Miracle-dz/UniFAR-FTUs huggingface dataset:
Biodegradation of Ephedrine Isomers by Arthrobacter sp. Strain TS-15: Discovery of Novel Ephedrine and Pseudoephedrine Dehydrogenases

Arthrobacter sp. TS-15 is a newly isolated bacterium with the unique ability to degrade ephedrine isomers. The initiating steps of the novel metabolic pathway are described. Arthrobacter sp. TS-15 and its isolated ephedrine-oxidizing enzymes have potential for use in decontamination and synthetic applications. ABSTRACT The Gram-positive soil bacterium Arthrobacter sp. strain TS-15 (DSM 32400), which is capable of metabolizing ephedrine as a sole source of carbon and energy, was isolated. According to 16S rRNA gene sequences and comparative genomic analysis, Arthrobacter sp. TS-15 is closely related to Arthrobacter aurescens. Distinct from all known physiological paths, ephedrine metabolism by Arthrobacter sp. TS-15 is initiated by the selective oxidation of the hydroxyl function at the α-C atom, yielding methcathinone as the primary degradation product. Rational genome mining revealed a gene cluster potentially encoding the novel pathway. Two genes from the cluster, which encoded putative short-chain dehydrogenases, were cloned and expressed in Escherichia coli. The obtained enzymes were strictly NAD+ dependent and catalyzed the oxidation of ephedrine to methcathinone. Pseudoephedrine dehydrogenase (PseDH) selectively converted (S,S)-(+)-pseudoephedrine and (S,R)-(+)-ephedrine to (S)- and (R)-methcathinone, respectively. Ephedrine dehydrogenase (EDH) exhibited strict selectivity for the oxidation of the diastereomers (R,S)-(–)-ephedrine and (R,R)-(–)-pseudoephedrine. IMPORTANCE Arthrobacter sp. TS-15 is a newly isolated bacterium with the unique ability to degrade ephedrine isomers. The initiating steps of the novel metabolic pathway are described. Arthrobacter sp. TS-15 and its isolated ephedrine-oxidizing enzymes have potential for use in decontamination and synthetic applications.
Targeted deletion of PD-1 in myeloid cells induces antitumor immunity

PD-1 ablation regulates metabolism-driven lineage fate commitment of myeloid progenitors and differentiation of effector myeloid cells (see the related Focus by Rudd). A twist in the PD-1 tale Immunotherapies targeting programmed cell death protein 1 (PD-1) that can reverse T cell exhaustion have revolutionized the treatment of cancer. Here, by generating Pdcd1 floxed mice and conditionally deleting PD-1 in T cells or in myeloid cells, Strauss et al. have uncovered a previously unappreciated role for PD-1 expressed on myeloid cells in dampening antitumor immunity. They found that selective ablation of PD-1 in myeloid cells was just as effective at limiting tumor growth as global deletion of PD-1 and have documented the importance of PD-1 in regulating the development and functions of myeloid cells. Although the study does not question the role of PD-1 in T cell exhaustion, the results call for a rethink of how PD-1–centric therapies work. PD-1, a T cell checkpoint receptor and target of cancer immunotherapy, is also expressed on myeloid cells. The role of myeloid-specific versus T cell–specific PD-1 ablation on antitumor immunity has remained unclear because most studies have used either PD-1–blocking antibodies or complete PD-1 KO mice. We generated a conditional allele, which allowed myeloid-specific (PD-1f/fLysMcre) or T cell–specific (PD-1f/fCD4cre) targeting of Pdcd1 gene. Compared with T cell–specific PD-1 ablation, myeloid cell–specific PD-1 ablation more effectively decreased tumor growth. We found that granulocyte/macrophage progenitors (GMPs), which accumulate during cancer-driven emergency myelopoiesis and give rise to myeloid-derived suppressor cells (MDSCs), express PD-1. In tumor-bearing PD-1f/fLysMcre but not PD-1f/fCD4cre mice, accumulation of GMP and MDSC was prevented, whereas systemic output of effector myeloid cells was increased. Myeloid cell–specific PD-1 ablation induced an increase of T effector memory cells with improved functionality and mediated antitumor protection despite preserved PD-1 expression in T cells. In PD-1–deficient myeloid progenitors, growth factors driving emergency myelopoiesis induced increased metabolic intermediates of glycolysis, pentose phosphate pathway, and TCA cycle but, most prominently, elevated cholesterol. Because cholesterol is required for differentiation of inflammatory macrophages and DC and promotes antigen-presenting function, our findings indicate that metabolic reprogramming of emergency myelopoiesis and differentiation of effector myeloid cells might be a key mechanism of antitumor immunity mediated by PD-1 blockade.
DETECTING AND ANALYZING BOTS ON FINNISH POLITICAL TWITTER

This master’s thesis develops a machine learning model for detecting Twitter bots and applying the model to assess if bots were used to influence the 2019 Finnish parliamentary election. The aim of the thesis is to contribute to the growing information systems science literature on the use of social media and information systems to influence voters as well as to increase the general awareness in Finland of the effects of bots on Twitter. The thesis relies primarily on quantitative analysis of a dataset consisting of 550,000 unique Twitter accounts. The data was collected from Twitter during March 2019. The accounts in the dataset belong to humans and bots that were following 14 prominent Finnish politicians on Twitter. To determine which accounts are bots and to assess the feasibility of a new method for Twitter bot detection, a machine learning model that utilizes metadata-based features for classifying Twitter accounts as bots or humans is developed and tested on the dataset. The findings of this thesis indicate that a metadata-based approach is suitable for detecting bots and that there are several large botnets in the Finnish Twittersphere. Over 30% of the 550,000 accounts are labeled as bots by the model, which implies that the prevalence of bots is much higher than previously suggested by Twitter’s official estimates. Furthermore, a majority of the accounts seem inactive and either no longer being used or dormant and waiting for activation. The purpose of most of the bot accounts is obscure, and it is not certain how many of them are following and inflating the politicians’ popularity on purpose. Although the bots clearly increase the visibility of certain politicians, the effects of the bots on Finnish political Twitter are deemed negligible.
Revision of leccinoid fungi, with emphasis on North American taxa, based on molecular and morphological data

ABSTRACT The leccinoid fungi are boletes and related sequestrate mushrooms (Boletaceae, Basidiomycota) that have traditionally been placed in Leccinum, Boletus, Leccinellum, and a handful of other less familiar genera. These mushrooms generally feature scabers or scaber-like dots on the surface of the stipe, and they are often fairly tall and slender when compared with other boletes. They are ectomycorrhizal fungi and appear to be fairly strictly associated with specific trees or groups of related trees. In the present study, we investigate the phylogenetic relationships among the leccinoid fungi and other members of the family Boletaceae using portions of three loci from nuc 28S rDNA (28S), translation elongation factor 1-α (TEF1), and the RNA polymerase II second-largest subunit (RPB2). Two DNA data sets (combined 28S-TEF1 and 28S-TEF1-RPB2), comprising sequences from nearly 270 voucher specimens, were evaluated using two different phylogenetic analyses (maximum likelihood and Bayesian inference). Five major clades were obtained, and leccinoid fungi appeared in four of them. Taxonomic proposals supported by our results, representing a broadly circumscribed Leccinum that includes several sequestrate genera, along with Leccinellum, are made.
Family social capital and life satisfaction among older adults living alone in urban China: the moderating role of functional health

Abstract Objectives: The present study examined the moderating effects of functional health on the association between family social capital and life satisfaction among older adults who live alone in urban China. Method: Data for this study were derived from a study “Survey on older adults aged 70 and above who live alone in urban China,” which was carried out in five Chinese cities between November 2013 and May 2015. 2801 respondents passed the screening test of cognitive capacities and successfully completed the survey. Family social capital was operationalized as family interaction, number of children, and family relationship. Random-effects logistic regression was conducted to test the proposed hypotheses. Results: The moderating effects of functional health on the association between family interaction and life satisfaction were identified. While family interaction was positively associated with life satisfaction among older adults without disabilities who live alone, family interaction was negatively associated with life satisfaction among those with disabilities. Furthermore, the association between number of children and life satisfaction was nonsignificant among older adults without disabilities, when family relationship was controlled. However, number of children was positively associated with life satisfaction among those with disabilities. Finally, the results showed family relationship were important protective factors of life satisfaction among older adults living alone, regardless of their functional health levels. Conclusion: Theoretical aspects on how family social capital, living alone, and functional health are interwoven and influence mental health in later life were deliberated. Policy and intervention implications were discussed.
Induced production of a new polyketide in Penicillium sp. HS-11 by chemical epigenetic manipulation

Abstract Chemical investigation into the culture broth of the plant endophyte Penicillium sp. HS-11 in the modified Martin’s medium supplemented with subemylanilide hydroxamic acid (SAHA), a well-known histone deacetylase (HDACs) inhibitor, led to the isolation and identification of two induced products 4-epipenicillone B (1) and (R)-(+)-chrysogine (2). 4-epipenicillone B (1) was obtained as a new compound whose structure was elucidated by comprehensive spectroscopic methods including 1 D/2D NMR, HRESMS, and quantum chemistry calculations including DFT GIAO 13C NMR and ECD calculation. Acquisition of 4-epipenicillone B (1) enriched the chemical diversities of fungal natural products possessing a tricyclo [5.3. 1.03,8] undecane skeleton. The cytotoxic activity of 1 was also evaluated.
Glycemic load, dietary fiber, and added sugar and fecundability in 2 preconception cohorts.

BACKGROUND Glycemic load (GL) reflects the quantity and quality of carbohydrates in the diet; dietary fiber and added sugar are components of GL. Few epidemiologic studies have assessed the association between these dietary factors and fecundability. OBJECTIVE We prospectively evaluated the associations of GL, total carbohydrates, dietary fiber, and added sugar with fecundability. METHODS Snart Foraeldre (SF) and Pregnancy Study Online (PRESTO) are parallel web-based prospective preconception cohorts of couples attempting to conceive in Denmark and North America. At baseline, female participants completed a web-based questionnaire on demographic and lifestyle factors and a validated FFQ. We calculated GL, total carbohydrate intake, total dietary fiber, carbohydrate-to-fiber ratio, and added sugar based on reported frequencies for individual foods, standard recipes for mixed foods, and average serving sizes. The analysis included 2709 SF participants and 4268 PRESTO participants. We used proportional probabilities regression models to estimate fecundability ratios (FR) and 95% CIs. RESULTS Compared with an average daily GL of ≤100, FRs for an average daily GL of ≥141 were 0.89 (95% CI: 0.73, 1.08) in SF and 0.87 (95% CI: 0.77, 0.98) in PRESTO participants. Compared with consuming ≤16 g/d of dietary fiber, FRs for consuming ≥25 g/d were 0.99 (95% CI: 0.81, 1.22) in SF and 1.06 (95% CI: 0.94, 1.20) in PRESTO. Compared with a carbohydrate-to-fiber ratio of ≤8, FRs for a ratio of ≥13 were 0.86 (95% CI: 0.73, 1.01) in SF and 0.87 (95% CI: 0.78, 0.98) in PRESTO. Compared with ≤27 g/d of added sugar, FRs for ≥72 g/d were 0.87 (95% CI: 0.68, 1.10) in SF and 0.86 (95% CI: 0.75, 0.99) in PRESTO participants. CONCLUSIONS Among women attempting to conceive in Denmark and North America, diets high in GL, carbohydrate-to-fiber ratio, and added sugar were associated with modestly reduced fecundability.
Collective directional movement and the perception of social cohesion

We argue that perceivers associate collective directional movement – groups moving from one place to the next – with higher levels of social cohesion. Study 1 shows that pairs are rated as being more cohesive when described as engaging in directional movement compared to non‐directional activities. Study 2 replicates this finding using film clips. Study 3 reveals that the proximity of directionally moving dyads is a better predictor of perceived cohesion than behavioural synchrony. Study 4 replicates the original finding and reveals that perceptions of common fate and shared goals both contribute to the effect, with the former having more predictive power than the latter. We suggest that collective directional movement is an invariant part of social environments and is utilized by perceivers to make inferences about social dynamics.
Sequencing artifacts derived from a library preparation method using enzymatic fragmentation

DNA fragmentation is a fundamental step during library preparation in hybridization capture-based, short-read sequencing. Ultra-sonication has been used thus far to prepare DNA of an appropriate size, but this method is associated with a considerable loss of DNA sample. More recently, studies have employed library preparation methods that rely on enzymatic fragmentation with DNA endonucleases to minimize DNA loss, particularly in nano-quantity samples. Yet, despite their wide use, the effect of enzymatic fragmentation on the resultant sequences has not been carefully assessed. Here, we used pairwise comparisons of somatic variants of the same tumor DNA samples prepared using ultrasonic and enzymatic fragmentation methods. Our analysis revealed a substantially larger number of recurrent artifactual SNVs/indels in endonuclease-treated libraries as compared with those created through ultrasonication. These artifacts were marked by palindromic structure in the genomic context, positional bias in sequenced reads, and multi-nucleotide substitutions. Taking advantage of these distinctive features, we developed a filtering algorithm to distinguish genuine somatic mutations from artifactual noise with high specificity and sensitivity. Noise cancelling recovered the composition of the mutational signatures in the tumor samples. Thus, we provide an informatics algorithm as a solution to the sequencing errors produced as a consequence of endonuclease-mediated fragmentation, highlighted for the first time in this study.
A New Method for the Prediction of Carbon Sequestration in Reforested Areas Using a Fuzzy-ART- BP Neural Network

Global emissions of carbon dioxide the main cause of greenhouse effects and, as consequence, global warming, endanger the lives of all living species on the planet. Thus, it becomes essential to adopt measures to reduce carbon emissions, aiming to environmental sustainability and also the development of efficient methods for quantifying the flow of carbon into the atmosphere. Therefore, this paper presents an intelligent system to quantify emissions and carbon sequestration in reforestation areas, medium and long term. The proposed system consists of a combination fuzzy-ART neural network architecture and a multilayer feedforward training based on the backpropagation algorithm. Aiming to test the proposed system, we present an application in an area located in a reforested area in the Amazon region of Mato Grosso-Brazil, on a farm with land area of approximately 8939 hectare.
Interaction of silver nanoparticles with aerobic granular sludge in textile wastewater treatment bioreactors

The use of silver nanoparticles (Ag NPs) in textile industry has been increasing and their occurrence in wastewater is expected to rise accordingly. The antimicrobial properties of Ag NPs suggest a potential negative impact on biological wastewater treatment systems. This study assessed the impacts of 5mg L Ag NPs on aerobic granular sludge (AGS) in sequencing batch reactors treating textile wastewater. Nuclear microscopy (NM) was applied for imaging and quantitative elemental analysis. Successful granulation was achieved after 35 days, irrespective of Ag NP presence. Although Ag NPs had induced an early AGS deterioration, in the long term they seemed to enhance AGS settling properties. Furthermore, AGS treatment performance and cell integrity were not affected by Ag NPs. A quantitative analysis of the major fractions of the extracellular polymeric substances (EPS) suggested that Ag NPs interacted with the protein fraction, which was further confirmed by NM. The Ag NPs-containing sample examination through NM also showed that < 10μm Ag NPs agglomerates were presumably distributed uniformly in the surface of both granular and floc-like structures, although in AGS it was preferentially associated with an external EPS layer. The Ag distribution in AGS demonstrated that the granule outer layers hindered the dispersion of Ag NPs into the central part. Overall, AGS showed the ability to withstand Ag NPs toxicity, but granule structural stability was negatively influenced by Ag NPs. Furthermore, the detailed NM compartmentalization of Ag NPs in sludge components provided new and relevant information concerning the pattern of Ag NPs retention.
A 3.4 GHZ FAST-LOCKING PLL USING TRANSMISSION GATE CHARGE-PUMP IN 0.18μM CMOS FOR HDMI APPLICATIONS

A 3.4 GHz Phase Locked Loop (PLL) with a Differential Ring oscillator is simulated in a 0. 18μm CMOS process with 1.8V power supply. The reference clock frequency is 212.5 MHz with a mod 16 frequency divider the PLL generates a 3.4 GHz frequency. The proposed PLL can be locked from 2.539 GHz to 5.0793 GHz with a lock range of 2.54 GHz with 48.4% of duty cycle. The peak-peak jitter is 8.786ps with an RMS jitter of 1.18 ps and pull-in time 170ns (fast lock-in time). The PLL consumes 18.8mW power from a 1.8V power supply. PLL Blocks are simulated with 1.8V, 0. 18μm CMOS Technology using Cadence-Virtuoso tool.
Communities of practice in a large distributed agile software development organization - Case

Context: Communities of practice—groups of experts who share a common interest or topic and collectively want to deepen their knowledge—can be an important part of a successful lean and agile adoption in particular in large organizations. Objective: In this paper, we present a study on how a large organization within Ericsson with 400 persons in 40 Scrum teams at three sites adopted the use of Communities of Practice (CoP) as part of their transformation from a traditional plan-driven organization to lean and agile. Methods: We collected data by 52 semi-structured interviews on two sites, and longitudinal non-partic-ipant observation of the transformation during over 20 site visits over a period of two years. Results: The organization had over 20 CoPs, gathering weekly, bi-weekly or on a need basis. CoPs had several purposes including knowledge sharing and learning, coordination, technical work, and organizational development. Examples of CoPs include Feature Coordination CoPs to coordinate between teams working on the same feature, a Coaching CoP to discuss agile implementation challenges and successes and to help lead the organizational continuous improvement, an end-to-end CoP to remove bottlenecks from the ﬂow, and Developers CoPs to share good development practices. Success factors of well-functioning CoPs include having a good topic, passionate leader, proper agenda, decision making authority, open community, supporting tools, suitable rhythm, and cross-site participation when needed. Organizational support include creating a supportive atmosphere and providing a suitable infrastructure for CoPs. Conclusions: In the case organization, CoPs were initially used to support the agile transformation, and as part of the distributed Scrum implementation. As the transformation progressed, the CoPs also took on the role of supporting continuous organizational improvements. CoPs became a central mechanism behind the success of the large-scale agile implementation in the case organization that helped mitigate some of the most
Progressive Si-nanowire Device Technology Scaling

As channel length of device shrink towards nanoscale regime, Nanowire Gate-All-Around (GAA) FET is a potential next generation candidate to achieve high performance target set by ITRS. In this paper, we report variation in the behavior of Sinanowire GAA FET by scaling the gate length from 180nm to 22nm. Both static and dynamic characteristic of CMOS inverter at 45nm is obtained by using 3-D fabrication process in TCAD. In device simulator, quantum potential and velocity saturation models are included. In inverter design the driving current of PFET is matched by using two Si-nanowires in channel region. A good static and dynamic behavior is observed for Si-nanowire GAA FET inverter. The high voltage gain and noise margin for a wide range of Vdd values is obtained, indicating excellent potential of these devices even for low power applications. The results are benchmarked with corresponding FINFET based technology for area, speed and power dissipation. We show that nanowire based CMOS offer upto 25% reduction in layout area and 74% reduction in power. KeywordsSi-nanowire GAA FET; device performance parameter; TCAD; CMOS
Clinical manifestation and imageological analysis of 52 cases of lung adenocarcinoma.

Objective: To investigate the clinical manifestation and imageological characteristic of these patients with lung adenocarcinoma.Methods: The clinical data of 52 patients with lung adenocarcinoma were analyzed retrospectively,these datum include their clinical manifestation and imageological characteristics.Results: Main clinical manifestation of these patients include cough,hemoptysis,chest pain and the manifestation of other metastatic lesions,and the cancer often transferred to brain,liver,bone,adrenal,etc,five-year survival rate of patients with lymph node metastasis decreased significantly.Forty seven cases were performed with common chest X-ray check,nothing were found in 6 cases,thirteen cases were central type lung cancer,twenty five cases were peripheral type lung cancer,three cases were bronchioloalveolar cancer.All patients were performed with computed tomographic (CT) screening,lesion region were round,oval,lobulated.Most edge of lesion region were incisural shape,small burred or spine-like protuberances.Conclusion: Considering clinical symptoms,we can make a more accurate diagnosis of lung cancer with CT,and histiocyte can finally be diagnosed as lung adenocarcinoma with histological examination.