Miracle-dz/UniFAR-FTUs huggingface dataset:
OmniReprodubileCellAnalysis: a comprehensive toolbox for the analysis of cellular biology data

Open science and reproducibility are two key pillars of modern scientific research. Open science is making scientific research and data accessible and transparent to the broader scientific community and the public. Reproducibility, on the other hand, is the ability to replicate and confirm research results by following the same methods and procedures. Reproducibility is thus crucial because it ensures the reliability and validity of scientific findings. The relationship between open science and reproducibility is intertwined; indeed open science practices, such as sharing raw data, detailed methodologies, and code, greatly facilitate the reproducibility of research. In recent years, concerns about the reproducibility of scientific research have gained prominence, and indeed scientists still lament the lack of details in the methods sections of published papers and the unavailability of raw data from the authors. To assist cellular biologists and immunologists and to promote a more transparent, open and reproducible research practice, we developed OmniReproducibleCellAnalysis (ORCA), a new Shiny Application based in R, for the semi-automated analysis of Western Blot (WB), Reverse Transcription-quantitative PCR (RT-qPCR), Enzyme-Linked ImmunoSorbent Assay (ELISA), Endocytosis and Cytotoxicity experiments. ORCA is open-source and approachable by scientists without advanced R language knowledge. Our application automatically compiles a report containing the finalized data analysis and all its preliminary and intermediate steps, ensuring data analysis standardization and reproducibility. Furthermore, ORCA allows to upload raw data and results directly on the data repository Harvard Dataverse, a valuable tool for promoting transparency and data accessibility in scientific research. By employing ORCA, scientists will cut down analysis time and human-dependent errors, while taking a step towards a research practice compliant with Open Science and FAIR principle.
Dissecting the properties of circulating IgG against Group A Streptococcus through a combined systems antigenomics-serology workflow

Most individuals maintain circulating antibodies against various pathogenic bacteria as a consequence of previous exposures. However, it remains unclear to what extent these antibodies contribute to host protection. This knowledge gap is linked to the need for better methods to characterize antimicrobial polyclonal antibodies, including their antigen and epitope repertoires, subclass distribution, glycosylation status, and effector functions. Here, we showcase a generic mass spectrometry-based strategy that couples systems antigenomics and systems serology to characterize human antibodies directly in clinical samples. The method is based on automated affinity purification workflows coupled to an integrated suite of high-resolution MS-based quantitative, structural- and glyco-proteomics readouts. We focused on Streptococcus pyogenes (Group A Streptococcus; GAS), a major human pathogen still awaiting an approved vaccine. Our methodology reveals that both healthy and GAS infected individuals have circulating Immunoglobulin G (IgG) against a subset of genomically conserved streptococcal proteins, including numerous toxins and virulence factors. The antigen repertoire targeted by these antibodies was relatively constant across healthy individuals, but considerably changed in GAS bacteremia. Detailed analysis of the antigen-specific IgG indicates inter-individual variation regarding titers, subclass distributions, and Fc-signaling capacity, but not in epitope and Fc-glycosylation patterns. Importantly, we show that the IgG subclass has a major impact on the ability of GAS-antibodies to trigger immune signaling, in an antigen- and Fc receptor-specific fashion. Overall, these results uncover exceeding complexity in the properties of GAS-specific IgG, and showcase our methodology as high-throughput and flexible workflow to understand adaptive immune responses to bacterial pathogens. Significance statement Most people develop polyclonal antibodies against bacterial pathogens during infections but their structural and functional properties are poorly understood. Here, we showcase a combined systems antigenomics and systems serology strategy to quantify key antibody properties directly in clinical samples. We applied this method to characterize polyclonal antibody responses against Streptococcus pyogenes, a major human pathogen. We mapped the antigen and epitope landscape of anti-streptococcal antibodies circulating in healthy adult plasma, and their changes during blood infections. We further demonstrate the analytical power of our approach to resolve individual variations in the structure and effector functions of antigen-specific antibodies, including a dependency between immunoglobulin subclass and Fc-signaling capacity.
NASTRA: Innovative Short Tandem Repeat Analysis through Cluster-Based Structure-Aware Algorithm in Nanopore Sequencing Data

Short-tandem repeats (STRs) are type of genetic markers distinguishing individuals and authenticating cell-lines. Nanopore sequencing is promising in STR typing for its convenience, but lack of analysis method. Here we proposed NASTRA, a tool for accurate STR genotyping with nanopore sequencing, which uses an STR-structure-aware algorithm to infer repeat numbers of STR motifs. In our real-time scenario tesing, NASTRA has 100% accuracies for diploid STRs, far exceeding method employing strategy that include all candidate STR allele sequences for alignments. NASTRA could be useful in applications as individual identification and cell-line authentication with nanopore sequencing. NASTRA is available via https://github.com/renzilin/NASTRA.
Empirical Evaluation of Dissimilarity Measures for Color and Texture

This paper empirically compares nine families of image dissimilarity measures that are based on distributions of color and texture features summarizing over 1000 CPU hours of computational experiments. Ground truth is collected via a novel random sampling scheme for color, and by an image partitioning method for texture. Quantitative performance evaluations are given for classification, image retrieval, and segmentation tasks, and for a wide variety of dissimilarity measure parameters. It is demonstrated how the selection of a measure, based on large scale evaluation, substantially improves the quality of classification, retrieval, and unsupervised segmentation of color and texture images. c © 2001 Elsevier Science (USA)
Geographical Reasoning and Biases: The View from Taiwan

The present paper sought to offer Asian perspectives on constructed geographical representations and possible biases derived from those using the Friedman and Brown paradigm (Friedman & Brown, 2000a, 2000b). Two studies assessed individuals' latitude and longitude estimates, as well as examining the effect of seed cities on these estimates. The results indicated that level of knowledge and physical distance might play roles in geographical biases. Level of knowledge completely mediated the effect of physical distance on geographical biases for latitude estimates, but only partially mediated this effect for longitude estimates. This evidence supported the physical proximity hypothesis for longitude but not latitude, indicating that the reasoning bases of geographical representations for latitude and longitude may be different. Moreover, the effect of seed cities has improved participants' second estimates. The possible seeding mechanism and the reasoning bases for latitude and longitude will also be discussed.
Chemical Mechanical Polishing Mechanism of Silicon Nitride Surface: Effect of Tribochemical Oxidation

In this presentation, we reported the chemical mechanical polishing (CMP) mechanisms of silicon nitride surface by ceria abrasive grains. We performed two simulations using first-principles molecular dynamics (FPMD) simulations which are high accuracy methods. First, surface conditions of silicon nitride under friction in CMP slurry were investigated. From the simulation results, surface oxidation by adsorption of a water molecule onto the silicon nitride surface was observed, and then a Si-N bond was broken with generating an ammonia molecule. It means that there are several kinds of silicon nitride surface from a new surface to a oxidized surface during the CMP process. Thus we performed the second simulations to study the effect of surface oxidation of silicon nitride on polishing behavior. Results clearly indicated that CMP was accelerated on a oxidized surface. It suggested that surface oxidation was the key reaction for controlling polishing rates of silicon nitride.
Human Gene-Centric Databases at the Weizmann Institute of Science : GeneCards , UDB , CroW 21 and HORDE

Recent enhancements and current research in the GeneCards (GC) (http://bioinfo.weizmann.ac.il/cards/) project are described, including the addition of gene expression profiles and integrated gene locations. Also highlighted are the contributions of specialized associated human gene-centric databases developed at the Weizmann Institute. These include the Unified Database (UDB) (http://bioinfo.weizmann.ac.il/udb) for human genome mapping, the human Chromosome 21 database at the Weizmann Insti-tute (CroW 21) (http:// bioinfo.weizmann.ac.il/crow21), and the Human Olfactory Receptor Data Explora-torium (HORDE) (http://bioinfo.weizmann.ac.il/HORDE). The synergistic relationships amongst these efforts have positively impacted the quality, quantity and usefulness of the GeneCards gene compendium.
Intrinsic ﬂexoelectricity of van der Waals epitaxial thin ﬁlms

The direct measurement of ﬂexoelectric coefﬁcients in epitaxial thin ﬁlms is an unresolved problem, due to the clamping effect of substrates which induces a net strain (and hence parasitic piezoelectricity) in addition to strain gradients and ﬂexoelectricity. Herein, we propose and demonstrate the use of van der Waals epitaxy as a successful strategy for measuring the intrinsic (clamping-free = ﬂexoelectric coefﬁcients of epitaxial thin ﬁlms. We have made, measured, and compared BaTiO 3 and SrTiO 3 thin ﬁlm capacitor heterostructures grown both by conventional oxide-on-oxide epitaxy and by van der Waals oxide-on-mica epitaxy, and found that, whereas the former is dominated by parasitic piezoelectricity, the response of the latter is truly ﬂexoelectric. The results are backed by theoretical calculations of the ﬁlm-substrate mechanical interaction, as well as by direct measurements that conﬁrm the strain-free state of the ﬁlms. van der Waals epitaxy thus emerges as powerful new tool in the study of ﬂexoelectricity and, in particular, they ﬁnally allow exploring ﬂexoelectric phenomena at the nanoscale (where strain gradients are highest) with direct experimental knowledge of the actual ﬂexoelectric coefﬁcients of thin ﬁlms.
Etiquette protocol for Ultra Low Power Operation in Sensor Networks

In this paper, we propose a novel Etiquette protocol for enabling extremely energy-eﬃcient communication among nodes in a multi-hop sensor network. Our key idea for energy eﬃciency is to allow dynamic, ﬂexible scheduling of inter-node communication, thereby minimizing energy wasted due to idle-listening. Scheduling communication is commonly used in single-hop networks for signiﬁcant energy savings (e
ADVANCES IN BUSINESS AND MANAGEMENT FORECASTING

The problem of missing children draws much attention of both governmental and nongovernmental organizations in China due to huge numbers of the missing children. According to the records of Baby Back Home network (BBHNet), a professional website to search missing children in China, 1,666 missing children have been found via releasing information on BBHNet; how-ever, there are still 30,561 families searching for their children and 24,603 missing children are searching for biological parents through this website and have not succeeded yet. What is the difference between successful and unsuccessful cases in the aspect of released information? Motivated by this ques-tion, our research proposes to determine the crucial information in the process of searching missing children. A logistic regression model was developed on the data summarized from 500 succeed cases and 500 cases which have not succeed yet from BBHNet for forecasting success rate of searching missing children. The model identiﬁes that the differences in terms of released information, number of children, address, and natural geographical features are the three most crucial factors that cause differences in the result of searching. This research can be used as a guide for improving the success rate of searching missing children and provide reference for developing a missing children information-sharing platform.
set of objects: a graph based least-square approach

—We consider the problem of ranking N objects starting from a set of noisy pairwise comparisons provided by a crowd of equal workers. We assume that objects are endowed with intrinsic qualities and that the probability with which an object is preferred to another depends only on the difference between the qualities of the two competitors. We propose a class of non-adaptive ranking algorithms that rely on a least-squares optimization criterion for the estimation of qualities. Such algorithms are shown to be asymptotically optimal (i.e., they require O ( N(cid:15) 2 log Nδ ) comparisons to be ( (cid:15),δ ) -PAC). Numerical results show that our schemes are very efﬁcient also in many non-asymptotic scenarios exhibiting a performance similar to the maximum-likelihood algorithm. Moreover, we show how they can be extended to adaptive schemes and test them on real-world datasets.
The use of deep counterfort drains as an effective method of stabilizing cuttings constructed in overconsolidated clays

Abstract Slope failures in cuttings constructed in heavily overconsolidated clays often occur after a period of 20 to 30 years due to the gradual dissipation of negative pore pressures and the effects of water ingress into the slopes. These slope failures are often stabilized with the installation of deep counterfort drains, which reduce the pore water pressures on the potential critical slip planes and act as a reinforcing element in the slope. Counterfort drains are normally designed using empirical methods. However there is little published data on drain performance. This paper summarizes the findings of a research project undertaken by Mouchel on behalf of the Highways Agency to assess the performance of counterfort drains installed in two highway cutting slopes that have been monitored over a number of years. The study has shown that measured pore water pressures can exceed the theoretical pressures, due mainly to what is believed to be the poor performance of the counterfort drains and that the apparent improved slope stability may be primarily due to the reinforcing effect of the drains within the slope. Further studies are required to determine the effects of construction techniques and materials used on the performance of counterfort drains before the efficiency of the existing empirical design methods can be fully assessed.
Pseudopolar-based estimation of large translations, rotations, and scalings in images

One of the major challenges related to image registration is the estimation of large motions without prior knowledge. This work presents a Fourier-based approach that estimates large translations, scalings, and rotations. The algorithm uses the pseudopolar (PP) Fourier transform to achieve substantial improved approximations of the polar and log-polar Fourier transforms of an image. Thus, rotations and scalings are reduced to translations which are estimated using phase correlation. By utilizing the PP grid, we increase the performance (accuracy, speed, and robustness) of the registration algorithms. Scales up to 4 and arbitrary rotation angles can be robustly recovered, compared to a maximum scaling of 2 recovered by state-of-the-art algorithms. The algorithm only utilizes one-dimensional fast Fourier transform computations whose overall complexity is significantly lower than prior works. Experimental results demonstrate the applicability of the proposed algorithms.
Estimation of All-Terminal Network Reliability Using an Artificial Neural Network

The exact calculation of all-terminal network reliability is an NP-hard problem, with computational effort growing exponentially with the number of nodes and links in the network. During optimal network design, a huge number of candidate topologies are typically examined with each requiring a network reliability calculation. Because of the impracticality of calculating all-terminal network reliability for networks of moderate to large size, Monte Carlo simulation methods to estimate network reliability and upper and lower bounds to bound reliability have been used as alternatives. This paper puts forth another alternative to the estimation of all-terminal network reliability – that of artificial neural network (ANN) predictive models. Neural networks are constructed, trained and validated using the network topologies, the link reliabilities, and a network reliability upperbound as inputs and the exact network reliability as the target. A hierarchical approach is used: a general neural network screens all network topologies for reliability followed by a specialized neural network for highly reliable network designs. Both networks with identical link reliability and networks with varying link reliability are studied. Results, using a grouped cross validation approach, show that the ANN approach yields more precise estimates than the upperbound, especially in the worst cases.
Exploring the Path of Compiling TBCL Chinese Digital Teaching Materials with Generative AI—Taking ChatGPT for Example

This study aims to integrate the Generative Artificial Intelligence (GenAI) platform—ChatGPT with the Taiwan Benchmarks for the Chinese Language (TBCL)[14] for digital teaching materials (DTM) composition, proposing a digital teaching material composition model, showcasing the role of GenAI plays in DTM features. At the same, it shows the necessary measures to reduce the effect caused by the hallucination phenomenon[5] on the materials. The research production will be presented by web-based DTM which demonstrates the potential of GenAI in enhancing Chinese DTM composition. By adopting the IDEE framework[9] as foundational principles for designing web-based DTM with ChatGPT and using prompt engineering[11] as the research method, the study explores the strategies for avoiding the effect caused by the hallucination phenomenon in DTM composition with GenAI. It also delves into the potential features that GenAI can play in a web-based DTM. The procedure is as follows: (1) The instructional design is designed based on the Reference Guidelines for TBCL Application(RGTA) [15] and transcript as a unit outline. (2) input the unit outline into ChatGPT through prompt engineering, and generate DTM content based on the unit outline. (3) Using the Teaching Materials Editing Assistance System(TMEAS), the text is examined to ensure the content aligns with the TBCL proficiency level. Beyond assisting in material composition, GenAI can enhance features in web-based DTM as well : (1) utilize the “chat” from ChatGPT for “situational dialogue” and “essay review” by using prompt engineering, and (2) integrating “chat” by using webpage builder's Hyper Text Markup Language (HTML), allowing learners to use “continue this chat” feature to replicates the “chat” to their accounts for self-practice. The study presents a web-based DTM, combining the GenAI platform with the RGTA and TMEAS for material composition and interactive features for web-based DTM. We hope to draw attention to the effect caused by GenAI in Chinese language education. The study provides preliminary insights, looking forward to offering a reference direction for the future development of GenAI-assisted Chinese language teaching and web-based DTM composition
Numerical Simulation of High Mach Number Astrophysical Jets

Computational fluid dynamics simulations using the WENO-LF method are applied to high Mach number nonrelativistic astrophysical jets, including the effects of radiative cooling. Our numerical methods have allowed us to simulate astrophysical jets at much higher Mach numbers than have been attained (Mach 20) in the literature. Mach 80 simulations of the HH 1-2 astrophysical jets and Mach 55 simulations of the XZ Tauri proto-jet are presented.
Multicultural and Multireligious Understanding

During last decades, the managerialism model has predominated to solve structural and managerial problems in public service organizations. The Iranian judiciary has used some components of this model for years to solve the problem of lack of resources and vast number of cases. Since judges are the main actors of managerialism in criminal proceedings and this area, like all social fields, is based on a mental semantic system, so identifying the set of conditions, strategies and consequences of adopting strategies in it requires the application of the qualitative methodological method. Considering these requirements and based on the grounded theory, the present article investigated and analyzed the grounded rules of managerialism in criminal proceedings through interviews with judges of Kerman’s criminal branches. The analysis of data showed that according to all interviewees, the officials of the criminal justice system have set efficiency-based managerialism in order to solve the problem of high volume of cases, while this policy has reduced the accuracy of trials, increased judicial errors, reduced judge resilience, made judges stressful and stayed away from scientific studies. Therefore, it may conclude that judgment has moved away from its original meaning and has undergone a fundamental transformation (metamorphosis).
UvA-DARE (Digital Academic Repository) Temperature-sensitive colloidal phase behavior induced by critical Casimir forces

We report Monte Carlo simulations of phase behavior of colloidal suspensions with near-critical binary solvents using effective pair potentials from experiments. At off-critical solvent composition, the calculated phase diagram agrees well with measurements of the experimental system, indicating that many-body effects are limited. Close to the critical composition, however, agreement between experiment and simulation becomes poorer, signaling the increased importance of many-body effects. Both at and off the critical solvent concentration, the colloidal phase diagram is qualitatively similar to those of molecular systems and obeys the principle of corresponding states with one striking difference: it occurs in a narrow temperature interval of < 1 ◦ C below the solvent phase separation temperature. © 2013 AIP Publishing LLC . [http://dx.doi. org/10.1063/1.4819896]