Miracle-dz/UniFAR-FTUs huggingface dataset:
Potato Juice, a Starch Industry Waste, as a Cost-Effective Medium for the Biosynthesis of Bacterial Cellulose

The unique properties of bacterial cellulose (BC) make it of great interest for numerous branches of industry. Nevertheless, the high cost of the dedicated, microbiological medium used for BC production significantly hinders possibility of widespread use. Searching for an alternative, we turned our attention to potato tuber juice (PJ), a major waste product of the potato starch industry. We verified the possibility of using PJ as a cost-effective, ecological-friendly medium that yielded BC with properties equivalent to those from conventional commercial Hestrin-Schramm medium. The BC yield from PJ medium (>4 g/L) was comparable, despite the lack of any pre-treatment. Likewise, the macro- and microstructure, physicochemical parameters, and chemical composition showed no significant differences between PJ and control BC. Importantly, BC obtained from PJ was not cytotoxic against fibroblast cell line L929 in vitro and did not contain any hard-to-remove impurities. These are very important aspects from an application standpoint, particularly in biomedicine. Therefore, we conclude that using PJ for BC biosynthesis is a path towards significant valorization of an environmentally problematic waste product of the starch industry and can help ultimately lower BC production costs. Highlights Potato juice (PJ) was used as a culture medium for cellulose-synthesizing bacteria. PJ was suitable as source of nutrients and did not required any pre-treatment. Yield of BC from PJ was equivalent to that obtained from conventional HS. PJ-BC did not differ from conventionally produced HS-BC in terms of its properties. PJ-BC can be used in the same applications as commercially produced BC. Graphical abstract
Global and Gene-specific Transcriptional Responses to Acute Stress

Nucleosomes may regulate transcription by controlling access to promoters by transcription factors and RNA polymerase II (Pol2). Potentially active genes display nucleosome depleted regions flanked by positioned -1 and +1 nucleosomes. On yeast genes, the transcription start site (TSS) is on the upstream face of the +1 nucleosome, but whether precise +1 nucleosome positioning controls Pol2 access to the TSS remains unclear. Here, using acute nutrient starvation to rapidly reprogramme the genome, we show highly dynamic upstream or downstream shifts in the position of +1 nucleosomes, coincident with levels of transcriptionally engaged Pol2 at 58% of genes. Transcript level changes broadly reflect Pol2 occupancy changes with a delay but can be further influenced by Pub1 or Puf3 dependent changes in transcript degradation rates. The response to acute stress has a second component as we also observed genome-wide changes in Pol2 distribution on genes, independent of changes in Pol2 occupancy, with Pol2 accumulating upstream of a +170 nt stalling site. Mathematical modelling supports a global increase in promoter-proximal early transcription termination as a major component of the global stress response. Thus, we uncover a two-component transcriptional response to stress, one focused on the +1 nucleosome, the second on Pol2 itself. A two-component responses to acute stress involving a gene-specific response and a global response Dynamic shifting of +1 nucleosome position with transcriptional activation or repression. Global targeting of Pol2 leading to early transcription termination on acute stress
Structure of bacterial communities in Japanese-style bathrooms: Comparative sequencing of bacteria in shower water and showerhead biofilms using a portable nanopore sequencer

Showers are one of the main exposure routes to diverse microbes for end users in built environments. Bacteria in water are responsible for biofilm formation on surfaces, and the inside of a showerhead is a specific niche. Here, for the purpose of microbial characterization, source estimation and possibility of infection, the bacterial compositions of both shower water and showerhead biofilms in the same bathroom were determined and compared using a portable nanopore sequencer. The results suggest that specific bacteria in source water would primarily adhere to the surface of the showerhead where they subsequently form biofilms, and the community compositions within biofilms largely vary depending on environmental factors. The relative abundance of several pathogenic bacterial genera in both water and biofilm samples was low. We suggest that it is important to manage risk of infection in each household, and rapid on-site analysis of microbial communities will allow the realization.
Phylogenomic and mitogenomic data can accelerate inventorying of tropical beetles during the current biodiversity crisis

Conservation efforts must be evidence-based, so rapid and economically feasible methods should be used to quantify diversity and distribution patterns. We have attempted to overcome current impediments to the gathering of biodiversity data by using integrative phylogenomic and three mtDNA fragment analyses. As a model, we sequenced the Metriorrhynchini beetle fauna, sampled from ∼700 localities in three continents. The species-rich dataset included ∼6,500 terminals, >2,300 putative species, more than a half of them unknown to science. The phylogenomic backbone enabled the integrative delimitation of robustly defined natural units that will inform future research. Using constrained mtDNA analysis, we identified the spatial structure of α-diversity, very high species-level endemism, a biodiversity hotspot in New Guinea, and high phylogenetic diversity in the Sundaland. We suggest that ∼20 person months of focused field research and subsequent laboratory and bioinformatic workflow steps would substantially accelerate the inventorying of any hyperdiverse tropical group with several thousand species. The outcome would be a scaffold for the incorporation of further data. The database of sequences could set a benchmark for the spatiotemporal evaluation of biodiversity, would support evidence-based conservation planning, and would provide a robust framework for systematic, biogeographic, and evolutionary studies.
Transcriptomic analysis of mdx mouse muscles reveals a signature of early human Duchenne muscular dystrophy

The mdx mouse (C57BL/10ScSn-DMDmdx/J) is the oldest model of Duchenne muscular dystrophy (DMD). Mdx remains popular and has not been replaced by newer mouse models, despite criticisms that mdx has a nearly normal lifespan and mild pathology while DMD remains a severe, fatal disease. At some point we noticed that the absence of mdx RNA-seq data limited our ability to assess the results of physiological work on the mouse model and to compare these results to human genetic data [1]. We carried out RNA-seq analysis of wild-type and mdx mice of 2 and 5 months of age, using three hindlimb muscles per mouse: the flexor digitorum brevis (FDB), the extensor digitorum longus (EDL) and the soleus (SOL), with a total of 55 samples. We then mined the data and found that each of the three muscles is a valid experimental model for DMD-related mouse work, even the FDB, despite a delayed pathology development. We also show that the mdx mouse muscles are enriched in metabolic, developmental, regenerational and structural pathways that have been found to be the “disease signature” of DMD in young and presymptomatic subjects [38, 39]. Additionally, we show that healthy human muscle fiber microtubules present the grid-like organization found in control rodents but perturbed in the mdx mouse. We conclude that the mdx mouse appropriately mimics the early stages of DMD, with its microtubule defects signaling fiber regeneration [35]. We hope that these results may contribute to a better understanding of the failure of regeneration as DMD progresses.
Reciprocal Regulation of Shh Trafficking and H2O2 Levels via a Noncanonical BOC-Rac1 Pathway

Among molecules that bridge environment, cell metabolism, and cell signaling, H2O2 recently appeared as an emerging but central player. Its level depends on cell metabolism and environment and was recently shown to play key roles during embryogenesis, contrasting with its long-established role in disease progression. We decided to explore whether the secreted morphogen Sonic hedgehog (Shh), known to be essential in a variety of biological processes ranging from embryonic development to adult tissue homeostasis and cancers, was part of these interactions. Here, we report that H2O2 levels control key steps of Shh delivery and that physiological in vivo modulation of H2O2 levels changes Shh distribution and tissue patterning. A feedback loop exists in which Shh trafficking controls H2O2 synthesis via a non-canonical BOC-Rac1 pathway, leading to cytoneme growth. Our findings reveal that Shh directly impacts its own distribution, thus providing a molecular explanation for the robustness of morphogenesis to both environmental insults and individual variability.
Speciation and determination of mercury by various analytical techniques

Abstract Mercury is one of the most important metals to environmental researchers due to its toxicity. In recent years, many authors determined the concentration of mercury and its different forms in the environment, such as soil, water, atmosphere and biota, with various analytical techniques, such as atomic absorption spectrometry, spectrophotometry, voltammetry, inductively coupled plasma mass spectrometry, inductively coupled plasma atomic emission spectrometry, spectrofluorometry and chromatography. The objective of this paper is to summarize the recent understanding of the available techniques for the analysis and speciation of mercury in environmental and biological samples reported worldwide during 2010–2011. We tabulated all the analytical parameters of about 129 research papers published in reputable international journals during 2010–2011 about mercury determination and speciation studies.
MFmap: A semi-supervised generative model matching cell lines to tumours and cancer subtypes

Translating in vitro results from experiments with cancer cell lines to clinical applications requires the selection of appropriate cell line models. Here we present MFmap (model fidelity map), a machine learning model to simultaneously predict the cancer subtype of a cell line and its similarity to an individual tumour sample. The MFmap is a semi-supervised generative model, which compresses high dimensional gene expression, copy number variation and mutation data into cancer subtype informed low dimensional latent representations. The accuracy (test set F1 score > 90%) of the MFmap subtype prediction is validated in ten different cancer datasets. We use breast cancer and glioblastoma cohorts as examples to show how subtype specific drug sensitivity can be translated to individual tumour samples. The low dimensional latent representations extracted by MFmap explain known and novel subtype specific features and enable the analysis of cell-state transformations between different subtypes. From a methodological perspective, we report that MFmap is a semi-supervised method which simultaneously achieves good generative and predictive performance and thus opens opportunities in other areas of computational biology. Author summary Cancer researchers perform experiments with cell lines to better understand the biology of cancer and to develop new anti-cancer treatments. A prerequisite to translate promising results from these in vitro experiments to clinical applications is to use the most appropriate cell line for a given tumour or cancer subtype. We present MFmap (model fidelity map), a deep learning technique to integrate cancer genomic data from patients with cell line data. The MFmap neural network compresses complex genomic features from thousands of genes into a small set of features called latent representations. This makes cell line and tumour data comparable and allows cancer researchers to select the best cell line which closely resembles a specific type of tumours or even an individual tumour. By classifying cancer cell lines into subtypes, MFmap offers a new possibility to predict the effect of therapeutic compounds in a particular tumour subtype. For the example of an aggressive brain tumour we demonstrate that MFmap can be used to study cell-state transformations during the disease course. In addition, MFmap is a promising machine learning method with potential applications in many other areas of biology and medicine.
Increased Microbial Diversity and Decreased Prevalence of Common Pathogens in the Gut Microbiomes of Wild Turkeys Compared to Domestic Turkeys

Due to the increasingly recognized problems associated with antibiotic use in agricultural settings, poultry producers need alternative methods to control common bacterial pathogens. In this study, we compare the microbiota of wild and domestic turkeys. ABSTRACT Turkeys (Meleagris gallopavo) provide a globally important source of protein and constitute the second most important source of poultry meat in the world. Bacterial diseases are common in commercial poultry production, causing significant production losses for farmers. Due to the increasingly recognized problems associated with large-scale/indiscriminate antibiotic use in agricultural settings, poultry producers need alternative methods to control common bacterial pathogens. In this study, we compared the cecal microbiota of wild and domestic turkeys, hypothesizing that environmental pressures faced by wild birds may select for a disease-resistant microbial community. Sequence analyses of 16S rRNA genes amplified from cecal samples indicate that free-roaming wild turkeys carry a rich and variable microbiota compared to domestic turkeys raised on large-scale poultry farms. Wild turkeys also had very low levels of Staphylococcus, Salmonella, and Escherichia coli compared to domestic turkeys. E. coli strains isolated from wild and domestic turkey cecal samples also belong to distinct phylogenetic backgrounds and differ in their propensity to carry virulence genes. E. coli strains isolated from factory-raised turkeys were far more likely to carry genes for capsule (kpsII and kpsIII) or siderophore (iroN and fyuA) synthesis than were those isolated from wild turkeys. These results suggest that the microbiota of wild turkeys may provide colonization resistance against common poultry pathogens. IMPORTANCE Due to the increasingly recognized problems associated with antibiotic use in agricultural settings, poultry producers need alternative methods to control common bacterial pathogens. In this study, we compare the microbiota of wild and domestic turkeys. The results suggest that free-ranging wild turkeys carry a distinct microbiome compared to farm-raised turkeys. The microbiome of wild birds contains very low levels of poultry pathogens compared to that of farm-raised birds. The microbiomes of wild turkeys may be used to guide the development of new ways to control disease in large-scale poultry production.
Effect of Geobacter metallireducens nanowire on electron transfer efficiency in microbial fuel cell

The inhibitory effect of electron mediator 2,6-anthraquinone disulphonate (AQDS) on Geobacter metallireducens nanowire in the microbial fuel cell (MFC) was studied. In the culture process of G.metallireducens with Fe(OH)3 as an electron acceptor, the concentration of reduction product Fe (II) in solution without AQDS was higher than that with AQDS after 10 days, due to the formation of microbial nanowires. The effects of nanowire on electron transfer efficiency and electrical current characteristic were studied using a double chamber MFC reactor. The transfer efficiency between biofilm and electrodes was increased by nanowire, which increased the maximum output voltage of MFC was 442 mV. The nanowire biofilm electrode had a bigger cyclic voltammetry curve peak, smaller activation resistance, and a stronger current response signal through electrochemical measurement, which indicates that the nanowire enhanced the electrochemical activity of the electrode.
Patient Preferences for Attributes of Chemotherapy for Lung Cancer: Discrete Choice Experiment Study in Japan

Our study objective was to determine lung cancer chemotherapy attributes that are important to patients in Japan. A discrete choice experiment survey in an anonymous web-based questionnaire format with a reward was completed by 200 lung cancer patients in Japan from November 25, 2019, to November 27, 2019. The relative importance of patient preferences for each attribute was estimated using a conditional logit model. A hierarchical Bayesian logit model was also used to estimate the impact of each demographic characteristic on the relative importance of each attribute. Of the 200 respondents, 191 with consistent responses were included in the analysis. In their preference, overall survival was the most important, followed by diarrhea, nausea, rash, bone marrow suppression (BMS), progression-free survival, fatigue, interstitial lung disease, frequency of administration, and duration of administration. The preferences were influenced by demographic characteristics (e.g., gender and age) and disease background (e.g., cancer type and stage). Interestingly, the experience of cancer drug therapies and adverse events had a substantial impact on the hypothetical drug preferences. For the Japanese lung cancer patients, improved survival was the most important attribute that influenced their preference for chemotherapy, followed by adverse events, including diarrhea, nausea, rash, and BMS. The preferences varied depending on the patient’s demographic and experience. As drug attributes can affect patient preferences, pharmaceutical companies should be aware of the patient preferences and develop drugs that respond to segmented market needs.
Comparing Exogenous Methods to Induce Plant-Resistance Against a Bark-Feeding Insect

Exogenous application of the plant hormone methyl jasmonate (MeJA) can trigger induced plant defenses against herbivores, and has been shown to provide protection against insect herbivory in conifer seedlings. Other methods, such as mechanical damage to seedlings, can also induce plant defenses, yet few have been compared to MeJA and most studies lack subsequent herbivory feeding tests. We conducted two lab experiments to: (1) compare the efficacy of MeJA to mechanical damage treatments that could also induce seedling resistance, (2) examine if subsequent insect damage differs depending on the time since induction treatments occurred, and (3) assess if these induction methods affect plant growth. We compared Scots pine (Pinus sylvestris) seedlings sprayed with MeJA (10 or 15 mM) to seedlings subjected to four different mechanical bark damage treatments (two different bark wound sizes, needle-piercing damage, root damage) and previous pine weevil (Hylobius abietis) damage as a reference treatment. The seedlings were exposed to pine weevils 12 or 32 days after treatments (early and late exposure, hereafter), and resistance was measured as the amount of damage received by plants. At early exposure, seedlings treated with needle-piercing damage received significantly more subsequent pine weevil feeding damage than those treated with MeJA. Seedlings treated with MeJA and needle-piercing damage received 84% less and 250% more pine weevil feeding, respectively, relative to control seedlings. The other treatments did not differ statistically from control or MeJA in terms of subsequent pine weevil damage. For the late exposure group, plants in all induction treatments tended to receive less pine weevil feeding (yet this was not statistically significant) compared to control seedlings. On the other hand, MeJA significantly slowed down seedling growth relative to control and all other induction treatments. Overall, the mechanical damage treatments appeared to have no or variable effects on seedling resistance. One of the treatments, needle-piercing damage, actually increased pine weevil feeding at early exposure. These results therefore suggest that mechanical damage shows little potential as a plant protection measure to reduce feeding by a bark-chewing insect.
Investor Sentiment and Stock Returns During the COVID-19 Pandemic

In this paper, we regard the Baidu index as an indicator of investors' attention to China's epidemic stocks. We believe that when seeking information to guide investment decisions, investor sentiment is usually affected by the information provided by the Baidu search engine, which may cause stock prices to fluctuate. Therefore, we constructed a GARCH extended model including the Baidu index to predict the return of epidemic stocks and compared it with the benchmark model. The empirical research in this paper finds that the forecast model including the Baidu index is significantly better than the benchmark model. This has important reference value both for investors in predicting stock trends and for the government's formulation of policies to prevent excessive stock market volatility.
L2 Processing of Words Containing English /æ/-/ɛ/ and /l/-/ɹ/ Contrasts, and the Uses and Limits of the Auditory Lexical Decision Task for Understanding the Locus of Difficulty

Second language (L2) learners often exhibit difficulty perceiving novel phonological contrasts and/or using them to distinguish similar-sounding words. The auditory lexical decision (LD) task has emerged as a promising method to elicit the asymmetries in lexical processing performance that help to identify the locus of learners’ difficulty. However, LD tasks have been implemented and interpreted variably in the literature, complicating their utility in distinguishing between cases where learners’ difficulty lies at the level of perceptual and/or lexical coding. Building on previous work, we elaborate a set of LD ordinal accuracy predictions associated with various logically possible scenarios concerning the locus of learner difficulty, and provide new LD data involving multiple contrasts and native language (L1) groups. The inclusion of a native speaker control group allows us to isolate which patterns are unique to L2 learners, and the combination of multiple contrasts and L1 groups allows us to elicit evidence of various scenarios. We present findings of an experiment where native English, Korean, and Mandarin speakers completed an LD task that probed the robustness of listeners’ phonological representations of the English /æ/-/ɛ/ and /l/-/ɹ/ contrasts. Words contained the target phonemes, and nonwords were created by replacing the target phoneme with its counterpart (e.g., lecture/*[ɹ]ecture, battle/*b[ɛ]ttle). For the /æ/-/ɛ/ contrast, all three groups exhibited the same pattern of accuracy: near-ceiling acceptance of words and an asymmetric pattern of responses to nonwords, with higher accuracy for nonwords containing [æ] than [ɛ]. For the /l/-/ɹ/ contrast, we found three distinct accuracy patterns: native English speakers’ performance was highly accurate and symmetric for words and nonwords, native Mandarin speakers exhibited asymmetries favoring [l] items for words and nonwords (interpreted as evidence that they experienced difficulty at the perceptual coding level), and native Korean speakers exhibited asymmetries in opposite directions for words (favoring [l]) and nonwords (favoring [ɹ]; evidence of difficulty at the lexical coding level). Our findings suggest that the auditory LD task holds promise for determining the locus of learners’ difficulty with L2 contrasts; however, we raise several issues requiring attention to maximize its utility in investigating L2 phonolexical processing.