Feeding stimulatory effects of Cyperus rotundus tuber on Cirrhinus mrigala

Traditionally tubers of cyperus (Cyperus rotundus) and its extracts have been used for alluring fish during harvesting in India. An experiment was conducted to evaluate its feeding stimulatory activity and effect on the growth of a commercially important freshwater fish, Cirrhinus mrigala. Three isonitrogenous and isocaloric formulated diets viz. plant ingredient based control and control supplemented with cyperus tuber (CS) at 1% and 5% levels were fed to the fingerlings of mrigal, C. mrigala (2.68+0.20 g) for a period of 45 days. The growth performance and the activity of metabolic enzymes, aspartate aminotransferase (AST) and alanine aminotransferase (ALT), in liver, gill and muscle tissues of mrigal were studied during every 15 days interval. Highest relative growth (72.28%) was obtained in the mrigal fed with the diet containing 5% cyperus (5% CS), while the relative growths were 66.18% and 43.40% for the fish fed with the 1% CS diet and control respectively. The activities of AST and ALT were significantly higher (p<0.01) in both 1% and 5% CS diets as compared to the control in all the tissues studied. Higher aminotransferase activities were observed in the tissues of 5% CS group than in those of 1% CS group throughout the experimental period. The observed higher enzymatic activity was concomitant with the higher growth rate in fish. The results suggested that cyperus tuber supplementation increased feed palatability and growth

Spectrum Preserving Tilings Enable Sparse and Modular Reference Indexing

The reference indexing problem for k-mers is to pre-process a collection of reference genomic sequences so that the position of all occurrences of any queried k-mer can be rapidly identified. An efficient and scalable solution to this problem is fundamental for many tasks in bioinformatics. In this work, we introduce the spectrum preserving tiling (SPT), a general representation of that specifies how a set of tiles repeatedly occur to spell out the constituent reference sequences in. By encoding the order and positions where tiles occur, SPTs enable the implementation and analysis of a general class of modular indexes. An index over an SPT decomposes the reference indexing problem for k-mers into: (1) a k-mer-to-tile mapping; and (2) a tile-to-occurrence mapping. Recently introduced work to construct and compactly index k-mer sets can be used to efficiently implement the k-mer-to-tile mapping. However, implementing the tile-to-occurrence mapping remains prohibitively costly in terms of space. As reference collections become large, the space requirements of the tile-to-occurrence mapping dominates that of the k-mer-to-tile mapping since the former depends on the amount of total sequence while the latter depends on the number of unique k-mers in. To address this, we introduce a class of sampling schemes for SPTs that trade off speed to reduce the size of the tile-to-reference mapping. We implement a practical index with these sampling schemes in the tool pufferfish2. When indexing over 30,000 bacterial genomes, pufferfish2 reduces the size of the tile-to-occurrence mapping from 86.3 GB to 34.6 GB while incurring only a 3.6 slowdown when querying k-mers from a sequenced readset. Availability: pufferfish2 is implemented in Rust and available at https://github.com/COMBINE-lab/pufferfish2

Scheduling Virtual Conferences Fairly: {A}chieving Equitable Participant and Speaker Satisfaction

Recently, almost all conferences have moved to virtual mode due to the pandemic-induced restrictions on travel and social gathering. Contrary to in-person conferences, virtual conferences face the challenge of efficiently scheduling talks, accounting for the availability of participants from different timezones and their interests in attending different talks. A natural objective for conference organizers is to maximize efficiency, e.g., total expected audience participation across all talks. However, we show that optimizing for efficiency alone can result in an unfair virtual conference schedule, where individual utilities for participants and speakers can be highly unequal. To address this, we formally define fairness notions for participants and speakers, and derive suitable objectives to account for them. As the efficiency and fairness objectives can be in conflict with each other, we propose a joint optimization framework that allows conference organizers to design schedules that balance (i.e., allow trade-offs) among efficiency, participant fairness and speaker fairness objectives. While the optimization problem can be solved using integer programming to schedule smaller conferences, we provide two scalable techniques to cater to bigger conferences. Extensive evaluations over multiple real-world datasets show the efficacy and flexibility of our proposed approaches.Comment: In proceedings of the Thirty-first Web Conference (WWW-2022). arXiv admin note: text overlap with arXiv:2010.1462

{FairRec}: {T}wo-Sided Fairness for Personalized Recommendations in Two-Sided Platforms

We investigate the problem of fair recommendation in the context of two-sided online platforms, comprising customers on one side and producers on the other. Traditionally, recommendation services in these platforms have focused on maximizing customer satisfaction by tailoring the results according to the personalized preferences of individual customers. However, our investigation reveals that such customer-centric design may lead to unfair distribution of exposure among the producers, which may adversely impact their well-being. On the other hand, a producer-centric design might become unfair to the customers. Thus, we consider fairness issues that span both customers and producers. Our approach involves a novel mapping of the fair recommendation problem to a constrained version of the problem of fairly allocating indivisible goods. Our proposed FairRec algorithm guarantees at least Maximin Share (MMS) of exposure for most of the producers and Envy-Free up to One item (EF1) fairness for every customer. Extensive evaluations over multiple real-world datasets show the effectiveness of FairRec in ensuring two-sided fairness while incurring a marginal loss in the overall recommendation quality.Comment: In Proceedings of The Web Conference (WWW) 202

Patch antenna in isotropic plasma : Resonant frequency

A method has been developed to compute the resonant frequency of a rectangular microstrip antenna immersed in a linear isotropic plasma medium using Wolf's dynamic dielectric constant model. The results obtained are in agreement with those obtained using spectral domain technique. It has been observed that the antenna resonates at a higher frequency inside the plasma than in free space

“Influence of plasmids, selection markers and auxotrophic mutations on Haloferax volcanii cell shape plasticity”

Haloferax volcanii and other Haloarchaea can be pleomorphic, adopting different shapes, which vary with growth stages. Several studies have shown that H. volcanii cell shape is sensitive to various external factors including growth media and physical environment. In addition, several studies have noticed that the presence of a recombinant plasmid in the cells is also a factor impacting H. volcanii cell shape, notably by favoring the development of rods in early stages of growth. Here we investigated the reasons for this phenomenon by first studying the impact of auxotrophic mutations on cell shape in strains that are commonly used as genetic backgrounds for selection during strain engineering (namely: H26, H53, H77, H98, and H729) and secondly, by studying the effect of the presence of different plasmids containing selection markers on the cell shape of these strains. Our study showed that most of these auxotrophic strains have variation in cell shape parameters including length, aspect ratio, area and circularity and that the plasmid presence is impacting these parameters too. Our results indicated that ΔhdrB strains and hdrB selection markers have the most influence on H. volcanii cell shape, in addition to the sole presence of a plasmid. Finally, we discuss limitations in studying cell shape in H. volcanii and make recommendations based on our results for improving reproducibility of such studies

Evidence from clinical trials on high-risk medical devices in children

BACKGROUND: Meeting increased regulatory requirements for clinical evaluation of medical devices marketed in Europe in accordance with the Medical Device Regulation (EU 2017/745) is challenging, particularly for high-risk devices used in children. METHODS: Within the CORE-MD project, we performed a scoping review on evidence from clinical trials investigating high-risk paediatric medical devices used in paediatric cardiology, diabetology, orthopaedics and surgery, in patients aged 0–21 years. We searched Medline and Embase from 1st January 2017 to 9th November 2022. RESULTS: From 1692 records screened, 99 trials were included. Most were multicentre studies performed in North America and Europe that mainly had evaluated medical devices from the specialty of diabetology. Most had enrolled adolescents and 39% of trials included both children and adults. Randomized controlled trials accounted for 38% of the sample. Other frequently used designs were before-after studies (21%) and crossover trials (20%). Included trials were mainly small, with a sample size <100 participants in 64% of the studies. Most frequently assessed outcomes were efficacy and effectiveness as well as safety. CONCLUSION: Within the assessed sample, clinical trials on high-risk medical devices in children were of various designs, often lacked a concurrent control group, and recruited few infants and young children

Unifying Parsimonious Tree Reconciliation

Evolution is a process that is influenced by various environmental factors, e.g. the interactions between different species, genes, and biogeographical properties. Hence, it is interesting to study the combined evolutionary history of multiple species, their genes, and the environment they live in. A common approach to address this research problem is to describe each individual evolution as a phylogenetic tree and construct a tree reconciliation which is parsimonious with respect to a given event model. Unfortunately, most of the previous approaches are designed only either for host-parasite systems, for gene tree/species tree reconciliation, or biogeography. Hence, a method is desirable, which addresses the general problem of mapping phylogenetic trees and covering all varieties of coevolving systems, including e.g., predator-prey and symbiotic relationships. To overcome this gap, we introduce a generalized cophylogenetic event model considering the combinatorial complete set of local coevolutionary events. We give a dynamic programming based heuristic for solving the maximum parsimony reconciliation problem in time O(n^2), for two phylogenies each with at most n leaves. Furthermore, we present an exact branch-and-bound algorithm which uses the results from the dynamic programming heuristic for discarding partial reconciliations. The approach has been implemented as a Java application which is freely available from http://pacosy.informatik.uni-leipzig.de/coresym.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript - specific expression in <i>Arabidopsis thaliana</i>

RNA-sequencing (RNA-seq) allows global gene expression analysis at the individual transcript level. Accurate quantification of transcript variants generated by alternative splicing (AS) remains a challenge. We have developed a comprehensive, nonredundant Arabidopsis reference transcript dataset (AtRTD) containing over 74 000 transcripts for use with algorithms to quantify AS transcript isoforms in RNA-seq. The AtRTD was formed by merging transcripts from TAIR10 and novel transcripts identified in an AS discovery project. We have estimated transcript abundance in RNA-seq data using the transcriptome-based alignment-free programmes Sailfish and Salmon and have validated quantification of splicing ratios from RNA-seq by high resolution reverse transcription polymerase chain reaction (HR RT-PCR). Good correlations between splicing ratios from RNA-seq and HR RT-PCR were obtained demonstrating the accuracy of abundances calculated for individual transcripts in RNA-seq. The AtRTD is a resource that will have immediate utility in analysing Arabidopsis RNA-seq data to quantify differential transcript abundance and expression.</p