Miracle-dz/UniFAR-FTUs huggingface dataset:
Gastric Mucosa-associated Lymphoid Tissue Lymphoma_ Posttransplant Lymphopoliferative Disorder

Epstein-Barr virus (EBV)-associated posttransplant lymphoproliferative disorder (PTLD) is a rare, but life-threatening, complication following solid organ transplantation or haematopoietic stem cell transplantation (HSCT). The clinical features of PTLD are usually nonspecific and patients present a series of clinical symptoms depending on the extent and severity of organ involvement. In addition to the lymph nodes, extra nodal sites include the central nervous system (CNS), skin, gastrointestinal tract, lungs, kidney and bone marrow. PTLD encompasses a wide range of diseases, including benign hyperplasia and malignant lymphomas. However, there are no reports of mucosa-associated lymphoid tissue (MALT) lymphoma after allogenic HSCT (allo-HSCT). EBV is known to play a major role in the development of PTLD after allo-HSCT, and monitoring of EBVDNA in high-risk patients after HSCT is necessary. Because of the wide spectrum of diseases and scarcity of prospective phase II and III studies, there are currently no uniformly applicable guidelines for the treatment of PTLD after allo-HSCT. The treatment strategy for PTLD is controversial, and the outcomes of common therapies including immune suppression reduction (ISR), multiagent chemotherapy and donor lymphocyte infusion are not satisfactory. In recent years, rituximab (a monoclonal antibody directed against CD20) has been confirmed to be efficient in the prevention and treatment of PTLD. Herein, we report a patient who developed gastric MALT lymphoma with elevation of the EBV-DNA load in the peripheral blood after receiving allo-HSCT against severe aplastic anemia (SAA). The patient was finally completely relieved using a combination of ISR and chemotherapy with a regimen of rituximab, cyclophosphamide, vincristine and prednisone (R-CVP). A 25-year-old EBV-seronegative woman with SAA received allo-HSCT from a 6/6 human leukocyte antigen-matched, EBV-seronegative related donor (her brother). The patient received a conditioning regimen of 50 mg/kg cyclophosphamide (CTX) (days 6 to 3) and 3.15 mg/kg rabbit anti-thyroglobulin antibodies (ATG) (days 6 to 3). At the same time, 1 mg/d kg methylprednisolone (days 6 to 3) was given as a
Chromatin mapping identifies BasR, a key regulator of bacteria-triggered production of fungal secondary metabolites

The eukaryotic epigenetic machinery can be modified by bacteria to reprogram the response of eukaryotes during their interaction with microorganisms. We discovered that the bacterium Streptomyces rapamycinicus triggered increased chromatin acetylation and thus activation of the silent secondary metabolism ors gene cluster in the fungus Aspergillus nidulans. Using this model, we aim understanding mechanisms of microbial communication based on bacteria-triggered chromatin modification. Using genome-wide ChIP-seq analysis of acetylated histone H3, we uncovered the unique chromatin landscape in A. nidulans upon co-cultivation with S. rapamycinicus and relate changes in the acetylation to that in the fungal transcriptome. Differentially acetylated histones were detected in genes involved in secondary metabolism, in amino acid and nitrogen metabolism, in signaling, and encoding transcription factors. Further molecular analyses identified the Myb-like transcription factor BasR as the regulatory node for transduction of the bacterial signal in the fungus and show its function is conserved in other Aspergillus species.
gene expression analyses identify a relationship between stanniocalcin 2 and the malignant behavior of colorectal cancer

Background: Colorectal cancer (CRC) is one of the main causes of cancer-related death worldwide. Stanniocalcin 2 (STC2), a secreted glycoprotein, has been suggested to exert various functions in progression of many cancers. However, the precise biological role in CRC is not fully understood. Therefore, this study based on several public datasets aims at investigating the roles of STC2 in CRC. Methods: We used The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases to evaluate the STC2 expression and its clinical significance in CRC. Cell migration and invasion by STC2 overexpression and knockdown were assessed using Transwell migration and Matrigel invasion assays. We next performed RNAseq analysis on SW480 cells with or without STC2 overexpression. Differentially expressed genes were selected by using fold-change . 5 and P -value , 0.05. Results: In this study, we found that STC2 level was significantly higher in CRC than that in adjacent noncancerous tissues from TCGA and GEO. Tumors with high mRNA levels of STC2 were more common in patients with rectal cancer, left-sided CRC, advanced T-stage (T3–T4), positive lymph node involvement and advanced AJCC-stage (III–IV) from TCGA. STC2 displayed the negative correlation with the expressions of epithelial cell markers, while it was positively correlated with the expressions of mesenchymal cell markers, MMPs and the epithelial-mesenchymal transition (EMT)-related transcriptional factors. Furthermore, we found that STC2 promoted cell migration and invasion in vitro. And a group of differentially expressed genes, which were modulated by STC2, were identified from RNAseq analyses. Conclusion: Our study demonstrates that STC2 is overexpressed in CRC compared with normal tissues, and promotes CRC cell migration and invasion. Our data suggest that STC2 may be used as a potential biomarker for clinical application and target therapy in future.
Comparative analysis of antioxidant and phenolic content of chloroform extract/fraction of Terminalia chebula

In the present study, two chloroform extracts of fruits of Terminalia chebula viz. “CHL1” and “CHL 2” prepared by maceration and sequential method respectively was compared for their antioxidant efficacy and phenolic content. The extraction procedure of plant material plays an important role in the activity of phytochemicals. Also, the assessment of antioxidant capacity of phytochemicals cannot be executed precisely by any single method due to complex nature of phytochemicals as multiple reaction characteristics and mechanisms can be involved. So, no single assay could accurately reflect comparison in a mixed or complex system. Therefore in the present study the comparison of extracts was done by using most widely used assays viz. DPPH, deoxyribose, reducing power, chelating power and lipid peroxidation assay. Furthermore, the UV-Vis spectrum of both extracts and the correlation between total phenolic content was examined in order to give an orientation to the search of phytochemicals responsible for their activity. From the results, it was concluded that antioxidant activity and phenolic compounds were predominant in the ‘CHL 2’ prepared by sequential method. The present study enlightening the useful extraction procedure of plant material.
Antifungal agents: their diversity and increasing sophistication

Since the 1950s, antifungal drug discovery has identified three classes of natural products (griseofulvin, polyenes and echinocandins) and four classes of synthetic chemicals (allylamines, azoles, flucytosine and phenylmorpho-lines) with clinical value against fungal infections. For life threatening fungal disease, the polyene amphotericin B is still a common choice despite toxic side-effects. The azoles remain the most widely used group of anti fungals active against a wide range of mycoses, benefiting from creative chemistry to boost their effectiveness. More recently, the echinocandins show great promise, with caspofungin licensed for clinical use in 2002 and two other molecules close to registration. New advances in molecular genetics afford the promise of revealing new antifungal targets, together with new agents to inhibit those targets specifically.
UvA-DARE (Digital voters? impact of on

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Pleistocene Amphibians and Reptiles in Britain and Europe

1. Introduction 2. The Pleistocene in Britain and Europe 3. The European herpetofauna, Paleocene through Pleistocene 4. A bestiary: annotated taxonomic accounts 5. Pleistocene herpetological localities 6. Herpetological species as paleoenvironmental indicators 7. Herpetological population adjustments in the Pleistocene of Britain and Europe 8. Extinction patterns in the herpetofaunas of Britain and Europe and North America compared 9. Pleistocene events in the herpetofaunas of Britain and Europe and North American compared
Title : Dumpster diving in RNA-sequencing to find the source of every last read Authors :

High throughput RNA sequencing technologies have provided invaluable research opportunities across distinct scientific domains by producing quantitative readouts of the transcriptional activity of both entire cellular populations and single cells. The majority of RNA-Seq analyses begin by mapping each experimentally produced sequence (i.e., read) to a set of annotated reference sequences for the organism of interest. For both biological and technical reasons, a significant fraction of reads remains unmapped. In this work we develop a read origin protocol (ROP) aimed at discovering the source of all reads, originated from complex RNA molecules, recombinant antibodies and microbial communities. Our approach can account for 98.8% of all reads across poly(A) and ribodepletion protocols. Furthermore, using ROP we show that immune profiles of asthmatic individuals are significantly different from the control individuals with decreased average per sample T-cell/B-cell receptor diversity and that immune diversity is inversely correlated with microbial load. This demonstrates the potential of ROP to exploit unmapped reads to better understand the functional mechanisms underlying the connection between immune system, microbiome, human gene expression, and disease etiology. The ROP pipeline is freely available at https://sergheimangul.wordpress. com/rop/ . CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not . http://dx.doi. org/10.1101/053041 doi: bioRxiv preprint first posted online May. 13, 2016;
A Synthetic Community Approach Reveals Plant Genotypes Affecting the Phyllosphere Microbiota

The identity of plant host genetic factors controlling the composition of the plant microbiota and the extent to which plant genes affect associated microbial populations is currently unknown. Here, we use a candidate gene approach to investigate host effects on the phyllosphere community composition and abundance. To reduce the environmental factors that might mask genetic factors, the model plant Arabidopsis thaliana was used in a gnotobiotic system and inoculated with a reduced complexity synthetic bacterial community composed of seven strains representing the most abundant phyla in the phyllosphere. From a panel of 55 plant mutants with alterations in the surface structure, cell wall, defense signaling, secondary metabolism, and pathogen recognition, a small number of single host mutations displayed an altered microbiota composition and/or abundance. Host alleles that resulted in the strongest perturbation of the microbiota relative to the wild-type were lacs2 and pec1. These mutants affect cuticle formation and led to changes in community composition and an increased bacterial abundance relative to the wild-type plants, suggesting that different bacteria can benefit from a modified cuticle to different extents. Moreover, we identified ein2, which is involved in ethylene signaling, as a host factor modulating the community's composition. Finally, we found that different Arabidopsis accessions exhibited different communities, indicating that plant host genetic factors shape the associated microbiota, thus harboring significant potential for the identification of novel plant factors affecting the microbiota of the communities.
“That's very nice, but will it get me pregnant?”

I have to confess, I didn't understand the question at the time. A year later, I am starting to. I was an eager new general practitioner and member of a research team investigating how the internet might influence patients' use of primary care, and we had just begun offering free internet access at our deprived inner city practice. I had filled the waiting room with posters advertising the service, and a member of staff was on hand to guide newcomers through the web. With our new PC and a cup of coffee, we would help …
A Coordinate-based Fuzzy Encoding Strategy for Compressing Grayscale Images

Image compression techniques realized in various ways have become an indispensable part in the practical storage and transmission of digital images. In this study, we present a novel method of lossy compression based on sampling and fuzzy encoding for grayscale images and discuss the problem of their reconstruction. First, an image is divided into a number of non-overlapping blocks of pixels. Next, we perform multiple rounds of random sampling. In each round, a number of pixels are selected as prototypes for the representing the corresponding block. Each pixel in the block is reconstructed based on the gray-levels of the prototypes and membership degrees computed with respect to the distances of each pixel to the prototypes. The reconstruction abilities delivered by the prototypes are quanti�ed by a certain objective �delity criterion and the prototypes leading to lowest reconstruction error are determined as representatives of current block. Finally, once the representatives in each block have been determined, we reconstruct the whole image based on these prototypes. Experimental studies as well as visual evaluations show that the proposed algorithm is able to achieve high compression ratios while preserving the overall �delity in the decompressed images.
End‐to‐end quantitative analysis modeling of near‐infrared spectroscopy based on convolutional neural network

During the near‐infrared spectroscopy analysis process, modeling the quantitative relationship between the collected spectral information and target components is an important procedure. Before using the traditional modeling methods, it is often necessary to select the most featured wavelengths and eliminate those uninformative wavelengths. However, the wavelength selection algorithms can not only increase the model complexity but also may contain some adjustable parameters, which need the users to have more expertise knowledge and experiences. To solve this problem, this paper proposed a novel end‐to‐end quantitative analysis modeling method for near‐infrared spectroscopy based on convolutional neural network (CNN), which directly takes the whole range of collected raw spectral information as input without wavelength selection. The public corn NIR dataset was taken as example to validate the efficiency of proposed method. The experimental results showed that, firstly, if all the whole range of raw spectral information was taken as the input of modeling, the generalized performance of CNN outperforms the traditional methods, and the difference is statistically significant; secondly, if the traditional methods were combined with wavelength selection algorithms, their generalized performances were similar to CNN model; there is no statistical difference. The results indicated that applying the deep learning methods (take CNN as representative) to establish the quantitative analysis model of near‐infrared spectroscopy is easy to use and has more potential popularize values.
Extracellular matrix proteomics identifies molecular signature of symptomatic carotid plaques

1 jci.org Introduction Atherosclerosis is a chronic and progressive disease of the arterial wall and the main underlying cause of stroke, myocardial infarction (MI), and cardiac death (1, 2). The evolution of atherosclerotic plaques involves endothelial dysfunction, accumulation of lipids and inflammatory cells, as well as remodeling of the extracellular matrix (ECM). Previously, atherosclerotic plaques were defined by histological appearance. Plaques with thin fibrous caps and a large lipid pool were classified as “vulnerable lesions. ” Lipid-poor plaques rich in ECM with thick fibrous caps were considered “stable. ” Recent findings have challenged this “vulnerable plaque” concept (3, 4): First, intravascular imaging revealed that only a small percentage of thin-capped plaques cause clinical events (4, 5). Second, shifts in risk factor profiles (e.g., smoking cessation) and widespread use of statins are associated with a change in histopathological appearance of atherosclerotic lesions: “vulnerable plaques” with large lipid pools are far less common (3). Instead, superficial plaque erosions may trigger more cardiovascular events (3, 4). BACKGROUND. The identification of patients with high-risk atherosclerotic plaques prior to the manifestation of clinical events remains challenging. Recent findings question histologyand imaging-based definitions of the “vulnerable plaque,” necessitating an improved approach for predicting onset of symptoms.
experience of insomnia, symptom attribution and treatment preferences in individuals with moderate to severe cOPD: a qualitative study

: Persons with chronic obstructive pulmonary disease (COPD) are known to have poor sleep quality. Acceptance of and adherence to therapies for sleep problems may depend on how the person with COPD regards the source of his sleep problem, yet little is known about their attribution as to the cause of these sleep symptoms. The objective of this study was to describe the subjective sleep complaints of individuals with COPD along with their attributions as to the cause of these symptoms, and their treatment preferences for insomnia. Three focus groups were conducted (N = 18) with participants who have moderate to severe COPD. Focus group data were transcribed, compared and contrasted to identify themes of attribution. Participants reported difficulty falling asleep, staying asleep, and daytime sleepiness. They attributed their sleep problems primarily to their pulmonary symptoms, but also poor air quality (thick humid air) and death anxiety when awake during the night. There was no clear preference for type of treatment to remedy this problem (medication, cognitive therapy), although they indicated that traveling to the clinic was difficult and should be avoided as much as possible. These data suggest that environmental manipulation to improve air quality (eg, air conditioning) and modifications to reduce death anxiety could be beneficial to persons with COPD. In-person multi-session therapy may not be acceptable to persons with moderate to severe COPD, however internet-based therapy might make treatment more accessible.
Association for the Development of Education in Africa

The Working Group on the Teaching Profession launched the Teacher Management and Support (TMS) programme in 1993. The initiative was a culmination of careful negotiations, consultations and consensus building among donors, ministries of education and teacher=s organisations on key TMS issues. The Working Group and ministries of education identified the following issues affecting teachers, performance, learning and conditions of service in general:
Hydration Status of Geriatric Patients Is Associated with Changes in Plasma Proteome, Especially in Proteins Involved in Coagulation

Due to multifactorial reasons, such as decreased thirst and decreased total body water, elderly patients are vulnerable to dehydration. The study aims to investigate whether moderate dehydration or hyperhydration affects the blood proteome. Blood samples, medication, and bioelectrical impedance analysis (BIA) details were collected from 131 geriatric patients (77 women and 54 men aged 81.1 ± 7.2 years). Based on an evaluation by Bioelectrical Impedance Vector Analyses (BIVAs) of this cohort, for each hydration status (dehydrated, hyperhydrated, and control), five appropriate blood plasma samples for both males and females were analyzed by liquid chromatography–mass spectrometry (LC-MS). Overall, 262 proteins for female patients and 293 proteins for male patients could be quantified. A total of 38 proteins had significantly different abundance, showing that hydration status does indeed affect the plasma proteome. Protein enrichment analysis of the affected proteins revealed “Wound Healing” and “Keratinization” as the two main biological processes being dysregulated. Proteins involved in clot formation are especially affected by hydration status.
Seafood Watch

Disclaimer Seafood Watch® strives to have all Seafood Reports reviewed for accuracy and completeness by external scientists with expertise in ecology, fisheries science and aquaculture. Scientific review, however, does not constitute an endorsement of the Seafood Watch® program or its recommendations on the part of the reviewing scientists. Seafood Watch® is solely responsible for the conclusions reached in this report. Tilapia Tilapia (Oreochromis spp.)
Developing quality indicators for the care of HIV-1-infected pregnant women in a Dutch Caribbean setting

Effective interventions to prevent mother-to-child HIV transmission (PMTCT) exist and, when properly applied reduce the risk of vertical HIV transmission. As part of optimizing PMTCT in the Dutch Caribbean we developed a set of valid, reliable and applicable indicators in order to assess the quality of prenatal and delivery care in HIV-infected (pregnant) women and their newborns. A multidisciplinary expert panel of 18 experts reviewed and prioritized recommendations extracted from locally used international PMTCT guidelines according a 3-step modified Delphi procedure. The content validity was assessed during 2 consecutive rounds with a panel meeting in-between. Subsequently, the feasibility, sample size, inter-observer reliability, sensitivity to change and case mixed stability of the potential indicators were tested for a data set of 153 HIV-infected women, 108 pregnancies of HIV-infected women and 79 newborns of HIV-infected women in outpatient and inpatient clinical setting of Aruba, Curaçao and St Maarten from 2000 to 2010. The panel selected and prioritized 13 potential indicators. Applicability could not be tested for 4 indicators regarding HIV-screening in pregnant women because of lack of data. Four indicators performed satisfactorily for Curaçao and 3 for St Maarten whilst none for Aruba. A systemic evidenceand consensus-based approach was used to develop quality indicators for PMTCT in 3 Dutch Caribbean settings. Applicability testing of quality indicators regarding PMTCT in different settings is essential before they are used in quality improvement approaches. R1 R2 R3 R4 R5 R6 R7 R8 R9 R10 R11 R12 R13 R14 R15 R16 R17 R18 R19 R20 R21 R22 R23 R24 R25 R26 R27 R28 R29 R30 R31 R32 R33 R34 R35 R36 R37 R38 R39 99 Developing quality indicators for HIV care