Miracle-dz/UniFAR-FTUs huggingface dataset:
New insights into Chlamydomonas reinhardtii hydrogen production processes by combined microarray/RNA-seq transcriptomics.

Hydrogen production with Chlamydomonas reinhardtii induced by sulphur starvation is a multiphase process while the cell internal metabolism is completely remodelled. The first cellular response is characterized by induction of genes with regulatory functions, followed by a total remodelling of the metabolism to provide reduction equivalents for cellular processes. We were able to characterize all major processes that provide energy and reduction equivalents during hydrogen production. Furthermore, C. reinhardtii showed a strong transcript increase for gene models responsible for stress response and detoxification of oxygen radicals. Finally, we were able to determine potential bottlenecks and target genes for manipulation to increase hydrogen production or to prolong the hydrogen production phase. The investigation of transcriptomic changes during the time course of hydrogen production in C. reinhardtii with microarrays and RNA-seq revealed new insights into the regulation and remodelling of the cell internal metabolism. Both methods showed a good correlation. The microarray platform can be used as a reliable standard tool for routine gene expression analysis. RNA-seq additionally allowed a detailed time-dependent study of gene expression and determination of new genes involved in the hydrogen production process.
Long-term spatiotemporal stability and dynamic changes in helminth infracommunities of bank voles (Myodes glareolus) in NE Poland

SUMMARY Parasites are considered to be an important selective force in host evolution but ecological studies of host-parasite systems are usually short-term providing only snap-shots of what may be dynamic systems. We have conducted four surveys of helminths of bank voles at three ecologically similar woodland sites in NE Poland, spaced over a period of 11 years, to assess the relative importance of temporal and spatial effects on helminth infracommunities. Some measures of infracommunity structure maintained relative stability: the rank order of prevalence and abundance of Heligmosomum mixtum, Heligmosomoides glareoli and Mastophorus muris changed little between the four surveys. Other measures changed markedly: dynamic changes were evident in Syphacia petrusewiczi which declined to local extinction, while the capillariid Aonchotheca annulosa first appeared in 2002 and then increased in prevalence and abundance over the remaining three surveys. Some species are therefore dynamic and both introductions and extinctions can be expected in ecological time. At higher taxonomic levels and for derived measures, year and host-age effects and their interactions with site are important. Our surveys emphasize that the site of capture is the major determinant of the species contributing to helminth community structure, providing some predictability in these systems.
A novel approach to identify genes that determine grain protein deviation in cereals.

Grain yield and protein content were determined for six wheat cultivars grown over 3 years at multiple sites and at multiple nitrogen (N) fertilizer inputs. Although grain protein content was negatively correlated with yield, some grain samples had higher protein contents than expected based on their yields, a trait referred to as grain protein deviation (GPD). We used novel statistical approaches to identify gene transcripts significantly related to GPD across environments. The yield and protein content were initially adjusted for nitrogen fertilizer inputs and then adjusted for yield (to remove the negative correlation with protein content), resulting in a parameter termed corrected GPD. Significant genetic variation in corrected GPD was observed for six cultivars grown over a range of environmental conditions (a total of 584 samples). Gene transcript profiles were determined in a subset of 161 samples of developing grain to identify transcripts contributing to GPD. Principal component analysis (PCA), analysis of variance (ANOVA) and means of scores regression (MSR) were used to identify individual principal components (PCs) correlating with GPD alone. Scores of the selected PCs, which were significantly related to GPD and protein content but not to the yield and significantly affected by cultivar, were identified as reflecting a multivariate pattern of gene expression related to genetic variation in GPD. Transcripts with consistent variation along the selected PCs were identified by an approach hereby called one-block means of scores regression (one-block MSR).
American Gastroenterological Association Institute Technical Review on the Medical Management of Opioid-Induced Constipation.

Abbreviations used in this paper: AE, adverse event; AGA, American Gastroenterological Association; BFI, Bowel Function Index; BM, bowel movement; BSFS, Bristol Stool Form Scale; CI, confidence interval; FDA, Food and Drug Administration; GI, gastrointestinal; GRADE, Grading of Recommendations Assessment, Development and Evaluation; MD, mean difference; OIC, opioid-induced constipation; PAC-QOL, Patient Assessment of Constipation-Quality of Life; PAMORA, peripherally acting m-opioid receptor antagonist; PEG, polyethylene glycol; PICO, population, intervention, comparator, and outcomes; PROM, patient-reported outcome measure; QOL, quality of life; RCT, randomized controlled trial; RFBM, rescue-free bowel movement; RR, relative risk; SBM, spontaneous bowel movement.
Successful intestinal Echinococcus multilocularis oncosphere invasion and subsequent hepatic metacestode establishment in resistant RccHan™:WIST rats after pharmacological immunosuppression

SUMMARY Susceptibility/resistance to larval Echinococcus multilocularis infection varies greatly depending on host species and strains. Whereas several mice strains and non-human primates are highly susceptible to alveolar echinococcosis, rats and most of humans are considered as more resistant. In this study, we aimed to elucidate factors responsible for host resistance in rats (Experiments A–D). (A) The parasite establishment was not observed in immunocompetent Wistar rats orally inoculated with sodium hypochlorite resistant eggs with/without pig bile, or activated/non-activated oncospheres (NAO). Peritoneal inoculation with NAO or metacestode tissue allowed the parasite establishment in rats. (B) T-cell-deficient athymic nude rats showed complete resistance against the metacestode establishment after oral inoculation with parasite eggs. This finding suggests that T-cell-independent parasite clearance occurred in the animals during early phase of the parasite invasion. Finally, Wistar rats that received pharmacological immunosuppression using either dexamethasone (DMS) alone or methotrexate (MTX) i.p. alone or a combination of these compounds were orally inoculated with the parasite's eggs. As a result (D), successful establishment of metacestode with protoscoleces was observed in all 3 rats treated with DMS (s.c.) alone or in all 6 rats treated with DMS (s.c.) plus MTX but not in 8 rats with MTX alone, suggesting that factors affected by DMS treatment are responsible to regulate the parasite invasion and establishment.
Hepatitis B e antigen in sera from individuals infected with hepatitis B virus of genotype G

Hepatitis B virus (HBV) genotype G (HBV/G) was detected in sera from four individuals by polymerase chain reaction with hemi‐nested primers deduced from an insertion of 36 nt in the core gene that is specific for this genotype. Despite two stop codons in the precore region characteristic of HBV/G, all patients were positive for hepatitis B e antigen (HBeAg) in serum. When 10 HBV clones were propagated from one patient, and sequenced within precore region and a section of the core gene, 6 clones were HBV/G while 2 were genotype A (HBV/A); a recombination between HBV/G and HBV/A occurred in the remaining 2 clones. Mixed infection of HBV/G and HBV/A, as well as the recombination, was demonstrated in the sequence of preS1 and preS2 regions also. Coinfection with HBV/G and HBV/A was demonstrated in the other three patients, and their recombination in two patients. Ten HBV clones were propagated from one patient at two time points separated by 1 year. Clones of HBV/A, HBV/G and their recombination were found in 9 : 1 : 0 when the patient was positive for HBeAg, while the proportion shifted to 0 : 8 : 2 after the patient seroconverted to anti‐HBe. In conclusion, HBV/G is frequently found as a coinfection with HBV/A. This coinfection would explain the presence of HBeAg in individuals infected with HBV/G. Along with seroconversion to anti‐HBe, HBV/G would be selected accompanied by the recombination with HBV/A. Further studies should be performed to confirm these findings.
Mouse A6–positive hepatic oval cells also express several hematopoietic stem cell markers

Hepatic oval cells (HOC) are thought to be a type of facultative stem cell that arises as a result of certain forms of hepatic injury. A new and more efficient model has been established to activate the oval cell compartment in mice by incorporating 3,5‐diethoxycarbonyl‐1,4‐dihydro‐collidine (DDC) in a standard chow at a concentration of 0.1%. At the present time, very few markers exist for the mouse oval cells. One accepted marker is A6, an uncharacterized epitope recognized by mouse hepatic oval cells and it is accepted to be an oval cell marker. Sca‐1 is a cell surface marker used to identify hematopoietic stem cells in conjunction with Thy‐1+, CD34+, and lineage‐specific markers. Both the CD34 and Sca‐1 antigens are not normally expressed in adult liver, but are expressed in fetal liver, presumably on the hematopoietic cells. We report herein that mouse oval cells express high levels of Sca‐1 and CD34, as well as CD45 surface proteins. Immunohistochemistry revealed that the cells expressing Sca‐1/CD34/CD45 were indeed oval cells because they co‐expressed the oval cell–specific marker A6 (94.57% ± 0.033%), as well as alpha‐fetoprotein (AFP) (75.92% ± 0.071%). By using Sca‐1 antibody in conjunction with magnetic activated cell sorting (MACS), followed with a flow cytometric cell sorting (FACS) method for CD34 and CD45, we have developed a rapid oval cell isolation protocol with high yields of greater than 90%. In conclusion, we have an efficient murine model for the production and isolation of large numbers of highly purified oval cells. Our system works with most strains of mouse, which will facilitate both in vivo and in vitro studies of mouse hepatic oval cells.
Engineering canker‐resistant plants through CRISPR/Cas9‐targeted editing of the susceptibility gene CsLOB1 promoter in citrus

Summary Citrus canker, caused by Xanthomonas citri subsp. citri (Xcc), is severely damaging to the global citrus industry. Targeted editing of host disease‐susceptibility genes represents an interesting and potentially durable alternative in plant breeding for resistance. Here, we report improvement of citrus canker resistance through CRISPR/Cas9‐targeted modification of the susceptibility gene CsLOB1 promoter in citrus. Wanjincheng orange (Citrus sinensis Osbeck) harbours at least three copies of the CsLOB1 G allele and one copy of the CsLOB1 − allele. The promoter of both alleles contains the effector binding element (EBEP thA4), which is recognized by the main effector PthA4 of Xcc to activate CsLOB1 expression to promote citrus canker development. Five pCas9/CsLOB1sgRNA constructs were designed to modify the EBEP thA4 of the CsLOB1 promoter in Wanjincheng orange. Among these constructs, mutation rates were 11.5%–64.7%. Homozygous mutants were generated directly from citrus explants. Sixteen lines that harboured EBEP thA4 modifications were identified from 38 mutant plants. Four mutation lines (S2‐5, S2‐6, S2‐12 and S5‐13), in which promoter editing disrupted CsLOB1 induction in response to Xcc infection, showed enhanced resistance to citrus canker compared with the wild type. No canker symptoms were observed in the S2‐6 and S5‐13 lines. Promoter editing of CsLOB1 G alone was sufficient to enhance citrus canker resistance in Wanjincheng orange. Deletion of the entire EBEP thA4 sequence from both CsLOB1 alleles conferred a high degree of resistance to citrus canker. The results demonstrate that CRISPR/Cas9‐mediated promoter editing of CsLOB1 is an efficient strategy for generation of canker‐resistant citrus cultivars.
High‐density genotyping of the A.E. Watkins Collection of hexaploid landraces identifies a large molecular diversity compared to elite bread wheat

Summary The importance of wheat as a food crop makes it a major target for agricultural improvements. As one of the most widely grown cereal grains, together with maize and rice, wheat is the leading provider of calories in the global diet, constituting 29% of global cereal production in 2015. In the last few decades, however, yields have plateaued, suggesting that the green revolution, at least for wheat, might have run its course and that new sources of genetic variation are urgently required. The overall aim of our work was to identify novel variation that may then be used to enable the breeding process. As landraces are a potential source of such diversity, here we have characterized the A.E. Watkins Collection alongside a collection of elite accessions using two complementary high‐density and high‐throughput genotyping platforms. While our results show the importance of using the appropriate SNP collection to compare diverse accessions, they also show that the Watkins Collection contains a substantial amount of novel genetic diversity which has either not been captured in current breeding programmes or which has been lost through previous selection pressures. As a consequence of our analysis, we have identified a number of accessions which carry an array of novel alleles along with a number of interesting chromosome rearrangements which confirm the variable nature of the wheat genome.
Positive density-dependent growth supports costs sharing hypothesis and population density sensing in a manipulative parasite

SUMMARY Parasites manipulate their hosts’ phenotype to increase their own fitness. Like any evolutionary adaptation, parasitic manipulations should be costly. Though it is difficult to measure costs of the manipulation directly, they can be evaluated using an indirect approach. For instance, theory suggests that as the parasite infrapopulation grows, the investment of individual parasites in host manipulation decreases, because of cost sharing. Another assumption is that in environments where manipulation does not pay off for the parasite, it can decrease its investment in the manipulation to save resources. We experimentally infected rainbow trout Oncorhynchus mykiss with the immature larvae of the trematode Diplostomum pseudospathaceum, to test these assumptions. Immature D. pseudospathaceum metacercariae are known for their ability to manipulate the behaviour of their host enhancing its anti-predator defenses to avoid concomitant predation. We found that the growth rate of individual parasites in rainbow trout increased with the infrapopulation size (positive density-dependence) suggesting cost sharing. Moreover, parasites adjusted their growth to the intensity of infection within the eye lens where they were localized suggesting population density sensing. Results of this study support the hypothesis that macroparasites can adjust their growth rate and manipulation investment according to cost sharing level and infrapopulation size.
MuMADS1 and MaOFP1 regulate fruit quality in a tomato ovate mutant

Summary Fruit ripening and quality are common botanical phenomena that are closely linked and strictly regulated by transcription factors. It was previously discovered that a banana MADS‐box protein named MuMADS1 interacted with an ovate family protein named MaOFP1 to regulate banana fruit ripening. To further investigate the role of MuMADS1 and MaOFP1 in the regulation of fruit quality, a combination of genetic transformation and transcriptional characterization was used. The results indicated that the co‐expression of MuMADS1 and MaOFP1 in the ovate mutant could compensate for fruit shape and inferior qualities relating to fruit firmness, soluble solids and sugar content. The number of differentially expressed genes (DEGs) was 1395 in WT vs. ovate, with 883 up‐regulated and 512 down‐regulated genes, while the numbers of DEGs gradually decreased with the transformation of MuMADS1 and MaOFP1 into ovate. ‘Starch and sucrose metabolism’ constituted the primary metabolic pathway, and the gene numbers in this pathway were obviously different when MuMADS1 and MaOFP1 were integrated into ovate. A series of metabolic genes involved in cell wall biosynthesis were up‐regulated in the WT vs. ovate, which probably resulted in the firmer texture and lower sugar contents in the ovate fruit. These results demonstrate that MuMADS1 and MaOFP1 are coregulators of fruit quality, facilitating the dissection of the molecular mechanisms underlying fruit quality formation.
Caregiver Service Use: A Complex Story of Care at the End of Life

ABSTRACT This study explored the impact of caregiving, service use, and unmet needs of caregivers of the dying and whether end-of-life caregiving differs from other types of caregiving. We hypothesized that end-of-life caregivers would have greater unmet needs before and after the death of their care recipient and that they would report lower levels of well-being than continuing caregivers. We looked specifically at the service use of caregivers whose care recipients died during the study period and whether or not such service use helped caregivers to manage end-of-life care. This study showed that, on average, end-of-life caregivers are older, more likely to be White, and provide care for individuals with greater Instrumental Activities of Daily Living (IADL) and Activities of Daily Living (ADL) needs and severe memory problems. In cross-sectional analyses, end-of-life caregivers experienced greater emotional stress, physical strain, and poorer health and used more supportive services than their caregiving counterparts. However, after controlling for other covariates in regression analyses, end of life care remained a predictor of only physical strain.
OsAUX1 controls lateral root initiation in rice (Oryza sativa L.).

Polar auxin transport, mediated by influx and efflux transporters, controls many aspects of plant growth and development. The auxin influx carriers in Arabidopsis have been shown to control lateral root development and gravitropism, but little is known about these proteins in rice. This paper reports on the functional characterization of OsAUX1. Three OsAUX1 T-DNA insertion mutants and RNAi knockdown transgenic plants reduced lateral root initiation compared with wild-type (WT) plants. OsAUX1 overexpression plants exhibited increased lateral root initiation and OsAUX1 was highly expressed in lateral roots and lateral root primordia. Similarly, the auxin reporter, DR5-GUS, was expressed at lower levels in osaux1 than in the WT plants, which indicated that the auxin levels in the mutant roots had decreased. Exogenous 1-naphthylacetic acid (NAA) treatment rescued the defective phenotype in osaux1-1 plants, whereas indole-3-acetic acid (IAA) and 2,4-D could not, which suggested that OsAUX1 was a putative auxin influx carrier. The transcript levels of several auxin signalling genes and cell cycle genes significantly declined in osaux1, hinting that the regulatory role of OsAUX1 may be mediated by auxin signalling and cell cycle genes. Overall, our results indicated that OsAUX1 was involved in polar auxin transport and functioned to control auxin-mediated lateral root initiation in rice.
A cross-ethnic comparison on incidence of suicide

Background Suicide rates vary widely across nations and ethnic groups. This study aims to explore potential factors contributing to inter-ethnic differences in suicide rates. Method Study subjects came from a case-control psychological autopsy study conducted in Taiwan, including 116 consecutive suicides from two aboriginal groups and Taiwanese Han; 113 of them each matched with two living controls. Gender-, age- and method-specific suicide rates, population attributable fraction (PAF) of suicide for five major risk factors, help-seeking before suicide and emergency medical aid after suicide were compared between the three ethnic groups. Results One aboriginal group (the Atayal) had significantly higher adjusted rate ratios (RR) of suicide than the other aboriginal group (the Ami) [RR 0.20, 95% confidence intervals (CI) 0.12–0.34] and the Han (RR 0.26, 95% CI 0.16–0.40). Such differences can be explained by higher PAFs of suicide for three major risk factors (substance dependence, PAF 47.6%, 95% CI 25.5–64.2; emotionally unstable personality disorder, PAF 52.7%, 95% CI 32.8–69.0; family history of suicidal behaviour, PAF 43.5%, 95% CI 23.2–60.2) in this group than in the other two groups. This higher suicide rate was substantially reduced from 68.2/100 000 per year to 9.1/100 000 per year, comparable with the other two groups, after stepwise removal of the effects of these three risk factors. Suicide rates by self-poisoning were also significantly higher in this group than in the other two groups. Conclusions Higher rates of specific risk factors and use of highly lethal pesticides for suicide contributed to the higher suicide rate in one ethnic group in Taiwan. These findings have implications for developing ethnicity-relevant suicide prevention strategies.
Structural Reductions and Stutter Sensitive Properties

Verification of properties expressed as $\omega$-regular languages such as LTL can benefit hugely from stutter insensitivity, using a diverse set of reduction strategies. However properties that are not stutter invariant, for instance due to the use of the neXt operator of LTL or to some form of counting in the logic, are not covered by these techniques in general. We propose in this paper to study a weaker property than stutter insensitivity. In a stutter insensitive language both adding and removing stutter to a word does not change its acceptance, any stuttering can be abstracted away; by decomposing this equivalence relation into two implications we obtain weaker conditions. We define a shortening insensitive language where any word that stutters less than a word in the language must also belong to the language. A lengthening insensitive language has the dual property. A semi-decision procedure is then introduced to reliably prove shortening insensitive properties or deny lengthening insensitive properties while working with a \emph{reduction} of a system. A reduction has the property that it can only shorten runs. Lipton's transaction reductions or Petri net agglomerations are examples of eligible structural reduction strategies. We also present an approach that can reason using a partition of a property language into its stutter insensitive, shortening insensitive, lengthening insensitive and length sensitive parts to still use structural reductions even when working with arbitrary properties. An implementation and experimental evidence is provided showing most non-random properties sensitive to stutter are actually shortening or lengthening insensitive.