Miracle-dz/UniFAR-FTUs huggingface dataset:
Response of sweet orange (Citrus sinensis) to 'Candidatus Liberibacter asiaticus' infection: microscopy and microarray analyses.

Citrus greening or huanglongbing (HLB) is a devastating disease of citrus. HLB is associated with the phloem-limited fastidious prokaryotic alpha-proteobacterium 'Candidatus Liberibacter spp. ' In this report, we used sweet orange (Citrus sinensis) leaf tissue infected with 'Ca. Liberibacter asiaticus' and compared this with healthy controls. Investigation of the host response was examined with citrus microarray hybridization based on 33,879 expressed sequence tag sequences from several citrus species and hybrids. The microarray analysis indicated that HLB infection significantly affected expression of 624 genes whose encoded proteins were categorized according to function. The categories included genes associated with sugar metabolism, plant defense, phytohormone, and cell wall metabolism, as well as 14 other gene categories. The anatomical analyses indicated that HLB bacterium infection caused phloem disruption, sucrose accumulation, and plugged sieve pores. The up-regulation of three key starch biosynthetic genes including ADP-glucose pyrophosphorylase, starch synthase, granule-bound starch synthase and starch debranching enzyme likely contributed to accumulation of starch in HLB-affected leaves. The HLB-associated phloem blockage resulted from the plugged sieve pores rather than the HLB bacterial aggregates since 'Ca. Liberibacter asiaticus' does not form aggregate in citrus. The up-regulation of pp2 gene is related to callose deposition to plug the sieve pores in HLB-affected plants.
Qualitative Meta-Synthesis: Reflections on the Utility and Challenges in Occupational Therapy

Background. A qualitative meta-synthesis is an approach to synthesizing relevant findings from across qualitative studies on a particular topic using methods consistent with qualitative research. Purpose. Using examples of recently completed qualitative meta-synthesis projects, the purpose of this paper is to present the meta-synthesis approach; highlight the key steps, processes, and issues involved; and demonstrate its potential to advance knowledge about occupation and occupation-based practice. Key Issues. The qualitative meta-synthesis approach allows us to take stock of the current state of knowledge in a given area in order to ensure that we have explored the phenomenon from different perspectives and to begin to push the field forward by allowing us to develop deeper insights and understandings. Implications. Despite certain limitations and challenges associated with the approach, qualitative meta-syntheses can provide new knowledge through critical analysis and interpretation to inform client, practitioner, and policy audiences.
Predictors of Nonstandard Helmet Use Among San Francisco Bay–Area Motorcyclists

Objective: The use of helmets that do not comply with safety standards is common in California. The objective of this study was to describe the use of these nonstandard helmets among San Francisco Bay–area (SFBA) motorcyclists and to identify personal and motorcycle characteristics that are associated with the use of nonstandard helmets. Methods: A survey of 860 SFBA motorcyclists was conducted. Log-binomial regression was used to estimate risk ratios to compare probabilities of nonstandard helmet use. Results: Fifteen percent of motorcyclists reported wearing a nonstandard helmet sometimes or often. BMW riders had the lowest use of nonstandard helmet (5%) and Harley-Davidson riders had the highest use (51%). Among non-Harley-Davidsons, riders of cruiser-style motorcycles were 3.1 times as likely to wear a nonstandard helmet as riders of motorcycles of other styles. African American riders were more than twice as likely to use nonstandard helmets compared to riders with other self-reported race. Discussion: Behavioral countermeasures are needed to improve motorcycle helmet choice in California. This study identified riders of Harley-Davidsons and riders of cruiser-style motorcycles of other brands as potential targets of interventions.
Levels and membrane localization of the c-K-ras p21 protein in lungs of mice of different genetic strains and effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and Aroclor 1254.

Mutational activation of the K-ras oncogene often occurs in human and mouse lung adenocarcinomas. Since K-ras p21 functions in trans-membrane signaling, we have investigated whether the amount of this protein in lung cell membranes is a variable that could influence lung tumorigenesis, either due to genetic differences or in response to tumor promoters. The six mouse strains assessed showed little difference in the total lung K-ras p21 after immunoprecipitation and immunoblotting. However, amount of ras p21 in the membrane fraction showed significant differences, with C57BL/6 and BALB/c having 3-5-fold more than NIH Swiss, AKR and DBA mice. Interestingly, a congenic AKR strain having the Ahr(b-1) Ah receptor allele from C57BL/6 mice (designated AKR.B6Ah) had high lung membrane K-ras p21 similar to that of C57BL/6. To test for possible changes related to lung tumor promotion, mice were treated with a promotional dose of TCDD (5 nmol/kg). After 48 h C57BL/6 lungs showed an increase in p21 in both total and membrane fractions. BALB/c, DBA and Swiss mice showed an increase only in membranes. There was no change in the AKR and AKR.B6Ah. Aroclor 1254 (250 mg/kg) caused an increase in membrane/cytosol ratio in Swiss mice. Thus the membrane:cytosol K-ras p21 ratio may be influenced by the Ahr phenotype, and TCDD and PCBs can induce p21 or increase its membrane level in certain strains, but these properties are not fully dependent on Ahr receptor type. In confirmation of the relevance of these findings for the tumor target cell type, the immortalized alveolar type 2 E10 cell line presented K-ras p21 in membrane, and this was increased 4-fold by treatment with 10 nM TCDD.
Drug Susceptibility Testing of Mycobacterium tuberculosis by a Nitrate Reductase Assay Applied Directly on Microscopy-Positive Sputum Samples

ABSTRACT Current methods for drug susceptibility testing of Mycobacterium tuberculosis are either costly or slow. As the prevalence of multidrug-resistant strains increases, the need for fast, reliable, and inexpensive methods that can also be applied in settings with scarce resources is obvious. We evaluated a rapid colorimetric nitrate reductase assay (NRA) for direct drug susceptibility testing of M. tuberculosis directly from clinical sputum samples with positive microscopy results for acid-fast bacilli with more than 10 acid-fast bacilli per high-power field. We have saved valuable time by omitting the preisolation step. The sensitivity (ability to detect true drug resistance) and specificity (ability to detect true drug susceptibility) of the direct NRA, using the direct proportion method as the reference, were 100 and 100%, 93 and 100%, 76 and 100%, and 55 and 99% for rifampin, isoniazid, streptomycin, and ethambutol, respectively, when tested on M. tuberculosis strains present in 121 samples. The results were in most cases available in 14 days. The direct NRA could be used as a rapid, inexpensive, and accurate method to determine rifampin and isoniazid susceptibility directly from sputum. The technique might become a valid alternative to traditional methods, especially in low-income countries.
Comparing dysphagia therapy in head and neck cancer patients in Australia with international healthcare systems

Abstract Purpose: The Australian healthcare system has invested heavily in multidisciplinary cancer care teams. Despite such investments, guidelines that clearly delineate standard of care dysphagia treatment are lacking and services provided to Head and Neck Cancer (HNC) patients are not always consistent. There is little consensus regarding the frequency and intensity of dysphagia therapy. This is largely due to a lack of well-designed clinical trials that establish the efficacy of any dysphagia therapy in this patient population. The aim of this study was to evaluate HNC dysphagia therapy patterns among Australian speech-language pathologists (SLPs). Method: A 22 question internet-based survey was administered to a web-based professional interest group. Results were analysed by institution type and individual clinical experience. Result: A response rate of 46% was achieved (67 out of 144 surveyed). This survey identified several aspects of dysphagia management that were provided uniformly in addition to many aspects of care that showed a lack of consensus. Conclusion: By comparing the results of this survey with existing international best-evidence treatment guidelines, the development of uniform Australian guidelines may be facilitated. However, more authoritative data on dysphagia treatment efficacy is needed to provide uniform evidence-based HNC dysphagia treatment guidelines.
Culture of Mouse Amniotic Fluid-Derived Cells on Irradiated STO Feeders Results in the Generation of Primitive Endoderm Cell Lines Capable of Self-Renewal in vitro

The cells present in amniotic fluid (AF) are currently used for prenatal diagnosis of fetal anomalies but are also a potential source of cells for cell therapy. To better characterize putative progenitor cell populations present in AF, we used culture conditions that support self-renewal to determine if these promoted the generation of stable cell lines from AF-derived cells (AFC). Cells isolated from E11.5 mouse were cultured on irradiated STO fibroblast feeder layers in human embryonic germ cell derivation conditions. The cultures grew multicellular epithelial colonies that could be repropagated from single cells. Reverse transcription semiquantitative polymerase chain reaction of established cell lines revealed that they belonged to the extraembryonic endoderm (ExEn) expressing high levels of Gata6, Gata4, Sox17, Foxa2 and Sox7 mRNA. Hierarchical clustering based on the whole transcriptome expression profile of the AFC lines (AFCL) shows significant correlation between transcription profiles of AFCL and blastocyst-derived XEN, an ExEn cell line. In vitro differentiation of AFCL results in the generation of cells expressing albumin and α-fetoprotein (AFP), while intramuscular injection of AFCL into immunodeficient mice produced AFP-positive tumors with primitive endodermal appearance. Hence, E11.5 mouse AF contains cells that efficiently produce XEN lines. These AF-derived XEN lines do not spontaneously differentiate into embryonic-type cells but are phenotypically stable and have the capacity for extensive expansion. The lack of requirement for reprogramming factors to turn AF-derived progenitor cells into stable cell lines capable of massive expansion together with the known ability of ExEn to contribute to embryonic tissue suggests that this cell type may be a candidate for banking for cell therapies.
Action of fat, four-jointed, dachsous and dachs in distal-to-proximal wing signaling

In the Drosophila wing, distal cells signal to proximal cells to induce the expression of Wingless, but the basis for this distal-to-proximal signaling is unknown. Here, we show that three genes that act together during the establishment of tissue polarity, fat, four-jointed and dachsous, also influence the expression of Wingless in the proximal wing. fat is required cell autonomously by proximal wing cells to repress Wingless expression, and misexpression of Wingless contributes to proximal wing overgrowth in fat mutant discs. Four-jointed and Dachsous can influence Wingless expression and Fat localization non-autonomously, consistent with the suggestion that they influence signaling to Fat-expressing cells. We also identify dachs as a gene that is genetically required downstream of fat, both for its effects on imaginal disc growth and for the expression of Wingless in the proximal wing. Our observations provide important support for the emerging view that Four-jointed, Dachsous and Fat function in an intercellular signaling pathway, identify a normal role for these proteins in signaling interactions that regulate growth and patterning of the proximal wing, and identify Dachs as a candidate downstream effector of a Fat signaling pathway.
Shared decision‐making in question

Over recent years, communication within the physician–patient relationship has been profoundly changing. New modes of conveying diagnostic and therapeutic information influence the way in which decisions regarding treatment are made. We propose a critical review of the various theoretical models as presented in the literature, from the paternalistic to the shared decision model, in order to reveal conceptual ambiguities and their related methodological problems. This analysis leads to a project for clarifying these problems through a research protocol based on shared decision‐making. Copyright © 2001 John Wiley & Sons, Ltd.
The complete mitochondrial genome of Sika deer Cervus nippon hortulorum (Artiodactyla: Cervidae) and phylogenetic studies

Abstract Sika deer (Cervus nippon Temminck 1836) are classified in the order Artiodactyla, family Cervidae, subfamily Cervinae. At present, the phylogenetic studies of C. nippon are problematic. In this study, we first determined and described the complete mitochondrial sequence of the wild C. nippon hortulorum. The complete mitogenome sequence is 16 566 bp in length, including 13 protein-coding genes, two rRNA genes, 22 tRNA genes, a putative control region (CR) and a light-strand replication origin (OL). The overall base composition was 33.4% A, 28.6% T, 24.5% C, 13.5% G, with a 62.0% AT bias. The 13 protein-coding genes encode 3782 amino acids in total. To further validate the new determined sequences and phylogeny of Sika deer, phylogenetic trees involving 15 most closely related species available in GenBank database were constructed. These results are expected to provide useful molecular data for deer species identification and further phylogenetic studies of Artiodactyla.
The Effects of Oil Inventories on Growth Prospects, Futures Markets, and Risk Premia

This paper studies the effects of introducing storable inputs into a general equilibrium model of endogenous growth. We explicitly account for an occasionally binding non-negativity constraint on storage. To solve the model, we rely on global non-linear solution methods, allowing us to make conditional statements on endogenous variables. We ﬁnd a substantial nonlinear impact of inventory levels on growth prospects in the economy. The state of commodity holdings has an important impact on utilization of production capacity. In an economy with endogenous growth risks, ﬁrms target an optimal level of inventories to be able to increase oil usage in boom times. In an economy with transitory shocks only, the opposite is true. Macroeconomic dynamics implied by the model explain major stylized fact of ﬁnancial markets, such as the term structure of futures premia and a negative co-movement of oil inventories with the risk-free rate.
Imaging predictors of the response to transarterial chemoembolization in patients with hepatocellular carcinoma: A radiological‐pathological correlation

Transarterial chemoembolization (TACE) is one of the standard therapies for bridging patients with hepatocellular carcinoma (HCC) to transplantation. This study was designed to determine which features on pre‐ and post‐TACE imaging are associated with tumor necrosis in pathological specimens. Records of 105 patients with 132 HCC lesions who underwent liver transplantation after TACE were retrospectively reviewed. In 70% of the nodules, >90% necrosis was achieved. The development of >90% lesion necrosis upon pathological analysis was associated with avid lesion enhancement (P = 0.03) and the presence of a feeding vessel larger than 0.9 mm in diameter on the pre‐TACE visceral angiogram (P = 0.01). Near‐complete lesion necrosis was also associated with an extensive accumulation of ethiodized oil within a lesion during TACE administration (P = 0.04). On post‐TACE computed tomography imaging, a lack of residual contrast enhancement (P < 0.0001), a decrease in the lesion size (P = 0.04), a high lesion density due to an accumulation of ethiodized oil (P = 0.03), and a diffuse distribution of ethiodized oil throughout the lesion (P = 0.0001) were also correlated with near‐complete lesion necrosis upon pathological analysis. In conclusion, this study found multiple pre‐ and post‐TACE imaging characteristics of HCC that were associated with near‐complete tumor necrosis upon histopathological analysis after TACE. These findings may help to guide the selection of an optimal treatment strategy for bridging patients with HCC to liver transplantation. Liver Transpl 18:727–736, 2012. © 2012 AASLD.
Activated Mitofusin 2 Signals Mitochondrial Fusion, Interferes with Bax Activation, and Reduces Susceptibility to Radical Induced Depolarization*[boxs]

Mitochondrial fusion in higher eukaryotes requires at least two essential GTPases, Mitofusin 1 and Mitofusin 2 (Mfn2). We have created an activated mutant of Mfn2, which shows increased rates of nucleotide exchange and decreased rates of hydrolysis relative to wild type Mfn2. Mitochondrial fusion is stimulated dramatically within heterokaryons expressing this mutant, demonstrating that hydrolysis is not requisite for the fusion event, and supporting a role for Mfn2 as a signaling GTPase. Although steady-state mitochondrial fusion required the conserved intermembrane space tryptophan residue, this requirement was overcome within the context of the hydrolysis-deficient mutant. Furthermore, the punctate localization of Mfn2 is lost in the dominant active mutants, indicating that these sites are functionally controlled by changes in the nucleotide state of Mfn2. Upon staurosporine-stimulated cell death, activated Bax is recruited to the Mfn2-containing puncta; however, Bax activation and cytochrome c release are inhibited in the presence of the dominant active mutants of Mfn2. The dominant active form of Mfn2 also protected the mitochondria against free radical-induced permeability transition. In contrast to staurosporine-induced outer membrane permeability transition, pore opening induced through the introduction of free radicals was dependent upon the conserved intermembrane space residue. This is the first evidence that Mfn2 is a signaling GTPase regulating mitochondrial fusion and that the nucleotide-dependent activation of Mfn2 concomitantly protects the organelle from permeability transition. The data provide new insights into the critical relationship between mitochondrial membrane dynamics and programmed cell death.
Association between Style of Living and General Health in Suburban Women: A Cross-sectional Study in South East of Iran.

INTRODUCTION In developing countries, suburban population is increasing. However, their health issues are rarely considered in studies. Socioeconomic and environmental factors in their neighbourhood can affect their lifestyle and health. Compared to men, women have fewer social resources and are more susceptible to an unfavourable environment, in general. AIM To investigate the association between lifestyle and general health status in suburban women. MATERIALS AND METHODS This correlation, cross-sectional study assessed the lifestyle and general health, among suburban women living in Shirabad neighbourhood, Zahedan, Iran. Randomized one stage cluster sampling was used and 132 people participated in the study. Lifestyle Questionnaire (LSQ) and General Health Questionnaire-28 (GHQ-28) were used for data collection. For data analysis, descriptive statistical methods, Pearson's correlation coefficient and multivariate regression analysis were performed. RESULTS Mean score of LSQ was 100.23±20.45 and mean GHQ-28 score was 28.46±16.41. There was a significant negative relationship between lifestyle and GHQ-28 total score (r=-0.619, p=0.01). Multivariate regression analysis showed that among predictor variables, education, sports and fitness and psychological health components had a significant relationship with GHQ-28 (p<0.001, p=0.01, p=0.002 respectively). CONCLUSION This study demonstrated that suburban women have poor lifestyle and health status. Also, it showed a significant relationship between education, sports and fitness and psychological health components and health. As a result, implementation of programs to modify lifestyle especially in the field of sports and improving the educational level could be useful in promoting women's health.
Common FMF alleles may predispose to development of Behcet's disease with increased risk for venous thrombosis

Background: Behcet's disease (BD) is an inflammatory disorder of unknown cause, associated with vasculitis. Arterial or venous thrombosis occurs in about 25% of BD patients. Familial Mediterranean fever (FMF) is another inflammatory disorder, which stems from mutations in the FMF gene (MEFV) and shares a number of features with BD. Objective: MEFV analysis in patients with BD suggests that mutated MEFV may act as a susceptibility gene in BD. We studied the rate and the clinical correlates of MEFV mutations in Israeli BD patients. Methods: Included were 54 BD patients who satisfied the International Study Group criteria for BD. All BD patients were genotyped using polymerase chain reaction (PCR) and restriction enzyme analysis for the three most common MEFV mutations (M694V, V726A, and E148Q). The association between BD manifestations and MEFV alleles was analysed. Results: Twenty‐one BD patients were found to carry a single MEFV mutation and three additional patients were compound heterozygotes, a frequency significantly higher than that expected for ethnically matched healthy individuals. There were no statistically significant differences between carriers and non‐carriers with respect to gender, frequency of HLA B5 antigen, cutaneous lesions, joint disease, and severity score. However, carriers did experience thrombosis more often [54% vs. 17%, p<0.005, odds ratio (OR) = 6.9, 95% confidence interval (CI) 1.75–26.9] and uveitis less often (20% vs. 40%, p<0.05, OR = 0.2, 95% CI 0.04–0.92). Conclusions: MEFV appears to be a susceptibility and modifier gene in BD.
Differential space-time-frequency coded OFDM with maximum multipath diversity

Addressing orthogonal frequency division multiplexing (OFDM) transmissions over frequency-selective Rayleigh fading channels, we propose a differential space-time-frequency (DSTF) coding scheme with maximum multipath diversity. Resorting to subcarrier grouping, we convert the system into a set of parallel DSTF systems, within which DSTF coding is considered. Through pairwise error probability (PEP) analysis, we prove that full diversity gain, which is the product of the number of transmit antennas, receive antennas, and the multipath channel length, can be achieved without channel state information (CSI) at the receiver. We analyze the performance of group DSTF coding over correlated fading channels and establish the design criteria for subcarrier selection and code selection. In addition to applying existing differential unitary diagonal codes, we propose a systematic approach to designing nondiagonal codes for DSTF systems, which are block diagonal (BD) and have the necessary unitary and full diversity properties. Based on permutation techniques, we have devised new excellent-performing BD DSTF codes, which significantly improve the coding gain as compared to their diagonal counterparts. Corroborating simulations confirm the merits of our approach.