Miracle-dz/UniFAR-FTUs huggingface dataset:
Batch Experiments Demonstrating a Two-Stage Bacterial Process Coupling Methanotrophic and Heterotrophic Bacteria for 1-Alkene Production From Methane

Methane (CH4) is a sustainable carbon feedstock source for aerobic CH4-oxidizing bacteria (methanotrophs) to produce value-added chemicals. Under O2-limiting conditions, CH4 oxidation results in the production of various short-chain organic acids and platform chemicals. However, these CH4-derived products are still limited to C2-C6 and could be extended by utilizing them as a feedstock for heterotrophic bacteria. A two-stage system for CH4 abatement and 1-alkene production was developed in this study. Gamma- and alphaproteobacterial methanotrophs, i.e. Methylobacter tundripaludum SV96 and Methylocystis rosea SV97, respectively, were investigated in batch tests under different gas supplementation schemes. Under O2 limiting conditions (O2/CH4 molar ratio ~0.3), M. tundripaludum SV96 could potentially produce formate, acetate, succinate, and malate, accounted for ~7.4% of mol-CH4 consumed. For the first time, the organic acids-rich spent media derived from O2 limited-methanotrophic cultivation were successfully used for 1-alkene production using engineered Acinetobacter baylyi ADP1 (‘tesA-undA) cells.
CNN based Heuristic Function for A* Pathfinding Algorithm: Using Spatial Vector Data to Reconstruct Smooth and Natural Looking Plant Roots

In this work we propose an extension to recent methods for the reconstruction of root architectures in 2-dimensions. Recent methods for the automatic root analysis have proposed deep learned segmentation of root images followed by path finding such as Dijkstra’s algorithm to reconstruct root topology. These approaches assume that roots are separate, and that a shortest path within the image foreground represents a reliable reconstruction of the underlying root structure. This approach is prone to error where roots grow in close proximity, with path finding algorithms prone to taking “short cuts” and overlapping much of the root material. Here we extend these methods to also consider root angle, allowing a more informed shortest path search that disambiguates roots growing close together. We adapt a CNN architecture to also predict the angle of root material at each foreground position, and utilise this additional information within shortest path searchers to improve root reconstruction. Our results show an improved ability to separate clustered roots.
Spatial analysis for highly multiplexed imaging data to identify tissue microenvironments

Highly multiplexed in situ imaging cytometry assays have made it possible to study the spatial organisation of numerous cell types simultaneously. We have addressed the challenge of quantifying complex multi-cellular relationships by proposing a statistical method which clusters local indicators of spatial association. Our approach successfully identifies distinct tissue architectures in datasets generated from three state-of-the-art high-parameter assays demonstrating its value in summarising the information-rich data generated from these technologies.
Tools in Their Toolbox: How Community College Faculty Transfer Industry Experience Into Their Teaching

Objective: This study is aimed at understanding the ways in which faculty at community colleges utilize their industry experiences to inform their teaching. Method: The research drew on Merriam’s basic qualitative approach in analyzing data from 14 semi-structured qualitative interviews. Results: Our findings expand upon prior research surrounding faculty development and community college faculty experiences. Our analysis revealed several themes in regard to how community college faculty with industry backgrounds follow diverse pathways leading to their teaching positions; how they teach using practical applications of concepts and sharing real-life examples; how they utilize their industry networks to enhance their academic programs and create practical opportunities for students; how they replicate workplace settings in their classrooms; and how they prepare students for their future careers. Contribution: Our study contributes new empirical evidence on the myriad ways in which faculty apply industry experiences in their instruction. The findings indicate that community colleges would benefit from offering targeted supports and pedagogical training for faculty with an industry background; encouraging faculty from all backgrounds and disciplines to share successful teaching strategies; and utilizing faculty members’ expertise, networks, and experiences from industry in mathematics-oriented classrooms.
A Randomized, Double-Blind, Placebo-Controlled Dose-Escalation Trial of Merimepodib (VX-497) and Interferon-α in Previously Untreated Patients with Chronic Hepatitis C

Inhibition of inosine monophosphate dehydrogenase (IMPDH) is one of several proposed mechanisms of action for ribavirin (RBV), a critical component of the current treatment for chronic hepatitis C (CHC). This study was a double-blind, placebo-controlled dose-escalation study of a novel, selective, orally active small molecule inhibitor of IMPDH, merimepodib (VX-497 or MMPD) in combination with standard interferon-alpha (IFN-α). Fifty-four treatment-naive patients with genotype-1 CHC were randomized to receive IFN-α 3 MIU subcutaneously three times a week, alone or in combination with 100 mg or 300 mg (every 8 h) of MMPD for 4 weeks. At the end of 4 weeks, all patients were offered 48 weeks of treatment with IFN-α/RBV. The objectives of the study were to evaluate the tolerability of the IFN-α/MMPD combination and to evaluate whether MMPD had an on-treatment effect on HCV-RNA, similar to RBV when added to IFN-α. The drug combination was generally well tolerated; one patient at the higher dose discontinued because of elevated alanine aminotransferase levels. No pharmacokinetic interactions were evident between the two drugs. Analysis of covariance that adjusted for a baseline imbalance in HCV-RNA in the intent-to-treat population did not show any significant differences between the treatment groups, or between MMPD plus IFN-α compared with IFN-α alone. However, the per-protocol primary efficacy analysis based on treatment-compliant patients demonstrated a greater reduction in mean HCV-RNA in the combination of 100 mg MMPD plus IFN-α compared with IFN-α alone (-1.78 log vs -0.86 log, P=0.037). In conclusion, the addition of a selective IMPDH inhibitor to IFN-α was well tolerated. In a low-dose range, the addition of MMPD may have the potential to add to the antiviral efficacy of IFN-α. Larger, longer duration trials incorporating pegylated IFN would be required to determine whether this combination, alone or with RBV, would increase either early or sustained virological response rates.
HIV Protease Inhibitors Prevent Mitochondrial Hyperpolarization and Redox Imbalance and Decrease Endogenous Uncoupler Protein-2 Expression in Gp120-Activated Human T Lymphocytes

It has been demonstrated that HIV protease inhibitors (PIs) are able to inhibit apoptosis of both infected and uninfected T cells. It was hypothesized that the mechanisms underlying this effect are associated with a specific activity of these drugs against mitochondrial modifications occurring in the execution phase of apoptosis. In this work, we investigated the activity of PIs towards the early changes occurring in mitochondrial membrane potential in freshly isolated uninfected human T lymphocytes sensitized to CD95/Fas-induced physiological apoptosis via pre-exposure to HIV envelope protein gp120. The results obtained clearly indicate that PIs are capable of hindering early morphogenetic changes bolstering T cell apoptosis, that is, cell polarization and mitochondrial hyperpolarization. The target effect on mitochondria appeared to be characterized by a specific activity of PIs in the maintenance of their homeostasis either in intact cells or in cell-free systems, that is, isolated mitochondria. PIs seem to act as boosters of mitochondrial defense mechanisms, including modulation of endogenous uncouplers. These results add new insights in the field of PI mitochondrial toxicity mechanisms and pharmacological perspectives for the use of these drugs in the control of immune system homeostasis.
Antiviral Therapy of Haemorrhagic Fevers and Arbovirus Infections

RNA viruses of the families Arena-, Bunya-, Filo-, Flavi-and Togaviridae cause illness in humans ranging from mild, non-specific febrile syndromes to fulminant, lethal haemorrhagic fever. They are transmitted from animals to humans and from human to human by arthropods, aerosols or contact with body fluids. Antiviral compounds, convalescent plasma and interferon inhibit many of these agents in vitro and in virus-infected animals. Drug or plasma treatment is now in use for several human diseases, and would probably be beneficial for a number of others for which there is only limited treatment experience. Success is linked to early diagnosis and initiation of therapy. Ribavirin is used to treat Lassa fever and haemorrhagic fever with renal syndrome, and would probably be effective for Crimean-Congo haemorrhagic fever and for all New World arenavirus diseases. The value of ribavirin in the early treatment of hantavirus pulmonary syndrome is under evaluation. Convalescent plasma is the therapy of choice for Argentine haemorrhagic fever, and would also probably be effective for other New World arenaviruses and some other infections if a safe supply of plasma could be maintained. Ribavirin and interferon-α have both shown protective efficacy in non-human primates infected with Rift Valley fever virus. No effective therapy has yet been identified for filovirus infections, but results in animal models are encouraging. More clinical research is urgently needed. Even if placebo-controlled drug trials cannot be performed, conscientious reports of the results of therapy in limited numbers of patients can still provide evidence of antiviral drug effects.
Net Tuition, Unmet Financial Need, and Cooling Out: A National Study of Degree Aspirations Among First-Time Community College Students

Objective: This study examined the statistical association between net tuition and changes in degree aspirations among community college students. In addition, the study explored the moderating influence of unmet financial need. Method: Analyses relied on data from the most recent iteration of the Beginning Postsecondary Students Longitudinal Study. Estimates were derived from a series of robust multinomial models controlling for student, institutional, and state-level covariates. Results: Net tuition was consistently associated with decreased risks of experiencing a “cool out,” regardless of model specification. Yet, this main effect of net tuition was moderated by unmet need, such that net tuition increased cool out risks among students with greater unmet need. Conclusions: The results of this study suggest that net reductions in tuition alone may not fully reduce or eliminate barriers to college access and student success. Future financial aid policies should focus on the full cost of college attendance.
Word Embeddings and Length Normalization for Document Ranking

—Distributed word representation techniques have been effectively integrated into the Information Retrieval retrieval task. The most basic approach to this is mapping a document and the query words into the vector space and calculating the semantic similarity between them. However, this has a bias problem towards documents with different lengths, which rank a small document higher compared to documents with larger vocabulary size. While averaging a document by mapping it into vector space, it allows each word to contribute equally, which results in increased distance between a query and the document vectors. In this paper, we propose that document length normalization should be applied to address the length bias problem while using embedding based ranking. Therefore, we have presented an experiment with traditional Length Normalization techniques over, word2vec (Skip-gram) model trained using the TREC Blog06 dataset for ad-hoc retrieval tasks. We have also attempted to include relevance signals introducing a simple Linear Ranking (LR) function, which considers the presence of query words in a document as evidence of relevancy while ranking. Our combined method of Length Normalization and LR signiﬁcantly increases the Mean Average Precision up to 47% over a simple embeddings based baseline.
On Guidable Index of Tree Automata

We study guidable parity automata over infinite trees introduced by Colcombet and Löding, which form an expressively complete subclass of all non-deterministic tree automata. We show that, for any non-deterministic automaton, an equivalent guidable automaton with the smallest possible index can be effectively found. Moreover, if an input automaton is of a special kind, i
Cross-Cultural Differences and Psychometric Properties of the Japanese Actions and Feelings Questionnaire (J-AFQ)

Aims: We aimed to assess the psychometric properties of a Japanese version of the Actions and Feelings Questionnaire (J-AFQ), an 18-item self-report measure of non-verbal emotional communication, as well as to examine its transcultural properties. Methods: The J-AFQ was administered to 500 Japanese adults (age 20–49, 250 male), alongside the Japanese Broad Autism Phenotype Questionnaire (BAPQ-J) and Empathy Quotient (EQ-J). These were compared to a group of 597 British and Irish participants (age 16–18, 148 male). J-AFQ was assessed in terms of validity by confirmatory factor analysis and convergence with BAPQ-J and EQ-J using Pearson correlation. Internal consistency and differential item functioning (DIF) were assessed and compared between Japanese and UK/Irish participants. Results: Reversed worded items (RWIs) showed poor item-total correlations but excluding these left a 13-item version of the J-AFQ with good internal consistency and content validity. Consistent with the English version, J-AFQ scores correlated with EQ and lower BAPQ scores. However, comparing across cultures, J-AFQ scores were significantly lower in the Japanese sample, and there was evidence of important DIF by country in over half of the J-AFQ items Conclusion: Cultural differences in attitudes to self-report, as well as increased acquiescence to RWI's also seen in previous studies, limit the value of the 18-item instrument in Japanese culture. However, the 13-item J-AFQ is a valid and reliable measure of motor empathy, which, alongside the English version, offers promise for research in motor cognition and non-verbal emotional communication across cultures.
Hydrodeoxygenation of Xylose Isopropylidene Ketal Over Pd/HBEA Catalyst for the Production of Green Fuels

1,2:3,5-Di-O-isopropylidene-α-D-xylofuranose (DX) is a major component of a new bio-crude: a viscous oil presenting petroleum-friendly properties produced by the ketalization of sugarcane bagasse. This article studies DX HDO (hydrodeoxygenation) over a Pd/HBEA catalyst in a batch reactor at 250°C. The effects of hydrogen pressure from 10 to 40 bar, catalyst/DX ratio from ½ to 2, and reaction time 0–24 h were investigated. A range of conditions for complete hydrodeoxygenated DX into alkanes with a Pd/HBEA catalyst was found. In these conditions, a low coke yield with water as the principal deoxygenated product was obtained. Further, higher amounts of alkanes containing seven or more carbons (A7+) were favored at 30 bar of hydrogen pressure, Cat/DX ratio = 2, and short reaction time. Products analysis that accompanied the above variations during reaction time led to general insights into reaction pathways. First, in the presence of DX, an effective n-hexane conversion was not observed on experiments of low catalyst/DX ratio (½) or in the initial period of high Cat/DX ratio, suggesting DX is much more successful than n-hexane to compete for active sites. Then, the formation of a pool of oxygenated compounds, such as furans, ketones, and carboxylic acids, along with lighter and heavier alkanes was observed. Hence, the aforementioned oxygenates may undergo reactions, such as aldol condensation with subsequent hydrodeoxygenation reaction, generating heavier alkanes.
Brief Episodes of Nocturnal Hypoxia and Acidification Reduce Survival of Economically Important Blue Crab (Callinectes sapidus) Larvae

Many shallow coastal systems experience diel fluctuations in dissolved oxygen (DO) and pH that can intensify throughout the summer season and expose estuarine organisms to repeated episodes of coastal hypoxia and acidification. In temperate regions, larval release of the economically important blue crab Callinectes sapidus occurs in the summer, and while the earliest stage (zoea I) larvae are susceptible to persistent low DO and low pH conditions, their sensitivity to diel fluctuations is unknown. Here, a series of short-term (≤96 h) experiments were conducted to investigate the survival of C. sapidus zoea I larvae exposed to a range of diel cycling hypoxic and acidified conditions and durations. Two experiments comparing a diel cycling DO/pH treatment (fluctuating from ∼30% air saturation to ∼103% averaging ∼66%/and from pH ∼7.26 to ∼7.80 averaging ∼7.53) to a static low DO/pH treatment (∼43%/∼7.35), a static moderate DO/pH treatment (∼68%/∼7.59), and a static control treatment (∼106%/∼7.94) indicated that survival in the diel cycling treatment was significantly lower than the moderate treatment (p < 0.05) by 75 and 48% over 96 and 48 h, respectively, despite comparable mean experimental DO/pH values. Three other experiments aimed at identifying the effective minimum duration of low DO/low pH to significantly depress larval survival under diel cycling conditions revealed that 8 h of low DO/low pH (∼28%/∼7.43) over a 24-h diel cycle consistently decreased survival (p < 0.05) relative to control conditions by at least 55% regardless of experimental duration (72-, 48-, and 24-h experiments). An increase in DO beyond saturation to supersaturation (160%) and pH beyond normocapnic to highly basified (8.34) conditions during the day phase of the diel cycle did not improve survival of larvae exposed to nocturnal hypoxia and acidification. Collectively, these experiments demonstrate that diel cycling does not provide newly hatched C. sapidus larvae a temporal refuge capable of ameliorating low DO/pH stress, but rather is more lethal than chronic exposure to comparable average DO/pH conditions. Given that larvae exposed to a single nocturnal episode of moderate hypoxia and acidification experience significantly reduced survival, such occurrences may depress larval recruitment.
A Complete and Low-Cost Cardiac Optical Mapping System in Translational Animal Models

Clinicians, biologists, physicists, engineers, and computer scientists are coming together to better understand heart disease, which is currently the leading cause of death globally. Optical mapping, a high-speed fluorescence imaging technique that visualizes and measures key cardiac parameters such as action potentials, cytosolic calcium transients, and fibrillation dynamics, is a core research tool that has arisen from such interdisciplinary collaborations. In an effort to broaden its use, especially among clinical scientists and students, we developed a complete and low-cost optical mapping system, including a constant-flow Langendorff perfusion system, which minimizes the economic threshold to widespread use of this powerful tool in cardiac electrophysiology research. The system described here provides high spatiotemporal resolution data about action potentials, intracellular calcium transients and fibrillation wave dynamics in isolated Langendorff-perfused hearts (pigs and rabbits), relevant for translational research. All system components and software elements are fully disclosed with the aim of increasing the use of this affordable and highly versatile tool among clinicians, basic scientists and students wishing to tackle their own research questions with their own customizable systems.
Global Identification and Systematic Analysis of Lysine Malonylation in Maize (Zea mays L.)

Lysine malonylation is a kind of post-translational modifications (PTMs) discovered in recent years, which plays an important regulatory role in plants. Maize (Zea mays L.) is a major global cereal crop. Immunoblotting revealed that maize was rich in malonylated proteins. We therefore performed a qualitative malonylome analysis to globally identify malonylated proteins in maize. In total, 1,722 uniquely malonylated lysine residues were obtained in 810 proteins. The modified proteins were involved in various biological processes such as photosynthesis, ribosome and oxidative phosphorylation. Notably, a large proportion of the modified proteins (45%) were located in chloroplast. Further functional analysis revealed that 30 proteins in photosynthesis and 15 key enzymes in the Calvin cycle were malonylated, suggesting an indispensable regulatory role of malonylation in photosynthesis and carbon fixation. This work represents the first comprehensive survey of malonylome in maize and provides an important resource for exploring the function of lysine malonylation in physiological regulation of maize.
Evolutionary Constraints on Connectivity Patterns in the Mammalian Suprachiasmatic Nucleus

The mammalian suprachiasmatic nucleus (SCN) comprises about 20,000 interconnected oscillatory neurons that create and maintain a robust circadian signal which matches to external light cues. Here, we use an evolutionary game theoretic framework to explore how evolutionary constraints can influence the synchronization of the system under various assumptions on the connection topology, contributing to the understanding of the structure of interneuron connectivity. Our basic model represents the SCN as a network of agents each with two properties—a phase and a flag that determines if it communicates with its neighbors or not. Communication comes at a cost to the agent, but synchronization of phases with its neighbors bears a benefit. Earlier work shows that when we have “all-to-all” connectivity, where every agent potentially communicates with every other agent, there is often a simple trade-off that leads to complete communication and synchronization of the system: the benefit must be greater than twice the cost. This trade-off for all-to-all connectivity gives us a baseline to compare to when looking at other topologies. Using simulations, we compare three plausible topologies to the all-to-all case, finding that convergence to synchronous dynamics occurs in all considered topologies under similar benefit and cost trade-offs. Consequently, sparser, less biologically costly topologies are reasonable evolutionary outcomes for organisms that develop a synchronizable oscillatory network. Our simulations also shed light on constraints imposed by the time scale on which we observe the SCN to arise in mammals. We find two conditions that allow for a synchronizable system to arise in relatively few generations. First, the benefits of connectivity must outweigh the cost of facilitating the connectivity in the network. Second, the game at the core of the model needs to be more cooperative than antagonistic games such as the Prisoner’s Dilemma. These results again imply that evolutionary pressure may have driven the system towards sparser topologies, as they are less costly to create and maintain. Last, our simulations indicate that models based on the mutualism game fare the best in uptake of communication and synchronization compared to more antagonistic games such as the Prisoner’s Dilemma.