Miracle-dz/UniFAR-FTUs huggingface dataset:
Long-chain fatty acids alter transcription of Helicobacter pylori virulence and regulatory genes

Infection with Helicobacter pylori is one of the most important risk factors for developing gastric cancer (GC). The type IV secretion system (T4SS) encoded in the cag pathogenicity island is the main virulence factor of H. pylori associated with GC. Additionally, other virulence factors have been shown to play a role in the H. pylori virulence, such as vacuolizing cytotoxin (VacA), urease, flagella, and adhesins. Long-chain fatty acids (LCFAs) are signaling molecules that affect the transcription of virulence genes in several pathogenic bacteria such as Salmonella enterica, Vibrio cholerae, Pseudomonas aeruginosa and Mycobacterium tuberculosis. However, the effect of LCFAs on the transcription of H. pylori virulence and regulatory genes remains unknown. Here we analyzed whether the transcription of virulence genes that encode T4SS and cellular envelope components, flagellins, adhesins, toxins, urease, as well as the transcription of different regulatory genes of the H. pylori strain 26695, are altered by the presence of five distinct LCFAs: palmitic, stearic, oleic, linoleic, and linolenic acids. Palmitic and oleic acids up-regulated the transcription of most of the virulence genes tested, including cagL, cagM, flaB, sabA, mraY and vacA, as well as that of the genes encoding the transcriptional regulators NikR, Fur, CheY, ArsR, FlgR, HspR, HsrA, Hup, and CrdR. In contrast, the other LCFAs differentially affected the transcription of the virulence and regulatory genes assessed. Our data show that LCFAs can act as signaling molecules that control the transcription of the H. pylori virulome.
Leveraging Transfer Learning to Identify Food Categories

In today's scenario, recognition of pictured food dishes automatically has significant importance. During the COVID-19 pandemic, there was a decline in people visiting restaurants for their dietary requirements. So many restaurants started offering their services online. This situation caused a demand for better categorization of food into various categories on a large scale by companies that facilitated these services. It is challenging to congregate a large dataset of food categories, so it is complex to build a generalized architecture. To solve this issue, In this paper, domain-specific transfer learning is used to build the model using some standard architectures like VGGNET, RESNET, and EFFICIENTNET family, which are trained on popular benchmark datasets such as IMAGENET, COCO, etc. The similarity between the source and target datasets is calculated to find the best source dataset, and the one with the highest similarity is chosen for transfer learning. The solution proposed in this paper outperforms some of the existing works on categorizing food items.
The Path to Contentless Experience in Meditation: An Evidence Synthesis Based on Expert Texts

In contentless experience (sometimes termed pure consciousness) there is an absence of mental content such as thoughts, perceptions, and mental images. The path to contentless experience in meditation can be taken to comprise the meditation technique, and the experiences (“interim-states”) on the way to the contentless “goal-state/s”. Shamatha, Transcendental, and Stillness Meditation are each said to access contentless experience, but the path to that experience in each practice is not yet well understood from a scientific perspective. We have employed evidence synthesis to select and review 135 expert texts from those traditions. In this paper we describe the techniques and interim-states based on the expert texts and compare them across the practices on key dimensions. Superficially, Shamatha and Transcendental Meditation appear very different to Stillness Meditation in that they require bringing awareness to a meditation object. The more detailed and systematic approach taken in this paper indicates that posturally Shamatha is closer to Stillness Meditation, and that on several other dimensions Shamatha is quite different to both other practices. In particular, Shamatha involves greater measures to cultivate attentional stability and vividness on an object, greater focusing, less tolerance of mind-wandering, more monitoring, and more deliberate doing/control. Achieving contentless experience in Shamatha is much slower, more difficult, and less frequent. The findings have important implications for consciousness, neuroscientific, and clinical research and practice.
Load Balancing Strategies for Slice-Based Parallel Versions of JEM Video Encoder

The proportion of video traffic on the internet is expected to reach 82% by 2022, mainly due to the increasing number of consumers and the emergence of new video formats with more demanding features (depth, resolution, multiview, 360, etc.). Efforts are therefore being made to constantly improve video compression standards to minimize the necessary bandwidth while retaining high video quality levels. In this context, the Joint Collaborative Team on Video Coding has been analyzing new video coding technologies to improve the compression efficiency with respect to the HEVC video coding standard. A software package known as the Joint Exploration Test Model has been proposed to implement and evaluate new video coding tools. In this work, we present parallel versions of the JEM encoder that are particularly suited for shared memory platforms, and can significantly reduce its huge computational complexity. The proposed parallel algorithms are shown to achieve high levels of parallel efficiency. In particular, in the All Intra coding mode, the best of our proposed parallel versions achieves an average efficiency value of 93.4%. They also had high levels of scalability, as shown by the inclusion of an automatic load balancing mechanism.
Micromolding fabrication of biocompatible dry micro-pyramid array electrodes for wearable biopotential monitoring

Thin dry electrodes are promising components in wearable healthcare devices. Assessing the condition of the human body by monitoring biopotentials facilitates the early diagnosis of diseases as well as their prevention, treatment, and therapy. Existing clinical-use electrodes have limited wearable-device usage because they use gels, require many preparation steps, and can be uncomfortable to wear. Dry electrodes can improve these issues and have demonstrated performance on par with gel-based electrodes, providing advantages in mobile and wearable applications. However, the materials and fabrication methods used are not yet at the level of disposable gel electrodes for low-cost mass manufacturing and wide adoption. Here, a low-cost manufacturing process for thin dry electrodes with a conductive micro-pyramidal array (MPA) is presented for large-scale on-skin wearable applications. The electrode is fabricated using micromolding techniques in conjunction with solution processes in order to guarantee ease of fabrication, high device yield, and the possibility of mass production compatible with current semiconductor production processes. Fabricated using a conductive paste and an epoxy resin that are both biocompatible, the developed MPA electrode operates in a conformal, non-invasive manner, with low skin irritation, which ensures improved comfort for brief or extended use. The operation of the developed electrode was examined by analyzing electrode-skin-electrode impedance, electroencephalography, electrocardiography, and electromyography signals and comparing them with those measured simultaneously using gel electrodes.
Understanding Help-Seeking Avoidance among EFL Students and the Social Climate of EFL Classrooms in Thailand

The important roles of help-seeking avoidance and the social climate of the classroom have been confirmed by research in the past two decades, yet little is known about how these two variables interact with each other. EFL students and classrooms at the university level in Asian countries have also been neglected by preceding research despite their large number and strong presence. On this premise, an investigation was conducted on 427 EFL students (76.6% females, 23.4% males) at a university in Thailand. It explored the patterns of help-seeking avoidance among EFL students and the social climate of EFL classrooms. The results of the Exploratory Factor Analysis (EFA) indicated the dimensionality of help-seeking avoidance and the six underlying factors of the social climate of EFL classrooms, with the existence of gender differences. Nonetheless, a direct connection between EFL students’ help-seeking avoidance and the social climate of their EFL classrooms was not identified. It was in the two-model hierarchical regression that the classroom social climate emerged as a significant predictor.
Kriging-Weighted Laplacian Kernels

Laplacian kernels, which are widely used as sharpening filters in image processing, are isotropic and tend to over-highlight fine details with a sharp discontinuity in images. To address this issue, this paper introduces a method that integrates anisotropic averaging with the Laplacian kernels. The proposed method can also be useful as a new type of image convolution for designing convolutional neural networks.
Developing ICT Competencies: New Skill Sets for Excellent Customer Service in Academic Libraries

This study seeks to examine the perception of academic librarians on the acquisition of ICT skills and customer service competencies in order to meet the diverse and increasingly complex information needs of library users in the digital environment. The study adopts the qualitative approach to research by using content analysis of job advertisements and semi-structured interviews with purposively selected academic librarians. Fifty (50) job advertisements published in newspapers and online portals from 2010-2019 were collected and studied. Ten (10) academic librarians were selected from five (5) academic libraries in Ghana to identify existing skill sets and customer service competencies within academic libraries. The findings of the study showed that ICT skills and competencies are an integral requirement for job placement within academic libraries. However, there is more to be done on the use of ICT skills to deliver excellent customer service online. The findings of the study would be useful for librarians, managers of tertiary institutions and policy makers who seek to address the issue of staff competency, skill sets and training for improved service delivery within academic libraries.
Maximization of Damage from a Non-Detected Cyber-Attack to a Control System with an Invariant-Set-Based Protection

The paper elaborates a cyber-attack on a control system that is realized as a distortion of its feedback signal. The control system has an implemented detection of this type of cyber-attack by means of a minimum robust positively invariant set computed for the closed-loop control system for the case of bounded measurement noise. The work explores how to maximize the damage to the control system from the side of a well-informed attacker that tries to remain non-discovered by the implemented detection system. The information obtained through this analysis is crucial to assess the effectiveness of the analyzed detection system in suppressing potential damages of the considered cyber-attack type. It gives an insight into how large the damage can be in the worst case with the implemented protection scheme. A demonstration is performed on a simple double-integrator process and an important conclusion is that even the fully-informed attacker cannot perform significant damage while remaining below the radar of the invariant-set-based cyber-threat detection.
Current Incidence and Risk Factors of Fecal Incontinence After Acute Stroke Affecting Functionally Independent People

Background: Previously published retrospective series show a high prevalence of fecal incontinence (FI) in stroke patients. We aimed to analyze in a prospective series the current incidence of FI in acute stroke in functionally independent patients and its evolution over time and the patient characteristics associated with the appearance of FI in acute stroke. Methods: We included consecutive patients with acute stroke admitted in our stroke unit who fulfilled the following inclusion criteria: a first episode of stroke, aged >18 years, with no previous functional dependency [modified Rankin Scale (mRS) ≤ 2] and without previous known FI. FI was assessed by a multidisciplinary trained team using dedicated questionnaires at 72 ± 24 h (acute phase) and at 90 ± 15 days (chronic phase). Demographic, medical history, clinical and stroke features, mortality, and mRS at 7 days were collected. Results: Three hundred fifty-nine (48.3%) of 749 patients (mean age 65.9 ± 10, 64% male, 84.1% ischemic) fulfilled the inclusion criteria and were prospectively included during a 20-month period. FI was identified in 23 patients (6.4%) at 72 ± 24 h and in 7 (1.9%) at 90 days ± 15 days after stroke onset. FI was more frequent in hemorrhagic strokes (18 vs. 5%, p 0.007) and in more severe strokes [median National Institute of Health Stroke Scale (NIHSS) 18 (14–22) vs. 5 (3–13), p < 0.0001]. No differences were found regarding age, sex, vascular risk factors, or other comorbidities, or affected hemisphere. Patients with NIHSS ≥12 (AUC 0.81, 95% CI 0.71 to 0.89) had a 17-fold increase for the risk of FI (OR 16.9, IC 95% 4.7–60.1) adjusted for covariates. Conclusions: At present, the incidence of FI in acute stroke patients without previous functional dependency is lower than expected, with an association of a more severe and hemorrhagic stroke. Due to its impact on the quality of life, it is necessary to deepen the knowledge of the underlying mechanisms to address therapeutic strategies.
Biological Insights Knowledge Graph: an integrated knowledge graph to support drug development

The use of knowledge graphs as a data source for machine learning methods to solve complex problems in life sciences has rapidly become popular in recent years. Our Biological Insights Knowledge Graph (BIKG) combines relevant data for drug development from public as well as internal data sources to provide insights for a range of tasks: from identifying new targets to repurposing existing drugs. Besides the common requirements to organisational knowledge graphs such as being able to capture the domain precisely and give the users the ability to search and query the data, the focus on handling multiple use cases and supporting use case-specific machine learning models presents additional challenges: the data models must also be streamlined for the performance of downstream tasks; graph content must be easily customisable for different use cases; different projections of the graph content are required to support a wider range of different consumption modes. In this paper we describe our main design choices in implementation of the BIKG graph and discuss different aspects of its life cycle: from graph construction to exploitation.
Design and Development of Portable Supervisory Unit and Programmable Automation Controller (PUSPAC)

This paper presents the design and development of an innovative industrial automation device named as “Portable Supervisory Unit and Programmable Automation Control (PUSP AC)” which works as a RTU (Remote Terminal Unit) and also as a PAC (Programmable Automation Controller). Typically, popular industrial automation systems like SCADA are implemented in larger industries over a robust network of various control, network, and peripheral devices. In some setups a compact standalone PLC like system ‘PAC’ is also used which includes the control, communication, and interface elements in a single device. The PUSP AC device gives the flexibility to use it with a remote MTU/computer or with implementation of local control logic through high-level programming languages. Though these automation devices are functionally similar across vendors, most of the commercial ones do not talk much about their hardware as well as software implementation. The PUSP AC is a modular platform for the students and researchers to learn and develop various industrial automation applications and protocols. The resources required for a typical automation setup is available in a single portable device along with the required software support.
A fiber laser temperature-sensing system with customizable sensitivity based on beat frequency demodulation method

In this paper, a customizable, sensitive fiber laser temperature-sensing scheme based on beat frequency demodulation method is proposed. The scheme adopts a ring fiber laser cavity structure and monitors temperature variations by tracking changes in the beat frequency signal (BFS). An erbium-doped fiber amplifier is used to provide gain for the optical fiber laser sensing system, and an ordinary single-mode fiber is used as the sensing head. Sensing fibers of different lengths were heated, and the sensitivities were estimated at -0.177, -0.538, and -1.116 kHz/°C for lengths of 1, 4, and 8 m, respectively. Meanwhile, by measuring the monitored frequency shifts, different sensitivities were obtained, estimated at -0.42 and -1.12 kHz/°C for monitored frequencies of 0.5 and 1.168 GHz, respectively. The BFS bandwidth reaches to 8.0 GHz, the signal-to-noise ratio is approximately 65 dB, and the -3dB linewidth is less than 2.5 kHz.
Optimal feedforward torque control for nonlinear induction machines considering stator and rotor copper losses and current and voltage limits

In order to analytically solve the optimal feedforward torque control (OFTC) problem of induction machines (IMs), the unified theory for synchronous machine introduced in [1] is extended by considering relevant IM nonlinearities and incorporating stator and rotor copper losses. Instead of the well known Maximum Torque per (stator) Current (MTPC) operation strategy, Maximum Torque per (copper) Losses (MTPLCu) is realized and extended by the Maximum (rotor) Current (MCr, ext) strategy due to stator and rotor current limitations. Modeling magnetic saturation and cross-coupling effects leads to a constrained nonlinear optimization problem which is solved based on the idea of sequential quadratic programming (SQP). The second order Taylor approximations are formulated in implicit form as quadrics. Applying the Lagrangian formalism to the quadratic problem leads to analytical solution for the optimal rotor currents. For a doubly-fed induction machine (DFIM), a decision tree for optimal operation management is presented and the OFTC is validated in simulations for a real nonlinear IM.
Modeling and development of new materials for fuel cells solid electrolyte

The Solid Oxide Fuel Cell (SOFC) defined by its ceramic and oxide electrolyte, is an electrochemical energy conversion device that produces electricity directly from the chemical reaction of fuel. Nowadays, apatite type rare earths silicates and germaniums attract many interests as the solid electrolyte due to the superior transport properties with high ionic conductivity and low activation energy. They can operate stably at intermediate temperature over a wide oxygen partial pressure range and maintain excellent performances, being considered as a candidate for IT-SOFC electrolytes. Among this series of conductors, the La-Si-O type has a higher conductivity and the performance would be modified by different doping elements.The objective of this thesis is to study the effects of element substitution/doping and synthesis methods on the structural and conductivity properties of apatite type lanthanum silicates. In this study, we use a double approach: a simulation approach and an experimental approach to optimize the electrolyte materials purity and performance.Using simulation approach, a first principle calculation based on DFT (Density Functional Theory) was carried out to investigate the effect on doping positions: Sr dopant at La position and Ge dopant at Si position. The calculation results give a connection to the ionic conductivity obtained by experiments.With experimental approach, we present the synthesis and characterization of Sr-doped La10Si6O27 (LSO) prepared through an optimized water-based sol-gel process. The results show that the ionic conductivity is thermally activated and values lies between 4.5×10-2 and 1×10-6 Scm-1 at 873 K as a function of the composition and powder preparation conditions.
Milankovic Pseudo-cycles Recorded in Sediments and Ice Cores Extracted by Singular Spectrum Analysis

Abstract. Milankovic cycles describe the changes in the Earth's orbit and rotation axis and their impact on its climate over thousands of years. Singular Spectrum Analysis (SSA) is a signal processing method that is best known for its ability to find and extract pseudo-cycles in complex signals. In this short paper, we propose to apply it to three time series that have been proposed as geological reference time scales, in order to retrieve, compare and identify their Milankovic periodicities: (1) LR04, a stack of Plio-Pleistocene benthic microfossil records (Lisiecki and Raymo, 2005), (2) the CO2 and CH4 records from the Vostok ice core (Petit et al, 1999) and (3) the long-term orbital solution La04 for the insolation of Laskar et al (2004). The Vostok CO2 and CH4 series share the first 7 SSA components, three main ones (98, 104, 39 kyr), and four smaller ones (18, 22, 65, 180 kyr). CO2 displays a component at 28 kyr and a doublet at 61 and 62 kyr. CH4 displays a doublet near 50 kyr. 18/22 ky is a precession doublet, 62 kyr an insolation component, and 95/105 kyr an insolation/eccentricity doublet. The 49/50 kyr doublet in CH4 is not found in the orbital model. The SSA results for the La04 orbital solution are in excellent agreement with the values obtained by Laskar et al (2004). Four SSA components of obliquity are almost identical (rounded figures are 41, 54, 29 and 39 kyr). As far as eccentricity is concerned, the first five components are 404, 95, 124, 99, and 132 kyr. The next components are not found in our list of components for eccentricity, but they are in the SSA of insolation, at 2338, 970, 488 and 684 kyr. With more than 20 components, the LR04 stack is the richest series. In order of decreasing amplitude, one encounters 41, 95 and 75 kyr components. Next are smaller 39.5 and 53.6 kyr components, and a 22.4 kyr component. One recognizes one of the two main precession components, the doublet of obliquity components, a line at 47.4 kyr that is not found in any of the other spectra, and a doublet at 53.6 and 55.7 kyr, corresponding to the line at 54 kyr found in all four orbital quantities. Next comes a line at 63.6 kyr that may correspond to a line in insolation, CH4 and CO2. Then come components from eccentricity variations at 75.2, 94.5, 107.2, 132.1, 198.6 and 400.9 kyr. The remaining components of LR04 show up in La04. The “elusive ~200 kyr eccentricity cycle” of Hilgen et al (2020) is actually present in all three series, in the La04 orbital model as a 195 ± 6 kyr component of eccentricity and in LR04 as a 198.6 ± 5.6 kyr component. Finding not only the main expected Milankovic periodicities but also many “secondary” components with much smaller amplitudes gives confidence in our iterative SSA method (iSSA), on the quality of the La04 model and on the remarkable LR04 sedimentary stack, with more than 15 “ Milankovic periods”.