Miracle-dz/UniFAR-FTUs huggingface dataset:
Lighting environment predicts the relative abundance of male colour morphs in bluefin killifish (Lucania goodei) populations

Animal communication occurs when an animal emits a signal, the signal is transmitted through the environment, and then detected by the receiver. The environment in which signalling occurs should govern the efficacy of this process. In this study, I examine the relationship of lighting environment (light transmission and tree cover), location and the relative abundances of male colour morphs across seven drainages and 30 populations in the bluefin killifish, Lucania goodei. I found that males with blue anal fins were more common in populations with low transmission of ultraviolet (UV) and blue wavelengths. By contrast, males with red anal fins (and to a lesser extent, males with yellow anal fins) were more common in populations with high transmission of UV and blue wavelengths. High UV–blue light transmission should create a blue visual background and may make blue males less conspicuous and red males more conspicuous to conspecifics. Colour contrast with the visual background may be more important than total brightness of the colour pattern. These results indicate that natural selection for effective intraspecific communication drives the relative abundance of male colour morphs in different lighting habitats.
Aspergillus flavus myositis in a patient after liver transplantation

Abstract: We describe the first case of Aspergillus myositis caused by Aspergillus flavus in a liver transplant patient. The patient was a 43‐year‐old man who underwent liver transplantation because of end‐stage hepatic cirrhosis. He experienced pain in his left calf two months after the operation. Nodules with weakness, swelling, and flaring were found in the calf two wk later. Color ultrasonic examination showed uneven resonance in the left gastrocnemius. Needle aspiration and biopsy of the muscle revealed septate hyphae consistent with Aspergillus species and focal necrosis of the muscle cells with inflammatory cell infiltration. A culture subsequently yielded A. flavus, confirming histopathologic diagnosis. Sequencing of the internal transcribed spacer region confirmed the morphologic identification. The patient was first given itraconazole 0.2 g twice daily for one wk and was then switched to terbinafine 0.25 g once a day. A three‐month regimen of terbinafine therapy cured the infection, though the cultured fungus showed resistance to a number of antifungal agents. Aspergillus, a genus of ubiquitous molds, may cause invasive and even fatal disease in immunosuppressed patients.
Metagenomic-Based Screening and Molecular Characterization of Cowpea-Infecting Viruses in Burkina Faso

Cowpea, (Vigna unguiculata L. (Walp)) is an annual tropical grain legume. Often referred to as “poor man’s meat”, cowpea is one of the most important subsistence legumes cultivated in West Africa due to the high protein content of its seeds. However, African cowpea production can be seriously constrained by viral diseases that reduce yields. While twelve cowpea-infecting viruses have been reported from Africa, only three of these have so-far been reported from Burkina Faso. Here we use a virion-associated nucleic acids (VANA)-based metagenomics method to screen for the presence of cowpea viruses from plants collected from the three agro-climatic zones of Burkina Faso. Besides the three cowpea-infecting virus species which have previously been reported from Burkina Faso (Cowpea aphid borne mosaic virus [Family Potyviridae], the Blackeye cowpea mosaic virus—a strain of Bean common mosaic virus—[Family Potyviridae] and Cowpea mottle virus [Family Tombusviridae]) five additional viruses were identified: Southern cowpea mosaic virus (Sobemovirus genus), two previously uncharacterised polerovirus-like species (Family Luteoviridae), a previously uncharacterised tombusvirus-like species (Family Tombusviridae) and a previously uncharacterised mycotymovirus-like species (Family Tymoviridae). Overall, potyviruses were the most prevalent cowpea viruses (detected in 65.5% of samples) and the Southern Sudan zone of Burkina Faso was found to harbour the greatest degrees of viral diversity and viral prevalence. Partial genome sequences of the two novel polerovirus-like and tombusvirus-like species were determined and RT-PCR primers were designed for use in Burkina Faso to routinely detect all of these cowpea-associated viruses.
Vitamin D and the musculoskeletal health of older adults.

BACKGROUND The scientific literature related to vitamin D and bone health in older adults is extensive. OBJECTIVE This article aims to summarise key practice points regarding vitamin D and bone health in older adults, relevant to general practitioners, and to provide an overview of the background literature to enable GPs to appreciate the extent of the supporting evidence. DISCUSSION Vitamin D supplementation can prevent falls, particularly in the vitamin D deficient elderly. However, adequate vitamin D levels and dietary calcium intake are needed for effective primary fracture prevention with greatest benefits occurring in the elderly with vitamin D deficiency and/or low dietary calcium intakes. For secondary fracture prevention, ie. preventing further fractures in the elderly who have already sustained a fragility fracture, specific anti-osteoporosis treatment is necessary. However, to maximise the benefits of these medications, vitamin D deficiency should be corrected and adequate dietary calcium consumed.
RNAplex: a fast tool for RNA-RNA interaction search

MOTIVATION Regulatory RNAs often unfold their action via RNA-RNA interaction. Transcriptional gene silencing by means of siRNAs and miRNA as well as snoRNA directed RNA editing rely on this mechanism. Additionally ncRNA regulation in bacteria is mainly based upon RNA duplex formation. Finding putative target sites for newly discovered ncRNAs is a lengthy task as tools for cofolding RNA molecules like RNAcofold and RNAup are too slow for genome-wide search. Tools like RNAhybrid that neglects intramolecular interactions have runtimes proportional to O(m x n), albeit with a large prefactor. Still in many cases the need for even faster methods exists. RESULTS We present a new program, RNAplex, especially designed to quickly find possible hybridization sites for a query RNA in large RNA databases. RNAplex uses a slightly different energy model which reduces the computational time by a factor 10-27 compared to RNAhybrid. In addition a length penalty allows to focus the target search on short highly stable interactions. AVAILABILITY RNAplex can be downloaded at http://www.tbi. univie.ac. at/~htafer/ SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Near-Infrared Spectroscopy Does Not Reliably Detect the Cerebral Status in Adults During Aortic Arch Surgery - A Retrospective Trial

Introduction: To investigate relationship between intraoperative regional oxygen cerebral desaturation (rScO2) and the incidence of neurological deficit after aortic arch surgery in adult patients. Methods: This study was conducted in a retrospective fashion. 53 patients undergoing aortic arch surgery with antegrade selective cerebral perfusion during deep hypothermic circulatory arrest between 2010 and 2012 were included. ln all patients cerebral monitoring was performed using the near-infrared spectroscopy (NIRS) and a bispectral index electroencephalography (BIS). Cumulative values of rScO2 decrease > 20% of the baseline level (min%) captured as the area under the curve (rScO2 AUC) were calculated. Patients were divided in two groups: patients with (N-group) and without (Non-N group) a nonreversible neurological deficit, and patients with (D-group) and without (Non-D group) a reversible neurological deficit. Results: Of 53 patients, 49 (93%) suffered an aortic dissection Stanford Type A/De Bakey Type I and 4 (8%) patients a De Bakey Type II. Six (11%) patients died. Eleven (21%) patients developed a nonreversible (stroke, hemorrhage) and 23 (43%) patients a reversible neurological deficit (postoperative delirium). Postoperative delirium was significantly more frequent in the N-group (91%) compared to the Non-N group (33%). No significant difference was found for absolute rScO2 values < 50% and for the rScO2 AUC in both hemispheres between all groups. Conclusion: Regional oxygen cerebral desaturation measured by NIRS appears to be a poor indicator for neurological outcome after aortic arch surgery in adults.
Gene Expression Analysis of Two Epithelial-mesenchymal Transition-related Genes: Long Noncoding RNA-ATB and SETD8 in Gastric Cancer Tissues

Background: Cancer is the second cause of death after cardiovascular diseases worldwide. Tumor metastasis is the main cause of death in patients with cancer; therefore, unraveling the molecular mechanisms involved in metastasis is critical. Epithelial-mesenchymal transition (EMT) is believed to promote tumor metastasis. Based on the critical roles of long noncoding RNA-ATB (lncRNA-ATB) and SETD8 genes in cancer pathogenesis and EMT, in this study, we aimed to assess expression profile and clinicopathological relevance of these two genes in human gastric cancer. Materials and Methods: Quantitative real-time polymerase chain reaction was performed to assess these gene expressions in gastric cancer tissues and various cell lines. The associations between these gene expressions and clinicopathological characteristics were also analyzed. Results: Insignificant downregulation of lncRNA-ATB and significant upregulation of SETD8 in cancerous versus noncancerous gastric tissues were observed. Among different examined cell lines, all displayed both genes expression. Except for a significant inverse correlation between the expression levels of lncRNA-ATB and depth of invasion (T) and a direct association between SETD8 levels and advanced tumor grades, no significant association was found with other clinicopathological characteristics. Conclusion: lncRNA-ATB and SETD8 genes may play a critical role in gastric cancer progression and may serve as potential diagnostic/prognostic biomarkers in cancer patients.
Onset of optimal P 2 Y 12-ADP receptor blockade after ticagrelor and prasugrel intake in Non-ST elevation acute coronary syndrome

Laurent Bonello1,2; Marc Laine1; Laurence Camoin-Jau3; Frederic Noirot1; Régis Guieu4; Françoise Dignat-George2,5; Franck Paganelli1; Corinne Frere2,3 1Département de cardiologie, Hôpital universitaire Nord de Marseille, Assistance-Publique Hôpitaux de Marseille, Marseille, France; 2Vascular Research Center of Marseille, INSERM UMR-S 1076, Aix-Marseille Université, Marseille, France; 3Laboratoire d’hématologie Hôpital de la Timone, Marseille, France; 4Research Unit of Physiology and Pathophysiology in Extreme Oxygenation Conditions (UMR MD2), Faculty of Medicine, Aix-Marseille University, Marseille, France; 5Laboratoire d‘Hématologie et de Biologie Vasculaire, AssistancePublique Hôpitaux de Marseille, Centre hospitalo-universitaire de la Conception, Marseille, France
Lung Carcinoma in the Era of Personalized Medicine: The Role of Cytology

The search for new, targetable mutations in lung cancer has resulted in discoveries and frustrations and dramatic changes in the pathology practice. In this evolving scenario some questions seem relevant: where does cytology fit into this new era? How is the practice of cytology poised to ask and answer the necessary questions? How does the cytologist do ‘more and more with less and less’? We know that most lung cancer patients present with advanced disease and that diagnosis will be made on cytology and small biopsy specimens [5] . According to the 2012 National Comprehensive Cancer Network (NCCN) guidelines [6] , the first step in the therapy for recurrent or metastatic NSCLC is the establishment of histologic subtype and the second step is testing for EGFR mutations and ALK fusions yet nowhere is the word cytology even mentioned. In some of these patients, the only diagnostic and analyzable material is the one obtained from an FNA biopsy. In an attempt to guide the cytopathologist and offer strategies to navigate this new territory, this issue of Acta Cytologica, devoted to lung cancer, brings together data and techniques from international experts in the field of diagnosis, testing, epidemiology, new discoveries, and markers, and offers a multidisciplinary approach to these In 2004, three groups working independently [1–3] , almost simultaneously, reported remarkable findings: that activating mutations in the epidermal growth factor receptor (EGFR) were common in certain lung carcinomas and that these mutations correlated with the response of those lung tumors to therapy with gefitinib and erlotinib, both EGFR tyrosine kinase inhibitors (TKIs). This was the first time driver mutations in lung cancer that responded to targeted therapy had been identified, marking the beginning of a new era of personalized medicine in lung cancer. Prior to the discovery of these mutations, patients had been treated with EGFR TKIs but predicting who would respond and who would not was only imperfectly correlated with the histologic appearance of the tumor and the clinical profile of the patient. The lung cancer landscape has rapidly shifted in less than a decade since these discoveries. Pathology now drives treatment selection with the knowledge that there are histology-specific mutations and treatment agents readily available [4] . Departments of pathology have responded by refining criteria for the separation of nonsmall cell lung cancer (NSCLC), increasing the size and scope of diagnostic molecular laboratories and collaborating with clinical colleagues on an unprecedented level. Published online: November 24, 2012
Asgard archaea are the closest prokaryotic relatives of eukaryotes

In Spang et al. [1], we reported the discovery of Lokiarchaeum (Loki1) and two related lineages (Loki2 and Loki3, now referred to as Heimdallarchaeote LC_2 and LC_3). These were the first known representatives of the subsequently described Asgard superphylum [2], which branches as a sister clade to the TACK archaea [3]. We provided extensive phylogenomic evidence for the emergence of eukaryotes from within the Asgard archaea (thus supporting the two-domains [2D] tree of life), and the investigation of the Lokiarchaeum genome revealed the presence of more eukaryotic signature proteins (ESPs) than in any other described archaeal lineage [1]. In the recent study by Da Cunha et al. [4], the authors argue against the findings reported in Spang et al. Their main claims are that (i) the published genome data contains extensive contamination from distantly related organisms; (ii) a subset of universal genes supports a three-domains (3D) tree of life; and (iii) removing the elongation factor 2 (EF2) from the phylogenomic analysis breaks the Lokiarchaeota–Eukarya affiliation. Below, we show that the claims by Da Cunha et al. are unfounded.
Diversity and distribution of coral-associated bacteria

Coral reefs are the most biodiverse of all marine ecosystems; however, very little is known about prokaryotic diversity in these systems. To address this issue, we sequenced over 1000 bacterial 16S rDNAs from 3 massive coral species (Montastraea franksi, Diploria strigosa, and Porites astreoides) in Panama and Bermuda. Analysis of only 14 coral samples yielded 430 distinct bacterial ribotypes. Statistical analyses suggest that additional sequencing would have resulted in a total of 6000 bacterial ribotypes. Half of the sequences shared <93% identity to previously published 16S sequences, and therefore probably represent novel bacterial genera and species; this degree of novelty was substantially higher than that observed for other marine samples. Samples from the Panama corals were more diverse than those from Bermuda, paralleling diversity gradients seen in metazoans. The coral-bacteria associations were non-random. Different coral species had distinct bacterial communities, even when physically adjacent, while bacterial communities from the same coral species separated by time (~1 yr) or space (3000 km) were similar. Analysis of the branching coral Porites furcata showed that bacterial ribotypes can also be structured spatially within colonies. Therefore, corals and reefs represent landscapes of diverse, ecologically structured prokaryotic communities.
Physical Fitness and Telomere Length in Patients with Coronary Heart Disease: Findings from the Heart and Soul Study

Background Short telomere length (TL) is an independent predictor of mortality in patients with coronary heart disease (CHD). However, the relationship between physical fitness and TL has not been explored in these patients. Methods In a cross sectional study of 944 outpatients with stable CHD, we performed exercise treadmill testing, assessed self-reported physical activity, and measured leukocyte TL using a quantitative PCR assay. We used generalized linear models to calculate mean TL (T/S ratio), and logistic regression models to compare the proportion of patients with short TL (defined as the lowest quartile), among participants with low, medium and high physical fitness, based on metabolic equivalent tasks achieved (METs). Results 229 participants had low physical fitness (<5 METS), 334 had moderate physical fitness (5–7 METS), and 381 had high physical fitness (>7 METS). Mean ± T/S ratio ranged from 0.86±0.21 (5349±3781 base pairs) in those with low physical fitness to 0.95±0.23 (5566±3829 base pairs) in those with high physical fitness (p<.001). This association remained strong after adjustment for numerous patient characteristics, including measures of cardiac disease severity and physical inactivity (p = 0.005). Compared with participants with high physical fitness, those with low physical fitness had 2-fold greater odds of having TL in the lowest quartile (OR 2.39, 95% CI 1.60–3.55; p<.001). This association was similar after multivariable adjustment (OR 1.94, 95%CI, 1.18–3.20; p = 0.009). Self-reported physical inactivity was associated with shorter TL in unadjusted analyses, but not after multivariable adjustment. Conclusions We found that worse objectively-assessed physical fitness is associated with shorter leukocyte telomere length in patients with CHD. The clinical implications of this association deserve further study.
Hearing It Again and Again: On-Line Subcortical Plasticity in Humans

Background Human brainstem activity is sensitive to local sound statistics, as reflected in an enhanced response in repetitive compared to pseudo-random stimulus conditions [1]. Here we probed the short-term time course of this enhancement using a paradigm that assessed how the local sound statistics (i.e., repetition within a five-note melody) interact with more global statistics (i.e., repetition of the melody). Methodology/Principal Findings To test the hypothesis that subcortical repetition enhancement builds over time, we recorded auditory brainstem responses in young adults to a five-note melody containing a repeated note, and monitored how the response changed over the course of 1.5 hrs. By comparing response amplitudes over time, we found a robust time-dependent enhancement to the locally repeating note that was superimposed on a weaker enhancement of the globally repeating pattern. Conclusions/Significance We provide the first demonstration of on-line subcortical plasticity in humans. This complements previous findings that experience-dependent subcortical plasticity can occur on a number of time scales, including life-long experiences with music and language, and short-term auditory training. Our results suggest that the incoming stimulus stream is constantly being monitored, even when the stimulus is physically invariant and attention is directed elsewhere, to augment the neural response to the most statistically salient features of the ongoing stimulus stream. These real-time transformations, which may subserve humans' strong disposition for grouping auditory objects, likely reflect a mix of local processes and corticofugal modulation arising from statistical regularities and the influences of expectation. Our results contribute to our understanding of the biological basis of statistical learning and initiate a new investigational approach relating to the time-course of subcortical plasticity. Although the reported time-dependent enhancements are believed to reflect universal neurophysiological processes, future experiments utilizing a larger array of stimuli are needed to establish the generalizability of our findings.
Efficacy and tolerability of weekly docetaxel, cisplatin, and 5-fluorouracil for locally advanced or metastatic gastric cancer patients with ECOG performance scores of 1 and 2.

BACKGROUND Docetaxel, cisplatin, 5-fluorouracil (DCF) given every three weeks is an effective, but palliative regimen and significantly toxic especially in patients who have a low performance score. Here, we aimed to evaluate the efficacy and tolerability of a weekly formulation of DCF in locally advanced and metastatic gastric cancer patients. MATERIALS AND METHODS 64 gastric cancer patients (13 locally advanced and 51 metastatic) whose ECOG (Eastern Cooperative Oncology Group) performance status (PS) was 1-2 and who were treated with at least two cycles of weekly DCF protocol as first-line treatment were included retrospectively. The weekly DCF protocol included 25mg/m2 docetaxel, 25mg/m2 cisplatin, and 24 hours infusion of 750mg/m2 5-fluorouracil, repeated every week. Disease and patient characteristics, prognostic factors, treatment response, grade 3-4 toxicity related to treatment, progression free survival (PFS) and overall survival (OS) were evaluated. RESULTS Of the patients, 41 were male and 23 were female; the median age was 63 (29-82) years. Forty-one patients were ECOG-1 and 23 were ECOG-2. Of the total, 81.2% received at least three cycles of chemotherapy. Partial response was observed in 28.1% and stabilization in 29.7%. Overall, the disease was controlled in 57.8% whereas progression was noted in 42.2%. The median time to progression was 4 months (95%CI, 2.8-5.2 months) and median overall survival was 12 months (95%CI, 9.2-14.8 months). The evaluation of patients for grade 3-4 toxicity revealed that 10.9% had anemia, 7.8% had thrombocytopenia and 10.9% had neutropenia. Non-hematologic toxicity included renal toxicity (7.8%) and thrombosis (1.6%). CONCLUSIONS In patients with locally advanced or metastatic gastric cancer who were not candidates for DCF administered every-3-weeks, a weekly formulation of DCF demonstrated modest activity with minimal hematologic toxicity, suggesting that weekly DCF is a reasonable treatment option for such patients.
1 1 DEVELOPMENT OF THE NEONATAL CEREBRAL CORTEX

The neonatal period is a unique time of brain development. The cortical neuron undergoes major changes in the first few weeks after birth. It is a period of rapid growth, formation of new connections and progressive maturation of electrical and synaptic activity that translates into the formation of functional modules and networks in the brain. It is also a period when genetically programmed activity patterns are influenced by early environmental influences that result in the development of cortical maps. The neonatal brain is known to be vulnerable to injury and seizures, which are likely to disrupt normal development. There is a greater potential for neuroplasticity and modification of the developing networks in response to injury. The interaction of drugs with developing neurotransmitter and neuromodulatory systems may also influence normal maturation of the cortex. Therefore, a better understanding of the maturation of neural activity and the development of cortical connections and networks in the neonatal cortex is an important prerequisite for our ability to evaluate the cause and effect of neonatal seizures and their treatment.