Miracle-dz/UniFAR-FTUs huggingface dataset:
The complete mitogenome of brown trout (Salmo trutta fario) and its phylogeny

Abstract The complete mitochondrial genome of Salmo trutta fario, commonly known as brown trout, was sequenced using NGS technology. The mitochondrial genome size was determined to be 16 677 bp and composed of 13 protein-coding gene (PCG), 22 tRNAs, 2 rRNA genes, and 1 putative control region. The overall mitogenome composition of S. trutta fario is A: 28.13%, G: 16.44%, C: 29.47%, and T: 25.96% with A + T content of 54.09% and G + C content of 45.91%. The gene arrangement and the order are similar to other vertebrates. The phylogenetic tree constructed using 42 complete mitogenomes of Salmonidae fishes confirmed the position of the present species under the genus Salmo of subfamily Salmoninae. NGS platform was proved to be a rapid and time-saving technology to reveal complete mitogenomes.
Adenosine A2A receptors play an active role in mouse bone marrow‐derived mesenchymal stem cell development

Bone marrow‐derived mesenchymal stem cells (BM‐MSCs) play a role in wound healing and tissue repair and may also be useful for organ regeneration. As we have demonstrated previously that A2A adenosine receptors (A2AR) promote tissue repair and wound healing by stimulating local repair mechanisms and enhancing accumulation of endothelial progenitor cells, we investigated whether A2AR activation modulates BM‐MSC proliferation and differentiation. BM‐MSCs were isolated and cultured from A2A‐deficient and ecto‐5′nucleotidase (CD73)‐deficient female mice; the MSCs were identified and quantified by a CFU‐fibroblast (CFU‐F) assay. Procollagen α2 type I expression was determined by Western blotting and immunocytochemistry. MSC‐specific markers were examined in primary cells and third‐passage cells by cytofluorography. PCR and real time‐PCR were used to quantitate adenosine receptor and CD73 expression. There were significantly fewer CFU‐Fs in cultures of BM‐MSCs from A2AR knockout (KO) mice or BM‐MSCs treated with the A2AR antagonist ZM241385, 1 μM. Similarly, there were significantly fewer procollagen α2 type I‐positive MSCs in cultures from A2AR KO and antagonist‐treated cultures as well. In late passage cells, there were significantly fewer MSCs from A2A KO mice expressing CD90, CD105, and procollagen type I (P<0.05 for all; n=3). These findings indicate that adenosine and adenosine A2AR play a critical role in promoting the proliferation and differentiation of mouse BM‐MSCs.
Differentiating pulmonary transfusion reactions using recipient and transfusion factors

It is increasingly recognized that recipient risk factors play a prominent role in possible transfusion‐related acute lung injury (pTRALI) and transfusion‐associated circulatory overload (TACO). We hypothesized that both transfusion and recipient factors including natriuretic peptides could be used to distinguish TRALI from TACO and pTRALI.
Progressive Loss of Speech: A Neuropsychological Profile of Premotor Dysfunction

Several patients with ‘progressive loss of speech output’ or ‘progressive anarthria’ of degenerative origin have been reported in the literature. We report 5 clinical cases with slowly progressive loss of speech output and initially no deficit in other cognitive domains. The early clinical features were analysed in an attempt to identify the anatomo-functional systems implied in the degenerative process. The first phase of the disorder was characterised by impaired articulation consistent with speech apraxia, telegraphic style and a difficulty to elaborate a series of orofacial or hand movements. It is argued that these symptoms result from an impairment of complex motor processing due to dysfunction of the ventral premotor system. In the second phase, a decrease in spontaneous speech and self-initiated action was combined with exaggerated dependency on external stimuli, interpreted as dysfunction of the dorsal premotor system. We suggest that the neuropsychological profile of the disorder may result from progressive degeneration of the premotor cortex.
Progesterone receptor isoforms, agonists and antagonists differentially reprogram estrogen signaling

Major roadblocks to developing effective progesterone receptor (PR)-targeted therapies in breast cancer include the lack of highly-specific PR modulators, a poor understanding of the pro- or anti-tumorigenic networks for PR isoforms and ligands, and an incomplete understanding of the cross talk between PR and estrogen receptor (ER) signaling. Through genomic analyses of xenografts treated with various clinically-relevant ER and PR-targeting drugs, we describe how the activation or inhibition of PR differentially reprograms estrogen signaling, resulting in the segregation of transcriptomes into separate PR agonist and antagonist-mediated groups. These findings address an ongoing controversy regarding the clinical utility of PR agonists and antagonists, alone or in combination with tamoxifen, for breast cancer management. Additionally, the two PR isoforms PRA and PRB, bind distinct but overlapping genomic sites and interact with different sets of co-regulators to differentially modulate estrogen signaling to be either pro- or anti-tumorigenic. Of the two isoforms, PRA inhibited gene expression and ER chromatin binding significantly more than PRB. Differential gene expression was observed in PRA and PRB-rich patient tumors and PRA-rich gene signatures had poorer survival outcomes. In support of antiprogestin responsiveness of PRA-rich tumors, gene signatures associated with PR antagonists, but not PR agonists, predicted better survival outcomes. The better patient survival associated with PR antagonists versus PR agonists treatments was further reflected in the higher in vivo anti-tumor activity of therapies that combine tamoxifen with PR antagonists and modulators. This study suggests that distinguishing common effects observed due to concomitant interaction of another receptor with its ligand (agonist or antagonist), from unique isoform and ligand-specific effects will inform the development of biomarkers for patient selection and translation of PR-targeted therapies to the clinic.
Morphological and physiological changes exhibited by a Cd-resistant Dictyosphaerium chlorelloides strain and its cadmium removal capacity

ABSTRACT Changes induced on freshwater microalga Dictyosphaerium chlorelloides (Dcwt) acclimated in the laboratory until their survival in culture media enriched with cadmium 100 µM have been studied. Cadmium removal by living cells of this Cd-resistant (DcCdR100) strain was tested in cultures exposed to 100 µM Cd during 30 days. Cell dimensions were measured under light microscopy, and cell growth was studied. Photosynthetic yield (ΦPSII) was analyzed and the photosynthetic oxygen development and respiration response was obtained. Results show that DcCdR100 strain exhibited significant cell morphology changes in comparison to Dcwt cells, which affected both surface area and cell biovolume. Malthusian fitness analysis showed that DcCdR100 strain living in Cd-enriched culture had developed a lower capacity of nearly 50% growth, and its photosynthetic oxygen development and respiration response were significantly reduced in both light and dark photosynthetic phases. DcCdR100 strain showed a very high capacity to remove cadmium from the aquatic environment (over 90%), although most of the removed heavy metal (≈70%) is adhered to the cell wall. These specific characteristics of DcCdR100 cells suggest the possibility of using this strain in conjunction with Dcwt strain as bioelements into a dual-head biosensor, and in bioremediation processes on freshwater polluted with Cd.
Latest Neoproterozoic to Mid-Cambrian age for the main deformation phases of the Transantarctic Mountains: new stratigraphic and isotopic constraints from the Pensacola Mountains, Antarctica

New isotopic ages and a fresh understanding of stratigraphic relations among siliciclastic strata in the Pensacola Mountains along the northern margin of the East Antarctic craton result in removal of some constraints for the Proterozoic break-up of Rodinia and necessitate revision of the subsequent history of the East Antarctic margin. These rocks, formerly all included in the Patuxent Formation, were thought to be of mid-Neoproterozoic age, to have formed as a consequence of Rodinia rifting, and to have been deformed during a Neoproterozoic orogenic event. Our data show, in contrast, that these siliciclastic strata were deposited in two chronologically distinct basins. The older basin, in which the Hannah Ridge Formation (new name) accumulated, received sediment that contains detrital zircons of latest Neoproterozoic or Early Cambrian age. It was deformed and its contents uplifted and eroded prior to the late Mid-Cambrian in an orogenic event that we interpret as the early stage(s) of the Ross orogeny. The second basin formed later, accumulated turbidite-rich sediments of the redefined Patuxent Formation of Mid- and probably Late Cambrian age, and was subsequently deformed, possibly in Ordovician time. Review of both biostratigraphic and isotopic ages along the length of the Transantarctic Mountains indicates that almost everywhere the main episodes of deformation predate 500 Ma and are thus older than latest Mid-Cambrian, rather than Ordovician, as they are commonly considered to be. Only in the accreted Bowers and Robertson Bay terranes of northern Victoria land, which reveal no clear record of pre-latest Mid-Cambrian or older folding, is the principal episode of Ross orogenic deformation demonstrably younger than Late Cambrian.
A Word Embeddings Informed Focused Topic Model

In natural language processing and related ﬁelds, it has been shown that the word embed-dings can successfully capture both the semantic and syntactic features of words. They can serve as complementary information to topics models, especially for the cases where word co-occurrence data is insuﬃcient, such as with short texts. In this paper, we propose a focused topic model where how a topic focuses on words is informed by word embeddings. Our models is able to discover more informed and focused topics with more representative words, leading to better modelling accuracy and topic quality. With the data argumentation technique, we can derive an eﬃcient Gibbs sampling algorithm that beneﬁts from the fully local conjugacy of the model. We conduct extensive experiments on several real world datasets, which demonstrate that our model achieves comparable or improved performance in terms of both perplexity and topic coherence, particularly in handling short text data.
Monopolar radiofrequency treatment in Asian skin: An update

Dear Editor, Noninvasive skin-tightening devices have become increasingly popular, improving skin laxity with minimal risk and recovery time (Burns & Holden, 2006; Carruthers, Fabi, & Weiss, 2014). In 2011, the authors have surveyed dermatologists practicing the Thermage® system (Solta Medical Inc., Hayward, CA) (Abraham & Mashkevich, 2007; Sukal & Geronemus, 2008) in Korea, to better understand monopolar RF in Asian skin (Suh, Chang, Ryou, Lee, & Kim, 2011). With this updated questionnaire based study, we have analyzed their latest view. A questionnaire, consisting of 15 questions on the effectiveness, practice patterns, and side effects of monopolar RF on Asians, was distributed to dermatologists who have had more than 2 years of experience or have treated more than 100 patients with Thermage. All questions were multiple-choice and respondents could choose one or more answers. Among the 75 dermatologists who handed-in the questionnaire, 97.3% were Thermage CPT system users, and 2.7% had Thermage NXT. In 2011, 83% replied to use the ThermaCool TC and 17% Thermage NXT. As in 2011 (Suh et al., 2011), Asians in their 40s (89.3%) were considered to benefit most from Thermage (Figure 1a). Facial fat was considered important in terms of responsiveness to monopolar RF but there was great variation in preference among
A review of theoretical study of graphene chemical vapor deposition synthesis on metals: nucleation, growth, and the role of hydrogen and oxygen

Graphene has attracted intense research interest due to its extraordinary properties and great application potential. Various methods have been proposed for the synthesis of graphene, among which chemical vapor deposition has drawn a great deal of attention for synthesizing large-area and high-quality graphene. Theoretical understanding of the synthesis mechanism is crucial for optimizing the experimental design for desired graphene production. In this review, we discuss the three fundamental steps of graphene synthesis in details, i.e. (1) decomposition of carbon feedstocks and formation of various active carbon species, (2) nucleation, and (3) attachment and extension. We provide a complete scenario of graphene synthesis on metal surfaces at atomistic level by means of density functional theory, molecular dynamics (MD), Monte Carlo (MC) and their combination and interface with other simulation methods such as quantum mechanical molecular dynamics, density functional tight binding molecular dynamics, and combination of MD and MC. We also address the latest investigation of the influences of the hydrogen and oxygen on the synthesis and the quality of the synthesized graphene.
Effective Priming of Herpes Simplex Virus-Specific CD8+ T Cells In Vivo Does Not Require Infected Dendritic Cells

ABSTRACT Resolution of virus infections depends on the priming of virus-specific CD8+ T cells by dendritic cells (DC). While this process requires major histocompatibility complex (MHC) class I-restricted antigen presentation by DC, the relative contribution to CD8+ T cell priming by infected DC is less clear. We have addressed this question in the context of a peripheral infection with herpes simplex virus 1 (HSV). Assessing the endogenous, polyclonal HSV-specific CD8+ T cell response, we found that effective in vivo T cell priming depended on the presence of DC subsets specialized in cross-presentation, while Langerhans cells and plasmacytoid DC were dispensable. Utilizing a novel mouse model that allows for the in vivo elimination of infected DC, we also demonstrated in vivo that this requirement for cross-presenting DC was not related to their infection but instead reflected their capacity to cross-present HSV-derived antigen. Taking the results together, this study shows that infected DC are not required for effective CD8+ T cell priming during a peripheral virus infection. IMPORTANCE The ability of some DC to present viral antigen to CD8+ T cells without being infected is thought to enable the host to induce killer T cells even when viruses evade or kill infected DC. However, direct experimental in vivo proof for this notion has remained elusive. The work described in this study characterizes the role that different DC play in the induction of virus-specific killer T cell responses and, critically, introduces a novel mouse model that allows for the selective elimination of infected DC in vivo. Our finding that HSV-specific CD8+ T cells can be fully primed in the absence of DC infection shows that cross-presentation by DC is indeed sufficient for effective CD8+ T cell priming during a peripheral virus infection.
Etk Interaction with PFKFB4 Modulates Chemoresistance of Small-cell Lung Cancer by Regulating Autophagy

Purpose: Epithelial and endothelial tyrosine kinase (Etk), also known as bone marrow X kinase (Bmx), was found to be critical in modulating the chemoresistance of small-cell lung cancer (SCLC) in our preliminary study. However, the molecular mechanisms of Etk in SCLC chemoresistance remain poorly understood. Experimental Design: We determined correlation of Etk with autophagy in SCLC. And direct inhibition of autophagy was performed to validate its effect on chemoresistance. Coimmunoprecipitation (co-IP) and GST-pull down experiments were conducted to verify the interaction of Etk and PFKFB4, after a microarray analysis. In vitro and in vivo gain or loss-of-function analyses and evaluation of PFKFB4 expression in SCLC specimens, were done to validate its role in chemoresistance. Ibrutinib was administrated in SCLC cells to verify its synergistic anti-tumor effect with chemotherapy using preclinical models including a PDX model. Results: Downregulation of Etk suppressed autophagy in chemoresistant SCLC cells, and direct inhibition of autophagy sensitized cells to chemotherapy. PFKFB4 (6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4) was identified as a downstream target of Etk and an Etk-interacting protein, which promoted chemoresistance in SCLC and was associated with poor therapeutic response and prognosis. Furthermore, ibrutinib was found to exhibit a synergistic anti-tumor effect with chemotherapy in targeting Etk. Conclusions: Our results demonstrated for the first time that Etk interacts with PFKFB4 to promote SCLC chemoresistance through regulation of autophagy. Aberrant Etk and PFKFB4 can be predictive factors for the chemotherapy response as well as potential therapeutic targets in SCLC. Clin Cancer Res; 24(4); 950–62. ©2017 AACR.
Mechanisms of Androgen Induction of Sebocyte Differentiation

It has been difficult to induce the expected sebocyte differentiation in vitro with dihydrotestosterone (DHT). We reasoned that our culture system lacks differentiating factors, and peroxisome proliferator-activated receptors (PPARs) were the prime candidates. We tested PPAR activators informative about diverse PPAR subtypes, with and without DHT (10–6 M): BRL-49653 (10–6 M, PPAR-γ), WY-14643 (10–6 M, PPAR-α), and linoleic acid (LIN, 10–4 M, PPAR-d). Treatments were added in serum-free medium to cultures of rat preputial sebocytes. Control, DHT, BRL and BRL + DHT treatments caused 11, 25, 66 and 80%, respectively, of preputial cell colonies to differentiate into lipid-forming colonies (LFCs) (p <0.001). WY induced 20% and LIN over 95% LFC formation. PPAR-γ mRNA was identified in preputial sebocytes by the RNase protection assay. These data suggest that differentiation of sebocytes is transduced by PPARs and have implications for the development of new treatments for acne.
The utility of myocardial perfusion imaging before renal transplantation: a retrospective analysis

Background Renal transplantation (RT) reduces morbidity and mortality in patients with end-stage renal failure. Myocardial perfusion imaging provides prognostic information in patients with renal failure, but its role before transplantation remains unclear. We performed a retrospective review assessing the prognostic value of technetium-99m sestamibi myocardial perfusion imaging at a tertiary UK centre. Patients and methods We included scans performed between 2005 and 2012. Available scans were reanalysed to calculate the semiquantitative summed scores: sum rest score (SRS), sum stress score (SSS), sum difference score and sum motion score (SMS). Kaplan–Meier survival estimates assessed all-cause mortality and cardiac events according to scan findings, transplant decision and SSS. Cox-proportional hazards tested for an association between clinical/scan variables and all-cause mortality, and combined all-cause mortality/cardiovascular (CV) events. Results One hundred and thirty-eight scans were identified with complete follow-up. During a median 40.4-month follow-up, 21 patients died, with 11 nonfatal CV events. There was no significant difference between groups according to scan findings for mortality (log-rank P=0.17) or mortality/CV events (P=0.06). An SSS greater than 8 was associated with higher mortality and CV events combined (P=0.028). An abnormal baseline ECG [hazard ratio (HR): 16.1] and higher SRS (HR: 2.3) were associated independently with higher mortality; an abnormal ECG (HR: 3.4) also predicted higher cardiac events/mortality. Conclusion Moderate to severe perfusion defects by SSS were associated with higher mortality and CV events. Higher SRS was associated independently with increased mortality on multivariable analysis, highlighting a key role for semiquantitative analysis methods for risk stratification. An abnormal ECG was associated strongly with both endpoints, and may be a useful screening tool to select patients for further investigation.
Facilitating effective digital game-based learning behaviors and learning performances of students based on a collaborative knowledge construction strategy

ABSTRACT Researchers have recognized the potential of educational computer games in improving students’ learning engagement and outcomes; however, facilitating effective learning behaviors during the gaming process remains an important and challenging issue. In this paper, a collaborative knowledge construction strategy was incorporated into an educational computer game to facilitate students’ knowledge sharing and organizing during the game-based learning process. An experiment was conducted to examine the students’ learning behavioral patterns, group efficacy, and problem-solving awareness. The experimental results revealed that the proposed approach improved the students’ learning achievements and awareness of problem-solving. Moreover, from the analysis of the students’ behavior sequences, it was found that, with the collaborative knowledge construction mechanism, the students revealed significantly more aggressive learning behavioral patterns, such as “comparing and observing the learning targets” and “seeking clues and answers” during the gaming process. This implies that integrating the collaborative knowledge construction mechanism into the gaming process has great potential for helping students effectively learn and organize knowledge as well as fostering their awareness of applying the acquired knowledge to dealing with problems.
Industrialization of a perfusion bioreactor: Prime example of a non‐straightforward process

Bioreactors are essential enabling technologies for the translation of advanced therapies medicinal products from the research field towards a successful clinical application. In order to speed up the translation and the spread of novel tissue engineering products into the clinical routine, tissue engineering bioreactors should evolve from laboratory prototypes towards industrialized products. In this work, we thus challenged the industrialization process of a novel technological platform, based on an established research prototype of perfusion bioreactor, following a GMP‐driven approach. We describe how the combination of scientific background, intellectual property, start‐up factory environment, wise industrial advice in the biomedical field, design, and regulatory consultancy allowed us to turn a previously validated prototype technology into an industrial product suitable for serial production with improved replicability and user‐friendliness. The solutions implemented enhanced aesthetics, ergonomics, handling, and safety of the bioreactor, and they allowed compliance with the fundamental requirements in terms of traceability, reproducibility, efficiency, and safety of the manufacturing process of advanced therapies medicinal products. The result is an automated incubator‐compatible device, housing 12 disposable independent perfusion chambers for seeding and culture of any perfusable tissue. We validated the cell seeding process of the industrialized bioreactor by means of the Design of Experiment approach, whilst the effectiveness of perfusion culture was evaluated in the context of bone tissue engineering.