Miracle-dz/UniFAR-FTUs huggingface dataset:
Rickettsia typhi Possesses Phospholipase A2 Enzymes that Are Involved in Infection of Host Cells

The long-standing proposal that phospholipase A2 (PLA2) enzymes are involved in rickettsial infection of host cells has been given support by the recent characterization of a patatin phospholipase (Pat2) with PLA2 activity from the pathogens Rickettsia prowazekii and R. typhi. However, pat2 is not encoded in all Rickettsia genomes; yet another uncharacterized patatin (Pat1) is indeed ubiquitous. Here, evolutionary analysis of both patatins across 46 Rickettsia genomes revealed 1) pat1 and pat2 loci are syntenic across all genomes, 2) both Pat1 and Pat2 do not contain predicted Sec-dependent signal sequences, 3) pat2 has been pseudogenized multiple times in rickettsial evolution, and 4) ubiquitous pat1 forms two divergent groups (pat1A and pat1B) with strong evidence for recombination between pat1B and plasmid-encoded homologs. In light of these findings, we extended the characterization of R. typhi Pat1 and Pat2 proteins and determined their role in the infection process. As previously demonstrated for Pat2, we determined that 1) Pat1 is expressed and secreted into the host cytoplasm during R. typhi infection, 2) expression of recombinant Pat1 is cytotoxic to yeast cells, 3) recombinant Pat1 possesses PLA2 activity that requires a host cofactor, and 4) both Pat1 cytotoxicity and PLA2 activity were reduced by PLA2 inhibitors and abolished by site-directed mutagenesis of catalytic Ser/Asp residues. To ascertain the role of Pat1 and Pat2 in R. typhi infection, antibodies to both proteins were used to pretreat rickettsiae. Subsequent invasion and plaque assays both indicated a significant decrease in R. typhi infection compared to that by pre-immune IgG. Furthermore, antibody-pretreatment of R. typhi blocked/delayed phagosomal escapes. Together, these data suggest both enzymes are involved early in the infection process. Collectively, our study suggests that R. typhi utilizes two evolutionary divergent patatin phospholipases to support its intracellular life cycle, a mechanism distinguishing it from other rickettsial species.
Relevance of Nck–CD3ε Interaction for T Cell Activation In Vivo

On TCR ligation, the adaptor Nck is recruited through its src homology 3.1 domain to a proline-rich sequence (PRS) in CD3ε. We have studied the relevance of this interaction for T cell activation in vitro and in vivo by targeting the interaction sites in both partners. The first approach consisted of studying a knockin (KI) mouse line (KI-PRS) bearing a conservative mutation in the PRS that makes the TCR incompetent to recruit Nck. This deficiency prevents T cell activation by Ag in vitro and inhibited very early TCR signaling events including the tyrosine phosphorylation of CD3ζ. Most important, KI-PRS mice are partly protected against the development of neurological symptoms in an experimental autoimmune encephalitis model, and show a deficient antitumoral response after vaccination. The second approach consisted of using a high-affinity peptide that specifically binds the src homology 3.1 domain and prevents the interaction of Nck with CD3ε. This peptide inhibits T cell proliferation in vitro and in vivo. These data suggest that Nck recruitment to the TCR is fundamental to mount an efficient T cell response in vivo, and that the Nck–CD3ε interaction may represent a target for pharmacological modulation of the immune response.
Internalized Chitosan Nanoparticles Persist for Long Time in Cultured Cells

Chitosan-based nanoparticles (chiNPs) are considered to be potentially good carriers for the sustained intracellular delivery of specific molecules. However, scarce attention has been paid to the long-lasting permanence of these NPs in the intracellular milieu, as well as to their intracellular fate (i.e., distribution, interaction with cell organelles, and degradation) in the long term. In the present study, the presence and subcellular location of FITC-labelled chiNPs were monitored in HeLa cells up to 14 days post-administration using multicolorfluorescence confocal microscopy and diaminobenzidine photo-oxidation at transmission electron microscopy. The main result of the present study is the demonstration that internalized chiNPs persist inside the cell up to two weeks, occurring in both the cytoplasm and nucleus; accordingly, chiNPs are able to pass from mother to daughter cells through several mitotic cycles. The cells did not show increased mortality or structural damage up to 14 days after chiNP exposure.
Cancer and the LGBTQ Population: Quantitative and Qualitative Results from an Oncology Providers’ Survey on Knowledge, Attitudes, and Practice Behaviors

Background: Despite growing social acceptance, the LGBTQ population continues to face barriers to healthcare including fear of stigmatization by healthcare providers, and providers’ lack of knowledge about LGBTQ-specific health issues. This analysis focuses on the assessment of quantitative and qualitative responses from a subset of providers who identified as specialists that treat one or more of the seven cancers that may be disproportionate in LGBTQ patients. Methods: A 32-item web-based survey was emailed to 388 oncology providers at a single institution. The survey assessed: demographics, knowledge, attitudes, and practice behaviors. Results: Oncology providers specializing in seven cancer types had poor knowledge of LGBTQ-specific health needs, with fewer than half of the surveyed providers (49.5%) correctly answering knowledge questions. Most providers had overall positive attitudes toward LGBTQ patients, with 91.7% agreeing they would be comfortable treating this population, and would support education and/or training on LGBTQ-related cancer health issues. Conclusion: Results suggest that despite generally positive attitudes toward the LGBTQ population, oncology providers who treat cancer types most prevalent among the population, lack knowledge of their unique health issues. Knowledge and practice behaviors may improve with enhanced education and training on this population’s specific needs.
Preclinical evaluation of a novel cyanine dye for tumor imaging with in vivo photoacoustic imaging

Abstract. Photoacoustic imaging (PA imaging or PAI) has shown great promise in the detection and monitoring of cancer. Although nanocarrier-based contrast agents have been studied for use in PAI, small molecule contrast agents are required due to their ease of preparation, cost-effectiveness, and low toxicity. Here, we evaluated the usefulness of a novel cyanine dye IC7-1-Bu as a PAI contrast agent without conjugated targeting moieties for in vivo tumor imaging in a mice model. Basic PA characteristics of IC7-1-Bu were compared with indocyanine green (ICG), a Food and Drug Administration approved dye, in an aqueous solution. We evaluated the tumor accumulation profile of IC7-1-Bu and ICG by in vivo fluorescence imaging. In vivo PAI was then performed with a photoacoustic tomography system 24 and 48 h after intravenous injection of IC7-1-Bu into tumor bearing mice. IC7-1-Bu showed about a 2.3-fold higher PA signal in aqueous solution compared with that of ICG. Unlike ICG, IC7-1-Bu showed high tumor fluorescence after intravenous injection. In vivo PAI provided a tumor to background PA signal ratio of approximately 2.5 after intravenous injection of IC7-1-Bu. These results indicate that IC7-1-Bu is a promising PAI contrast agent for cancer imaging without conjugation of targeting moieties.
Integrated Weed Management in Aerobic Rice

Field experiment was conducted at the Wetlands Farm of Department of Farm Management, Tamil Nadu Agricultural University to find an effective integrated weed management strategy for the control of complex weed flora of aerobic rice. Pre emergence (PE) application of pendimethalin (1.0 kg ha-1) on 3 DAS + Early post emergence (EPOE) application of bispyribac sodium (25 g ha-1) on 20 DAS significantly lowered weed density and dry weight. This sequential application of pendimethalin and bispyribac sodium recorded 61.11 per cent increased yield over weedy check. The net return was higher in PE application of pendimethalin (1.0 kg ha-1) on 3 DAS + EPOE application of bispyribac sodium (25 g ha-1) on 20 DAS (`35,973 ha-1). Mean while growing intercrops as living mulch showed promising results for using it as a component of integrated weed management practice.
“Maybe It Could Be a Heart Attack . . . But I'm Only 31”: Young Men's Lived Experience of Myocardial Infarction—An Exploratory Study

This study examines the lived experience of myocardial infarction (MI) in younger men. Seven men, aged between 32 and 58, all of whom had suffered MI within the previous 12 months, were interviewed. Thematic analysis of the interview transcripts revealed four main themes. The themes were “disillusionment with life,” “tension and stress,” “keeping up appearances,” and “invincibility. ” Collectively the four themes reflected the complexities, subtleties, and consensus of the experiences of these younger men who have survived MI. This study reveals that the individuals within the authors' sample appear to allude to the ideal or hegemonic form of masculine identity. Utilization of a qualitative approach with this younger male sample has enabled the authors to elicit the defining features of their experience as identified by themselves. Implications for these findings are discussed.
How strong is the evidence of a link between environmental chemicals and adverse effects on human reproductive health?

Surveys show that the public suspects that synthetic (manmade) chemicals released into the environment, especially pesticides, have adverse effects on human health and cause disease, including cancer. In reality, few scientifically documented examples support this view, especially for effects on the general population.1 However, the observation that many synthetic chemicals have intrinsic hormonal activity—they are “endocrine disruptors”—has reopened this debate.1 Pressure groups have called for all synthetic environmental chemicals with the potential to cause harm to be phased out or banned, whereas the chemical industry argues that such action must be based on proof of harm. Vociferous cases have been made on both sides, each lacking definitive data. Yet it is clear that environmental and lifestyle factors are key determinants of human disease—accounting for perhaps 75% of most cancers.2 New understanding and emerging results are reshaping our thinking, as is the recognition that establishing cause and effect for environmental chemical exposures is a daunting task. Though this article is primarily an overview of the current evidence for reproductive effects resulting from exposure to environmental synthetic chemicals, it is relevant to the debate on wider potential health effects of such exposures. The review was compiled after detailed literature searches and cross referencing and scrutiny of relevant websites on environmental chemicals (see educational resources box). After revising the article in light of reviewers' comments, we sought the opinion of an expert toxicologist in industry to ensure balance in the review. In this hugely contentious area, polarised opinions predominate (because of the lack of definitive data). There are enormous difficulties in establishing whether exposure to individual chemicals or to chemical mixtures causes harm, as adverse effects may not manifest until many years after exposure (for example, in adulthood after fetal exposure). This difficulty must be factored into any discussion of …
Live conjunctiva-associated lymphoid tissue analysis in rabbit under inflammatory stimuli using in vivo confocal microscopy.

PURPOSE Conjunctiva-associated lymphoid tissue (CALT) plays an important role in ocular surface immunity. No study until now has been able to show its in vivo aspects, and few have demonstrated its reactions after pathologic patterns. The authors investigated in rabbit eyes the cell reactions occurring in the organized CALT during conjunctival inflammation models. METHODS Using in vivo confocal microscopy (IVCM), the authors analyzed, for the first time in vivo inflammatory cell infiltration and circulation inside the lymph vessels in rabbit CALT after inflammatory stimuli (LPS, TNFalpha, LPS+/-anti-TNF). Cresyl violet staining was performed to observe the morphology of CALT, and immunohistology was performed in whole mount conjunctiva and cryosections for detecting CD45(+) lymphocytes. Human CALT in vivo aspects were also explored in a patient with vernal keratoconjunctivitis (VKC). RESULTS The conjunctivitis model induced by LPS was characterized by inflammatory cell infiltration in the dome and intrafollicular layers of CALT and cell circulation inside the lymph vessels. TNF alone induced moderate inflammatory infiltration in CALT. However anti-TNF antibodies could significantly decrease LPS/TNFalpha-induced inflammation. CD45(+) lymphocytes were strongly expressed in the CALT after injection of LPS or TNFalpha at 4 hours and decreased with injection of anti-TNFalpha. The authors also showed the presence of the CALT pattern in VKC. CONCLUSIONS The authors showed for the first time the in vivo aspects of normal and pathologic cell reactions in rabbit CALT after inflammatory stimuli. IVCM-CALT could be a pertinent tool in the future for the comprehension of ocular surface defense mechanisms, and inflammatory cell analysis in CALT could constitute a new criterion for evaluating ocular surface inflammation.
Hierarchical Classification of Emotional Speech

Speech emotion as anger, boredom, fear, gladness, etc. is high semantic information and its automatic analysis may have many applications such as smart human-computer interactions or multimedia indexing. Main difficulties for an efficient speech emotion classification reside in complex emotional class borders leading to necessity of appropriate audio feature selection. While current work in the literature only relies on classical frequency and energy based features and make use of a global classifier with a identical feature set for different emotion classes, we propose in this paper some new harmonic and Zipf based features for better emotion class characterization and a hierarchical classification scheme as we discovered that different emotional classes need different feature set for a better discrimination. Experimented on Berlin dataset [11] with 68 features, our emotion classifier reaches a classification rate of 76.22% and up to 79.47% when a first gender classification is applied, whereas current works in the literature usually display, as far as we know, a classification rate from 55% to 70%.
Modeling Brain Activation in fMRI Using Group MRF

Noise confounds present serious complications to functional magnetic resonance imaging (fMRI) analysis. The amount of discernible signals within a single dataset of a subject is often inadequate to obtain satisfactory intra-subject activation detection. To remedy this limitation, we propose a novel group Markov random field (GMRF) that extends each subject's neighborhood system to other subjects to enable information coalescing. A distinct advantage of GMRF over standard fMRI group analysis is that no stringent one-to-one voxel correspondence is required. Instead, intra- and inter-subject neighboring voxels are jointly regularized to encourage spatially proximal voxels to be assigned similar labels across subjects. Our proposed group-extended graph structure thus provides an effective means for handling inter-subject variability. Also, adopting a group-wise approach by integrating group information into intra-subject activation, as opposed to estimating a single average group map, permits inter-subject differences to be characterized and studied. GMRF can be elegantly implemented as a single MRF, thus enabling all subjects' activation maps to be simultaneously and collaboratively segmented with global optimality guaranteed in the case of binary labeling. We validate our technique on synthetic and real fMRI data and demonstrate GMRF's superior performance over standard fMRI analysis.
Large-Scale Comparative Genomics Meta-Analysis of Campylobacter jejuni Isolates Reveals Low Level of Genome Plasticity

ABSTRACT We have used comparative genomic hybridization (CGH) on a full-genome Campylobacter jejuni microarray to examine genome-wide gene conservation patterns among 51 strains isolated from food and clinical sources. These data have been integrated with data from three previous C. jejuni CGH studies to perform a meta-analysis that included 97 strains from the four separate data sets. Although many genes were found to be divergent across multiple strains (n = 350), many genes (n = 249) were uniquely variable in single strains. Thus, the strains in each data set comprise strains with a unique genetic diversity not found in the strains in the other data sets. Despite the large increase in the collective number of variable C. jejuni genes (n = 599) found in the meta-analysis data set, nearly half of these (n = 276) mapped to previously defined variable loci, and it therefore appears that large regions of the C. jejuni genome are genetically stable. A detailed analysis of the microarray data revealed that divergent genes could be differentiated on the basis of the amplitudes of their differential microarray signals. Of 599 variable genes, 122 could be classified as highly divergent on the basis of CGH data. Nearly all highly divergent genes (117 of 122) had divergent neighbors and showed high levels of intraspecies variability. The approach outlined here has enabled us to distinguish global trends of gene conservation in C. jejuni and has enabled us to define this group of genes as a robust set of variable markers that can become the cornerstone of a new generation of genotyping methods that use genome-wide C. jejuni gene variability data.
Assessment of sugarcane grown in wetlands polluted with wastewater

Abstract Wastewater effluents directly discharged into nearby stream are eventually used to irrigate plants like sugarcane in Ghana. In this study, 24 triplicates sugarcane stems (sugarcane juice was extracted), 24 triplicates soil samples and 8 triplicates water samples were collected from sugarcane farms in four communities in Ashanti region of Ghana. Two of the communities were exposed to wastewater while the other two without wastewater contamination served as control. Metals (Pb, Cd, Cr, Cu, and Fe) concentration were determined in the digested samples using Spectra AA 220 flame atomic absorption spectrometer. The Pb concentration in all sugarcane juice samples ranged between 12.65 and 145.0 μg/L. The mean Cu concentration of the sugarcane juice samples varied between 11.28 and 156.00 μg/L. In general, there were decrease in metals investigated in sugarcane juice as you move away from the stream. However, the reduction was more pronounced in the hotspot sampling areas than control sampling areas. The EDI value was 9.76 × 10−4, 2.94 × 10−5, 1.09 × 10−3, and 9.07 × 10−3 (mg/kg-day) for Pb, Cd, Cu, and Fe, respectively. Mean hazard quotient (HQ) for the metals studied ranged from 0.036 (Fe) to 0.286 (Pb). The results of this study indicate that sugarcane is able to grow in soils where some metals are accumulated. High levels of metals were pronounced in sugarcane originating from wastewater polluted soils as those considered in this study. The consumption of normal quantity of sugarcane juice may not present detrimental health concerns through a lifetime based on the metals contents alone.
Point Count Length and Detection of Forest Neotropical Migrant Birds

Comparisons of bird abundances among years or among habitats assume that the rates at which birds are detected and counted are constant within species. We use point count data collected in forests of the Mid-Atlantic states to estimate detection probabilities for Neotropical migrant bird species as a function of count length. For some species, significant differences existed among years or observers in both the probability of detecting the species and in the rate at which individuals are counted. We demonstrate the consequence that variability in species' detection probabilities can have on estimates of population change, and discuss ways for reducing this source of bias in point count studies.
Controlling threshold in soil salinity when planting spring wheat and sequential cropping silage corn in Northern Xinjiang using drip irrigation

Xinjiang Region of China is one of the most typical and representative arid areas worldwide, along with severe soil salinization issue. Planting spring wheat and sequential cropping silage corn in Northern Xinjiang using drip irrigation has become an effective way to relieve soil salinity stress, which improves the simple agricultural structure in the past and ensures food security in this area. However, neither the effects of different soil salinities on the growth and yield of spring wheat and silage corn, nor their desalination effect correspondingly was clear until now. Therefore, a pot experiment was conducted at Shihezi, Xinjiang from March to June 2015. The study aimed to establish the quantitative correlations between the parameters mentioned above and came up with the appropriate soil salinity threshold in Northern Xinjiang area. The results confirmed that the soils in all treatments were desalinated after the whole growth period, and the decreasing rates varied within 18.89%-44.08% and 11.06%-30.83% for two plants, which showed linear and quadratic correlations with initial soil salinity, respectively (R2 > 0.92**, p 0.92**, p <0.01). The inhibition effect was enhanced with larger initial soil salinity. After the comprehensive consideration of soil salinity variation, crop growth and yield, the initial soil salinity was recommended under 8.91 g/kg and 5.54 g/kg to plant spring wheat and sequential cropping silage corn in Northern Xinjiang using drip irrigation. Keywords: soil salinity, drip irrigation, spring wheat sequential silage corn, quantitative correlations, critical controlling threshold DOI: 10.25165/j.ijabe. 20181102.3621 Citation: Wang Z H, Zhou B, Pei L, Zhang J Z, He X L, Lin H. Controlling threshold in soil salinity when planting spring wheat and sequential cropping silage corn in Northern Xinjiang using drip irrigation. Int J Agric & Biol Eng, 2018; 11(2): 108–114.
The Role of PTPN22 C1858T Gene Polymorphism in Diabetes Mellitus Type 1: First Evaluation in Greek Children and Adolescents

Type 1 diabetes mellitus (T1DM) is an autoimmune multifactorial disease. Protein tyrosine phosphatase nonreceptor type 22 (PTPN22) gene encodes lymphoid-specific tyrosine phosphatase (Lyp), an inhibitor of T cell activation. PTPN22 C1858T polymorphism was associated with T1DM in populations of Caucasian origin. The aim of this study was the investigation for the first time of the association of PTPN22 C1858T polymorphism with T1DM in Greek population. We studied 130 children and adolescents with T1DM and 135 healthy individuals of Greek origin. The polymorphism was genotyped using polymerase chain reaction with restriction fragment length polymorphism. C1858T and T1858T genotypes as well as 1858T allele were found more frequently in patients (10.8% and 5.8%, resp.) than in healthy individuals (5.9% and 3.0%, resp.) but at non statistically significant level. There was no statistically significant association found with gender, age at diagnosis, severity of onset, history of Hashimoto thyroiditis or family history of T1DM. Increased frequency of 1858T allele in patients than in controls, implying a probable association, agrees with results of similar studies on other populations. The inability to find a statistically significant difference is probably due to the decreased frequency of minor allele in Greek population, indicating the need for a larger sample.