Miracle-dz/UniFAR-FTUs huggingface dataset:
Computational Language Assessments of Harmony in Life — Not Satisfaction With Life or Rating Scales — Correlate With Cooperative Behaviors

Different types of well-being are likely to be associated with different kinds of behaviors. The first objective of this study was, from a subjective well-being perspective, to examine whether harmony in life and satisfaction with life are related differently to cooperative behaviors depending on individuals’ social value orientation. The second objective was, from a methodological perspective, to examine whether language-based assessments called computational language assessments (CLA), which enable respondents to answer with words that are analyzed using natural language processing, demonstrate stronger correlations with cooperation than traditional rating scales. Participants reported their harmony in life, satisfaction with life, and social value orientation before taking part in an online cooperative task. The results show that the CLA of overall harmony in life correlated with cooperation (all participants: r = 0.18, p < 0.05, n = 181) and that this was particularly true for prosocial participants (r = 0.35, p < 0.001, n = 96), whereas rating scales were not correlated (p > 0.05). No significant correlations (measured by the CLA or traditional rating scales) were found between satisfaction with life and cooperation. In conclusion, our study reveals an important behavioral difference between different types of subjective well-being. To our knowledge, this is the first study supporting the validity of self-reported CLA over traditional rating scales in relation to actual behaviors.
What Influences Bureaucrats’ Support for Red Tape Reduction Reform in Taipei City Government?

ABSTRACT Resistance from bureaucrats affected by the reforms is an often-cited challenge and it is important to know what influences their support for reform. Based on theories of organizational change, this paper examines how bureaucrats’ perceptions of reform benefits and risks, process and context influence their support for a structural reform in Taipei city government. Interviews of key informants were conducted to identify potential risks and benefits involved in the reform. An online survey was used to collect data to test the relationship between reform benefits, risks, process, context and reform support. The analysis confirms a positive relationship between individual efficiency gains and reform support, and of a negative relationship between risk of decision-making quality and reform support. The context of reform, demonstrated by the level of red tape, also enhances bureaucrats’ support for reform. This study provides important evidence of public sector reform beyond the U.S. context. Implications for future practices and research are provided.
Alphavirus and flavivirus infectivity is disrupted by components of the bacterial cell wall

The impact of the host microbiome on arbovirus infections is currently not clearly understood. Arboviruses are viruses transmitted through the bites of infected arthropods, predominantly mosquitoes or ticks. The first site of arbovirus inoculation is the biting site in the host skin, which is colonized by a complex microbial community that could possibly influence arbovirus infection. We demonstrated that pre-incubation of arboviruses with certain components of the bacterial cell wall, including lipopolysaccharides (LPS) of some Gram-negative bacteria and lipoteichoic acids or peptidoglycan of certain Gram-positive bacteria, significantly reduced arbovirus infectivity in vitro. This inhibitory effect was observed for arboviruses of different virus families, including chikungunya virus of the Alphavirus genus and Zika virus of the Flavivirus genus, showing that this is a broad phenomenon. A modest inhibitory effect was observed following incubation with a panel of heat-inactivated bacteria, including bacteria residing on the skin. No viral inhibition was observed after pre-incubation of cells with LPS. Furthermore, a virucidal effect of LPS on viral particles was noticed by electron microscopy. Therefore, the main inhibitory mechanism seems to be due to a direct effect on the virus particles. Together, these results suggest that bacteria are able to decrease the infectivity of alphaviruses and flaviviruses.
Multivalent interactions make adherens junction–cytoskeletal linkage robust during morphogenesis

Embryogenesis requires cells to change shape and move without disrupting epithelial integrity. This requires robust, responsive linkage between adherens junctions and the actomyosin cytoskeleton. Using Drosophila morphogenesis we define molecular mechanisms mediating junction-cytoskeletal linkage and explore the role of mechanosensing. We focus on the junction-cytoskeletal linker Canoe, a multidomain protein. We engineered the canoe locus to define how its domains mediate its mechanism of action. To our surprise, the PDZ and FAB domains, which we thought connected junctions and F-actin, are not required for viability or mechanosensitive recruitment to junctions under tension. The FAB domain stabilizes junctions experiencing elevated force, but in its absence most cells recover, suggesting redundant interactions. In contrast, the Rap1-binding RA domains are critical for all Cno functions and for enrichment at junctions under tension. This supports a model in which junctional robustness derives from a large protein network assembled via multivalent interactions, with proteins at network nodes and some node connections more critical than others.
Beneficial and detrimental genes in the cellular response to replication arrest

DNA replication is essential for all living organisms, and a variety of events can perturb replication, including DNA damage (e.g., pyrimidine dimers, crosslinking) and replication arrest due to “roadblocks” such as DNA-binding proteins or transcription. Bacteria have several well-characterized mechanisms for repairing damaged DNA and restoring functional replication forks. However, little is known about the repair of stalled or arrested replication forks in the absence of DNA lesions. Using a library of random transposon insertions in Bacillus subtilis, we identified 35 genes that affect the ability of cells to survive arrest of replication elongation, in the absence of DNA damage. Genes identified included those involved in iron-sulfur homeostasis, cell envelope biogenesis, and DNA repair and recombination. In B. subtilis, and many bacteria, two nucleases (AddAB and RecJ) are involved in early steps in repairing replication forks arrested by DNA damage. Loss of either one causes increased sensitivity to DNA damage. These single-strand nucleases resect DNA ends, leading to assembly of the recombinase RecA onto the single stranded DNA. Notably, we found that disruption of recJ increased survival of cells following replication arrest, indicating that, in the absence of DNA damage, RecJ is detrimental to surviving replication arrest. In contrast, and as expected, disruption of addA decreased survival of cells following replication arrest, indicating that AddA promotes survival. The different phenotypes of addA and recJ mutants appeared to be due to differences in assembly of RecA onto DNA. RecJ promoted too much assembly of RecA, and loss of RecA compensated for the detrimental effects of RecJ. Our results indicate that in the absence of DNA lesions, RecA is dispensable for cells to survive replication arrest and the stable RecA nucleofilaments favored by the RecJ pathway may lead to cell death by preventing proper processing of the arrested replication fork.
Frontostriatal functional connectivity underlies self-enhancement during social evaluation

Self-enhancement, the tendency to view oneself positively, is a pervasive social motive widely investigated in social and personality psychology. Despite research on the topic over the past several decades, relatively little is known about the neurocognitive mechanisms underlying this motive, specifically in social evaluative situations. To investigate whether positive emotion regulation circuitry, neural circuitry involved in modulating positive affect, relates to the operation of the self-enhancement motive in social contexts, we conducted an fMRI study in a sample of healthy young adults. We hypothesized that self-enhancement indices (state, trait self-esteem) relate to greater positive functional connectivity between right ventrolateral prefrontal cortex (RVLPFC), a neural region implicated in emotion regulation, and the ventral striatum (VS), a region associated with reward-related affect, during a social feedback task. Following social-evaluative feedback, participants maintained stable self-esteem or experienced a drop in state self-esteem. We found stable state self-esteem and higher trait self-esteem related to greater positive connectivity in RVLFPC-VS circuitry during receipt of positive (vs. neutral) feedback. These findings implicate the neurocognitive mechanisms underlying emotion regulation in the functioning of the self-enhancement motive and highlight a pathway through which self-enhancement may restore feelings of self-worth during threatening circumstances.
Host Bioenergetic Parameters Reveal Cytotoxicity of Antituberculosis Drugs Undetected Using Conventional Viability Assays

High attrition rates in tuberculosis (TB) drug development have been largely attributed to safety, which is likely due to the use of endpoint assays measuring cell viability to detect drug cytotoxicity. In drug development for cancer, metabolic, and neurological disorders and for antibiotics, cytotoxicity is increasingly being assessed using extracellular flux (XF) analysis, which measures cellular bioenergetic metabolism in real time. ABSTRACT High attrition rates in tuberculosis (TB) drug development have been largely attributed to safety, which is likely due to the use of endpoint assays measuring cell viability to detect drug cytotoxicity. In drug development for cancer, metabolic, and neurological disorders and for antibiotics, cytotoxicity is increasingly being assessed using extracellular flux (XF) analysis, which measures cellular bioenergetic metabolism in real time. Here, we adopt the XF platform to investigate the cytotoxicity of drugs currently used in TB treatment on the bioenergetic metabolism of HepG2 cells, THP-1 macrophages, and human monocyte-derived macrophages (hMDMs). We found that the XF analysis reveals earlier drug-induced effects on the cells’ bioenergetic metabolism prior to cell death, measured by conventional viability assays. Furthermore, each cell type has a distinct response to drug treatment, suggesting that more than one cell type should be considered to examine cytotoxicity in TB drug development. Interestingly, chemically unrelated drugs with different modes of action on Mycobacterium tuberculosis have similar effects on the bioenergetic parameters of the cells, thus discouraging the prediction of potential cytotoxicity based on chemical structure and mode of action of new chemical entities. The clustering of the drug-induced effects on the hMDM bioenergetic parameters are reflected in the clustering of the effects of the drugs on cytokine production in hMDMs, demonstrating concurrence between the effects of the drugs on the metabolism and functioning of the macrophages. These findings can be used as a benchmark to establish XF analysis as a new tool to assay cytotoxicity in TB drug development.
Mouse Adapted SARS-CoV-2 protects animals from lethal SARS-CoV challenge

The emergence of SARS-CoV-2 has resulted in a worldwide pandemic causing significant damage to public health and the economy. Efforts to understand the mechanisms of COVID-19 disease have been hampered by the lack of robust mouse models. To overcome this barrier, we utilized a reverse genetic system to generate a mouse-adapted strain of SARS-CoV-2. Incorporating key mutations found in SARSCoV-2 variants, this model recapitulates critical elements of human infection including viral replication in the lung, immune cell infiltration, and significant in vivo disease. Importantly, mouse-adaptation of SARS-CoV-2 does not impair replication in human airway cells and maintains antigenicity similar to human SARS-CoV-2 strains. Utilizing this model, we demonstrate that SARS-CoV-2 infected mice are protected from lethal challenge with the original SARS-CoV, suggesting immunity from heterologous CoV strains. Together, the results highlight the utility of this mouse model for further study of SARS-CoV-2 infection and disease.
Minian, an open-source miniscope analysis pipeline

Miniature microscopes have gained considerable traction for in vivo calcium imaging in freely behaving animals. However, extracting calcium signals from raw videos is a computationally complex problem and remains a bottleneck for many researchers utilizing single-photon in vivo calcium imaging. Despite the existence of many powerful analysis packages designed to detect and extract calcium dynamics, most have either key parameters that are hard-coded or insufficient step-by-step guidance and validations to help the users choose the best parameters. This makes it difficult to know whether the output is reliable and meets the assumptions necessary for proper analysis. Moreover, large memory demand is often a constraint for setting up these pipelines since it limits the choice of hardware to specialized computers. Given these difficulties, there is a need for a low memory demand, user-friendly tool offering interactive visualizations of how altering parameters at each step of the analysis affects data output. Our open-source analysis pipeline, Minian (Miniscope Analysis), facilitates the transparency and accessibility of single-photon calcium imaging analysis, permitting users with little computational experience to extract the location of cells and their corresponding calcium traces and deconvolved neural activities. Minian contains interactive visualization tools for every step of the analysis, as well as detailed documentation and tips on parameter exploration. Furthermore, Minian has relatively small memory demands and can be run on a laptop, making it available to labs that do not have access to specialized computational hardware. Minian has been validated to reliably and robustly extract calcium events across different brain regions and from different cell types. In practice, Minian provides an open-source calcium imaging analysis pipeline with user-friendly interactive visualizations to explore parameters and validate results.
YAP/TAZ Maintain the Proliferative Capacity and Structural Organization of Radial Glial Cells During Brain Development

The Hippo pathway regulates the development and homeostasis of many tissues and in many species. It controls the activity of two paralogous transcriptional coactivators, YAP and TAZ (YAP/TAZ). Although previous studies have established that aberrant YAP/TAZ activation is detrimental to mammalian brain development, whether and how endogenous levels of YAP/TAZ activity regulate brain development remain unclear. Here, we show that during mammalian cortical development, YAP/TAZ are specifically expressed in apical neural progenitor cells known as radial glial cells (RGCs). The subcellular localization of YAP/TAZ undergoes dynamic changes as corticogenesis proceeds. YAP/TAZ are required for maintaining the proliferative potential and structural organization of RGCs, and their ablation during cortical development reduces the numbers of cortical projection neurons and causes the loss of ependymal cells, resulting in hydrocephaly. Transcriptomic analysis using sorted RGCs reveals gene expression changes in YAP/TAZ-depleted cells that correlate with mutant phenotypes. Thus, our study has uncovered essential functions of YAP/TAZ during mammalian brain development and revealed the transcriptional mechanism of their action.
Incorporating Sub-Word Level Information in Language Invariant Neural Event Detection

Detection of TimeML events in text have traditionally been done on corpora such as TimeBanks. However, deep learning methods have not been applied to these corpora, because these datasets seldom contain more than 10,000 event mentions. Traditional architectures revolve around highly feature engineered, language specific statistical models. In this paper, we present a Language Invariant Neural Event Detection (ALINED) architecture. ALINED uses an aggregation of both sub-word level features as well as lexical and structural information. This is achieved by combining convolution over character embeddings, with recurrent layers over contextual word embeddings. We find that our model extracts relevant features for event span identification without relying on language specific features. We compare the performance of our language invariant model to the current state-of-the-art in English, Spanish, Italian and French. We outperform the F1-score of the state of the art in English by 1.65 points. We achieve F1-scores of 84.96, 80.87 and 74.81 on Spanish, Italian and French respectively which is comparable to the current states of the art for these languages. We also introduce the automatic annotation of events in Hindi, a low resource language, with an F1-Score of 77.13.
Alexithymia, Emotional Distress, and Perceived Quality of Life in Patients With Hashimoto’s Thyroiditis

Emotion-processing impairment represents a risk factor for the development of somatic illness, affecting negatively both health-related quality of life (HRQoL) and disease management in several chronic diseases. The present pilot study aims at (i) investigating the associations between alexithymia and depression, anxiety, and HRQoL in patients with Hashimoto’s thyroiditis (HT); (ii) examining the association between these three psychological conditions together with HRQoL, and thyroid autoantibodies status as well as thyroid echotexture in patients with HT; and (iii) comparing the intensity of all these clinical psychological features in patients with HT versus controls. Twenty-one patients with serologically or ultrasonographically verified HT and 16 controls with non-toxic goiter or postsurgical hypothyroidism were recruited for this study. Serum thyrotropin (TSH) and free thyroxine, as well as thyroid autoantibodies (thyroglobulin antibodies and thyroid peroxidase antibodies), were assayed. Alexithymia, depression, anxiety, and HRQoL were assessed with Toronto Alexithymia Scale; Beck Depression Inventory, second edition; Hamilton Anxiety Rating Scale; and Health Survey Short-Form 36, respectively. A negative relationship between the difficulty to describe feelings and the cognitive component of depression was found (r = -0.46, p = 0.04). Besides, patients with seronegative HT had lower somatic anxiety than patients with HT who tested positive (r = -0.68, p = 0.01 and r = -0.59, p = 0.04, respectively). Besides, no statistically significant difference was found between patients with HT and controls with regard to somatic anxiety. The present study suggests the relevance of alexithymia in patients suffering from HT, which may be intertwined with a possible state of underreported depression that is mainly expressed through physical complaints. Promoting the capability to describe and communicate feelings could contribute to psychological elaboration and coping with the disease and, consequently, to the improvement of self-management and perceived HRQoL.
Design and Fabrication of PTFE Substrate Integrated Waveguide Coupler by SR Direct Etching

The microfabrication technique based on synchrotron radiation (SR) direct etching process has recently been applied to construct PTFE microstructures. This paper proposes a PTFE substrate integrated waveguide (PTFE SIW). It is expected that the PTFE SIW contributes to the improvement of the structural strength. A rectangular through-hole is introduced taking the advantage of the SR direct etching process. First, a PTFE SIW for the Q-band is designed. Then, a cruciform 3-dB directional coupler consisting of the PTFE SIW is designed and fabricated by the SR direct etching process. The validity of the PTFE SIW coupler is confirmed by measuring the frequency characteristics of the S -parameters. The mechanical strength of the PTFE SIW and the peeling strength of its Au film are also additionally investigated. key words: microstructure, X-ray lithography, dielectric loaded waveguides, couplers, millimeter wave circuits
Recovery of Pyruvate from Fermentation Broth by Using Ion Exchange Resin Chromatography

resin was chosen to decolor the pyruvate fermentation broth. Excellent decoloration result was achieved under the following conditions: pH 3.0, 60 g/L pyruvate concentration of broth, 1.8 mL/(mL·h). 330 weakly basic anion resin was selected for its superior separation performance to purify pyruvate. In the fixed bed ion exchange operation, high total exchange capacity was obtained when pH and pyruvate concentration of the influent were kept around 4.0 and 40 g/L, respectively. High effective exchange capacity (0.604 mol/L) was achieved under lower flow rate of influent. Elution experiments demonstrated that 2 mol/L hydrochloric acid and lower flow rate (0.44 mL/ (mL·h) ) benefit high elution efficiency. Under the optimal conditions, the recovery percent of pyruvate from fermentation broth achieved 97.0% in ion exchange operation unit.
A Review on Structure Based Therapeutic Approach for Huntington Disease

Huntington disease (HD) is a fatal and progressive neurodegenerative disease that has affected the social and personal life of patients. The disease causes the most disturbing symptoms of chorea, which is characterized by uncontrolled body movements. HD patients are being treated by providing drugs that maintain neurotransmission balance and relieve chorea symptoms. HD has been associated with mutant Huntingtin protein (mHtt) with more than thirty-six polyQ stretches at N terminal of 34 kDaHtt protein. mHtt protein undergoes misfolding, which leads to accumulation of toxic mHtt aggregates in the brain. The phenomenon of protein aggregation initiates a cascade of events, eventually leading to endoplasmic reticulum (ER) stress and misregulated unfolding protein response (UPR). Different molecular targets have been identified from ER stress and UPR pathways for finding potential molecules that can treat HD. Overall, the mechanism causes structural transitions in mHtt, which can be controlled at the subatomic and molecular level by molecular dynamic simulations (MDS). The MDS strategies help to observe structural changes in the mHtt protein and association pattern between the protein and novel drug compounds. Hence, this study explains the journey of HD research to computational strategies and the scope of structural drug designing in psychologically disturbing Huntington’s disease.
The Development and Application of Support Vector Machine

Support Vector Machine(SVM) algorithm has the advantages of complete theory, global optimization, strong adaptability, and good generalization ability because of it on the basis of Statistical Learning Theory’s(SLT). It is a new hot spot in machine learning research. This article first systematically studies some basic concepts of SVM and the optimization of SVM. In addition, this article also discusses the application of SVM in modern machining, protein prediction and face detection. Through these applications, the performance characteristics and advantages of SVM can be reflected. At the end of the article, some shortcomings of SVM are introduced, and the development trend of subsequent SVM is pointed out accordingly.