Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of resistance to complex infection of SPFMVs in transgenic sweet potato

Viral diseases of the sweet potato (Ipomoea batatas L. (Lam)) are highly prevalent and often cause serious damage to the plants, particularly the severe strain of the sweet potato feathery mottle virus (SPFMV-S) that causes ‘obizyo-sohi’ disease in Japan. To confer viral resistance to SPFMV using current biotechnology, a transgenic sweet potato has been developed by introducing SPFMV-S coat protein (CP) genes, which have shown significant resistance to SPFMV-S; however, ecological distribution in the field of SPFMVs is unclear. This study investigated the ecological distribution of SPFMVs in field-infected sweet potato, and virus resistance nearer to the field was evaluated in transgenic sweet potato. SPFMV was not capable of independent infection; rather, infection by SPFMVs was coincidentally complex under natural conditions. Furthermore, infection was by a dominant strain between complex infecting SPFMVs, and was differentiated by the area of infection. Transgenic sweet potato plants expressing the SPFMV-S CP gene were challenged by graft inoculation with field-infected SPFMVs. All of the transgenic sweet potato plants were highly protected in the long term against SPFMV complex infection compared to control plants. These results suggest that transgenic sweet potato can acquire resistance to SPFMVs in the field.
Untapped Potential: A Qualitative Study of a Hospital-Based Dengue Surveillance System

Abstract. The incidence and geographical distribution of dengue fever has increased in recent decades. The actual disease burden is unknown owing to frequent underreporting and misclassification of cases. A well-functioning system for diagnosing, treating, and reporting cases is of prime importance as disease statistics is the foundation for decisions aiming to control the disease. This study aimed to explore the hospital-based disease surveillance system in Yogyakarta, a dengue-endemic region on Java, Indonesia. Semi-structured interviews were performed with 16 informants from four hospitals, including five general practitioners, three internists, four pediatricians, and four administrative staff working with administration relating to dengue diagnostics and reporting. Data were analyzed using content analysis. A theme arose from the analysis “Dengue surveillance stands and falls by the rigor of the health system. ” The theme, and underlying categories and subcategories, describes a surveillance system that in the best-case scenario works well and is likely to produce reliable dengue case data. However, there is a lack of synchronization between regulations and guidelines in different hospitals and some friction between regulatory bodies and the care provider. Knowledge among the staff appears to vary, and many clinical and financial decisions are made rather arbitrarily, which ultimately might lead to unequal health service delivery. In conclusion, the dengue surveillance system under study could improve further, particularly by ensuring that all regulations and recommended procedures are standardized and that all staff are given the best opportunity to stay updated on dengue-related matters, clinical as well as regulatory, on a regular basis.
Basin‐Wide Effects of Game Harvest on Vertebrate Population Densities in Amazonian Forests: Implications for Animal‐Mediated Seed Dispersal

Vertebrate responses to hunting are widely variable for target and nontarget species depending on the history of hunting and productivity of any given site and the life history traits of game species. We provide a comprehensive meta‐analysis of changes in population density or other abundance estimates for 30 mid‐sized to large mammal, bird and reptile species in 101 hunted and nonhunted, but otherwise undisturbed, Neotropical forest sites. The data set was analyzed using both an unnested approach, based on population density estimates, and a nested approach in which pairwise comparisons of abundance metrics were restricted to geographic groups of sites sharing similar habitat and soil conditions. This resulted in 25 geographic clusters of sites within which 1811 population abundance estimates were compared across different levels of hunting pressure. Average nested changes in abundance across increasingly greater levels of hunting pressure ranged from moderately positive to highly negative. Populations of all species combined declined across greater differences in hunting pressure by up to 74.8 percent from their numeric abundance in less intensively hunted sites, but harvest‐sensitive species faired far worse. Of the 30 species examined, 22 declined significantly at high levels of hunting. Body size significantly affected the direction and magnitude of abundance changes, with large‐bodied species declining faster in overhunted sites. Frugivorous species showed more marked declines in abundance in heavily hunted sites than seed predators and browsers, regardless of the effects of body size. The implications of hunting for seed dispersal are discussed in terms of community dynamics in semi‐defaunated tropical forests.
Numerical Taxonomy and Deoxyribonucleic Acid Reassociation in the Taxonomy of Some Gram-Negative Fermentative Bacteria

One hundred and five strains of gram-negative, fermentative bacteria, representing members of the Enterobacteriaceae together with strains of Vibrio and Aeromonas, were subjected to numerical taxonomy and deoxyribonucleic acid (DNA)/DNA reassociation studies. The numerical taxonomy sorted the strains into major clusters corresponding to Edwardsiella tarda, Escherichia coli, Citrobacter freundii, the tribe Klebsielleae, and Vibrio alginolyticus. Smaller clusters could be identified as Serratia marcescens, Hafnia alvei, and Shigella species. Seven reference strains were used in the DNA/DNA reassociation studies. Klebsiella pneumoniae at 60 C shared reassociation values of 80 to 100% with other strains of Klebsiella, 37 to 64% with Enterobacter spp. , and lower values with Hafnia, Citrobacter, Serratia, and Escherichia coli. Phenetically, K. pneumoniae and Enterobacter aerogenes shared high relatedness, although they are only 41 to 64% related in the reassociation studies. Hafnia, Salmonella typhimurium, and Edwardsiella tarda showed little relatedness to any of the other strains included in this study. Both reference strains of Escherichia coli shared genetic resemblances greater than 65% at 60 C with Shigella and at least 70% with other strains of Escherichia coli. Overall, the agreement between numerical taxonomy and the DNA/DNA reassociation studies was satisfactory, with correlation coefficients ranging from 0.5 to 0.9. The choice of reference strains may well affect the correlation between the two techniques, and it is suggested that hypothetical median organisms be determined from the phenetic groupings and that actual strains that approximate to the hypothetical median organisms be used as reference strains for DNA reassociation.
Flexibility and Preorganization of Fluorescent Nucleobase-Pyrene Conjugates Control DNA and RNA Recognition

We synthesized a new amino acid-fluorescent nucleobase derivative (qAN1-AA) and from it two new fluorescent nucleobase–fluorophore (pyrene) conjugates, whereby only the analogue with the longer and more flexible linker (qAN1-pyr2) self-folded into intramolecularly stacked qAN1/pyrene conformation, yielding characteristic, 100 nm-red-shifted emission (λmax = 500 nm). On the contrary, the shorter and more rigid linker resulted in non-stacked conformation (qAN1-pyr1), characterized by the emission of free pyrene at λmax = 400 nm. Both fluorescent nucleobase–fluorophore (pyrene) conjugates strongly interacted with ds-DNA/RNA grooves with similar affinity but opposite fluorescence response (due to pre-organization), whereas the amino acid-fluorescent base derivative (qAN1-AA) was inactive. However, only intramolecularly self-folded qAN1-pyr2 showed strong fluorescence selectivity toward poly U (Watson–Crick complementary to qAN1 nucleobase) and poly A (reverse Hoogsteen complementary to qAN1 nucleobase), while an opposite emission change was observed for non-complementary poly G and poly C. Non-folded analogue (qAN1-pyr1) showed no ss-RNA selectivity, demonstrating the importance of nucleobase-fluorophore pre-organization.
Multipurpose chemical liquid sensing applications by microwave approach

In this work, a novel sensor based on printed circuit board (PCB) microstrip rectangular patch antenna is proposed to detect different ratios of ethanol alcohol in wines and isopropyl alcohol in disinfectants. The proposed sensor was designed by finite integration technique (FIT) based high-frequency electromagnetic solver (CST) and was fabricated by Proto Mat E33 machine. To implement the numerical investigations, dielectric properties of the samples were first measured by a dielectric probe kit then uploaded into the simulation program. Results showed a linear shifting in the resonant frequency of the sensor when the dielectric constant of the samples were changed due to different concentrations of ethanol alcohol and isopropyl alcohol. A good agreement was observed between the calculated and measured results, emphasizing the usability of dielectric behavior as an input sensing agent. It was concluded that the proposed sensor is viable for multipurpose chemical sensing applications.
Stay‐green compared with non‐stay‐green Lolium perenne in field swards with different cutting and nitrogen treatments

Wilman, D. , Irianni, R. A. M. , Humphreys, M. O. (2004). Stay-green compared with non-stay-green Lolium perenne in field swards with different cutting and nitrogen treatments. Annals of Applied Biology, 144, 95-101 Key words: Stay-green, Lolium perenne, perennial ryegrass, colour, yield, N, leaves
Improved Process to Obtain Nanofibrillated Cellulose (CNF) Reinforced Starch Films with Upgraded Mechanical Properties and Barrier Character

Nowadays, the interest on nanofibrillated cellulose (CNF) has increased owing to its sustainability and its capacity to improve mechanical and barrier properties of polymeric films. Moreover, this filler shows some drawbacks related with its high capacity to form aggregates, hindering its dispersion in the matrix. In this work, an improved procedure to optimize the dispersability of CNF in a thermoplastic starch was put forward. On the one hand, CNF needs a hydrophilic dispersant to be included in the matrix, and on the other, starch needs a hydrophilic plasticizer to obtain a thermoformable material. Glycerol was used to fulfil both targets at once. CNF was predispersed in the plasticizer before nanofibrillation and later on was included into starch, obtaining thin films. The tensile strength of these CNF–starch composite films was 60% higher than the plain thermoplastic starch at a very low 0.36% w/w percentage of CNF. The films showed a noticeable correlation between water uptake, and temperature and humidity. Regarding permeability, a ca. 55% oxygen and water vapor permeability drop was found by nanofiller loading. The hydrolytic susceptibility of the composite was confirmed, being similar to that of the thermoplastic starch.
Plasma Galectin-3 predicts deleterious vascular dysfunction affecting post-myocardial infarction patients: An explanatory study

Objectives In a previous analysis of a post-myocardial infarction (MI) cohort, abnormally high systemic vascular resistances (SVR) were shown to be frequently revealed by MRI during the healing period, independently of MI severity, giving evidence of vascular dysfunction and limiting further recovery of cardiac function. The present ancillary and exploratory analysis of the same cohort was aimed at characterizing those patients suffering from high SVR remotely from MI with a large a panel of cardiovascular MRI parameters and blood biomarkers. Methods MRI and blood sampling were performed 2–4 days after a reperfused MI and 6 months thereafter in 121 patients. SVR were monitored with a phase-contrast MRI sequence and patients with abnormally high SVR at 6-months were characterized through MRI parameters and blood biomarkers, including Galectin-3, an indicator of cardiovascular inflammation and fibrosis after MI. SVR were normal at 6-months in 90 patients (SVR-) and abnormally high in 31 among whom 21 already had high SVR at the acute phase (SVR++) while 10 did not (SVR+). Results When compared with SVR-, both SVR+ and SVR++ exhibited lower recovery in cardiac function from baseline to 6-months, while baseline levels of Galectin-3 were significantly different in both SVR+ (median: 14.4 (interquartile range: 12.3–16.7) ng.mL-1) and SVR++ (13.0 (11.7–19.4) ng.mL-1) compared to SVR- (11.7 (9.8–13.5) ng.mL-1, both p < 0.05). Plasma Galectin-3 was an independent baseline predictor of high SVR at 6-months (p = 0.002), together with the baseline levels of SVR and left ventricular end-diastolic volume, whereas indices of MI severity and left ventricular function were not. In conclusion, plasma Galectin-3 predicts a deleterious vascular dysfunction affecting post-MI patients, an observation that could lead to consider new therapeutic targets if confirmed through dedicated prospective studies.
A New Method Based on Coding Sequence Density to Cluster Bacteria

Bacterial evolution is an important study field, biological sequences are often used to construct phylogenetic relationships. Multiple sequence alignment is very time-consuming and cannot deal with large scales of bacterial genome sequences in a reasonable time. Hence, a new mathematical method, joining density vector method, is proposed to cluster bacteria, which characterizes the features of coding sequence (CDS) in a DNA sequence. Coding sequences carry genetic information that can synthesize proteins. The correspondence between a genomic sequence and its joining density vector (JDV) is one-to-one. JDV reflects the statistical characteristics of genomic sequence and large amounts of data can be analyzed using this new approach. We apply the novel method to do phylogenetic analysis on four bacterial data sets at hierarchies of genus and species. The phylogenetic trees prove that our new method accurately describes the evolutionary relationships of bacterial coding sequences, and is faster than ClustalW and the existing alignment-free methods.
The Relation between Volume and Outcome of Transcatheter and Surgical Aortic Valve Replacement: A Systematic Review and Meta-Analysis

Transcatheter aortic valve replacement (TAVR) and surgical aortic valve replacement (SAVR) are standard procedures for dealing with severe aortic stenosis patients. Researchers have not carried out a systematic review of the volume-outcome relationship in TAVR and SAVR. Our study is intended to address this problem. We systemically searched databases through MEDLINE, EMBASE, PUBMED, and the Cochrane Library up to September 2019. Two reviewers independently screened for the studies and evaluated bias. We used short-term mortality (in-hospital or 30-day mortality) as an outcome. A meta-analysis of TAVR with 115,596 patients ranging from 2005 to 2016 showed a result significantly in favor of high-volume hospitals (OR 0.43 (CI 0.36-0.51)). The subgroup of population period, region, data type, and cut-off value did not show any difference. A meta-analysis of SAVR comprising 418,384 patients ranging from 1994 to 2011 revealed that the OR of short-term mortality for a high-volume hospital compared with that of a low-volume hospital was 0.73 (CI 0.71, 0.74). No difference was observed in subgroups based on population period and cut-off. In conclusion, we found that short-term mortality was lower in high-volume hospitals for both TAVR and SAVR.
Plasmids of novel incompatibility group IncpRBL16 from Pseudomonas species.

OBJECTIVES To dissect genomic features of IncpRBL16 plasmids from Pseudomonas. METHODS An extensive genomic comparison was applied to all 17 available sequenced IncpRBL16 plasmids, including 8 sequenced in this study and another 2 sequenced in two of our previous studies. RESULTS Conserved IncpRBL16 backbone markers repAIncpRBL16 together with its iterons, parB2-parA, che, pil and ter were present in all 17 plasmids. At least 18 regions or sites across IncpRBL16 genomes exhibited major modular differences, including insertion of accessory modules, deletion of backbone regions surrounding insertion sites and substitution of multiple-gene backbone regions. Ten plasmids carried a sole IncpRBL16 replicon, while exogenous acquisition of an auxiliary replicon (located in an accessory module) besides the primary IncpRBL16 replicon was observed in each of the remaining seven plasmids. The 17 IncpRBL16 plasmids carried at least 71 different accessory modules, notably including Tn1403-related regions, Tn7-family transposons, Tn6571-family transposons, integrative and conjugative elements, and integrative and mobilizable elements. There were a total of 40 known resistance genes, which were involved in resistance to 15 categories of antibiotics and heavy metals, notably including blaIMP-9, blaIMP-45, blaVIM-2, blaDIM-2, blaOXA-246, blaPER-1, aphA and armA. CONCLUSIONS Different IncpRBL16 plasmids contain different profiles of accessory modules and thus diverse collections of resistance genes. To the best of our knowledge, this is the first report of fully sequenced blaOXA-246-carrying (p12939-PER) and blaPER-1-carrying (p12939-PER and pA681-IMP) IncpRBL16 plasmids and also that of 14 novel (first identified in this study) and additionally 31 newly named (first designated in this study, but with previously determined sequences) mobile elements.
Long-term safety and durability of effect with a combination of olanzapine and samidorphan in patients with schizophrenia: results from a 1-year open-label extension study

Abstract Background Combination olanzapine and samidorphan (OLZ/SAM), in development for schizophrenia and bipolar I disorder, is intended to provide the efficacy of olanzapine while mitigating olanzapine-associated weight gain. OLZ/SAM safety, tolerability, and efficacy from a 52-week open-label extension study in patients with schizophrenia are reported. Methods Patients previously completing the 4-week, double-blind ENLIGHTEN-1 study switched from OLZ/SAM, olanzapine, or placebo to OLZ/SAM. Assessments included adverse events (AEs), weight, vital signs, Positive and Negative Syndrome Scale (PANSS), and Clinical Global Impression-Severity (CGI-S) scores. Baseline was prior to first dose of OLZ/SAM in the extension study. Results In total, 281 patients enrolled, 277 received ≥1 OLZ/SAM dose, and 183 (66.1%) completed 52 weeks. Reasons for discontinuation included patient withdrawal (15.5%), loss to follow-up (6.9%), AEs (5.8%), and lack of efficacy (1.8%). AEs were reported in 136 (49.1%) patients; increased weight (13%) and somnolence (8%) were most common. Ten serious AEs were reported in eight patients (2.9%); none were considered treatment related. There were no deaths. Mean (SD) baseline weight was 79.1 (17.8) kg. Mean weight change from baseline to week 52 was 1.86 kg (2.79% increase). PANSS total and CGI-S scores continued to decline over 52 weeks (mean [95% CI] changes from baseline to week 52: −16.2 [−18.5, −14.0] and −0.9 [−1.0, −0.8], respectively). Conclusion OLZ/SAM was generally well tolerated in this extension study; most patients completed the 52-week treatment period with sustained improvement in schizophrenia symptoms. Mean increases in weight stabilized by week 6 with limited subsequent change through end of treatment.
The ties that bind: Cancer history, communication, and screening intention associations among diverse families

Objective Breast and cervical cancers are screen-detectable; yet, challenges exist with ensuring uptake of mammography and Pap smear. Family, a central factor in developing knowledge to carry out health promotion behaviors, may be an asset to improving intention to screen among non-adherent women from underrepresented minority groups. We explored familial cancer; communication; and breast and cervical screening intention among non-adherent Black, Latina, and Arab women in the United States who participated in a randomized controlled trial of the Kin KeeperSM Cancer Prevention Intervention study. The intervention was a culturally-targeted breast and cervical cancer literacy tool for Black, Latina, and Arab women, consisting of two family-focused education sessions on the cancers, their screening guidelines, and risk-reducing health-related behaviors. Methods For this secondary analysis, we assessed family cancer history, family communication, and screening intention for breast and cervical cancer in age-eligible, non-adherent participants. Descriptive statistics examined sample characteristics of the intervention and control groups. Odds ratios were estimated from logistic regression modeling to assess the intervention and sample characteristic effects on screening intention. Results Of the 516 participants, 123 and 98 were non-adherent to breast and cervical cancer screening, respectively. The intervention (OR = 1.95 for mammography; OR = 1.62 for Pap smear) and highly communicative (OR = 2.57 for mammography; OR = 3.68 for Pap smear) families reported greater screening intention. Family history of cancer only increased screening intention for mammography (OR = 2.25). Conclusion Family-focused approaches supporting communication may increase breast and cervical cancer screening intention among non-adherent, underrepresented minority groups.
Density compensated diodes for small field dosimetry: comprehensive testing and implications for design

Purpose. In small megavoltage photon fields, the accuracies of an unmodified PTW 60017-type diode dosimeter and six diodes modified by adding airgaps of thickness 0.6–1.6 mm and diameter 3.6 mm have been comprehensively characterized experimentally and computationally. The optimally thick airgap for density compensation was determined, and detectors were micro-CT imaged to investigate differences between experimentally measured radiation responses and those predicted computationally. Methods. Detectors were tested on- and off-axis, at 5 and 15 cm depths in 6 and 15 MV fields ≥ 0.5 × 0.5 cm2. Computational studies were carried out using the EGSnrc/BEAMnrc Monte Carlo radiation transport code. Experimentally, radiation was delivered using a Varian TrueBeam linac and doses absorbed by water were measured using Gafchromic EBT3 film and ionization chambers, and compared with diode readings. Detector response was characterized via the kQclin,Qmsrfclin,fmsr formalism, choosing a 4 × 4 cm2 reference field. Results. For the unmodified 60017 diode, the maximum error in small field doses obtained from diode readings uncorrected by kQclin,Qmsrfclin,fmsr factors was determined as 11.9% computationally at +0.25 mm off-axis and 5 cm depth in a 15 MV 0.5 × 0.5 cm2 field, and 11.7% experimentally at −0.30 mm off-axis and 5 cm depth in the same field. A detector modified to include a 1.6 mm thick airgap performed best, with maximum computationally and experimentally determined errors of 2.2% and 4.1%. The 1.6 mm airgap deepened the modified dosimeter’s effective point of measurement by 0.5 mm. For some detectors significant differences existed between responses in small fields determined computationally and experimentally, micro-CT imaging indicating that these differences were due to within-tolerance variations in the thickness of an epoxy resin layer. Conclusions. The dosimetric performance of a 60017 diode detector was comprehensively improved throughout 6 and 15 MV small photon fields via density compensation. For this approach to work well with good detector-to-detector reproducibility, tolerances on dense component dimensions should be reduced to limit associated variations of response in small fields, or these components should be modified to have more water-like densities.