Miracle-dz/UniFAR-FTUs huggingface dataset:
In Vivo Reduction of Medium‐ to Long‐Chain Fatty Acids by Carboxylic Acid Reductase (CAR) Enzymes: Limitations and Solutions

Fatty aldehyde production by chemical synthesis causes an immense burden to the environment. Within this study, we explored a sustainable, aldehyde‐selective and mild alternative approach by utilizing carboxylic acid reductases (CARs). CARs from Neurospora crassa (NcCAR), Thermothelomyces thermophila (TtCAR), Nocardia iowensis (NiCAR), Mycobacterium marinum (MmCAR) and Trametes versicolor (TvCAR) were overexpressed in E. coli K‐12 MG1655 RARE (DE3) and screened for medium‐ to long‐chain fatty acid (C6–C18) reduction. MmCAR showed the broadest tolerance towards all carbon‐chain lengths and was selected for further investigations of fatty aldehyde synthesis in whole cells. To yield relevant product concentrations, different limitations of CAR whole‐cell conversions were elucidated and compensated. We coupled an in vitro cofactor recycling system to a whole‐cell biocatalyst to support cofactor supply and achieved 12.36 g L−1 of octanal (STY 0.458 g L−1 h−1) with less than 1.5 % of 1‐octanol.
Research on Stock Selection Strategy Based on AdaBoost Algorithm

In this paper, we propose a new direction of stock selection strategy, coining the AdaBoost-Decision Tree (Ada-DT) model, which uses the AdaBoost lifting algorithm and Decision Tree to predict stock movements and select superior stocks. As for financial investment, people are more sensitive to losses than the same amount of gains. Therefore, we add this consideration to the use of AdaBoost algorithm. We use quality indicators, growth indicators, per-share indicators, and sentiment indicators, 24 in total, as the feature space, and try to identify the stocks that may outperform the broader market and have high yield from the Shanghai Stock Exchange (SSE) 50 constituent stocks. The stock selection result of Ada-DT is that the average correct rate of the out-of-sample test set is 72.84%, and the AUC is 0.634. At the same time, we compare the Ada-DT with AdaBoost-Support Vector Machine (Ada-SVM) prediction model and find that Ada-DT provides a higher correct rate and better cumulative returns, indicating that the Ada-DT algorithm is reasonable for complex nonlinear stock markets.
Evaluation of Forensic Data Using Logistic Regression-Based Classification Methods and an R Shiny Implementation

We demonstrate the use of classification methods that are well-suited for forensic toxicology applications. The methods are based on penalized logistic regression, can be employed when separation occurs in a two-class classification setting, and allow for the calculation of likelihood ratios. A case study of this framework is demonstrated on alcohol biomarker data for classifying chronic alcohol drinkers. The approach can be extended to applications in the fields of analytical and forensic chemistry, where it is a common feature to have a large number of biomarkers, and allows for flexibility in model assumptions such as multivariate normality. While some penalized regression methods have been introduced previously in forensic applications, our study is meant to encourage practitioners to use these powerful methods more widely. As such, based upon our proof-of-concept studies, we also introduce an R Shiny online tool with an intuitive interface able to perform several classification methods. We anticipate that this open-source and free-of-charge application will provide a powerful and dynamic tool to infer the LR value in case of classification tasks.
Convergent Associative Motor Cortical Plasticity Induced by Conditional Somatosensory and Motor Reaction Afferents

Objective: Associative motor cortical plasticity can be non-invasively induced by paired median nerve electric stimulation and transcranial magnetic stimulation (TMS) of the primary motor cortex (M1). This study investigates whether a simultaneous motor reaction of the other hand advances the associative plasticity in M1. Methods: Twenty-four right-handed subjects received conventional paired associative stimulation (PAS) and PAS with simultaneous motor reaction (PASmr) with at least a 1-week interval. The PASmr protocol additionally included left abductor pollicis brevis muscle movement responding to a digital sound. The motor reaction time was individually measured. The M1 excitability was examined by the motor evoked potential (MEP), short-interval intracortical inhibition (SICI), and intracortical facilitation (ICF) before and after the PAS protocols. Results: The conventional PAS protocol significantly facilitated MEP and suppressed SICI. A negative correlation between the reaction time and the MEP change, and a positive correlation between the reaction time and the ICF change were found in the PASmr protocol. By subgrouping analysis, we further found significant facilitation of MEP and a reduction of ICF in the subjects with fast reaction times but not in those with slow reaction times. Conclusion: Synchronized motor reaction ipsilateral to the stimulated M1 induces associative M1 motor plasticity through the spike-timing dependent principle. MEP and ICF change could represent this kind of plasticity. The current findings provide a novel insight into designing rehabilitation programs concerning motor function.
Weekend Box Office Forecasting Based on MF-DCCA and Multiple Neural Networks Approach

The forecasting of box office receipts is always a difficult and challenging problem. In this paper, a forecasting approach is proposed to accurately forecasting weekend box office receipts based on multifractal detrend cross-correlation analysis (MF-DCCA) and multiple neural networks (DNN, CNN, LSTM). The MF-DCCA quantitatively finds that there is a long-range cross-correlation between each factor and box office receipts, which is multifractal. Its rolling window can reflect the intrinsic mechanism of neural network, and extract effective data that can improve the generalization ability of the model from the original data. The predictive performance of these frameworks is able to meet or exceed the method based on a single neural network. For (MF-DCCA)-DNN, the classification accuracy is 0.843, (MF-DCCA)-CNN is 0.786, and (MF-DCCA)-LSTM is 0.986. This research provides a theoretical method to further to enrich and improve the accuracy of box office receipts prediction and the extraction of effective feature.
Interclass GPCR heteromerization affects localization and trafficking

Serotonin 5-HT2A receptors heterodimerize with mGluR2 and trigger internalization. GPCR heteromers go intracellular together Whereas some GPCRs (such as the metabotropic glutamate mGluR2 receptor) are largely found on the cell surface, others (such as the serotonin 5-HT2A receptor) are mainly localized in intracellular compartments. Toneatti et al. found that 5-HT2A receptors promoted the internalization of cell surface mGluR2 in unstimulated cells, an effect that required the heteromerization of these two GPCRs. The intracellular localization of mGluR2 was increased by 5-HT2A receptor stimulation but decreased by mGluR2 activation or exposure to clozapine, an inverse antagonist of 5-HT2A receptors. Neurons from mice lacking 5-HT2A receptors showed greater surface localization of mGluR2 compared to those from wild-type mice. Thus, 5-HT2A receptors influence the intracellular localization of mGluR2 in a manner dependent on the activation state of the receptors in the heteromer. Membrane trafficking processes regulate G protein–coupled receptor (GPCR) activity. Although class A GPCRs are capable of activating G proteins in a monomeric form, they can also potentially assemble into functional GPCR heteromers. Here, we showed that the class A serotonin 5-HT2A receptors (5-HT2ARs) affected the localization and trafficking of class C metabotropic glutamate receptor 2 (mGluR2) through a mechanism that required their assembly as heteromers in mammalian cells. In the absence of agonists, 5-HT2AR was primarily localized within intracellular compartments, and coexpression of 5-HT2AR with mGluR2 increased the intracellular distribution of the otherwise plasma membrane–localized mGluR2. Agonists for either 5-HT2AR or mGluR2 differentially affected trafficking through Rab5-positive endosomes in cells expressing each component of the 5-HT2AR–mGluR2 heterocomplex alone, or together. In addition, overnight pharmacological 5-HT2AR blockade with clozapine, but not with M100907, decreased mGluR2 density through a mechanism that involved heteromerization between 5-HT2AR and mGluR2. Using TAT-tagged peptides and chimeric constructs that are unable to form the interclass 5-HT2AR–mGluR2 complex, we demonstrated that heteromerization was necessary for the 5-HT2AR–dependent effects on mGluR2 subcellular distribution. The expression of 5-HT2AR also augmented intracellular localization of mGluR2 in mouse frontal cortex pyramidal neurons. Together, our data suggest that GPCR heteromerization may itself represent a mechanism of receptor trafficking and sorting.
Xylem Anatomical Variability in White Spruce at Treeline Is Largely Driven by Spatial Clustering

The ecological function of boreal forests is challenged by drastically changing climate conditions. Although an increasing number of studies are investigating how climate change is influencing growth and distribution of boreal tree species, there is a lack of studies examining the potential of these species to genetically adapt or phenotypically adjust. Here, we sampled clonally and non-clonally growing white spruce trees (Picea glauca [Moench] Voss) to investigate spatial and genetic effects on tree ring width and on six xylem anatomical traits representing growth, water transport, mechanical support, and wood density. We compared different methods for estimating broad sense heritability (H2) of each trait and we evaluated the effects of spatial grouping and genetic grouping on the xylem anatomical traits with linear models. We found that the three different methods used to estimate H2 were quite robust, showing overall consistent patterns, while our analyses were unsuccessful at fully separating genetic from spatial effects. By evaluating the effect size, we found a significant effect of genetic grouping in latewood density and earlywood hydraulic diameter. However, evaluating model performances showed that spatial grouping was a better predictor than genetic grouping for variance in earlywood density, earlywood hydraulic diameter and growth. For cell wall thickness neither spatial nor genetic grouping was significant. Our findings imply that (1) the variance in the investigated xylem anatomical traits and growth is mainly influenced by spatial clustering (most probably caused by microhabitat conditions), which (2) makes it rather difficult to estimate the heritability of these traits in naturally grown trees in situ. Yet, (3) latewood density and earlywood hydraulic diameter qualified for further analysis on the genetic background of xylem traits and (4) cell wall thickness seems a useful trait to investigate large-scale climatic effects, decoupled from microclimatic, edaphic and genetic influences.
Dimerization regulates the human APC/C-associated ubiquitin-conjugating enzyme UBE2S

The E2 enzyme UBE2S may be stored as a dimer to prevent its degradation between mitotic cycles. Protected from destruction by dimerization The activity of the anaphase-promoting complex/cyclosome (APC/C), an E3 ubiquitin ligase complex, is critical for mitotic progression and exit. The APC/C ubiquitinates substrates in conjunction with the E2 ubiquitin-conjugating enzyme UBE2S. This enzyme can autoubiquitinate itself and promote its own turnover, raising the question of how appropriate amounts of UBE2S are maintained in nonmitotic cells. Liess et al. found that dimerization of UBE2S prevented its autoubiquitination and kept this protein in an inactive state. Cells that expressed wild-type UBE2S maintained UBE2S concentrations high enough to exit from drug-induced mitotic arrest, unlike those expressing the dimerization-defective form of UBE2S. Thus, UBE2S may dimerize to prevent its autoubiquitination and turnover in noncycling cells and ensure its availability for future mitotic cycles. At the heart of protein ubiquitination cascades, ubiquitin-conjugating enzymes (E2s) form reactive ubiquitin-thioester intermediates to enable efficient transfer of ubiquitin to cellular substrates. The precise regulation of E2s is thus crucial for cellular homeostasis, and their deregulation is frequently associated with tumorigenesis. In addition to driving substrate ubiquitination together with ubiquitin ligases (E3s), many E2s can also autoubiquitinate, thereby promoting their own proteasomal turnover. To investigate the mechanisms that balance these disparate activities, we dissected the regulatory dynamics of UBE2S, a human APC/C-associated E2 that ensures the faithful ubiquitination of cell cycle regulators during mitosis. We uncovered a dimeric state of UBE2S that confers autoinhibition by blocking a catalytically critical ubiquitin binding site. Dimerization is stimulated by the lysine-rich carboxyl-terminal extension of UBE2S that is also required for the recruitment of this E2 to the APC/C and is autoubiquitinated as substrate abundance becomes limiting. Consistent with this mechanism, we found that dimerization-deficient UBE2S turned over more rapidly in cells and did not promote mitotic slippage during prolonged drug-induced mitotic arrest. We propose that dimerization attenuates the autoubiquitination-induced turnover of UBE2S when the APC/C is not fully active. More broadly, our data illustrate how the use of mutually exclusive macromolecular interfaces enables modulation of both the activities and the abundance of E2s in cells to facilitate precise ubiquitin signaling.
Design of Distributed Simulation Training System Based on IoT Technology

The distributed missile simulation training system has several parts whose controller is placed far away from each other. The upper control computer needs some communication protocol with the distributed controller and the Internet of Things (IoT) technology can be used in the system. In this research, the communication topology based on RS-485 bus and LoRa WAN is designed. RS-485 bus including interface circuits, Lora interface circuits, transmission protocol, Cyclic Redundancy Check (CRC) method and test software was designed and proposed. And the designed network was tested. The results show that the communication is effective using the RS-485 and LoRa protocol and has a strong stability and a better communication capability of long distance with a complex environment before the missile launching.
Generación de frases literarias: un experimento preliminar

espanolEn este trabajo abordamos la generacion automatica de frases literarias en espanol. Proponemos un modelo de generacion textual basado en algoritmos estadisticos y analisis sintactico superficial. Presentamos resultados preliminares que son bastante alentadores. EnglishIn this paper we address the automatic generation of literary phrases in Spanish. We propose a model for text generation based on statistical algorithms and Shallow Parsing. We present preliminary results that are quite encouraging.
A Seat at the Table

Game-based second language (L2) learning represents an ideal alternative to foreign language classroom instruction. However, despite a diverse player demographic, the design of L2 games is often not informed by players representative of marginalized populations, especially women of color (i.e., Black women). Such oversight in the design process contributes to games that perpetuate gendered and racist stereotypes, and therefore, are less appealing to women of color. In response this dilemma, we utilize Black Feminist Thought (BFT) as a critical framework to engage Black women, a marginalized and understudied population within the gaming subculture, and more broadly, the Computer Supported Cooperative Work (CSCW) community in game design. Twenty-five Black women take on multiple roles as game designers, foreign language instructor, and informants who represent both producers and consumers throughout the conceptualization phase of a L2 mobile game prototype. Applying BFT principles, we leverage Black women\textquotesingle s lived intersectional experiences to transform the traditional game design process into a more inclusive design experience for Black women. In the context of games that support L2 learning, our findings reveal that Black women appreciate games that: 1. provide authentic cultural experiences; 2. feature intersectional game characters that reflect real life experiences; 3. accurately portray the diversity of Black women's bodies; and 4. provide opportunities for players to customize game assets. As a disruptor to traditional game design, BFT makes salient oppressive design practices within the gaming culture that also extend to the larger CSCW community, signifying the need to embrace more inclusive design practices that benefit Black women and other marginalized populations.
Human intestinal models to study interactions between intestine and microbes

Implementations of suitable in vitro cell culture systems of the human intestine have been essential tools in the study of the interaction among organs, commensal microbiota, pathogens and parasites. Due to the great complexity exhibited by the intestinal tissue, researchers have been developing in vitro/ex vivo systems to diminish the gap between conventional cell culture models and the human intestine. These models are able to reproduce different structures and functional aspects of the tissue. In the present review, information is recapitulated on the most used models, such as cell culture, intestinal organoids, scaffold-based three-dimensional models, and organ-on-a-chip and their use in studying the interaction between human intestine and microbes, and their advantages and limitations are also discussed.
Limitations of Neural Networks-based NER for Resume Data Extraction

espanolProporcionamos investigacion sobre las capacidades de los modelos REN basados en redes neuronales, la calidad y sus limitaciones para resolver entidades de diferentes tipos de dificultad (correos electronicos, nombres, habilidades, etc.). Se ha demostrado que la calidad depende del tipo y la complejidad de la entidad, y estima los limites, que la calidad del modelo puede lograr en el caso de una realizacion adecuada y un corpus bien etiquetado. EnglishWe provided research about the abilities of neural network-based NER models, quality, and their limitations in resolving entities of different types of complexity (emails, names, skills, etc.). It has been shown that the quality depends on the entity type and complexity, and estimate \ceilings", which model quality can achieve in the case of proper realization and well-labelled dataset.
Protein engineering to capture and kill cancer cells

The formation of protein assemblies to carry out sophisticated functions is constantly gaining attention in nano-biotechnology. However protein assemblies are often linked through non-covalent interactions, limiting the stability of the complexes and the resilience to forces. Force resistance is crucial for magnetic isolation of circulating tumour cells (CTCs), when a specific protein interaction must withstand the forces pulling a captured cell in the magnetic field. CTCs are present in the blood of cancer patients at very low frequency, making their isolation extremely challenging. However, CTC isolation provides an important approach to enable cancer prognosis and personalised therapy. By optimizing the nanotechnology of the antibody-magnetic bead linkage, the membrane fluidity of the cancer cells, and the affinity of the antibody binding we developed a new approach to minimize the level of tumour markers required to immunomagnetically capture cancer cells. To improve the sensitivity of cancer cell detection even further, a peptide-peptide covalent ligation system was used to generate self-assembled polymers of affibodies (an antibody-like scaffold). Affibody polymers allowed the establishment of multivalent interactions with cell-surface tumour markers, greatly improving the recovery of tumour cells expressing low levels of cancer biomarkers. However, those polymers had a mixture of lengths and there was no control over polymer sequence. Using orthogonal sequential isopeptide bond formation, we synthesized sequence-controlled proteins chains and used these immuno-assemblies as potent inducers of apoptosis of cancer cells. The approaches presented in this thesis show the importance of generating covalent protein polymers for cell isolation and killing, potentially opening up new directions for cancer biotechnology.
Complement C1q Interacts With LRP1 Clusters II and IV Through a Site Close but Different From the Binding Site of Its C1r and C1s-Associated Proteases

LRP1 is a large endocytic modular receptor that plays a crucial role in the scavenging of apoptotic material through binding to pattern-recognition molecules. It is a membrane anchored receptor of the LDL receptor family with 4 extracellular clusters of ligand binding modules called cysteine rich complement-type repeats that are involved in the interaction of LRP1 with its numerous ligands. Complement C1q was shown to interact with LRP1 and to be implicated in the phagocytosis of apoptotic cells. The present work aimed at exploring how these two large molecules interact at the molecular level using a dissection strategy. For that purpose, recombinant LRP1 clusters II, III and IV were produced in mammalian HEK293F cells and their binding properties were investigated. Clusters II and IV were found to interact specifically and efficiently with C1q with KDs in the nanomolar range. The use of truncated C1q fragments and recombinant mutated C1q allowed to localize more precisely the binding site for LRP1 on the collagen-like regions of C1q (CLRs), nearby the site that is implicated in the interaction with the cognate protease tetramer C1r2s2. This site could be a common anchorage for other ligands of C1q CLRs such as sulfated proteoglycans and Complement receptor type 1. The use of a cellular model, consisting in CHO LRP1-null cells transfected with full-length LRP1 or a cluster IV minireceptor (mini IV) confirmed that mini IV interacts with C1q at the cell membrane as well as full-length LRP1. Further cellular interaction studies finally highlighted that mini IV can endorse the full-length LRP1 binding efficiency for apoptotic cells and that C1q has no impact on this interaction.
Expression, Purification, Refolding, and Characterization of a Neverland Protein From Caenorhabditis elegans

Steroid hormones that serve as vital compounds are necessary for the development and metabolism of a variety of organisms. The neverland (NVD) family genes encode the conserved Rieske-type oxygenases, which are accountable for the dehydrogenation during the synthesis and regulation of steroid hormones. However, the His-tagged NVD protein from Caenorhabditis elegans expresses as inclusion bodies in Escherichia coli BL21 (DE3). This bottleneck can be solved through refolding by urea or the introduction of a maltose-binding protein (MBP) tag at the N-terminus. Through further research on purification after the introduction of a MBP tag at the N-terminus, the CD measurement and fluorescence-based thermal shift assay indicated that MBP was favorable for the NVD proteins’ solubility and stability, which may be beneficial for the large-scale manufacture of NVD protein for further research. The structural model contained the Rieske [2Fe–2S] domain and non-heme iron-binding motif, which were similar to 3-ketosteroid 9 α-hydroxylase.