Miracle-dz/UniFAR-FTUs huggingface dataset:
The phenotypic association between the interval to post-partum ovulation and traditional measures of fertility in dairy cattle

The relationship between the interval to post-partum (PP) commencement of luteal activity (CLA) and traditional measures of fertility was studied in 1733 lactations of British Friesian cows. Milk progesterone (P 4 ) concentrations were used to determine the interval to PP ovulation and to confirm pregnancy. Milk samples were taken thrice weekly from cows in 20 commercial herds and daily in the University of Nottingham research herd. Commencement of luteal activity was defined as the day of first PP occurrence ofP 4 levels >3 μg/l which was then maintained for at least two consecutive readings in the commercial herds and for 4 days in the university herd. Records from animals with retained placenta, uterine infection or those treated with reproductive hormone preparations for reproductive disorders were excluded for this analysis from the original database of cows during 2503 lactations. The interval to PP CLA averaged 27·0 (s.d. 12·1) days (no. = 1733), interval to first service 71·2 (s.d. 19·9) days (no. = 1646), interval to conception 87·2 (s.d. 35·0) days (no. = 1510), number of services per conception 1·50 (s.d. 0·83, no. = 1510) and conception to first service was 0·65. Linear models were then fitted to subsets of the data with complete information to assess the influences of lactation number, season and herd (at least 1243 observations in all analyses). The interval to PP CLA was favourably correlated with measures of fertility such that for every day delay in the interval to CLA there was an average delay of 0·24 and 0·41 days (P
Environmental Performance of Pseudomonas putida with a Uracylated Genome

A variant of the soil bacterium Pseudomonas putida with a genome containing a ∼20 % replacement of the whole of thymine (T) by uracil (U) was made by deleting genes ung (uracil DNA glycosylase) and dut (deoxyuridine 5′‐triphosphate nucleotide hydrolase). Proteomic comparisons revealed that, of 281 up‐regulated and 96 down‐regulated proteins in the Δung Δdut cells, as compared to the wild‐type, many were involved in nucleotide metabolism. Unexpectedly, genome uracylation did not greatly change the gross environmental endurance profile of P. putida, increased spontaneous mutagenesis by only twofold and supported expression of heterologous proteins well. As U‐enriched DNA is potentially degraded by the base excision repair of recipients encoding a uracil DNA glycosylase, we then tested the spread potential of genetic material originating in the Δung Δdut cells either within the same species or in a commonly used Escherichia coli strain. Transformation and conjugation experiments revealed that horizontal gene transfer of U‐containing plasmids fared worse than those made of standard DNA by two orders of magnitude. Although this figure does not guarantee the certainty of containment, it suggests a general strategy for curbing the dispersal of recombinant genetic constructs.
Woodland mouse and vole response to increased structural diversity following midrotation commercial thinning in spruce plantations

We assessed whether commercially thinning (CT) spruce (Picea spp.) plantations (40% basal area removal) can cause structural changes in fine woody debris (FWD) and understory vegetation to improve habitat quality for small rodents in northwestern New Brunswick, Canada. We created three contrasting environments (FWD rich – understory vegetation rich, FWD poor – understory vegetation rich, and FWD poor – understory vegetation poor) by establishing CT with debris retention (merchantable trunk removal), CT with all debris removed (full tree removal), and non-CT (plantation without CT) in six midrotation white spruce (Picea glauca (Moench) Voss) plantations. We live-trapped small mammals in each plantation during spring and summer of 2011 and 2012 and estimated animal density and survival with capture–recapture models. Southern red-backed vole (Myodes gapperi (Vigors, 1830)) density was two to three times greater in CT with debris retention than in either non-CT or CT with debris removal, and their survival ra.
Meta-Analysis of the Association Between the rs228570 Vitamin D Receptor Gene Polymorphism and Arterial Hypertension Risk.

The association between FokI polymorphism in the vitamin D receptor (VDR) gene and susceptibility to arterial hypertension (HT) is controversial. Thus, we evaluated the relation between FokI and HT according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines using MEDLINE® (Medical Literature Analysis and Retrieval System Online)/PubMed, Scopus, and Cochrane Library CENTRAL databases. Data from case-control studies, including the number of participants, age, 25-hydroxyvitamin D concentrations, systolic and diastolic blood pressure values, FokI allele, and genotype frequency were extracted by 2 independent authors and OR was calculated with the 95% CI to assess the strength of the association between the FokI variant and odds of HT. In general and subgroup analyses, we used allelic (f compared with F), common (ff compared with FF + Ff), risk (ff + Ff compared with FF), and additive (ff compared with FF) models. Six case-control studies including 3140 cases and 3882 controls were reviewed in the meta-analysis. Global assessment revealed a correlation between FokI and reduced odds of HT in the additive/homozygote model (ff compared with FF; OR: 0.65; 95% CI: 0.45-0.94) and common/recessive model (ff compared with FF + Ff; OR: 0.75; 95% CI: 0.57-0.99). In Asian subjects, there was a significant reduction in the odds of HT in additive (ff compared with FF; OR: 0.84; 95% CI: 0.73-0.98) and risk models (ff + Ff compared with FF; OR: 0.87, 95% CI: 0.78-0.97), in particular, for Indians (South). In Africans, the statistically significant association occurred in the additive and common models. Allele f in the FokI polymorphism of the VDR gene was associated with reduced odds of HT in the general population based on the risk model. Thus, nutritional genomics can help understand the influence of nutrition on metabolic homeostasis pathways and the clinical consequences of hypertension. This study shows the need for healthy, anti-inflammatory, and antioxidant compounds to prevent or treat chronic complications.
Useofaninert marker (phenol red) toimprove accuracyingastric secretion studies

SUMMARY Gastric secretion from24subjects was collected bycontinuous nasogastric aspiration during theplateau ofsecretion evokedbyintravenous histamine diphosphate, 0.01mg/kg/hr. Simultaneously, phenol redwas instilled ata constant rateintotheproximal partofthestomach. Concentrations ofphenol redin15-minute aspirates weremeasured, andusedtodeduce pyloric losses andthe reasonsforrandom variation inthevolumes aspirated. Theaveragecoefficient ofvariation inthevolume was26%, irrespective ofthenature ofthenasogastric tube. Correction byphenol redreduced this value to21%. Thecoefficient ofvariation of volume diminished assecretion rateincreased. Pyloric losses amounted to7ml/15 min, andwere independent ofthesecretion rate. Thequantitative effect ofthese errorsupon theassessment of gastric secretion wasminimal athigh secretion rates butimportant atlowrates. Clinical studies designed tomeasure humangastric secretory activity rely uponthecomplete collection ofthegastric secretion asanessential first step. Thetechnique usually employed iscontinuous aspiration viaa nasogastric tube, positioned so thatitstiplies inthemostdependent partofthe stomach. Rovelstad (1963) showed that continuous aspiration, rather thanintermittent, wasessential toreduce theerrors duetolosses ofgastric juice through thepylorus, butdidnotprovethatthis source oferror wasnegligible iftheaspiration was carried outcontinuously. Machine suction has beenshowntobeinferior tohandsuction (Johnston andMcCraw,1958). RoyleandCatchpole (1967) reported that considerable losses ofgastric secretion didoccurviathepylorus evenduring continuous aspiration; their measurements ofthese losses were indirect andinferential. Thepresent article reports studies designed tomeasurepyloric losses under various conditions using anon-absorbable marker during astate ofsubmaximal butconstant secretory activity.
The p21‐activated kinase 2 (PAK2), but not PAK1, regulates contraction‐stimulated skeletal muscle glucose transport

Muscle contraction stimulates skeletal muscle glucose transport. Since it occurs independently of insulin, it is an important alternative pathway to increase glucose transport in insulin‐resistant states, but the intracellular signaling mechanisms are not fully understood. Muscle contraction activates group I p21‐activated kinases (PAKs) in mouse and human skeletal muscle. PAK1 and PAK2 are downstream targets of Rac1, which is a key regulator of contraction‐stimulated glucose transport. Thus, PAK1 and PAK2 could be downstream effectors of Rac1 in contraction‐stimulated glucose transport. The current study aimed to test the hypothesis that PAK1 and/or PAK2 regulate contraction‐induced glucose transport.
Motility and orientation of a dinoflagellate, Gymnodinium, impaired by solar and ultraviolet radiation

The effects of solar and artificial ultraviolet radiation on the motility and orientation of the dinoflagellate Y-100 were studied. The cells show a weak photokinesis but a pronounced phototaxis which is consistently positive between 1 and 100 klx (= 4 mW m−2 to 400 mW m−2); the precision of orientation increases with the fluence rate. Unfiltered solar radiation as well as artificial ultraviolet radiation reduce the percentage of motile cells increasingly with exposure time but the velocity of the still motile cells is less affected. Unirradiated control cells show a negative gravitaxis. After short exposure to solar or artificial ultraviolet radiation the precision of gravitaxis decreases and after prolonged exposure the cells start to actively move downward in the water column (positive gravitaxis). Phototaxis is also strongly impaired by ultraviolet radiation.
A NEW SQUAT LOBSTER OF THE GENUS RAYMUNIDA (DECAPODA: GALATHEIDAE) FROM TAIWAN

Abstract The galatheid genus Raymunida Macpherson and Machordom, 2000, is reported for the first time from Taiwan, and the species collected is also new to science. The new species is most closely related to R. confundens Macpherson and Machordom, 2001, but differs in having a more robust cheliped and walking legs covered with distinct squammae. The coloration of the new species is probably unique in the genus by both the carapace and abdomen being uniform in color. Analysis of the mitochondrial cytochrome oxidase I gene sequences also supports the specific status of this Taiwanese form.
Mechanism of translation inhibition by type II GNAT toxin AtaT2

Abstract Type II toxin–antitoxins systems are widespread in prokaryotic genomes. Typically, they comprise two proteins, a toxin, and an antitoxin, encoded by adjacent genes and forming a complex in which the enzymatic activity of the toxin is inhibited. Under stress conditions, the antitoxin is degraded liberating the active toxin. Though thousands of various toxin–antitoxins pairs have been predicted bioinformatically, only a handful has been thoroughly characterized. Here, we describe the AtaT2 toxin from a toxin–antitoxin system from Escherichia coli O157:H7. We show that AtaT2 is the first GNAT (Gcn5-related N-acetyltransferase) toxin that specifically targets charged glycyl tRNA. In vivo, the AtaT2 activity induces ribosome stalling at all four glycyl codons but does not evoke a stringent response. In vitro, AtaT2 acetylates the aminoacyl moiety of isoaccepting glycyl tRNAs, thus precluding their participation in translation. Our study broadens the known target specificity of GNAT toxins beyond the earlier described isoleucine and formyl methionine tRNAs, and suggest that various GNAT toxins may have evolved to specificaly target other if not all individual aminoacyl tRNAs.
Effect of plantation age on organoleptic traits of a typical Italian green asparagus crop

Asparagus is a very common and important vegetable in Italy especially in the North-east regions where it is also a typical and historical product. For green asparagus, and in particular for typical cultivar grown in Northern Italy, the information on these issues are limited. For these reasons experiments have been carried out in order to evaluate nitrates, nitrites, polyphenols and pigments contents and antioxidants activity of marketable product of green asparagus cv Eros. The qualitative analysis on green shoots were performed on samples coming from 2 plantations with different age: 3 years old crop (YC) and 8 years old crop (OC). During harvest (from April till May), six samplings were performed. After each harvest, shoots were calibrated, washed and placed at 4 C° till next day. For qualitative analysis only extra class shoots (diameter >16 mm) were used. Shoots were weighted and then cut to 270 mm from the apex in order to separate not marketable portion from the commercial one. The latter fraction was cut in 3 parts 90 mm long (apical (A), intermediate (I) and basal (B)) to evaluate quality characteristics of each part. Results showed that OC asparagus had a higher content of dry matter and a greater weight. The nitrate content, which was always far below the recommended WHO limits, was not influenced by location, while considering the part of shoot, as expected, a decreasing trend from the base to the apex was observed. For nitrites there were no significant differences between locations and among shoot parts. The pigments content increased during the advancing of the harvest season in OC that showed the highest values. The content of these compounds strongly increased moving from the base to the top of the shoot and the chlorophyll a content was higher than the chlorophyll b and the pool xanthophylls + carotenoids. The antioxidant activity and polyphenol analysis showed that the upper part is the richest in these compounds mainly because directly exposed to stress situations.
Survey or genetic variation in European tree populations

Muller-Starck. G. : Survey of genetic variation in European tree populations. - Bocconea 7: 43-49.1997 . - ISSN 1120-4060. The paper reviews the present state of knowledge of genetic variation in the main native European forest trees species. Isozyrne te sts have already shown that as a group these forest trees are extremely variable both in terrns of number of alleles per locus and the level of heterozygosity in populations. The maintenance of high levels of intrapopulation genetic variation in many of these trees is interpreted as a necessary strategy to survive in the heterogeneous environmental conditions that these long-lived plants fac e. Suggestions are offered how to preserve such vital genetic variation in forest tree populations in face of increasing environrnental stresses . Compared to environmental conditions of crops and other economically important plant species, forest environments are extremely heterogeneous in time and in space. Most fOl'est tree populations can be considered as wild populations which are exposed to highly variable constellations of stress factors. Due to limited efficiency, provisions for plant protection and amelioration of forest sites are rather the exception than the rule. Changes in environmental stress conditions cannot be predicted in long-lived tree popu lations. Such environmental heterogeneity severely challenges the ability of forest tree populations to adapt genetically and thus to survive. The adaptive potential of forest tree populations is determined by the realized amount and pattern of genetic variation. Consequently, genetic variation (e.g. heterozygosities, genetic multiplicity, diversity, differentiation) is considered as a parameter of stability of complex forest ecosystems. The objective of this contribution is to review the present state of knowledge on genetic variation within predominant native European forest tree species and to infer briefly on short comings and research needs.
Oral vancomycin prophylaxis for the prevention of Clostridium difficile infection: A systematic review and meta-analysis

Abstract Objective: Recently, oral vancomycin prophylaxis (OVP) has been suggested for the prevention of Clostridium difficile infection (CDI). We conducted a systematic review and meta-analysis to investigate the efficacy and safety of this approach. Design: Systematic review and meta-analysis. Methods: We conducted a computerized search of MEDLINE, EMBASE, and Cochrane databases from inception to March 2019 for publications investigating OVP for CDI prevention. Results were screened for eligibility. Relevant data were extracted and analyzed. Publication bias was assessed using the Egger test. Results: Ultimately, 8 retrospective studies and 1 prospective study examining 2174 patients, published between 2016 and 2019 were included in the review. OVP was associated with decreased CDI (odds ratio, 0.263; 95% confidence interval, 0.13–0.52) with considerable heterogeneity (I2 = 61%). Meta-regression showed that total daily dose of OVP correlated with CDI, explaining 100% of heterogeneity between studies. Furthermore, 3 studies evaluated the risk of vancomycin-resistant enterococci (VRE) infection after OVP and found no significant increase. Conclusion: Our results suggest that OVP might decrease CDI rates in at-risk populations, although this conclusion should be interpreted with caution. Higher daily doses of OVP might increase CDI. Although the use of OVP in high-risk patients may reduce CDI, this suggestion has yet to be validated by prospective blinded randomized controlled trials.
Adaptation of rat fast‐twitch muscle to endurance activity is underpinned by changes to protein degradation as well as protein synthesis

Muscle adaptations to exercise are underpinned by alterations to the abundance of individual proteins, which may occur through a change either to the synthesis or degradation of each protein. We used deuterium oxide (2H2O) labeling and chronic low‐frequency stimulation (CLFS) in vivo to investigate the synthesis, abundance, and degradation of individual proteins during exercise‐induced muscle adaptation. Independent groups of rats received CLFS (10 Hz, 24 h/d) and 2H2O for 0, 10, 20, or 30 days. The extensor digitorum longus (EDL) was isolated from stimulated (Stim) and contralateral non‐stimulated (Ctrl) legs. Proteomic analysis encompassed 38 myofibrillar and 46 soluble proteins and the rates of change in abundance, synthesis, and degradation were reported in absolute (ng/d) units. Overall, synthesis and degradation made equal contributions to the adaptation of the proteome, including instances where a decrease in protein‐specific degradation primarily accounted for the increase in abundance of the protein.
Adherence to prescribed medications in patients with heart failure - insights from liquid chromatography-tandem mass spectrometry-based urine analysis.

AIMS None of the existing studies on adherence have directly measured levels of medications (or their metabolites) in patients with heart failure. METHODS AND RESULTS We used liquid chromatography-tandem mass spectrometry to measure the presence of prescribed drugs (diuretics, angiotensin converting enzyme inhibitors, angiotensin receptor blockers, beta-blockers and mineralocorticoid receptor antagonists) in the urine of patients reviewed 4 to 6 weeks after hospitalisation with heart failure. Patients were unaware that adherence was being assessed. Of the 341 patients studied, 281 (82.4%) were adherent i.e. had all prescribed drugs of interest detectable in their urine. Conversely, 60 patients (17.6%) were partially or completely non-adherent. Notably, 24 of the 60 were non-adherent to only diuretic therapy and only 7 out of all 341 patients studied (2.1%) were completely non-adherent to all prescribed heart failure drugs. There were no major differences in baseline characteristics between adherent and non-adherent patients. CONCLUSION Non-adherence, assessed using a single spot urine measurement of drug levels, was confirmed in 1 of 5 patients evaluated 4 to 6 weeks after hospitalisation with heart failure.
Evolutionary Modification of Pereopods in Phronimid Amphipods (Crustacea: Amphipoda: Hyperiidea: Phronimidae) Reflects Host Differences

Phronimid amphipods are oceanic crustaceans associated with gelatinous zooplankters. Their host organisms belong mainly to two taxonomic groups: tunicates (salps or pyrosomes; subphylum Tunicata) and siphonophores (Cnidaria). After these amphipods devour the inner tissues of their hosts, they display the unique behavior of modifying their hosts into hollow barrel-shaped shelters, which are then utilized as neonatal nurseries by the females. Although previous studies have revealed the host specificity of these amphipods, it has not been inferred which types of hosts ancestral phronimids could have originally used. Moreover, morphological changes associated with host switching have not yet been studied. To deduce the evolutionary patterns of host switching, we investigated the phylogenetic relationships of phronimid species by using two genes: (1) cytochrome c oxidase subunit I (COI) and (2) 18S ribosomal RNA (18S). In addition, a morphometric analysis was conducted in order to better understand the morphological relationships between phronimids and their host organisms. Our phylogenetic analysis suggests that the ancestral host animals of phronimids could have been tunicates and that the host organisms have independently switched from tunicates to siphonophores at least twice in the family Phronimidae. Our morphometric analysis revealed that phronimids using siphonophores as hosts have a relatively shorter pereopod 5 compared to those using tunicates. The shortening of pereopod 5 seems to be an adaptation to the narrower internal space of siphonophore barrels compared to those of tunicates.
IS PLASTICITY IN RESPONSE TO LIGHT AND TO SOIL INVOLVED IN THE ECOTYPIC DIFFERENTIATION OF A TREE SPECIES FROM CERRADO AND ATLANTIC FOREST

1 Universidade Federal dos Vales do Jequitinhonha e Mucuri, Departamento de Ciencias Biologicas, Rua da Gloria 187, Centro, 39100 000, Diamantina, Minas Gerais, Brazil. 2 Universidade Federal de Minas Gerais, Departamento de Botânica, Av. Antonio Carlos 6627, 31270 010, Belo Horizonte, Minas Gerais, Brazil. 3 Universidade Federal de Minas Gerais, Departamento de Biologia Geral, Av. Antonio Carlos 6627, 31270 010, Belo Horizonte, Minas Gerais, Brazil. Phone number: 55 38 3532 1200-mfgoulart@biotropicos.org. br
Copepod vital rates under CO2-induced acidification: a calanoid species and a cyclopoid species under short-term exposures

Although copepods have been considered tolerant against the direct inﬂuence of the ocean acidiﬁcation (OA) projected for the end of the century, some recent studies have challenged this view. Here, we have examined the direct impact of short-term exposure to a pCO 2 / pH level relevant for the year 2100 ( pH NBS , control: 8.18, low pH : 7.78), on the physiological performance of two representative marine copepods: the calanoid Acartia grani and the cyclopoid Oithona davisae . Adults of both species, from laboratory cultures, were preconditioned for four consecutive days in algal suspensions ( Akashiwo sanguinea ) prepared with ﬁltered sea water pre-adjusted to the targeted pH values via CO 2 bub-bling. We measured the feeding and respiratory activity and reproductive output of those pre-conditioned females. The largely unaffected fatty acid composition of the prey offered between OA treatments and controls supports the absence in the study of indirect OA effects (i.e. changes of food nutritional quality). Our results show no direct effect of acidiﬁcation on the vital rates examined in either copepod species. Our ﬁndings are compared with results from previous short- and long-term manipulative experiments on other copepod species.