beam forming to occur within the material, with summing of the time domain signals performed in hardware on reception. These time domain signals are then typically stacked in software to produce B-scan images. Since the introduction of full matrix capture there has been advancement in post-processing algorithms, allowing for fully-focused inspections to be undertaken by dividing the area to be inspected into a grid of pixels and treating each as a focal point (the total focusing method). However, due to the large number of time domain signals associated with this approach, processing speed is often a limiting factor. Virtual source aperture (VSA) is an ultrasonic technique in which a highly divergent beam is generated using a focal law to simulate emission from a virtual point positioned some distance behind the transducer. When combined with each element of the array acting as a receiver, sufficient time domain signals may be acquired to allow B-scan images to be generated in real-time. In this paper, various imaging algorithms are presented, where the ability to image a series of point-like reflectors is demonstrated. Due to its high data acquisition speed, low computational requirement and reduced data size, VSA is shown to offer significant performance advantages over other advanced ultrasonic techniques, such as FMC.
Effects of circadian rhythm disruption on retinal physiopathology: Considerations from a consensus of experts

The circadian rhythms originate within the organism and synchronize with cyclic fluctuations in the external environment. It has been demonstrated that part of the human genome is under control of the circadian clock and that a synchronizer that helps to maintain daily rhythms is Melatonin, a neuro-hormone primarily synthesized by the pineal gland during the night. The chronic disruption of circadian rhythm has been linked to many conditions such as obesity, metabolic syndrome, type 2 diabetes, cancer, and neurodegenerative diseases. Studies in the mice showed that the disruption of the retinal circadian rhythm increases the decline during the aging of photoreceptors, accelerating age-related disruption of cone cell structure, function, and viability and that the melatonin receptor deletion seems to influence the health of retinal cells, speeding up their aging. In conclusion, preserving the circadian rhythms could be to add to the prevention and treatment of age-related degenerative retinal diseases, and although additional studies are needed, melatonin could be a valid support to favor this “chronoprotection action”.
Association between Ancestry-Specific 6q25 Variants and Breast Cancer Subtypes in Peruvian Women

Abstract Background: Breast cancer incidence in the United States is lower in Hispanic/Latina (H/L) compared with African American/Black or Non-Hispanic White women. An Indigenous American breast cancer–protective germline variant (rs140068132) has been reported near the estrogen receptor 1 gene. This study tests the association of rs140068132 and other polymorphisms in the 6q25 region with subtype-specific breast cancer risk in H/Ls of high Indigenous American ancestry. Methods: Genotypes were obtained for 5,094 Peruvian women with (1,755) and without (3,337) breast cancer. Associations between genotype and overall and subtype-specific risk for the protective variant were tested using logistic regression models and conditional analyses, including other risk-associated polymorphisms in the region. Results: We replicated the reported association between rs140068132 and breast cancer risk overall [odds ratio (OR), 0.53; 95% confidence interval (CI), 0.47–0.59], as well as the lower odds of developing hormone receptor negative (HR−) versus HR+ disease (OR, 0.77; 95% CI, 0.61–0.97). Models, including HER2, showed further heterogeneity with reduced odds for HR+HER2+ (OR, 0.68; 95% CI, 0.51–0.92), HR−HER2+ (OR, 0.63; 95% CI, 0.44–0.90) and HR−HER2− (OR, 0.77; 95% CI, 0.56–1.05) compared with HR+HER2−. Inclusion of other risk-associated variants did not change these observations. Conclusions: The rs140068132 polymorphism is associated with decreased risk of breast cancer in Peruvians and is more protective against HR− and HER2+ diseases independently of other breast cancer-associated variants in the 6q25 region. Impact: These results could inform functional analyses to understand the mechanism by which rs140068132-G reduces risk of breast cancer development in a subtype-specific manner. They also illustrate the importance of including diverse individuals in genetic studies.
How the Glasgow Declaration on Forests can help keep alive the 1.5 °C target

At last year’s 26th UN Climate Change Conference of the Parties (COP26) in Glasgow, 141 countries committed to halt and reverse forest loss and land degradation by 2030 (1). It was part of one of several side deals designed to keep the objectives of the Paris agreement within reach. The UK government boasted that these nations had made a landmark pledge to end deforestation (2). Yet, one crucial detail was left out: whether that deforestation will be gross or net. The distinction matters, because differing interpretations of how countries can “end deforestation” significantly impact future carbon dioxide emissions. Put simply, ending gross deforestation would be a major step forward for the climate. But considering only net deforestation could be anecdotal and even be detrimental to biodiversity. Overall, human activities related to land use emit 4 gigatonnes (Gt) of carbon dioxide (CO2) per year to the atmosphere (3). These are net emissions, comprising both carbon losses and carbon gains. On the loss side, the destruction of tree biomass during deforestation, for large-scale agriculture, cattle ranching, or shifting cultivation (cycles of cutting forest for agriculture, then abandoning to recover soil fertility, then returning), and the legacy emissions from harvested wood products, form the bulk of gross emissions, totaling 14 Gt CO2 per year (3). On the gain side, secondary forest regrowth after reforestation, agricultural abandonment, or during shifting cultivation form the bulk of the gross carbon Differing interpretations as to how countries can “end deforestation” will have significant impacts on future carbon dioxide emissions. Only ending gross deforestation would be a major step forward for the climate. Image credit: Shutterstock/guentermanaus.
SubsidyExplorer: A decision-support tool to improve our understanding of the ecological and economic effects of reforming fisheries subsidies

The magnitude of subsidies provided to the fishing sector by governments worldwide is immense—an estimated $35.4 billion USD per year. The majority of these subsidies may be impeding efforts to sustainably manage fisheries by incentivizing overfishing and overcapacity. Recognizing the threat these subsidies pose, the World Trade Organization has set a goal of reaching an agreement that would end fisheries subsidies that contribute to overcapacity, overfishing, and illegal fishing. However, negotiations have been hampered by uncertainty around the likely effects of reforming these subsidies. Here we present a novel method for translating a bioeconomic model into an interactive online decision support tool that draws upon real-world data on fisheries subsidies and industrial fishing activity so users can directly compare the relative ambition levels of different subsidy reform options.
E-learning Environments: Are our students e-ready?

technologies have advanced, modes of learning have evolved and educators now must be innovative and adaptable to new methods of teaching content. There are a variety of ways in which educational content is delivered and multiple tools and features to support learning activities, collaboration and communication. Students learning preferences, sense of preparedness, and knowledge of e-learning environments must be considered to ensure learning goals are supported by quality learning experiences. The proposed research study will explore first time e-learners perceptions of a one day introductory e-learning tutorial and subsequent weekly supplementary instructor-made-videos in an effort to bridge the distance gap between e-learners and lecturers. A mixed methods approach will also allow for a survey evaluation of student preferences and the influence course design elements in Moodle and Adobe Connect have on the educational experience of e-learners at Diploma level who are studying through the Eastern Institute of Technology.
Avoiding entry into intracellular protein degradation pathways by signal mutations increases protein secretion in Pichia pastoris

In our previous study, we serendipitously discovered that protein secretion in the methylotrophic yeast Pichia pastoris is enhanced by a mutation (V50A) in the mating factor alpha (MFα) prepro‐leader signal derived from Saccharomyces cerevisiae. In the present study, we investigated 20 single‐amino‐acid substitutions, including V50A, located within the MFα signal peptide, indicating that V50A and several single mutations alone provided significant increase in production of the secreted proteins. In addition to hydrophobicity index analysis, both an unfolded protein response (UPR) biosensor analysis and a microscopic observation showed a clear difference on the levels of UPR induction and mis‐sorting of secretory protein into vacuoles among the wild‐type and mutated MFα signal peptides. This work demonstrates the importance of avoiding entry of secretory proteins into the intracellular protein degradation pathways, an observation that is expected to contribute to the engineering of strains with increased production of recombinant secreted proteins.
Nutrient intake and adherence to the Nordic nutrition recommendations in a Swedish cohort with abdominal obesity

Background The Nordic Nutrition Recommendations (NNR) are developed to promote public health and to prevent food-related diseases such as obesity and cardiovascular diseases. Objective To investigate the nutrient intake and adherence to the NNR in a Swedish cohort with abdominal obesity. Design Dietary intake data were collected using 3-day food diaries and anthropometry and clinical chemistry parameters were measured at baseline of a long-term intervention studying weight-loss management. Results Eighty-seven subjects with abdominal obesity successfully completed a 3-day food diary. Twelve of these subjects were excluded for further analysis due to implausible low-energy reporting. The remaining 75 subjects (76% females) had mean age of 52.3 ± 10.1 years and a mean body mass index of 34.3 ± 3.1 kg/m2. Mean total fat intake (41.2 ± 7.0E%) was exceeded by 56% of the sample size compared to the maximum recommended intake (RI) of 40E%, whereas mean carbohydrate intake (40.4 ± 8.0E%) was lower than the RI (45–60E%). The intake of saturated fatty acids was high compared to the NNR with only 2 women and none of men reported intakes within the RI of <10 E%. Adherence to the RI for dietary fibre was very low (16.0% and 13.3% when expressed as g/d and g/MJ, respectively). Analyses of micronutrient intake showed lowest adherences for vitamin D and sodium. Conclusions The nutrient intake in our subjects compared to NNR was rather low with a high total fat intake, particularly too high intake of saturated fatty acids, high salt consumption, and very low dietary fibre and vitamin D intake. More effort is clearly needed to promote healthy dietary habits among subjects with obesity.
Redox‐engineering enhances maize thermotolerance and grain yield in the field

Summary Increasing populations and temperatures are expected to escalate food demands beyond production capacities, and the development of maize lines with better performance under heat stress is desirable. Here, we report that constitutive ectopic expression of a heterologous glutaredoxin S17 from Arabidopsis thaliana (AtGRXS17) can provide thermotolerance in maize through enhanced chaperone activity and modulation of heat stress‐associated gene expression. The thermotolerant maize lines had increased protection against protein damage and yielded a sixfold increase in grain production in comparison to the non‐transgenic counterparts under heat stress field conditions. The maize lines also displayed thermotolerance in the reproductive stages, resulting in improved pollen germination and the higher fidelity of fertilized ovules under heat stress conditions. Our results present a robust and simple strategy for meeting rising yield demands in maize and, possibly, other crop species in a warming global environment.
Multilevel Anti-Discrimination and Privacy Preservation Correlativity

In the fast growing technology, most organizations will need to reveal their crucial data which includes the sensitive information that discloses one's identity during their business analytics and to provide services. To limit the access to such sensitive data, various privacy preservation techniques are applied based on the level of priority assumed. The multilevel privacy preserved discrimination free data transmission deals with the correlation of discrimination prevention and privacy preservation. By applying appropriate privacy preservation techniques, it can be shown that the discrimination prevention can be easily accomplished along with secure transmission of data to different levels of users. On the basis of sociological aspect, discrimination is the unfair treatment of an individual or group based on their membership on a particular category. So, the decision attribute that leads to discrimination needs to be hided or transformed. The unified discrimination prevention method is available which avoids both direct and indirect discrimination simultaneously or both at the same time. Although discriminatory biases are eliminated, it results in huge data loss which drops down the data transmission efficiency. The data quality is much preserved since encryption technique is included. The proposed system is dynamic in nature and can be implemented in any organization. The experimental evaluation aids us to conclude that the proposed work is efficient for data transmission without discrimination and with maximum privacy preservation.
Seizure Semiology, Location of Lesion on Neuroimaging, and Interictal Electroencephalographic (EEG) Abnormalities in Children With Single-Lesion Neurocysticercosis—Is There a Correlation?

Background: Single-lesion neurocysticercosis provides a model of seizure genesis secondary to an acquired lesion. We aimed to study the correlation of seizure semiology with the location of the lesion and interictal electroencephalographic (EEG) abnormalities in children with single-lesion neurocysticercosis. Methods: Prospective, observational study in children with single-lesion neurocysticercosis and seizures. Seizure classification was done after an interview with the parent/onlooker and the child. Localization and lateralization of the lesion were done by neuroimaging. The EEG abnormalities were classified based on their morphology and location. Results: Ninety-two children (7.9 ± 2.4 years) were included. Focal-onset seizures were the commonest (n = 54; 58.6%) seizures. Majority of the lesions were located in the frontal (n = 43; 47%) and parietal cortex (n = 34; 37%). EEG showed focal slowing (n = 15; 53.6%) and epileptiform spikes/spike-wave complexes (n = 13; 46.4%). There was a perfect agreement of clinical semiology with imaging lateralization (K = 1.0) and moderate agreement with imaging localization (K = 0.4). There was no significant agreement of clinical localization with EEG slowing (K = 0.1) or sharps (K = 0). There was moderate agreement (K = 0.6) of EEG slowing and substantial agreement (K = 0.7) of EEG sharps with clinical lateralization. Focal EEG slowing had moderate (K = 0.5) agreement with imaging lateralization. Focal sharps/spikes had substantial (K = 0.7) agreement with imaging lateralization. The positive predictive value (PPV) of seizure semiology for lateralization and localization was 100% and 68%, respectively. PVV of focal sharps for lateralization and localization was 84% and 70%, respectively. PPV of focal slowing for lateralization and localization was 77% and 65%, respectively. Conclusion: Seizure semiology in single-lesion neurocysticercosis correlates very well with lateralization but not so well with localization of lesion on neuroimaging. Focal EEG abnormalities are seen in nearly one-third of children with single-lesion neurocysticercosis. EEG often predicts the side of the lesion but has poor localizing value.
Encoding Manipulation of DNA‐Nanoparticle Assembled Nanorobot Using Independently Charged Array Nanopores

During the past decades, scientists have developed different kinds of nanorobots based on various driving principles to realize controlled manipulation of them for potential applications like medical diagnosis and directed cargo delivery. In order to design a nanorobot with advantages of simple operation and precise control that can enrich the family of intelligent nanorobots, an encoding manipulation method is proposed to control the movement of a DNA‐nanoparticle assembled nanorobot by combing electrophoresis and electroosmosis effect in independently charged array nanopores. The nanorobot is composed of one nanoparticle and one or two ssDNAs. ssDNAs act as the legs of the nanorobot. The selective ion transport through charged nanopores can induce cooperation and competition between the electroosmosis and electrophoresis, which is the main power to activate the nanorobot. Thus by simply switching the applied electric field and surface charge density of each nanopore which is defined as the encoded nanopore according to a predetermined strategy, the well‐controlled encoding manipulation including capturing, releasing, jumping, and crawling of the nanorobot is realized in this work. The study is expected to realize its value in many interesting applications like drug delivery, nanosurgery, and so on in the near future.