Genome sequence of a novel alloherpesvirus isolated from glass catfish (Kryptopterus bicirrhis)

The 149,343-bp genome of silurid herpesvirus 1, which was isolated in Thailand from glass catfish, was sequenced. The genome was most closely related to that of ictalurid herpesvirus 2, which infects black bullhead catfish. To our knowledge, this was the first silurid catfish alloherpesvirus genome to be sequenced

Using collocation segmentation to augment the phrase table

This paper describes the 2010 phrase-based statistical machine translation system developed at the TALP Research Center of the UPC1 in cooperation with BMIC2 and VMU3. In phrase-based SMT, the phrase table is the main tool in translation. It is created extracting phrases from an aligned parallel corpus and then computing translation model scores with them. Performing a collocation segmentation over the source and target corpus before the alignment causes that di erent and larger phrases are extracted from the same original documents. We performed this segmentation and used the union of this phrase set with the phrase set extracted from the nonsegmented corpus to compute the phrase table. We present the con gurations considered and also report results obtained with internal and o cial test sets.Postprint (published version

UPC-BMIC-VDU system description for the IWSLT 2010: testing several collocation segmentations in a phrase-based SMT system

This paper describes the UPC-BMIC-VMU participation in the IWSLT 2010 evaluation campaign. The SMT system is a standard phrase-based enriched with novel segmentations. These novel segmentations are computed using statistical measures such as Log-likelihood, T-score, Chi-squared, Dice, Mutual Information or Gravity-Counts. The analysis of translation results allows to divide measures into three groups. First, Log-likelihood, Chi-squared and T-score tend to combine high frequency words and collocation segments are very short. They improve the SMT system by adding new translation units. Second, Mutual Information and Dice tend to combine low frequency words and collocation segments are short. They improve the SMT system by smoothing the translation units. And third, Gravity- Counts tends to combine high and low frequency words and collocation segments are long. However, in this case, the SMT system is not improved. Thus, the road-map for translation system improvement is to introduce new phrases with either low frequency or high frequency words. It is hard to introduce new phrases with low and high frequency words in order to improve translation quality. Experimental results are reported in the Frenchto- English IWSLT 2010 evaluation where our system was ranked 3rd out of nine systems.Postprint (published version

Interventions for improving clinical outcomes and health-related quality-of-life for people living with skeletal dysplasias: an evidence gap map

Purpose: Skeletal dysplasias are rare genetic disorders that are characterized by abnormal development of bone and cartilage. There are multiple medical and non-medical treatments for specific symptoms of skeletal dysplasias e.g. pain, as well as corrective surgical procedures to improve physical functioning. The aim of this paper was to develop an evidence-gap map of treatment options for skeletal dysplasias, and their impact on patient outcomes. Methods: We conducted an evidence-gap map to identify the available evidence on the impact of treatment options on people with skeletal dysplasias on clinical outcomes (such as increase in height), and dimensions of health-related quality of life. A structured search strategy was applied to five databases. Two reviewers independently assessed articles for inclusion in two stages: titles and abstracts (stage 1), and full text of studies retained at stage 2. Results: 58 studies fulfilled our inclusion criteria. The included studies covered 12 types of skeletal dysplasia that are non-lethal with severe limb deformities that could result in significant pain and numerous orthopaedic interventions. Most studies reported on the effect of surgical interventions (n = 40, 69%), followed by the effect of treatments on dimensions of health quality-of-life (n = 4, 6.8%) and psychosocial functioning (n = 8, 13.8%). Conclusion: Most studies reported on clinical outcomes from surgery for people living with Achondroplasia. Consequently, there are gaps in the literature on the full range of treatment options (including no active treatment), outcomes and the lived experience of people living with other skeletal dysplasias. More research is warranted to examine the impact of treatments on health-related quality-of-life of people living with skeletal dysplasias, including their relatives to enable them to make preference- and valued based decisions about treatment

Assessment of genotypes, endosymbionts and clinical characteristics of Acanthamoeba recovered from ocular infection

Introduction: Acanthamoeba is an emerging pathogen, infamous for its resilience against antiprotozoal compounds, disinfectants and harsh environments. It is known to cause keratitis, a sight-threatening, painful and difficult to treat corneal infection which is often reported among contact lens wearers and patients with ocular trauma. Acanthamoeba comprises over 24 species and currently 23 genotypes (T1-T23) have been identified. Aims: This retrospective study was designed to examine the Acanthamoeba species and genotypes recovered from patients with Acanthamoeba keratitis (AK), determine the presence of endosymbionts in ocular isolates of Acanthamoeba and review the clinical presentations. Methodology: Thirteen culture-confirmed AK patients treated in a tertiary eye care facility in Hyderabad, India from February to October 2020 were included in this study. The clinical manifestations, medications and visual outcomes of all patients were obtained from medical records. The Acanthamoeba isolates were identified by sequencing the ribosomal nuclear subunit (rns) gene. Acanthamoeba isolates were assessed for the presence of bacterial or fungal endosymbionts using molecular assays, PCR and fluorescence in situ hybridization (FISH). Results: The mean age of the patients was 33 years (SD ± 17.4; 95% CI 22.5 to 43.5 years). Six (46.2%) cases had AK associated risk factors; four patients had ocular trauma and two were contact lens wearers. A. culbertsoni (6/13, 46.2%) was the most common species, followed by A. polyphaga and A. triangularis. Most of the isolates (12/13) belonged to genotype T4 and one was a T12; three sub-clusters T4A, T4B, and T4F were identified within the T4 genotype. There was no significant association between Acanthamoeba types and clinical outcomes. Eight (61.5%) isolates harboured intracellular bacteria and one contained Malassezia restricta. The presence of intracellular microbes was associated with a higher proportion of stromal infiltrates (88.9%, 8/9), epithelial defect (55.6%, 5/9) and hypopyon (55.6%, 5/9) compared to 50% (2/4), 25% (1/4) and 25% (1/4) AK cases without intracellular microbes, respectively. Conclusions: Genotype T4 was the predominant isolate in southern India. This is the second report of T12 genotype identified from AK patient in India, which is rarely reported worldwide. The majority of the Acanthamoeba clinical isolates in this study harboured intracellular microbes, which may impact clinical characteristics of AK

Preferencias hacia carne de cordero en supermercados de Temuco, región de la Araucanía, Chile

Lobos, G (Lobos, German). Univ Talca, Escuela Ingn Comercial, Talca, ChileThe low levels of consumption of lamb meat in Chile suggest the need for studies on consumer preferences in order to orient production. A study with this object was carried out to evaluate preferences for various cuts, breeds, state (fresh or frozen) and price of lamb's meat among supermarket buyers in Temuco, Chile, and the existence of different market segments, through a survey of 400 persons. Using a fractional factorial design for conjoint analysis, it was determined that the state of the meat was more important than the cut, the price and the breed, with a preference for meat in half carcasses and quarters, Araucano lamb, fresh, at a medium price level. Four consumer segments were distinguished by analysis of hierarchic conglomerates. The majority group (47.7%) was sensitive to the state and the cut, with preference for meat in quarters, fresh, Texel breed. The second group (25.3%) was sensitive to the breed, presenting the strongest preferences for meat in whole carcass, fresh, Araucano lamb. The third group (14.3%) was sensitive to the price, preferred meat in quarters, fresh, Araucano lamb. The minority group (12.7%) was sensitive to the state and price, preferring meat in quarters, Texel breed, and was the only group which preferred frozen meat and would pay a higher price. The segments were distinguished by age, ethnic origin and satisfaction with food-related life. Thus the commercialisation strategy for lamb in supermarkets in Temuco should concentrate principally on the sale of fresh meat cut in quarter

A phase 3 multicenter, prospective, open-label efficacy and safety study of immune globulin (human) 10% caprylate/chromatography purified in patients with myasthenia gravis exacerbations

Background: Myasthenia gravis (MG) is an autoimmune disorder affecting neuromuscular transmission. Exacerbations may involve increasing bulbar weakness and/or sudden respiratory failure, both of which can be critically disabling. Management of MG exacerbations includes plasma exchange and intravenous immunoglobulin (IVIG); they are equally effective, but patients experience fewer side effects with IVIG. The objective of this study was to assess the efficacy and safety of immune globulin caprylate/chromatography purified (IGIV-C) in subjects with MG exacerbations. Methods: This prospective, open-label, non-controlled 28-day clinical trial was conducted in adults with MG Foundation of America class IVb or V status. Subjects received IGIV-C 2 g/kg over 2 consecutive days (1 g/kg/day) and were assessed for efficacy/safety on Days 7, 14, 21, and 28. The primary efficacy endpoint was the change from Baseline in quantitative MG (QMG) score to Day 14. Secondary endpoints of clinical response, Baseline to Day 14, included at least a 3-point decrease in QMG and MG Composite and a 2-point decrease in MG-activities of daily living (MG-ADL). Results: Forty-nine subjects enrolled. The change in QMG score at Day 14 was significant (p < 0.001) in the Evaluable (-6.4, n = 43) and Safety (-6.7, n = 49) populations. Among evaluable subjects, Day 14 response rates were 77, 86, and 88% for QMG, MG Composite, and MG-ADL, respectively. IGIV-C showed good tolerability with no serious adverse events. Conclusions: The results of this study show that IGIV-C was effective, safe, and well tolerated in the treatment of MG exacerbations

Comparison of Chloroplast Genomes among Species of Unisexual and Bisexual Clades of the Monocot Family Araceae

The chloroplast genome provides insight into the evolution of plant species. We de novo assembled and annotated chloroplast genomes of four genera representing three subfamilies of Araceae: Lasia spinosa (Lasioideae), Stylochaeton bogneri, Zamioculcas zamiifolia (Zamioculcadoideae), and Orontium aquaticum (Orontioideae), and performed comparative genomics using these chloroplast genomes. The sizes of the chloroplast genomes ranged from 163,770 bp to 169,982 bp. These genomes comprise 113 unique genes, including 79 protein-coding, 4 rRNA, and 30 tRNA genes. Among these genes, 17–18 genes are duplicated in the inverted repeat (IR) regions, comprising 6–7 protein-coding (including trans-splicing gene rps12), 4 rRNA, and 7 tRNA genes. The total number of genes ranged between 130 and 131. The infA gene was found to be a pseudogene in all four genomes reported here. These genomes exhibited high similarities in codon usage, amino acid frequency, RNA editing sites, and microsatellites. The oligonucleotide repeats and junctions JSB (IRb/SSC) and JSA (SSC/IRa) were highly variable among the genomes. The patterns of IR contraction and expansion were shown to be homoplasious, and therefore unsuitable for phylogenetic analyses. Signatures of positive selection were seen in three genes in S. bogneri, including ycf2, clpP, and rpl36. This study is a valuable addition to the evolutionary history of chloroplast genome structure in Araceae

Nitrogen Assimilation in Picocyanobacteria Inhabiting the Oxygen-Deficient Waters of the Eastern Tropical North and South Pacific

Prochlorococcus and Synechococcus are the most abundant free-living photosynthetic microorganisms in the ocean. Uncultivated lineages of these picocyanobacteria also thrive in the dimly illuminated upper part of oxygen-deficient zones (ODZs), where an important portion of ocean nitrogen (N) loss takes place via denitrification and anaerobic ammonium oxidation. Recent metagenomic studies revealed that ODZ Prochlorococcus have the genetic potential for using different N forms, including nitrate and nitrite, uncommon N sources for Prochlorococcus, but common for Synechococcus. To determine which N sources ODZ picocyanobacteria are actually using in nature, the cellular 15N natural abundance (δ15N) and assimilation rates of different N compounds were determined using cell sorting by flow cytometry and mass spectrometry. The natural δ15N of the ODZ Prochlorococcus varied from −4.0‰ to 13.0‰ (n = 9), with 50% of the values in the range of −2.1–2.6‰. While the highest values suggest nitrate use, most observations indicate the use of nitrite, ammonium, or a mixture of N sources. Meanwhile, incubation experiments revealed potential assimilation rates of ammonium and urea in the same order of magnitude as that expected for total N in several environments including ODZs, whereas rates of nitrite and nitrate assimilation were very low. Our results thus indicate that reduced forms of N and nitrite are the dominant sources for ODZ picocyanobacteria, although nitrate might be important on some occasions. ODZ picocyanobacteria might thus represent potential competitors with anammox bacteria for ammonium and nitrite, with ammonia-oxidizing archaea for ammonium, and with nitrite-oxidizing bacteria for nitrite