PyNAST: a flexible tool for aligning sequences to a template alignment

Motivation: The Nearest Alignment Space Termination (NAST) tool is commonly used in sequence-based microbial ecology community analysis, but due to the limited portability of the original implementation, it has not been as widely adopted as possible. Python Nearest Alignment Space Termination (PyNAST) is a complete reimplementation of NAST, which includes three convenient interfaces: a Mac OS X GUI, a command-line interface and a simple application programming interface (API)

Determining clinical pharmacy workload by patient disease classification in medical and surgical patients

Aim: To determine the time needed to provide clinical pharmacy services to individual patient episodes for medical and surgical patients and the effect of patient presentation and complexity on the clinical pharmacy workload. Method: During a 5-month period in 2006 at two general hospitals, pharmacists recorded a defined range of activities that they provided for patients, including the actual times required for these tasks. A customised database linked to the two hospitals\u27 patient administration systems stored the data according to the specific patient episode number. The influence of patient presentation and complexity on the clinical pharmacy activities provided was also examined. Results: The average time required by pharmacists to undertake a medication history interview and medication reconciliation was 9.6 (SD 4.9) minutes. Interventions required 5.7 (SD 4.6) minutes, clinical review of the medical record 5.5 (SD 4.0) minutes and medication order review 3.5 (SD 2.0) minutes. For all of these activities, the time required for medical patients was greater than for surgical patients and greater for \u27complicated\u27 patients. The average time required to perform all clinical pharmacy activities for 1071 completed patient episodes was 14.4 (SD 10.9) minutes and was greater for medical and \u27complicated\u27 patients. Conclusion: The time needed to provide clinical pharmacy services was affected by whether the patients were medical or surgical. The existence of comorbidities or complications affected these times. The times required to perform clinical pharmacy activities may not be consistent with recently proposed staff ratios for the provision of a basic clinical pharmacy service.<br /

Modulation of morphology and glycan composition of mucins in farmed guinea fowl (Numida meleagris) intestine by the multi-strain probiotic slab51®

Probiotics have become highly recognized as supplements for poultry.Since gut health can be considered synonymous withanimal health, the effects of probiotic Slab51® on the morphology and the glycan composition of guineafowlintestine were examined. The probiotics were added in drinking water (2 × 1011 UFC/L) throughout the grow-out cycle.Birds were individually weighed andslaughtered after four months. Samples from the duodenum, ileum and caecum were collected and processed for morphological, morphometric, conventional and lectin glycohisto-chemical studies.The results were analyzed for statistical significance by Student’s t test. Compared with control samples, probiotic group revealed (1) significant increase in villus height (p &lt; 0.001 in duodenum and ileum; p &lt; 0.05 in caecum), crypt depth (p &lt; 0.001 in duodenum and caecum;p &lt; 0.05 in ileum) and goblet cells (GCs) per villus (p &lt; 0.001) in all investigated tracts; (2) increase in galac-toseβl,3N-acetylgalacyosamine(Galβl,3GalNAc)terminating O-glycans and αl,2-fucosylated glycans secretory GCs in the duodenum; (3) increase in α2,6-sialoglycans and high-mannose N-linked glycans secretory GCs but reduction in GCs-secreting sulfoglycans in the ileum; (4) increase in Galβl,3GalNAc and high-mannose N-linked glycans secretory GCs and decrease in GCs-producing sulfomucins in the caecum; (5) increase in the numbers of crypt cells containing sulfate and non-sulfated acidic glycans. Overall, dietary Slab51® induces morphological and region-specific changes in glycoprotein composition of guinea fowl intestine, promoting gut health

Testicular activity and sperm glycoproteins in giant red shrimp Aristaeomorpha foliacea

The reproduction of male giani red shrimp Aristaeomorpha foliacea, collected from thè late winterto thè summer in thè north-western lonian Sea (Mediterranean Sea), was investigated using histological and histochemistry methods. Seasonal changes in thè spermiogenesis and thè glycoprotein pattern were found and sperm glycoproteins matured as gametes moved from thè testis to thè terminal ampliila. In serial sections stained with hematoxylin and eosin thè testicular activity appeared to be discontinuous. In late winter thè testes had no meiotic activity and thè seminiferous epithelium consisted of interkinetic spermatogonia and spermatozoa. In spring, spermiogenetic activity was high and thè seminiferous epithelium mainly consisted of spermatocytes and spermatozoa while in summer, thè testes were again inactive since both spermatocytes and spermatozoa were lacking. The use of twelve different lectins indicated that thè intratesticular spermatozoa from late winter to summer contain surface binding sites for SNA, MAA, Con A and KOH-sialidase (si)-WGA. In March and July they also exhibited nuclear and cytoplasmic reactivity for SNA and Con A. In thè hemispermatophore thè spermatozoa displayed a more complex lectin-binding pattern because they also reacted with PNA, DBA, HPA, OSA II. The staining with DBA, KOH-si- DBA, and OSA II showed differences between thè spermatozoa from late winter-spring hemispermatophores and summer hemispermatophores: thè former showed a nuclear affinity whereas thè latter displayed surface and/or cytoplasm staining. No reaction was observed with SBA, GSAI-B4, UEA I, and LTA

Competing with stationary prediction strategies

In this paper we introduce the class of stationary prediction strategies and construct a prediction algorithm that asymptotically performs as well as the best continuous stationary strategy. We make mild compactness assumptions but no stochastic assumptions about the environment. In particular, no assumption of stationarity is made about the environment, and the stationarity of the considered strategies only means that they do not depend explicitly on time; we argue that it is natural to consider only stationary strategies even for highly non-stationary environments.Comment: 20 page

Role of extracellular vesicle-based cell-to-cell communication in multiple myeloma progression

Multiple myeloma (MM) progression closely depends on the bidirectional crosstalk between tumor cells and the surrounding microenvironment, which leads to the creation of a tumor supportive niche. Extracellular vesicles (EVs) have emerged as key players in the pathological interplay between the malignant clone and near/distal bone marrow (BM) cells through their biologically active cargo. Here, we describe the role of EVs derived from MM and BM cells in reprogramming the tumor microenvironment and in fostering bone disease, angiogenesis, immunosuppression, drug resistance, and, ultimately, tumor progression. We also examine the emerging role of EVs as new therapeutic agents for the treatment of MM, and their potential use as clinical biomarkers for early diagnosis, disease classification, and therapy monitoring

Effects of Mefepronic Acid (2-Phenoxy-2-Methyl Propionic Acid) on Hepatic Metabolism and Reproductive Parameters in Postpartum Dairy Cows.

This study investigates the effects of mefepronic acid (MA), a PPAR-α agonist, on hepatic metabolic functions and reproduction of postpartum dairy cows. Sixty Friesian cows were divided into Group A (administered 5g of MA IM, within 24 hrs after calving, on the 3rd and 5th day postpartum) and Group B (control). All the cows were blood sampled within 24 hrs of calving (Day 0), on Day 3, 5, 10, 15, 30, and 40 postpartum. On plasma, metabolic and biochemical parameters were determined. Liver biopsies were performed on Day 0, 15 and 30 for the evaluation of hepatic lipid and glycogen content. Reproductive parameters were also evaluated. In Group A, blood HDL, glucose and cholesterol increased till the end of the study, in accordance with the histological results. PPAR-α immunopositive cells increased in liver slices of Group A, too. Reproductive parameters improved in Group A. This study highlights the beneficial effects of mefepronic acid on the hepatic metabolism and reproductive parameters of post-partum dairy cows

Histochemical analysis of glycoconjugates in the domestic cat testis

The localization and characterization of oligosaccharide sequences in the cat testis was investigated using 12 lectins in combination with the ßelimination reaction, N-Glycosidase F and sialidase digestion. Leydig cells expressed O-linked glycans with terminal aGalNAc (HPA reactivity) and N-glycans with terminal/internal aMan (Con A affinity). The basement membrane showed terminal Neu5Aca2,6Gal/GalNAc, Galß1,3GalNAc, a/ßGalNAc, and GlcNAc (SNA, PNA, HPA, SBA, GSA II reactivity) in O-linked oligosaccharides, terminal Galß1,4GlcNAc (RCA120 staining) and aMan in N-linked oligosaccharides; in addition, terminal Neu5Aca2,3Galß1,4GlcNac, Forssman pentasaccharide, aGal, aL-Fuc and internal GlcNAc (MAL II, DBA, GSA I-B4, UEA I, KOH-sialidase-WGA affinity) formed both O- and N-linked oligosaccharides. The Sertoli cells cytoplasm contained terminal Neu5Ac- Galß1,4GlcNAc, Neu5Ac-ßGalNAc as well as internal GlcNAc in O-linked glycans, aMan in N-linked glycoproteins and terminal Neu5Aca2,6Gal/ GalNAc in both O- and N-linked oligosaccharides. Spermatogonia exhibited cytoplasmic N-linked glycoproteins with aMan residues. The spermatocytes cytoplasm expressed terminal Neu5Aca2,3Galß1,4 GlcNAc and Galß1,3GalNAc in O-linked oligosaccharides, terminal Galß1,4GlcNAc and a/ßGalNAc in N-linked glycoconjugates. The Golgi region showed terminal Neu5aca2,3Galß1,4GlcNac, Galß1,4GlcNAc, Forssman pentasaccharide, and aGalNAc in O-linked oligosaccharides, aMan and terminal ßGal in N-linked oligosaccharides. The acrosomes of Golgi-phase spermatids expressed terminal Galß1,3GalNAc, Galß1,4GlcNAc, Forssmann pentasaccharide, a/ßGalNAc, aGal and internal GlcNAc in O-linked oligosaccharides, terminal a/ßGalNAc, aGal and terminal/internal aMan in N-linked glycoproteins. The acrosomes of cap-phase spermatids lacked internal Forssman pentasaccharide and aGal, while having increased a/ßGalNAc. The acrosomes of elongated spermatids did not show terminal Galß1,3GalNAc, displayed terminal Galß1,4GlcNAc and a/ßGalNAc in N-glycans and Neu5Ac-Galß1,3GalNAc in O-linked oligosaccharides