Miracle-dz/UniFAR-FTUs huggingface dataset:
Bicarbonate Resensitization of Methicillin-Resistant Staphylococcus aureus to β-Lactam Antibiotics

Endovascular infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are a major health care concern, especially infective endocarditis (IE). Standard antimicrobial susceptibility testing (AST) defines most MRSA strains as “resistant” to β-lactams, often leading to the use of costly and/or toxic treatment regimens. In this investigation, five prototype MRSA strains, representing the range of genotypes in current clinical circulation, were studied. ABSTRACT Endovascular infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are a major health care concern, especially infective endocarditis (IE). Standard antimicrobial susceptibility testing (AST) defines most MRSA strains as “resistant” to β-lactams, often leading to the use of costly and/or toxic treatment regimens. In this investigation, five prototype MRSA strains, representing the range of genotypes in current clinical circulation, were studied. We identified two distinct MRSA phenotypes upon AST using standard media, with or without sodium bicarbonate (NaHCO3) supplementation: one highly susceptible to the antistaphylococcal β-lactams oxacillin and cefazolin (NaHCO3 responsive) and one resistant to such agents (NaHCO3 nonresponsive). These phenotypes accurately predicted clearance profiles of MRSA from target tissues in experimental MRSA IE treated with each β-lactam. Mechanistically, NaHCO3 reduced the expression of two key genes involved in the MRSA phenotype, mecA and sarA, leading to decreased production of penicillin-binding protein 2a (that mediates methicillin resistance), in NaHCO3-responsive (but not in NaHCO3-nonresponsive) strains. Moreover, both cefazolin and oxacillin synergistically killed NaHCO3-responsive strains in the presence of the host defense antimicrobial peptide (LL-37) in NaHCO3-supplemented media. These findings suggest that AST of MRSA strains in NaHCO3-containing media may potentially identify infections caused by NaHCO3-responsive strains that are appropriate for β-lactam therapy.
Fear of Childbirth: A Mini Review

Fear of childbirth is one of the common problems found among pregnant women. It affects on a negative impact on a birth process. The objectives of this review are to explore factor related to fear of childbirth, consequences of fear of childbirth and assessment of fear of childbirth. A review was conducted in the electronic databases Pub Med, Science Direct, and CINAHL. Keywords used in the search were ‘fear’ in conjunction with ‘childbirth’. Combination of components of the Problem, Intervention, Comparison and Outcome strategy were used. The timeframe was limited to the years 1947-2019, as it was the timeframe where fear of childbirth made an appearance in the literature. The search was limited to English language articles. The results revealed factor related to fear of childbirth as prospective fear which composed of social aspect and personal aspect and retrospective fear. Consequences of fear of childbirth were decisions for future pregnancy and prolong labor. The measurements scales of fear of childbirth were Childbirth Attitudes Questionnaire and Wijma Delivery Expectancy/Experience Questionnaire (W-DEQ).
Aquatic macroinvertebrates as water quality bioindicators in Colombia: A systematic review

The use of aquatic macroinvertebrates to assess water quality has been growing during the last 50 years in Colombia. We conducted a systematic review of 109 references to analyze scientific production related to the evaluation of water quality in Colombian freshwater ecosystems, using aquatic macroinvertebrates. We describe bibliographical, geographical, ecological, and methodological characteristics of these studies. In the last two decades, there was an increase of more than 50% of publications. The Andean region was the most studied, while the other regions had few research. Lotic ecosystems were widely studied, unlike the lentic ones. The main land use management was agricultural. BMWP and diversity indices were the most used in the analyses. Further research is necessary in lentic ecosystems since they are being severely impacted by anthropogenic pressures, but were not assessed yet. Different regions that harbor diverse aquatic ecosystems (e.g. Amazon, Orinoquia) have been little studied. There is a critical need to revisit traditional indices, aiming at avoiding wrong assumptions about the relation between aquatic macroinvertebrates communities and water quality. For this purpose, it is recommended that assumptions and conditions required for using the indices, high taxonomic resolution, and new approaches, such as effective number of species, are taken into account. Keywords: aquatic insects, biotic indices, BMWP, diversity indices, lentic ecosystems, lotic ecosystems, water pollution.
Quantifying Flesh Browning, Polyphenoloxidase, Total Phenolic Content And Vitamin C In Select Apple Varieties And Progeny

Enzymatic browning of apples is a significant problem in the fresh cut and processing industries. Quantifying the rates and extent of flesh browning across a range of cultivars can assist breeders in selecting low-browning parents to use in crosses. The browning reaction uses phenolic compounds as the substrate and the enzyme polyphenoloxidase (PPO) as the catalyst. This study quantified flesh browning, PPO activity, and total phenolic content in twelve commercial cultivars and five advanced breeding selections. ‘Liberty’, ‘McIntosh’, and selection #2 (a ‘McIntosh’ x ‘Fuji’ hybrid) were consistently the highest browning apples. ‘AutumnCrisp’ (previously designated as NY674) and selection #5 (‘AutumnCrisp’ x ‘Braeburn’) were the lowest browning apples. Flesh browning tended to decrease over time in cold storage for most cultivars, and was lower near the peel than near the core. Cultivars ‘AutumnCrisp’, ‘Cortland’, ‘Zestar’, and ‘McIntosh’ had the lowest measured PPO activity. Selection #2, #3 (‘Braeburn’ x ‘AutumnCrisp’), and ‘Braeburn’ had the highest PPO activity. ‘McIntosh’, #4 (‘AutumnCrisp’ x ‘Fuji’), #5, and #2 had the highest phenolic content. Selection #3 and ‘Braeburn’ had the lowest phenolic content. Phenolic content and PPO were correlated to total color change only in some cultivars.
Preliminary evidence for altered interoceptive processing in smokers

Background Neuroimaging evidence suggests that interoceptive processing might be altered in nicotine addiction, however this has not yet been confirmed with behavioral measures. Therefore, we investigated the perception of internal bodily states in smokers (49) and people who had never smoked (n=51), by measuring interoceptive sensitivity (IS) and interoceptive awareness (IA). Methods IS was measured with a heartbeat tracking task and a heartbeat discrimination task. Performance on the heartbeat tracking task may be influenced by one's ability to estimate an elapsed time interval so this was controlled by a time-estimation (TE) task. IA was measured using two sub-scales from the Multidimensional Assessment of Interoceptive Awareness (MAIA). Participants in the ‘addiction’ group completed the Revised Fagerström Test for Nicotine Dependence (FTND-R) to measure addiction severity. Results Independent-samples t-tests revealed that non-smokers performed significantly better than smokers on the heartbeat tracking task (p = 0.007, d = 0.22). There were no group differences observed for the remaining variables. Furthermore, none of the variables predicted addiction severity. Conclusions This is the first demonstration of behavioral differences in interoception in participants with nicotine addiction. When considered in the context of previous research, these findings support the hypothesis that interoceptive processing may be disturbed in addiction. These data also support the hypothesis that behavioral and self-report measures of interoception assess two separate constructs.
Germline Pathogenic Variants in Homologous Recombination and DNA Repair Genes in an Asian Cohort of Young-Onset Colorectal Cancer

Abstract Background Growing evidence suggests a role for cancer susceptibility genes such as BRCA2 and PALB2 in young-onset colorectal cancers. Using a cohort of young colorectal cancer patients, we sought to identify and provide functional evidence for germline pathogenic variants of DNA repair genes not typically associated with colorectal cancer. Methods We recruited 88 patients with young-onset colorectal cancers seen at a general oncology center. Whole-exome sequencing was performed to identify variants in DNA repair and colorectal cancer predisposition genes. Pathogenic BRCA2 and PALB2 variants were analyzed using immunoblot and immunofluorescence on patient-derived lymphoblastoid cells. Results In general, our cohort displayed characteristic features of young-onset colorectal cancers. Most patients had left-sided tumors and were diagnosed at late stages. Four patients had familial adenomatous polyposis, as well as pathogenic APC variants. We identified 12 pathogenic variants evenly distributed between DNA repair and colorectal cancer predisposition genes. Six patients had pathogenic variants in colorectal cancer genes: APC (n = 4) and MUTYH monoallelic (n = 2). Another six had pathogenic variants in DNA repair genes: ATM (n = 1), BRCA2 (n = 1), PALB2 (n = 1), NTHL1 (n = 1), and WRN (n = 2). Pathogenic variants BRCA2 c.9154C>T and PALB2 c.1059delA showed deficient homologous recombination repair, evident from the impaired RAD51 nuclear localization and foci formation. Conclusion A substantial portion of pathogenic variants in young-onset colorectal cancer was found in DNA repair genes not previously associated with colorectal cancer. This may have implications for the management of patients. Further studies are needed to ascertain the enrichment of pathogenic DNA repair gene variants in colorectal cancers.
Synthesis, characterization and investigation on the magnetic and electronic structure of strontium iron oxides

The relationship of the crystallographic, magnetic, and electronic structure have long been of highinterest in research. Strontium iron oxides have structural, charge, spin, and orbital degrees offreedom, and thus give rich information to study for the condensed matter scientists. In this thesis,we have systematically studied the strontium iron oxides based on the freedom of the iron charge:Fe3+ and Fe4+ mixed valence compound SrFeO2,75 , Fe3+ compound Sr3Fe2O6 and SrFeO2,5 with differentcoordination around Fe3+ and Fe2+ compound SrFeO2. The synthesis of the polycrystalline compoundsare through either solid state reaction or sol-gel method. Single crystals of SrFeO2,75 and SrFeO2,5have been prepared by floating zone furnace. The purity of all the compounds is checked by lab x-raydiffraction and Mossbauer spectroscopy. Electronic structures have been studied by x-ray absorptionspectroscopy for all these compounds. Special efforts have been used to investigate the magneticstructure of SrFeO2,75 and Sr3Fe2O6 .
Unraveling the effects of spatial variability and relic DNA on the temporal dynamics of soil microbial communities

Few studies have comprehensively investigated the temporal variability in soil microbial communities despite widespread recognition that the belowground environment is dynamic. In part, this stems from the challenges associated with the high degree of spatial heterogeneity in soil microbial communities1 and because the presence of relic DNA2 may mask temporal dynamics. Here we disentangle the relationships among spatial, temporal, and relic DNA effects on microbial communities in soils collected from contrasting hillslopes in Colorado, USA. These sites were chosen because they have distinct soil microbial communities and experience strong seasonal changes in precipitation and temperature regimes. We intensively sampled plots on each hillslope over one year to discriminate between temporal variability, the intra-plot spatial heterogeneity, and relic DNA effects on the soil prokaryotic and fungal communities. We show that the intra-plot spatial variability in microbial community composition was strong and independent of relic DNA effects and these spatial patterns persisted throughout the study. When controlling for intra-plot spatial variability, we identified significant temporal variability in both plots, particularly after relic DNA was removed, suggesting that relic DNA hinders the detection of important temporal dynamics in soil microbial communities. We also identified microbial taxa that exhibited shared temporal responses and we show that these responses were often predictable from temporal changes in soil conditions. These findings highlight approaches that can be used to better characterize temporal shifts in soil microbial communities, information that is critical for predicting the environmental preferences of individual soil microbial taxa and identifying linkages between soil microbial community composition and belowground dynamics.
Chromosome dynamics in bacteria: triggering replication at opposite location and segregation in opposite direction

The accurate onset of chromosome replication and segregation are fundamental for the survival of the cell. In bacteria, regulation of chromosome replication lies primarily at the initiation step. The bacterial replication initiator DnaA recognizes the origin of replication (ori) and opens this double stranded site allowing for the assembly of the DNA replication machinery. Following the onset of replication initiation, the partitioning protein ParA triggers the onset of chromosome segregation by direct interactions with ParB-bound to the centromere. The subcellular organization of ori and centromere are maintained after the completion of each cell cycle. It remains unclear what triggers the onset of these key chromosome regulators DnaA and ParA. One potential scenario is that the microenvironment of where the onset of replication and segregation take place hosts the regulators that trigger the activity of DnaA and ParA. In order to address this, we analyzed whether the activity of DnaA and ParA are restricted to only one site within the cell. In non-dividing cells of the alpha proteobacterium Caulobacter crescentus, ori and centromere are found near the stalked pole. To test DnaA’s ability to initiate replication away from the stalked pole, we engineered a strain where movement of ori was induced in the absence of chromosome replication. Our data show that DnaA can initiate replication of the chromosome independently of the subcellular localization of ori. Furthermore, we discovered that the partitioning protein ParA was functional and could segregate the replicated centromere in the opposite direction from the new pole toward the stalked pole. We showed that the organization of the ParA gradient can be completely reconstructed in the opposite orientation by rearranging the location of the centromere. Our data reveal the high flexibility of the machineries that trigger the onset of chromosome replication and segregation in bacteria. Our work also provides insights into the coordination between replication and segregation with the cellular organization of specific chromosomal loci.
Virus-induced gene silencing for functional analysis of eds1 gene in tomato infected with Ralstonia solanacearum

The efficiency of virus-induced gene silencing (VIGS) can be identified by monitoring the level of silencing of the target genes in plants. In this study, enhanced disease susceptibility 1 (eds1) gene was silenced in tomato (Lycopersicon esculentum L.) plants by VIGS, using Tobacco rattle virus (TRV) expression vector. Tomato plants at different growth stages (fully-opened cotyledon and eight-leaf) were co-infected with Agrobacterium tumefaciens C58C1 strain containing eds1 complementary deoxyribonucleic acid (cDNA) at different (20°C and 28°C) temperatures and bacterial concentrations with 1.0 × 106 and 1.5 × 108 colony forming unit (CFU) mL-1. The reverse transcriptase-polymerase chain reaction (RT-PCR) method was used to analyse the suppression level of the eds1 gene and the VIGS efficiency assay. Data analysis showed a high eds1 gene silencing at fully-opened cotyledon stage at 20°C using a A. tumefaciens at a concentration of 1.0 × 106 CFU rather than other conditions. In addition, the percentage of wilted plants was significantly varied in different conditions and the most wilted plants were observed at the 1.0 × 106 CFU and 20°C. Based on our results, we suggest that eds1 gene silencing can be used as a possible screening marker to select bacterial wilt-resistant species.
Detecting Opisthonema libertate (Gunther, 1867) phenotypic stocks in northwestern coast of Mexico using geometric morphometrics based on body and otolith shape

Stock discrimination is essential for biomass population assessment and essential for the fisheries management. The analysis of shape differences in anatomical structures ( e.g ., body shape, otoliths, scales) has been relevant issue in the study of population structure. We evaluated the hypothesis on the existence of a stockstructured population of Pacific thread herring Opisthonema libertate in the northwestern coast of Mexico. Geometric morphometric methods were used to analyze body and otolith shape. Samples come from at three commercial fishery-landing sites: Magdalena Bay, Guaymas, and Mazatlan, Mexico. Results based on body and otolith shape support the existence of different morphotypes by location. Body shape allowed better discrimination than otolith shape. The differences observed between the phenotypic stocks suggest seasonal movements, which are linked to the marine current system in this region, particularly to the California Current and the North Equatorial Counter Current.
Fatty acid oxidizing enzymes in Lobosphaera incisa

Green microalgae are a model in biotechnology because of their capacity to accumulate neutral lipids, as part of a general lipid remodeling mechanism under stress. The species L. incisa is of special interest for its unique TAG acyl chain composition, especially 20:4 (n-6) that can reach up to 21 % of dry weight after nitrogen starvation. In order to identify lead actors of this remodeling, special focus was put on lipid oxidizing processes, which have been described to be of major importance in flowering plants. Investigation of the available genome, transcriptome and proteome of L. incisa allowed the identification of a putative LOX, which so far has not been studied in green microalgae. The identification as a LOX was first confirmed in silico, by alignments and 3D structure prediction. The heterologous expression of LiLOX in E. coli was achieved in mg quantities, allowing further characterization of the LOX via enzymatic assays in vitro. Throughout the study, LiLOX was found to be a good model to study plastidic plant LOXs, as it shares highest identity with this class of enzymes and was found to have identical regio- and stereospecificity. This hypothesis was further confirmed by the localization of LiLOX in plastids, investigated via transient expression in epithelial onion cells. In order to further characterize this class of enzymes, mutational studies and attempts at crystallizations were performed and are presented in this thesis. An important part of this work focused on identification of the endogenous substrate of LiLOX. In this regards, an ex vivo enzymatic assay, coupled with non-targeted analysis via mass spectrometry allowed the identification of MGDG, DGDG and PC as three substrate candidates, later confirmed via in vitro assays. Further investigation revealed that LiLOX has preferences towards the lipid class MGDG, which seems in agreement with its localization in the galactolipid rich plastid. Altogether, this study shows the first characterization of plastidic LOX from green algae, showing preference for MGDGs. Finally, this study targeted the role of LiLOX in the general lipid remodeling taking place in L. incisa during nitrogen starvation. Since this remodeling is accompanied with the degradation of the plastidic membrane, the involvement of LiLOX in this process was discussed.
STUDI FENOMENOLOGI BUDAYA PERENCANAAN KEUANGAN KELUARGA MUSLIM DI SIDOARJO & SURABAYA

Abstrac: This paper is interested in exploring the phenomenon of planning and management of the Muslim family finances in Sidoarjo and Surabaya. The Muslim families that this paper focuses on are those with high religious commitment judged from their regular attendance to religious rituals and gatherings such as Majlis Taklim and the likes. The towns of Sidoarjo and Surabaya are being chosen to obtain specific findings on the one hand, and to have a better picture of the culture of wealth management among the urban Muslims on the other. The study is qualitative in its methods, and phenomenological in its analysis. Data were extracted from 20 informants, 7 of whom are categorised as lower income, 8 are middle income, and 5 are upper income laborers. One of the findings that this paper comes about is the fact that better understanding to the teachings of religion obtained from religious gatherings does not necessarily make a family better in its financial planning and management. On the other hand, with some exceptions, many informants among the lower classes are capable of managing their household and running their finances well making them better off to prepare their future needs. Keywords : Planning, management, Muslim household, family Abstrak: Fenomena perencanaan dan pengelolaan keuangan rumah tangga keluarga Muslim selalu menarik untuk dibahas, terlebih keluarga dengan intensitas yang tinggi untuk mempelajari agama Islam melalui Majlis Taklim dan kajian-kajian agama lainnya. Penelitian ini membatasi lokasi hanya di Surabaya dan Sidoarjo saja, untuk mendapatkan temuan yang spesifik. Penelitian dilakukan dengan metode kualitatatif, dengan alat analisis fenomenologi. Data digali dari 20 informan, dengan spesifikasi 7 informan dari kategori pendapatan kelas bawah, 8 informan dari kategori pendapatan kelas menengah dan 5 informan dari kategori pendapatan kelas atas. Dari beberapa informan tersebut dihasilkan satu temuan, bahwa semakin tinggi pemahaman keagamaan yang didapatkan dari kajian-kajian agama tidak serta merta menjadikan sebuah keluarga cerdas dalam merencanakan dan mengelola keuangan rumah tangga mereka. Walaupun ada beberapa pengecualian, yaitu terdapat informan di kalangan bawah yang mampu memanaj keuangan rumah tangga mereka dengan baik sehingga mereka bisa mempersiapkan kebutuhan masa depan dengan bijak. Kata Kunci: Perencanaan, pengelolaan, rumah tangga Muslim, keluarga
Ozone induced alterations in the metabolite pools and enzyme activities of plants

Acute or chronic ozone exposure may reduce plant growth and cause greater reductions in root growth than in top growth. These growth reductions are associated with metabolic alterations. When soybean leaves and pine needles were exposed to ozone, there was an initial decrease in the levels of soluble sugars followed by a subsequent increase. Ozone exposure also caused a decrease in the activity of the glycolytic pathway and the decrease in the activity was reflected in a lowered rate of nitrate reduction. Ozone increased the activities of enzymes involved in phenol metabolism (phenylalanine ammonia lyase and polyphenoloxidase). Leachates from fescue leaves exposed to ozone inhibited nodulation. Ozone-induced reductions in root growth resulted from altered foliage metabolism rather than from direct action upon the roots themselves. Soluble carbohydrates and starch were at lower levels in roots of ponderosa pine exposed to low levels of ozone at the end of the growing season, while the levels of amino acids and Kjeldahl nitrogen were higher. Nodulation of legumes exposed to ozone was reduced suggesting a reduction in the amount of nitrogen fixed per plant. Root exudates from plants exposed to ozone also inhibited root growth and nodulation in other plants. 23 references, 9more » figures, 5 tables. « less