Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimating efficiency of survey and commercial trawl gears from comparisons of catch-ratios

Assumptions about gear efficiency and catchability influence estimates of abundance, mortality, reference points and catch potential. Despite the need to better quantify fishing effects on some target species and on many non-target species taken as bycatch, there are few gear efficiency estimates for some of the most widely deployed towed fishing gears in the northeast Atlantic. Here, we develop a method that applies generalised additive models to catch-at-length data from trawl surveys and a commercial catch and discard monitoring program in the North Sea to estimate catch-ratios. We then rescale these catch-ratios and fit relationships to estimate gear efficiency. When catches of individuals by species were too low to enable species-specific estimates, gear efficiency was estimated for species-groups. Gear efficiency (and associated uncertainty) at length was ultimately estimated for 75 species, seven species-groups and for up to six types of trawl gear per species or species-group. Results are illustrated for dab (Limanda limanda), grey gurnard (Eutrigula gurnardus) and thornback ray (Raja clavata), two common non-target species and a depleted elasmobranch. All estimates of gear efficiency and uncertainty, by length, species, species-group and gear, are made available in a supplementary data file.
Molecular microbial eukaryote diversity in five rift valley lakes and description of three ciliates species from lake Bogoria, Kenya

Die molekulare Diversitat, Phylogenie und taxonomische Zusammensetzung von Protisten-Gesellschaften aus funf Rift Valley Seen in Kenia wurden mit klassischer Mikroskopie und der 454 Pyrosequenzierungs-Technik untersucht. Insgesamt erhielt ich 96.555 Amplikons (Durchschnittslange 250 bp), von denen 33,8% Metazoen und andere Nicht-Zielorganismen waren. Die restlichen eukaryotischen Amplikons wurden taxonomischen Einheiten (operational taxonomic units – OTUs) zugeordnet, die durch den besten Treffer fur jedes Amplikon des Basic Local Alignment Search Toolfur Nukleotide (BLAST) in der National Center for Biotechnology Information Datenbank (NCBI) definiert wurden. Die taxonomische Vielfalt der Protisten war hoch und die 18s-rRNA-Amplikons wurden neun hochrangigen taxonomischen Gruppen zugeordnet. Die 746 eingruppierten OTUs hatten eine Ubereinstimmung mit den Referenzsequenzen von 97%. Die meisten gefundenen Sequenzen wurden den Alveolata zugeordnet (27,2% der Gesamtsequenzen, zumeist Ciliophora). Weitere taxonomische Gruppen, denen viele Sequenzen zugeordnet wurden, waren: Stramenopiles (14,2%), Fungi (11,2%), Chlorophyta (11,1%) und Cryptophyta (9%). Auch nicht weiter klassifizierte Sequenzen (unclassified environmetal Sequentes – ES) machten mit 13,2% einen grosen Teil der Gesamtsequenzen aus. Nach der Analyse uber rarefaction ergab sich bei einem Level von je 1000 Einzelsequenzen eine Zuordnung zu 13 bis 148 OTUs pro Probe. Die Diverstitat der Protisten zeigte spezifische raumliche Verteilungsmuster in den Seen, die mit vorliegenden Umweltvariablen, insbesondere dem Salzgehalt, korrelierten. Vertiefende Analysen mit dem Fokus auf Ciliaten und Chlorophyta zeigten eine Vielfalt, die durch eine hohe Anzahl von Amplikons in den Suswasserseen gekennzeichnet war. Des Weiteren fuhre ich eine taxonomische Beschreibungen der drei Ciliatenspezies (Frontonia alkalina sp. cand., Euplotes endoroisi sp. cand. und Condylostoma bogoriense sp. cand.) aus dem Lake Bogoria basierend auf morphologischen Merkmalen durch. Die vorliegende Arbeit gibt einen breiten Uberblick uber die molekulare Vielfalt der Protisten-Gesellschaften der funf untersuchten Seen, die den Bereich von Suswasser bis mesosalin umfassen (0,3 - 34,1 ‰ Salzgehalt). Sie zeigt die Rift Valley Seen als wichtiges Reservoir eukaryotisch-protistischer Vielfalt und macht deutlich, dass unser Verstandnis der Community-Struktur und molekularen Diversitat mikrobieller Eukaryoten in diesen tropischen Seen noch begrenzt ist.
The complex case of Ceratitis cosyra (Diptera: Tephritidae) and relatives. A DNA barcoding perspective

The mango fruit fly, Ceratitis (Ceratalaspis) cosyra, is a major agricultural pest affecting mango production in sub‐Saharan Africa. Morphological differences between C. cosyra and five closely related Ceratitis (Ceratalaspis) species (C. discussa, C. pallidula, C. quinaria, C. silvestrii, C. striatella) are subtle, so that their identification often requires specialized expertise. A previous study based on nuclear molecular markers (microsatellites) showed cryptic genetic variation within C. cosyra with separate microsatellite genotypic clusters also occurring in sympatry. This study aimed at verifying whether DNA barcoding can (a) separate C. cosyra from morphologically similar Ceratitis (Ceratalaspis) species and (b) resolve the cryptic genetic variation previously observed within C. cosyra. A subset of 62 C. cosyra specimens previously genotyped at 16 microsatellite loci was subjected to DNA barcoding. This data set was integrated with 130 DNA barcodes of C. cosyra, C. discussa, C. quinaria, C. silvestrii and C. striatella. Neighbor Joining, maximum likelihood and Bayesian tree reconstructions confirmed the presence of two main C. cosyra genotypic groups and resolved well‐supported groups corresponding to C. discussa, C. pallidula, C. striatella and to C. quinaria/C. silvestrii. The analysis of morphological characters did not show consistent morphological differences between the two groups of C. cosyra and called into question the morphological characters currently implemented in the identification of C. striatella. These results further support the hypothesis of cryptic speciation within the mango fruit fly and suggest that DNA barcoding represents a suitable complementary tool for the problematic diagnosis of C. cosyra and C. striatella.
Effect of hydric stress on intake, growth performance and nutritional status of Nguni goats

Abstract Limited water intake affects livestock. Though small ruminants are more resilient to suboptimum water intake compared to other species of livestock, tolerance abilities differ among breeds. This study was aimed at investigating the effect of water deprivation levels on intake, growth performance and nutritional status of Nguni goats. Thirty-six Nguni goats (initial weight, 18 ± 3.2 kg) were assigned to one of three treatments: without water deprivation, water deprivation for 24 and 48 h in a completely randomised design for 40 days. Performance traits, body condition score (BCS), faecal egg count (FEC) and FAffa MAlan CHArt (FAMACHA) were determined weekly while blood metabolites were determined on the last day of the experiment and analysed with PROC GLM of SAS software. The average daily water intake (WI) and feed intake (FI) increased (p < .05) with increased period of water deprivation. The average daily gain (ADG) and feed conversion ratio (FCR) declined (p < .01) with increased period of water deprivation. Final body weight, BCS and FAMACHA decreased (p < .05) while faecal egg count, glucose and creatine increased (p < .05) with increased period of water deprivation. Water deprivation period had negative correlations with ADFI, WFR, ADG, FCR, FAMACHA, BCS and BW. The correlation of BW was negative with FEC and positive with serum glucose. It was concluded that water deprivation impacts negatively on the nutritional status, blood metabolites and growth performance of Nguni goats. Highlights Limited water intake in small ruminants decreases body weight and body condition score. Rehydration, after prolonged dehydration of 48 h in small ruminants, results in increased average daily water and feed intake. Under dehydration effect, bodyweight positively correlates with body condition scores and negatively correlates with faecal egg count.
Assessing P‐T variability in mélange blocks from the Catalina Schist: Is there differential movement at the subduction interface?

In subduction‐related tectonic mélange, thermobarometry on individual blocks can in principle constrain the scale of lithological mixing along the subduction interface. Previous thermobarometric investigation of the tectonic amphibolite facies mélange unit in the Catalina Schist, Santa Catalina Island, California, USA, has suggested relatively limited mixing among blocks (≤12 km). Here we further investigate scales of mixing among metamorphically disparate (‘exotic’) blocks within epidote‐amphibolite and lawsonite‐blueschist facies mélange of the Catalina Schist using field and petrographic observations, Zr‐in‐rutile thermometry, and quartz‐in‐garnet elastic barometry. A new statistically based method is presented for calculating elastic barometry maximum pressures. The exotic blocks record peak metamorphic temperatures between 580 and 735°C and peak pressures between 1.16 and 1.65 GPa. Temperatures primarily fall in between those recorded by rocks in the amphibolite facies and epidote amphibolite facies units (643–735°C and 553–596°C respectively). The pressure estimates encompass those recorded by blocks from the amphibolite facies mélange (1.34–1.44 GPa), although the exotic blocks record a much larger range of pressures. The large range of recorded temperatures and pressures suggests that blocks within the epidote amphibolite unit were sourced from and mixed along a 20–30 km region of the subduction interface while an exotic block from the lawsonite blueschist facies unit appears to have been sourced from at least 70 km deeper than the unit it is hosted in. Metre‐ to kilometre‐scale variations in matrix mineral rheology likely control strain partitioning at the interface and permit differential transport of mélange blocks over variable length scales.
#MeToo as a Connective Movement: Examining the Frames Adopted in the Anti-Sexual Harassment Movement in China

This study was aimed to contribute to understanding how networked yet fragmented online actors create meaning in digital media–enabled movements like #MeToo. By drawing upon a multidimensional framing analysis, this study investigated how personal action frames, collective action frames, and issue-specific frames were adopted in #MeToo movement in China, and it also shed light on how different groups of social actors respond to sexual harassment issues on Sina Weibo, a Chinese social media platform. This study employed computational content analysis to extract frames from a huge amount of traceable data (i.e., 16,187 Weibo posts) and uncovered seven specific types of frames categorized as personal experiences and emotional commentary (as personal action frames), injustice and opposition (as collective action frames), and problem definition, treatment recommendation, and related news (as issue-specific frames). The results revealed that personal action frames and collective action frames were widely adopted by females and ordinary users, whereas issue-specific frames were more commonly applied by males and organizational users. These empirical findings enhance our understanding of meaning construction with regard to digital media–enabled movements.
Nasty Prophages and the Dynamics of Antibiotic-Tolerant Persister Cells

Bacterial persisters are phenotypic variants that survive antibiotic treatment in a dormant state and can be formed by multiple pathways. We recently proposed that the second messenger (p)ppGpp drives Escherichia coli persister formation through protease Lon and the activation of toxin-antitoxin (TA) modules. This model found support in the field, but also generated controversy as part of recent heated debates on the validity of significant parts of the literature. In this study, we therefore used our previous work as a model to critically examine common experimental procedures in order to understand and overcome the inconsistencies often observed between results of different laboratories. Our results show that seemingly simple antibiotic killing assays are very sensitive to variation of culture conditions and bacterial growth phase. Additionally, we found that some assay conditions cause the killing of antibiotic-tolerant persisters via induction of cryptic prophages. Similarly, the inadvertent infection of mutant strains with bacteriophage φ80, a notorious laboratory contaminant, has apparently caused several phenotypes that we reported in our previous studies. We therefore reconstructed all infected mutants and probed the validity of our model of persister formation in a refined assay setup that uses robust culture conditions and unravels the dynamics of persister cells through all bacterial growth stages. Our results confirm the importance of (p)ppGpp and Lon, but do not anymore support a role of TA modules in E. coli persister formation. We anticipate that the results and approaches reported in our study will lay the ground for future work in the field. Importance The recalcitrance of antibiotic-tolerant persister cells is thought to cause relapsing infections and antibiotic treatment failure in various clinical setups. Previous studies have identified multiple genetic pathways involved in persister formation, but also revealed reproducibility problems that sparked controversies about adequate tools to study persister cells. In this study we unraveled how typical antibiotic killing assays often fail to capture the biology of persisters and instead give widely different results based on ill-controlled experimental parameters and artifacts caused by cryptic as well as contaminant prophages. We therefore established a new, robust assay that enabled us to follow the dynamics of persister cells through all growth stages of bacterial cultures without distortions by bacteriophages. This system also favored adequate comparisons of mutant strains with aberrant growth phenotypes. We anticipate that our results will contribute to a robust, common basis of future studies on the formation and eradication of antibiotic-tolerant persisters.
Bacteriological Profile and Antimicrobial Sensitivity Pattern of Blood Culture Isolates

BACKGROUND Blood stream infections are the leading cause of morbidity and mortality in children in developing countries. Blood culture remains the golden reference standard for the laboratory diagnosis of bloodstream infections (BSIs) and helps in the prevention of emergence of multidrug resistant bacterial strains which poses a major challenge in the management of bacteraemia. Knowledge about the bacteriological profile and antimicrobial susceptibility patterns in the local unit helps the clinician in rationalizing the empirical treatment protocols and optimizing the duration of therapy. A hospital based retrospective observational study was carried out by reviewing the records of 318 blood cultures received from children aged 1 month to 12 years admitted with clinically suspected sepsis at Institute of Child Health, Niloufer Hospital for Women and Children, Hyderabad over a 4 month period (April 2019 August 2019). Blood samples were collected under aseptic conditions, identification of isolates and their antibiotic sensitivity pattern was done by disc diffusion method as per CLSI standards 2019. %) samples of the positive 57 %) samples showed Gram-positive bacteria and 48 %) samples %)] epidermidis 18 (17.1 %), Pseudomonas aeruginosa 12 (11.4 %), Enterococcus species 6 (5.7 %), Staphylococcus aureus 3 (2.8 %), Acinetobacter species 4 (3.8 %), and each one isolate of E. coli, Citrobacter species and Streptococcus pyogenes. The antibiotic sensitivity patterns have shown a high degree of resistance to the Cephalosporins among the Gram-negative cultures and high sensitivity pattern to Carbapenems and Fluoroquinolones. The present study emphasizes the need for continuous scrutiny and surveillance for the most common pathogens isolated in children with blood stream infections along with antibiotic sensitivity pattern in paediatric units for formulating rationalized antibiotic treatment protocols and infection control strategies for prevention of septicaemia in children.
Exploiting Network Methodology for Rare Variant Association Ana lysis

In this communication, we propose a new analysis approach for rare variant analysis that exploits network methodology. The approach is designed for large genomic regions, varying effect directions, and enables the analysis of the relationships between the variants. First, we construct networks based on the collapsed allele counts of rare variants in cases and in controls. Subsequently, we introduce a test statistic that compares the derived networks of cases and controls. In simulation studies, we assess the power of the methodology and compare it with standard rare variant approaches for association analysis. For scenarios with 100-500 loci, our approach achieves up 100% more power than standard approaches. We illustrate the practical aspect of the approach by application to a sequencing study for nonsyndromic cleft lip with or without cleft palate.
Comprehensive skin microbiome analysis reveals the uniqueness of human-associated microbial communities among the class Mammalia

Skin is the largest organ of the body and represents the primary physical barrier between mammals and their external environment. The objective of this research was to generate a skin microbiota baseline for members of the class Mammalia, testing the effects of host species, geographic location, body region, and biological sex. The back, torso, and inner thigh regions of 177 non-human mammals were collected to include representatives from 38 species and 10 mammalian orders. Animals were collected from local farms, zoos, households, and the wild. All samples were amplified using the V3-V4 16S rRNA gene region and sequenced using a MiSeq (Illumina). For reference, previously published skin microbiome data from 20 human participants, sampled using an identical protocol to the non-human mammals, were included in the analysis. Human skin was significantly less diverse than all other mammalian orders and the factor most strongly associated with community variation for all samples was whether the host was a human. Within non-human samples, host taxonomic order was the most significant factor influencing the skin community, followed by the geographic location of the habitat. By comparing the congruence between known host phylogeny and microbial community dendrograms, we observed that Artiodactyla (even-toed ungulates) and Perissodactyla (odd-toed ungulates) had significant congruence, providing first evidence of phylosymbiosis between skin communities and their hosts. Significance Skin forms a critical protective barrier between a mammal and its external environment. Baseline data on the mammalian skin microbiome is crucial for making informed decisions related to veterinary research and biodiversity conservation strategies, in addition to providing insight into mammalian evolutionary history. To our knowledge, this study represents the largest mammalian skin microbiota project to date. These findings demonstrate that human skin is distinct, not only from other Primates, but from all 10 mammalian orders sampled. Using phylosymbiosis analysis, we provide the first evidence that co-evolution may be occurring between skin communities and their mammalian hosts, which warrants more in-depth future studies of the relationships between mammals and their skin microbiota.
THE EFFECT OF LIQUIDITY ON TAX AVOIDANCE WITH PROFITABILITY MEDIATION VARIABLE IN BUMN COMPANIES LISTED ON THE IDX IN 2017-2018

The research objective was to determine the effect of liquidity on tax avoidance with profitability mediation variable in bumn companies listed on the idx in 2017-2018. This study uses a descriptive method with a population of 20 companies and uses a sample of 40 research samples based on 20 BUMN companies listed on the Indonesia Stock Exchange for the year 2017-2018 period. Analysis of the data is the coefficient of determination, F test, t-test, multiple regression. The significant test results show that in model 1 there is no significant effect between liquidity and tax avoidance, this is evidenced by the F-test 4.089 and a significant value of 0.05 at α = 5%. Whereas in model 2, it is found that with the mediation of profitability it is found that the effect of liquidity, profitability on tax avoidance is significant with a significant level of 0.032 at a significant level of 5% with an F-test of 3.779. The significant test results show that the independent variable shows that in model 1 there is no significant effect on the liquidity variable on tax avoidance with a significant value of 0.50 at the 10% significant level. Whereas in model 2, it is found that there is a mediation of profitability, it is found that liquidity and tax avoidance have a significant effect, namely 0.060 at a significant level of 10%. And related to profitability and tax avoidance, there is a significant effect with a significant level of 0.080 at a significant level of 10%. Thus, the existence of profitability does partially mediate the effects of liquidity and tax avoidance. So it is concluded that liquidity has a significant effect on tax avoidance, and profitability has a significant effect on tax avoidance.
Expression of Narcissus pseudonarcissus lectin and mannose receptor positive macrophages predict progression and prognosis of patients with gastric cancer

Background Mannose receptor (MR) is an immune adhesion molecule and is mainly expressed in macrophages and nonmature dendritic cells. The ligand mannose, one of the natural ligands of MR, is a monosaccharide, which is localized in the envelope or cytoplasm of macrophages. The aim of this study was to investigate expression of MR and its ligand mannose in tumor tissues of primary advanced gastric cancer and to evaluate the predictive and prognostic value of the positive cells in gastric cancer patients. Methods Histochemical staining for Narcissus pseudonarcissus lectin (NPL) and immunohistochemical envision two-step assay for MR were used to detect expression of NPL and MR in primary advanced gastric adenocarcinoma tissues. Adjacent non-cancerous gastric tissues of the patients were used as controls. Relationship of NPL and MR expression in the tumor tissues with clinicopathological features and survival time of the gastric cancer patients were analyzed. Results Numbers of NPL+ and MR+ macrophages in stromal tissues of gastric cancer were significantly higher than those in the adjacent non-cancerous gastric tissues (P=0.006; P<0.001). NPL expression in the primary tumor tissues was significantly more dominant than that in the adjacent non-cancerous gastric tissues (P=0.003). Expression of both the molecules in macrophages in tumor tissues was negatively correlated (r=−0.363, P=0.009). TNM stage of the patients was closely correlated to number of MR+ macrophages and NPL expression in the stromal tissues of gastric cancer (P=0.009 and P=0.020). Kaplan-Meier survival model data showed that the patients with low counting of NPL+ macrophages and high counting of MR+ macrophages significantly led to worse disease progression and poorer prognosis (P=0.008). Cox regression analysis further demonstrated that high expression of MR+ macrophages was an independent predictor of poor prognosis in patients with gastric cancer (P=0.033). Conclusions Occurrence of mannose and MR in tumor tissues of gastric cancer might be prognostic factors for estimating risk of gastric cancer patients.