Miracle-dz/UniFAR-FTUs huggingface dataset:
Reproductive cycles of two Australian freshwater fishes: the spangled perch, Therapon unicolor Gunther, 1859 and the East Queensland rainbowfish, Nematocentris splendida Peters, 1866

The reproductive cycles of the spangled perch Therapon unicolor Gunther, 1859 and the East Queensland rainbowfish Nematocentris splendida Peters, 1866 are described in terms of maturity stages, sex-ratio, gonosomatic indices, oocyte diameters, fecundity and rearing experiments. T. unicolor has a well-defined reproductive cycle with gonad development stimulated by rising temperatures and increasing daylength; with spawning induced by the ‘wet’, possibly by rising water levels and increasing turbidities. In contrast, N. splendida has a protracted spawning period with a peak of spawning activity in pre-flood and flood periods, although individuals in spawning condition and juveniles may be found throughout the year.
The Changes in the p53 Protein across the Animal Kingdom Point to Its Involvement in Longevity

Recently, the quest for the mythical fountain of youth has turned into extensive research programs aiming to extend the healthy lifespan in humans. Despite advances in our understanding of the aging process, the surprisingly extended lifespan and cancer resistance of some animal species remains unexplained. The p53 protein plays a crucial role in tumor suppression and in tissue homeostasis and aging. Long-lived, cancer-free African elephants, have 20 copies of TP53 gene including 19 retrogenes (38 alleles) which are partially active, whereas humans possess only one copy of TP53 and have an estimated cancer mortality of 11-25%. The mechanism through which p53 contributes to the resolution of the Peto’s paradox in the Animalia remains vague. Thus, in this work, we took advantage of the available datasets and inspected the p53 amino acid sequence of phylogenetically related organisms that show variations in the lifespan. We discovered new correlations between specific amino acid deviations in p53 and the lifespans across different animal species. We found that species with extended lifespan have certain characteristic amino acid substitutions in the p53 DNA binding domain that alter its function as depicted from the Phenotypic Annotation of p53 Mutations, using PROVEAN tool or SWISS-MODEL workflow. Our findings show a direct association between specific amino acid residues in p53 protein, changes in p53 functionality and the extended animal lifespan, and further highlight the importance of p53 protein in aging.
Validation of a PNA clamping method for reducing host DNA amplification and increasing eukaryotic diversity in rhizosphere microbiome studies

Protists and microscopic animals are important but poorly understood determinants of plant health. Plant-associated eukaryotes could be surveyed by high-throughput sequencing of 18S ribosomal RNA (rRNA) genes, but the abundance of plant DNA in rhizosphere samples makes 18S rRNA gene amplification with universal primers unfeasible. Here we applied a pipeline to generate peptide nucleic acid (PNA) clamps to suppress the amplification of plant host DNA during 18S rRNA gene library preparation. We designed a PNA clamp, PoacV9_01, specific to the V9 region of the 18S rRNA gene for plants in the family Poaceae. PoacV9_01 suppressed the amplification of five species of grain crops in quantitative PCR reactions. In an 18S rRNA gene sequencing survey of the rhizosphere of maize, PoacV9_01 reduced the relative abundance of plant reads from 65% to 0.6%, while drastically increasing the number and diversity of animal, fungal, and protist reads detected. Thus, PoacV9_01 can be used to facilitate the study of eukaryotes present in grass phytobiomes. In addition, the pipeline developed here can be used to develop PNA clamps that target other plant species.
Plasmids shape the diverse accessory resistomes of Escherichia coli ST131

The human gut microbiome includes beneficial, commensal and pathogenic bacteria that possess antimicrobial resistance (AMR) genes that exchange these predominantly through conjugative plasmids. Escherichia coli is a significant component of the gastrointestinal microbiome and is typically non-pathogenic in this niche. In contrast, extra-intestinal pathogenic E. coli (ExPEC) including ST131 may occupy other environments like the urinary tract or bloodstream where they express genes enabling AMR and host cell adhesion like type 1 fimbriae. The extent to which commensal E. coli and uropathogenic ExPEC ST131 share AMR genes remains understudied at a genomic level, and here we examined this using a preterm infant resistome. Here, individual ST131 had small differences in AMR gene content relative to a larger shared resistome. Comparisons with a range of plasmids common in ST131 showed that AMR gene composition was driven by conjugation, recombination and mobile genetic elements. Plasmid pEK499 had extended regions in most ST131 Clade C isolates, and it had evidence of a co-evolutionary signal based on protein-level interactions with chromosomal gene products, as did pEK204 that had a type IV fimbrial pil operon. ST131 possessed extensive diversity of selective type 1, type IV, P and F17-like fimbriae genes that was highest in subclade C2. The structure and composition of AMR genes, plasmids and fimbriae vary widely in ST131 Clade C and this may mediate pathogenicity and infection outcomes. Data Summary The following files are available on the FigShare project “Plasmids_ST131_resistome_2020” : The set of 794 AMR genes derived from [74] are available (with their protein sequence translation) at FigShare at doi: dx.doi. org/10.6084/m9.figshare. 11961402. The AMR gene profiles per sample determined by their BLAST sequence similarity results against CARD are available at FigShare at doi: dx.doi. org/10.6084/m9.figshare. 11961612. This dataset includes the PlasmidFinder results. It also includes other AMR database comparisons (ARG-ANNOT, ResFinder, MegaRes, VFDB and VirulenceFinder). The BLAST sequence similarity results for the fim, pil, pap and ucl operons’ genes versus 4,071 E. coli ST131 assemblies from Decano & Downing (2019) are available at FigShare at doi: dx.doi. org/10.6084/m9.figshare. 11961711. The genome sequences and annotation files for reference genomes NCTC13441, EC958 and SE15, along with the assembled contigs for 83972 and 3_2_53FAA are available at FigShare at doi: dx.doi. org/10.6084/m9.figshare. 11961813. The 4,071 E. coli ST131 genome assemblies from Decano & Downing (2019) are available at FigShare at doi: 10.6084/m9.figshare. 11962278 (the first 1,680 assemblies) and at doi: dx.doi. org/10.6084/m9.figshare. 11962557 (the second 2,391 assemblies).
Enhanced activity of the bacteriophage λ PL promoter at low temperature

We found that the activity of the phage λ PL promoter is inversely dependent on temperature. Both in vivo and in vitro transcription assays revealed that the rather unique temperature response of PL is a sum of an intrinsic property of the promoter and its activation by integration host factor. We also found that at low temperature, phage λ can lysogenize efficiently but cannot complete the lytic cycle. We hypothesize that by sensing the low environmental temperature the PL promoter plays a role in determining the direction of phage λ development.
Effect of extrusion processing on the nutritive value of canola meal for chinook salmon (Oncorhynchus tshawytscha) in seawater

This study was conducted to evaluate three canola protein products as partial replacements of steam-dried whole herring meal (HM) in a practical diet for juvenile chinook salmon in seawater. Groups of 30–40 g chinook salmon held in 9.5–12°C seawater on a natural photoperiod were fed one of seven equivalent protein (390 g kg−1) and isoenergetic (20 MJ gross energy kg−1) diets to satiation. Each of three test protein sources, namely, commercial canola meal (CM), low-temperature extruded CM (90°C; LT), and high-temperature extruded CM (150°C; HT) comprised about 120 and 240 g kg−1 of dietary protein by replacement of 15 and 30%, respectively, of the HM protein in the control diet. Chinook salmon growth and feed intake were markedly depressed by replacing HM protein with a high level of CM, but these responses were not lowered by replacement with LT and HT. The phytic acid content in commercial canola meal was reduced by about 10 and 30% from the original level by extrusion cooking at low (90°C) and high (150°C) temperature, respectively. Therefore, the diets containing HT still had significant amounts of phytic acid. Terminal whole-body zinc contents were inversely related to the dietary levels of the different canola protein products. Thyroid function was altered by CM but this effect was offset by heat treatment. The results suggest that extrusion cooking of CM improves its nutritive value for chinook salmon in seawater. Indeed, it was found that HT could comprise 240 g kg−1 of the dietary protein without adversely affecting performance.
The monophyly of Euparkeriidae (Reptilia: Archosauriformes) and the origins of Archosauria: a revision of Dorosuchus neoetus from the Mid‐Triassic of Russia

Euparkeria capensis is resolved as the sister taxon to Archosauria in many cladistic phylogenies and provides a key outgroup which may approximate the ancestral archosaur morphology. Several other taxa have been referred to the family Euparkeriidae, but the monophyly of this taxon remains doubtful and largely untested. To test this monophyly, the archosauriform and putative euparkeriid Dorosuchus neoetus from the Mid‐Triassic of Russia is re‐examined in the light of recent work on the evolution of stem archosaurs. Dorosuchus neoetus is found to possess a number of morphological features that place it close to Archosauria, including a sigmoidal femur with a clear attachment region for the m. caudifemoralis musculature, but no unambiguous archosaurian apomorphies. Dorosuchus neoetus is included for the first time in a numerical cladistic analysis and is recovered as the sole sister taxon to Archosauria + Phytosauria. A monophyletic Euparkeriidae including D. neoetus and E. capensis is slightly less parsimonious. In addition, a mandible and pterygoid that were previously referred to D. neoetus subsequent to the original description of the species are also included separately within the phylogenetic analysis and are recovered within Archosauria, possibly raising questions as to their correct taxonomic referral. However, this phylogenetic placement is based primarily on the absence of palatal teeth, but the presence or absence of palatal teeth exhibits considerable homoplasy within Archosauriformes. Based on other aspects of their morphology, we do not reject the referral of these elements to D. neoetus.
Effect of Seeding Rate on Seed and Hay Yield in Common Vetch (Vicia sativa L.)

The effects of six seeding rates (50-300 seeds m−2:) on some morphological traits with hay and seed yield were evaluated in common vetch (Vicia sativa L.) under fall and spring sowing conditions. The mutual correlations among yield and yield components were also determined. The sowing seasons and seeding rates significantly affected hay and seed yield, and most of the yield components. Fall sowings resulted in significantly higher hay and seed yield than spring sowings at all seeding rates, and the highest seed and hay yield was achieved in densities of 250 and 300 seeds m−2. In spring sowings there was a positive response in hay yield up to 250 seeds m−2 while no further increase in seed yield at the seeding rates higher than 150 seeds m−2. Average protein content of hay and seed was found to be higher in spring sown crops than fall. The highest protein yields of hay and seed were obtained at 250 seeds m−2 in fall sowings, and 150 seeds m−2 in spring sowings. Most of the correlations between both hay and seed yields with the yield components were not consistent and differed with the sowing time. Only the correlations between number of the plants per unit area with hay yield, and number of the pods and seeds per unit area with seed yield were statistically significant in both sowing seasons. Close positive associations were obtained between hay and seed yield.
AGA Institute Rapid Review of the Gastrointestinal and Liver Manifestations of COVID-19, Meta-Analysis of International Data, and Recommendations for the Consultative Management of Patients with COVID-19

Abstract Background Multiple gastrointestinal (GI) symptoms including diarrhea, nausea/vomiting, and abdominal pain, as well liver enzyme abnormalities have been variably reported in patients with COVID-19. The AGA) Institute Clinical Guideline Committee and Clinical Practice Updates Committee performed a systematic review and meta-analysis of international data on GI and liver manifestations of COVID-19. Methods We performed a systematic literature search to identify published and unpublished studies using OVID Medline and pre-print servers (medRxiv, LitCovid, and SSRN) up until April 5 2020; major journal sites were monitored for US publications until April 19 2020. We analyzed the prevalence of diarrhea, nausea, vomiting, and abdominal pain as well as LFT abnormalities using a fixed effect model and assessed the certainty of evidence using GRADE. Results We identified 118 studies and used a hierarchal study selection process to identify unique cohorts. We performed a meta-analysis of 47 studies including 10,890 unique patients. Pooled prevalence estimates of GI symptoms was diarrhea 7.7% (95% CI 7.2-8.2), nausea/vomiting 7.8% (95% CI 7.1-8.5), abdominal pain 2.7% (95% CI 2.0-3.4). Most studies reported on hospitalized patients. The pooled prevalence of elevated liver abnormalities was: AST 15.0% (13.6 to 16.5) and ALT 15.0% (13.6 to 16.4). When analyzed comparing data from China to studies from countries other than China, diarrhea, nausea/vomiting, liver abnormalities were more prevalent outside of China with diarrhea reported in 18.3% (16.6 to 20.1). Isolated GI symptoms were rarely reported. We also summarized of the Gl and liver adverse effects of the most commonly utilized medications for COVID19 Conclusions GI symptoms are associated with COVID-19 in less than 10% of patients. In studies outside of China, estimates are higher. Further studies are needed with standardized GI symptoms questionnaires and LFT checks on admission to better quantify and qualify the association of these symptoms with COVID-19. Based on findings from our meta-anlaysis, we make several Best Practice Statements for the consultative management of COVID-19.
Combining ability of salinity tolerance on the basis of NaCl-induced K+ flux from roots of barley

Salinity is a major abiotic stress affecting agricultural production. To understand the genetic behavior of salinity tolerance traits, a half-diallel cross was made among six barley cultivars (Hordeum vulgare L.), with contrasting levels of known tolerance, to study the combining ability of salinity tolerance on the basis of K+ loss from plant roots under saline conditions. The glasshouse pot experiments showed that the six parents were significantly different in salinity tolerance and those tolerances were highly correlated with the K+ flux measurements. The combining ability analysis showed that the variances of both general combining ability (GCA) and specific combining ability (SCA) were highly significant. Two tolerant cultivars, CM72 and Numar, showed significantly higher GCA for salinity tolerance (less K+ loss under salinity stress). Cultivars with medium GCA were YU6472 and Yan90260. Salinity tolerance was mainly controlled by additive effects with the tolerance allele showing partial dominance. High positive SCA was also found between two tolerant cultivars and between tolerant and medium-tolerant cultivars, indicating possible different tolerant genes or some minor genes in these cultivars. The combination of these genes from different sources of tolerant cultivars should produce cultivars with even greater tolerance. © Crop Science Society of America. All rights reserved.
Recovery of surface orientation from diffuse polarization

When unpolarized light is reflected from a smooth dielectric surface, it becomes partially polarized. This is due to the orientation of dipoles induced in the reflecting medium and applies to both specular and diffuse reflection. This paper is concerned with exploiting polarization by surface reflection, using images of smooth dielectric objects, to recover surface normals and, hence, height. This paper presents the underlying physics of polarization by reflection, starting with the Fresnel equations. These equations are used to interpret images taken with a linear polarizer and digital camera, revealing the shape of the objects. Experimental results are presented that illustrate that the technique is accurate near object limbs, as the theory predicts, with less precise, but still useful, results elsewhere. A detailed analysis of the accuracy of the technique for a variety of materials is presented. A method for estimating refractive indices using a laser and linear polarizer is also given.
Characterization of Bacillus luciferensis Strain KJ2C12 from Pepper Root, a Biocontrol Agent of Phytophthora Blight of Pepper

In this study, we characterized the bacterial strain KJ2C12 in relation with its biocontrol activity against Phytophthora capsici on pepper, and identified this strain using morphological, physiological, biochemical, fatty acid methyl ester, and 16S rRNA gene sequence analyses. Strain KJ2C12 significantly (P
A review of the biology and ecology of Calanus agulhensis off South Africa

Calanus agulhensis is the dominant large copepod on South Africa's Agulhas Bank, and is an important food item for pelagic fish. This paper reviews current knowledge and understanding of its biology and ecology and includes comparisons with other Calanus species. Its distribution is influenced by the prevailing hydrography, being advected from the eastern to the western Agulhas Bank and then north along the edge of the west coast shelf. Highest biomass of C. agulhensis is on the central Agulhas Bank in the vicinity of a cool ridge of upwelled water that is thought to enhance local retention. Daily vertical migration on the Agulhas Bank is linked to food concentration, with a strong correlation between the extent of migration of large stages (C4-female) and food abundance in the chlorophyll-rich layer. A diel feeding rhythm has been observed, independent of whether or not animals are migrating vertically. Females offered natural assemblages show a preference for the larger particles of the dominant size classes. Development time from egg to adult (20.3 d at 15.5°C) is fast compared with other Calanus species. The long N3 stage duration suggests that it is the first feeding stage. Isochronal growth is approximated, but the equiproportional rule is not adhered to. In the field, growth rate is influenced more by food than by temperature, particularly larger stages that are more frequently food-limited. This is probably because the small phytoplankton cells that dominate at warm temperatures are generally at low concentrations (<2 mg chlorophyll a m–3), insufficient for fast growth of large stages. Egg production following short periods (1–3 d) of starvation returns quickly to normal on the reintroduction of food, an adaptation that may be beneficial in the relatively stable food environment of the Agulhas Bank. Following long periods (9 d) without food, however, many females are unable to regain normal levels of egg production. At present, there is no information on the extent of omnivory in C. agulhensis, and little on the ecology of the naupliar and young copepodite stages. These may be fruitful areas for future research.
Perioperation ulinastatin intervention protects liver function in hepatectomy: a systematic review of randomized controlled trials and meta-analysis.

BACKGROUND Vascular occlusion during hepatectomy accompanies ischemia-reperfusion (IR) injury, which can cause liver dysfunction and affect patients' outcome. Ulinastatin or urinary trypsin inhibitor (UTI), a polyvalent inhibitor of various enzymes, has been confirmed of anti-IR injury effect in recent studies. Here we performed a systematic review and meta-analysis to assess the benefits of perioperation UTI using to protect liver function in hepatectomy. METHODS Randomized controlled trials (RCTs) evaluating UTI in hepatectomy were identified. Two independent reviewers extracted data on basic characteristics and risk of bias in the studies, and on outcomes such as alanine transaminase (ALT), aspartate transaminase (AST), and total bilirubin (TBIL) from 1 to 7 days after operation. RESULTS A total of 9 RCTs including 408 UTI and 372 control participants were identified. There was no significant difference in basic characteristics such as age or sex. The majority of the patients who underwent hepatectomy had primary liver carcinoma, liver metastases and benign liver lesions. A significant improvement in liver function was associated with UTI use not only at 1 and 3 days postoperatively, but also at 7 days (all P≤0.01). However, significant heterogeneity existed between the pooled studies (all P<0.01). CONCLUSIONS UTI has positive protective effects against IR injury in hepatectomy. However, further highquality RCTs are needed to confirm this conclusion.
Mid-term results of a prospective randomised controlled trial comparing large-head metal-on-metal hip replacement to hip resurfacing using patient-reported outcome measures and objective functional task-based outcomes

Background: The early outcomes of large head-metal-on-metal total hip arthroplasty (MoM THA) are compromised by adverse local tissue reaction to metal debris. This study is the mid-term follow-up of a prospective randomised control trial (pRCT) comparing MoM THA to MoM HR. We sought to answer whether there was a difference between MoM THA and MoM HR at mid-term follow-up in the implant survival; patient-reported outcome measures (PROMs); and when performing objective functional tasks? Methods: A total of 104 patients were studied. Of these 56 had MoM THA (50 male) and 48 had HR (43 male). Mean age at surgery was 52 years in both groups. We reviewed this cohort at mid-term follow-up [minimum 8 years (mean 9 years; range 8–10; SD 0.7)]. PROMs that were completed were OHS, WOMAC, SF-12, and the UCLA. For objective functional task-based outcomes, gait parameters for operated legs were assessed in a subgroup of 17 patients with high UCLA. Results: Revision rate in MoM THA group was 7/56 (12.5%) and in the HR group was 1/48 (2.1%). Overall revision rate at minimum 8-year follow-up was 7.7% (8 of 104 patients). PROMs data comparing MoM THA versus HR showed no difference between the groups. 4 (8.5%) of the non-revised (47) HR patients had WOMAC function or pain score below 70. 3 (6.4%) patients had both pain and function scores <70. In the THA group, 5 (10.2%) of the non-revised (49) patients had WOMAC pain or function scores <70. 3 (6.1%) patients had both pain and function scores <70. The comparison of HA versus THA showed several gait parameters in the HR group to be better but not statistically significant (p > 0.05 Mann-Whitney U-test). Conclusions: At mid-term follow-up, the revision rate of MoM articulation for THA is high (7.7%), being higher in large head MoM total hips versus resurfacing. Overall probability of 10-year survival is 92.3% (KM analysis, 95% for MoM THA and 98% for HR). The HR group had better functional parameters on gait-based tasks compared to THA group but this difference did not reach statistical significance.