Miracle-dz/UniFAR-FTUs huggingface dataset:
Attitudes to, and experience of, pooled sampling for sexually transmitted infection testing: a web-based survey of English sexual health services

Chlamydia trachomatis and Neisseria gonorrhoeae testing guidance recommends extragenital screening with locally validated nucleic acid amplification tests, with anatomical sites tested separately. Evidence supports multi-patient combined aliquot pooled sampling (PS) for population screening; evidence for within-patient PS is sparse. Within-patient PS could be more cost-effective for triple-site testing, but requires distinct clinical pathways and consideration over loss of information to guide risk assessments and treatment. We explored PS attitudes and practices amongst clinicians in England. A cross-sectional web-based survey was distributed to clinical leads of sexual health services throughout England in February 2016. Fifty-two (52/216, 23%) services responded. One service reported current within-patient PS and two were awaiting implementation. Of the 49 services not pooling, five were considering implementation. Concerns raised included the inability to distinguish infection site(s) (36/52, 69%), absence of national guidance (34/52, 65%) and reduced assay performance (18/52, 34%). Only 8/52 (15%) considered the current level of evidence sufficient to support PS, with 40/52 (77%) requesting further validation studies and 39/52 (77%) national guidance. PS was rarely used by respondents to this survey, although the response rate was low. The clinical challenges presented by PS need to be addressed through further development of the evidence base.
Biological Characteristics of Grapholita molesta (Lepidoptera: Tortricidae) Induced to Diapause in Laboratory

Abstract In southern Brazil, Grapholita molesta (Busck) (Lepidoptera: Tortricidae) uses diapause as survival strategy during the winter (May–August). In our study, we evaluated the effect of diapause on biological characteristics of the species for 4 months in laboratory. Newly hatched larvae of G. molesta were induced to diapause changing the photoperiod and temperature (T) (12 ± 1°C), relative humidity (RH) (70 ± 10%), and a photophase of 12 h and, when they started diapause in the prepupal stage, the conditions were kept for 4 months. Afterwards, the insects were induced to finalize the diapause process at T 25 ± 1°C, RH 70 ± 10%, and a photophase of 16 h. We evaluated the duration and viability of the larval stages and pupae, pupae weight at 24 h and sex ratio (sr), periods of preoviposition, oviposition, and postoviposition; adult life span (males and females); fecundity (daily and total); embryonic period duration and eggs viability, comparing the data with insects nondiapause. The results show that diapause greatly affected the viability of pupal–adult stages of the population (21.8%) when compared with insects’ nondiapause (80.0%). Total fecundity (83.0 eggs) and mean life span (12.0 d) of insects diapause was significantly lower compared with insects nondiapause (173.0 and 17.0), respectively. However, these differences were not observed in the sr, which was similar to insects diapause (sr = 0.41) and insects nondiapause (sr = 0.49). The diapause induced for 4 months negatively affects reproduction and life span of adults of G. molesta.
Nitrogen Limitation and Slow Drying Induce Desiccation Tolerance in Conjugating Green Algae (Zygnematophyceae, Streptophyta) from Polar Habitats

Background Filamentous Zygnematophyceae are typical components of algal mats in the polar hydro-terrestrial environment. Under field conditions, they form senescent vegetative cells, designated as pre-akinetes, which are tolerant to desiccation and osmotic stress. Key Findings Pre-akinete formation and desiccation tolerance was investigated experimentally under monitored laboratory conditions in four strains of Arctic and Antarctic isolates with vegetative Zygnema sp. morphology. Phylogenetic analyses of rbcL sequences revealed one Arctic strain as genus Zygnemopsis, phylogenetically distant from the closely related Zygnema strains. Algae were cultivated in liquid or on solidified medium (9 weeks), supplemented with or lacking nitrogen. Nitrogen-free cultures (liquid as well as solidified) consisted of well-developed pre-akinetes after this period. Desiccation experiments were performed at three different drying rates (rapid: 10% relative humidity, slow: 86% rh and very slow); viability, effective quantum yield of PS II, visual and ultrastructural changes were monitored. Recovery and viability of pre-akinetes were clearly dependent on the drying rate: slower desiccation led to higher levels of survival. Pre-akinetes survived rapid drying after acclimation by very slow desiccation. Conclusions The formation of pre-akinetes in polar Zygnema spp. and Zygnemopsis sp. is induced by nitrogen limitation. Pre-akinetes, modified vegetative cells, rather than specialized stages of the life cycle, can be hardened by mild desiccation stress to survive rapid drying. Naturally hardened pre-akinetes play a key role in stress tolerance and dispersal under the extreme conditions of polar regions, where sexual reproduction and production of dormant stages is largely suppressed.
Transfusion of recently donated (fresh) red blood cells (RBCs) does not improve survival in comparison with current practice, while safety of the oldest stored units is yet to be established: a meta‐analysis

Preclinical studies generated the hypothesis that older stored red blood cells (RBCs) can increase transfusion risks. To examine the most updated and complete clinical evidence and compare results between two trial designs, we assessed both observational studies and randomized controlled trials (RCTs) studying the effect of RBC storage age on mortality.
Effect of duration of alcohol consumption on calcium and bone metabolism during pregnancy in the rat.

BACKGROUND Little is known about the consequences of drinking during pregnancy for the long-term health of the mother. Alcohol (ethanol) has been shown to disrupt calcium (Ca) homeostasis and is known to have deleterious effects on bone. During pregnancy, bone turnover is increased to maintain Ca homeostasis; therefore, pregnancy may be a time of life when maternal bone is particularly susceptible to the effects of ethanol. This study investigated the effect of duration of ethanol consumption on Ca homeostasis and bone during pregnancy in the rat. METHODS Rats were fed ethanol (36% ethanol-derived calories) in liquid diets for 3 (21 days gestation only) or 6 (3 weeks before and throughout 21 days gestation) weeks. Maternal blood was analyzed for Ca (total and ionized Ca [iCa]), the Ca-regulating hormones (parathyroid hormone [PTH], 1,25(OH)2D, calcitonin), and osteocalcin (a marker for bone formation). Bone was analyzed for ash (mineral) content. RESULTS Dams consuming ethanol (E dams) had decreased blood Ca levels (total and iCa) at both 3 and 6 weeks, but iCa was lower in E dams after 6 compared with 3 weeks. Importantly, ethanol seemed to interfere with the normal compensatory response to these decreased Ca levels. In contrast to pair-fed controls, serum PTH levels actually were decreased, 1,25(OH)2D levels failed to increase, and calcitonin levels were increased in ethanol-consuming dams, regardless of duration. Moreover, ethanol decreased bone formation, as indicated by serum osteocalcin levels, after both 3 and 6 weeks consumption, and after 6 weeks, the ash content of bone also was decreased. In addition, a relationship was found between the blood alcohol concentration (BAC) and some measures of Ca and bone metabolism. Serum 1,25(OH)2D and osteocalcin levels varied inversely, whereas serum calcitonin varied directly with BAC, suggesting that time of sampling after drinking may be an important variable for interpreting ethanol's effects on Ca and bone metabolism. In all rats, serum osteocalcin levels varied directly with PTH and 1,25(OH)2D levels. CONCLUSIONS Ethanol consumption during pregnancy impaired Ca homeostasis in the dam, regardless of duration of consumption, and resulted in decreased bone formation and ash content of bone. Significant relationships among the Ca-regulating hormones, BAC, and osteocalcin support the hypothesis that ethanol's effects on the Ca-regulating hormones may mediate some of its effects on bone.
Earlier-Season Vegetation Has Greater Temperature Sensitivity of Spring Phenology in Northern Hemisphere

In recent decades, satellite-derived start of vegetation growing season (SOS) has advanced in many northern temperate and boreal regions. Both the magnitude of temperature increase and the sensitivity of the greenness phenology to temperature–the phenological change per unit temperature–can contribute the advancement. To determine the temperature-sensitivity, we examined the satellite-derived SOS and the potentially effective pre-season temperature (T eff) from 1982 to 2008 for vegetated land between 30°N and 80°N. Earlier season vegetation types, i.e., the vegetation types with earlier SOSmean (mean SOS for 1982–2008), showed greater advancement of SOS during 1982–2008. The advancing rate of SOS against year was also greater in the vegetation with earlier SOSmean even the T eff increase was the same. These results suggest that the spring phenology of vegetation may have high temperature sensitivity in a warmer area. Therefore it is important to consider temperature-sensitivity in assessing broad-scale phenological responses to climatic warming. Further studies are needed to explore the mechanisms and ecological consequences of the temperature-sensitivity of start of growing season in a warming climate.
Cross-Linking of a CD4-Mimetic Miniprotein with HIV-1 Env gp140 Alters Kinetics and Specificities of Antibody Responses against HIV-1 Env in Macaques

ABSTRACT Evaluation of the epitope specificities, locations (systemic or mucosal), and effector functions of antibodies elicited by novel HIV-1 immunogens engineered to improve exposure of specific epitopes is critical for HIV-1 vaccine development. Utilizing an array of humoral assays, we evaluated the magnitudes, epitope specificities, avidities, and functions of systemic and mucosal immune responses elicited by a vaccine regimen containing Env cross-linked to a CD4-mimetic miniprotein (gp140-M64U1) in rhesus macaques. Cross-linking of gp140 Env to M64U1 resulted in earlier increases of both the magnitude and avidity of the IgG binding response than those with Env protein alone. Notably, IgG binding responses at an early time point correlated with antibody-dependent cellular cytotoxicity (ADCC) function at the peak immunity time point, which was higher for the cross-linked Env group than for the Env group. In addition, the cross-linked Env group developed higher IgG responses against a linear epitope in the gp120 C1 region of the HIV-1 envelope glycoprotein. These data demonstrate that structural modification of the HIV-1 envelope immunogen by cross-linking of gp140 with the CD4-mimetic M64U1 elicited an earlier increase of binding antibody responses and altered the specificity of the IgG responses, correlating with the rise of subsequent antibody-mediated antiviral functions. IMPORTANCE The development of an efficacious HIV-1 vaccine remains a global priority to prevent new cases of HIV-1 infection. Of the six HIV-1 efficacy trials to date, only one has demonstrated partial efficacy, and immune correlate analysis of that trial revealed a role for binding antibodies and antibody Fc-mediated effector functions. New HIV-1 envelope immunogens are being engineered to selectively expose the most vulnerable and conserved sites on the HIV-1 envelope, with the goal of eliciting antiviral antibodies. Evaluation of the humoral responses elicited by these novel immunogen designs in nonhuman primates is critical for understanding how to improve upon immunogen design to inform further testing in human clinical trials. Our results demonstrate that structural modifications of Env that aim to mimic the CD4-bound conformation can result in earlier antibody elicitation, altered epitope specificity, and increased antiviral function postimmunization.
Phylogeography of the Tropical Planktonic Foraminifera Lineage Globigerinella Reveals Isolation Inconsistent with Passive Dispersal by Ocean Currents

Morphologically defined species of marine plankton often harbor a considerable level of cryptic diversity. Since many morphospecies show cosmopolitan distribution, an understanding of biogeographic and evolutionary processes at the level of genetic diversity requires global sampling. We use a database of 387 single-specimen sequences of the SSU rDNA of the planktonic foraminifera Globigerinella as a model to assess the biogeographic and phylogenetic distributions of cryptic diversity in marine microplankton on a global scale. Our data confirm the existence of multiple, well isolated genetic lineages. An analysis of their abundance and distribution indicates that our sampling is likely to approximate the actual total diversity. Unexpectedly, we observe an uneven allocation of cryptic diversity among the phylogenetic lineages. We show that this pattern is neither an artifact of sampling intensity nor a function of lineage age. Instead, we argue that it reflects an ongoing speciation process in one of the three major lineages. Surprisingly, four of the six genetic types in the hyperdiverse lineage are biogeographically restricted to the Indopacific. Their mutual co-occurrence and their hierarchical phylogenetic structure provide no evidence for an origin through sudden habitat fragmentation and their limitation to the Indopacific challenges the view of a global gene flow within the warm-water provinces. This phenomenon shows that passive dispersal is not sufficient to describe the distribution of plankton diversity. Rather, these organisms show differentiated distribution patterns shaped by species interactions and reflecting phylogenetic contingency with unique histories of diversification rates.
Mammals of Australia's Tropical Savannas: A Conceptual Model of Assemblage Structure and Regulatory Factors in the Kimberley Region

We construct a state-and-transition model for mammals in tropical savannas in northern Australia to synthesize ecological knowledge and understand mammalian declines. We aimed to validate the existence of alternative mammal assemblage states similar to those in arid Australian grasslands, and to speculate on transition triggers. Based on the arid grassland model, we hypothesized that assemblages are partitioned across rainfall gradients and between substrates. We also predicted that assemblages typical of arid regions in boom periods would be prevalent in savannas with higher and more regular rainfall. Data from eight mammal surveys from the Kimberley region, Western Australia (1994 to 2011) were collated. Survey sites were partitioned across rainfall zones and habitats. Data allowed us to identify three assemblage states: State 0:- low numbers of mammals, State II:- dominated by omnivorous rodents and State III:- dominated by rodents and larger marsupials. Unlike arid grasslands, assemblage dominance by insectivorous dasyurids (State I) did not occur in savannas. Mammal assemblages were partitioned across rainfall zones and between substrates as predicted, but—unlike arid regions—were not related strongly to yearly rainfall. Mammal assemblage composition showed high regional stability, probably related to high annual rainfall and predictable wet season resource pulses. As a consequence, we speculate that perpetually booming assemblages in savannas allow top-down control of the ecosystem, with suppression of introduced cats by the dingo, the region's top predator. Under conditions of low or erratic productivity, imposed increasingly by intense fire regimes and introduced herbivore grazing, dingoes may not limit impacts of cats on native mammals. These interacting factors may explain contemporary declines of savanna mammals as well as historical declines in arid Australia. The cat-ecosystem productivity hypothesis raised here differs from the already-articulated cat-habitat structure hypothesis for mammal declines, and we suggest approaches for explicit testing of transition triggers for competing hypotheses.
CALR, JAK2 and MPL mutation status in Argentinean patients with BCR-ABL1- negative myeloproliferative neoplasms

ABSTRACT Objectives: To establish the frequency of JAK2, MPL and CALR mutations in Argentinean patients with BCR-ABL1-negative myeloproliferative neoplasms (MPN) and to compare their clinical and haematological features. Methods: Mutations of JAK2V617F, JAK2 exon 12, MPL W515L/K and CALR were analysed in 439 Argentinean patients with BCR-ABL1-negative MPN, including 176 polycythemia vera (PV), 214 essential thrombocythemia (ET) and 49 primary myelofibrosis (PMF). Results: In 94.9% of PV, 85.5% ET and 85.2% PMF, we found mutations in JAK2, MPL or CALR. 74.9% carried JAK2V617F, 12.3% CALR mutations, 2.1% MPL mutations and 10.7% were triple negative. In ET, nine types of CALR mutations were identified, four of which were novel. PMF patients were limited to types 1 and 2, type 2 being more frequent. Discussion: In ET, patients with CALR mutation were younger and had higher platelet counts than those with JAK2V617F and triple negative. In addition, JAK2V617F patients had high leucocyte and haemoglobin values compared with CALR-mutated and triple-negative patients. In PMF, patients with mutant CALR were associated with higher platelet counts. Conclusion: Our study underscores the importance of JAK2, MPL and CALR genotyping for accurate diagnosis of patients with BCR-ABL1-negative MPN.
Steady-State Growth under Inorganic Carbon Limitation Conditions Increases Energy Consumption for Maintenance and Enhances Nitrous Oxide Production in Nitrosomonas europaea

ABSTRACT Nitrosomonas europaea is a chemolithoautotrophic bacterium that oxidizes ammonia (NH3) to obtain energy for growth on carbon dioxide (CO2) and can also produce nitrous oxide (N2O), a greenhouse gas. We interrogated the growth, physiological, and transcriptome responses of N. europaea to conditions of replete (>5.2 mM) and limited inorganic carbon (IC) provided by either 1.0 mM or 0.2 mM sodium carbonate (Na2CO3) supplemented with atmospheric CO2. IC-limited cultures oxidized 25 to 58% of available NH3 to nitrite, depending on the dilution rate and Na2CO3 concentration. IC limitation resulted in a 2.3-fold increase in cellular maintenance energy requirements compared to those for NH3-limited cultures. Rates of N2O production increased 2.5- and 6.3-fold under the two IC-limited conditions, increasing the percentage of oxidized NH3-N that was transformed to N2O-N from 0.5% (replete) up to 4.4% (0.2 mM Na2CO3). Transcriptome analysis showed differential expression (P ≤ 0.05) of 488 genes (20% of inventory) between replete and IC-limited conditions, but few differences were detected between the two IC-limiting treatments. IC-limited conditions resulted in a decreased expression of ammonium/ammonia transporter and ammonia monooxygenase subunits and increased the expression of genes involved in C1 metabolism, including the genes for RuBisCO (cbb gene cluster), carbonic anhydrase, folate-linked metabolism of C1 moieties, and putative C salvage due to oxygenase activity of RuBisCO. Increased expression of nitrite reductase (gene cluster NE0924 to NE0927) correlated with increased production of N2O. Together, these data suggest that N. europaea adapts physiologically during IC-limited steady-state growth, which leads to the uncoupling of NH3 oxidation from growth and increased N2O production. IMPORTANCE Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, is an important process in the global nitrogen cycle. This process is generally dependent on ammonia-oxidizing microorganisms and nitrite-oxidizing bacteria. Most nitrifiers are chemolithoautotrophs that fix inorganic carbon (CO2) for growth. Here, we investigate how inorganic carbon limitation modifies the physiology and transcriptome of Nitrosomonas europaea, a model ammonia-oxidizing bacterium, and report on increased production of N2O, a potent greenhouse gas. This study, along with previous work, suggests that inorganic carbon limitation may be an important factor in controlling N2O emissions from nitrification in soils and wastewater treatment.
Deeper and wider: income and mortality in the USA over three decades.

BACKGROUND Literature on the socio-economic 'gradient' in health often asserts that income is associated with better health not only for the very poor, but also across the entire income distribution. In addition, changes in the shape of the association between incomes during a period of increasing economic inequality have not been previously studied. The goal of the current study was to estimate and compare the shape of the relationship between income and mortality in the USA for the 1970s, the 1980s and the 1990s. METHODS Using income and mortality data from the Panel Study of Income Dynamics for respondents aged 35-64 years, we used a Bayesian Cox Model with regression splines to model the risk of mortality over three 10-year follow-up periods. To identify whether income was more strongly associated with mortality at different parts of the income distribution, we treated income as a linear spline with an unknown knot location. RESULTS The shape of the association between income and mortality was quite non-linear, with a much stronger association at lower levels of income. The relationship between income and mortality in the USA was also not invariant across time, with the increased risk of death associated with lower income applying to an increasing proportion of the US population over time (9th percentile of income in 1970-79, 20th percentile in 1980-89 and 32nd percentile in 1990-99). CONCLUSIONS Our analyses do not support the claim that income is associated with mortality throughout the income distribution, nor is the association between income and mortality the same across periods. Based on our analyses, a focus on the bottom 30% of the income distribution would seem to return the greatest benefits in reducing socio-economic inequalities in health.
Extended Long‐Term Effects of Cervical Vagal Nerve Stimulation on Headache Intensity/Frequency and Affective/Cognitive Headache Perception in Drug Resistant Complex‐Partial Seizure Patients

Invasive vagal nerve stimulation (iVNS) is an established treatment option for drug‐resistant focal seizures and has been assumed to diminish frequent co‐incidental daily headache/migraine. However, long‐term effects on cognitive/affective head pain perception, headache intensity/frequency are lacking. We therefore investigated potential iVNS‐induced effects in patients with drug‐resistant focal seizure and daily headache/migraine.
A contribution to the analysis of the intrinsic shear behavior of fabrics

The in-plane shear behavior of textile performs is the most studied mechanical property because this mode of deformation is necessary for forming on double curvature surfaces. The resulting mechanical behavior is complex and specific considering the possibilities of relative movements between yarns and fibers. Two main tests are used: the hinged framework or ‘picture frame’ and the tensile test at 45° or ‘bias test’. Nevertheless, the results obtained by different labs using these two tests on the same fabric can be significantly different. Using a simplified analytical model of the picture frame test and a specific instrumented picture frame that enables us to track and adjust yarns tensions and to measure the strain field through optical measurements, this article analyzes and explains the origin of these discrepancies and concludes in dealing with the association between the experimental test used and the intrinsic in-plane shear behavior of a fabric.