Miracle-dz/UniFAR-FTUs huggingface dataset:
Ability of Bicarbonate Supplementation To Sensitize Selected Methicillin-Resistant Staphylococcus aureus Strains to β-Lactam Antibiotics in an Ex Vivo Simulated Endocardial Vegetation Model

Supplementation of standard growth media (cation-adjusted Mueller-Hinton Broth [CAMHB]) with bicarbonate (NaHCO3) increases β-lactam susceptibility of selected methicillin-resistant Staphylococcus aureus (MRSA) strains (“NaHCO3 responsive”). This “sensitization” phenomenon translated to enhanced β-lactam efficacy in a rabbit model of endocarditis. ABSTRACT Supplementation of standard growth media (cation-adjusted Mueller-Hinton Broth [CAMHB]) with bicarbonate (NaHCO3) increases β-lactam susceptibility of selected methicillin-resistant Staphylococcus aureus (MRSA) strains (“NaHCO3 responsive”). This “sensitization” phenomenon translated to enhanced β-lactam efficacy in a rabbit model of endocarditis. The present study evaluated NaHCO3-mediated β-lactam MRSA sensitization using an ex vivo pharmacodynamic model, featuring simulated endocardial vegetations (SEVs), to more closely mimic the host microenvironment. Four previously described MRSA strains were used: two each exhibiting in vitro NaHCO3-responsive or NaHCO3-nonresponsive phenotypes. Cefazolin (CFZ) and oxacillin (OXA) were evaluated in CAMHB with or without NaHCO3. Intra-SEV MRSA killing was determined over 72-h exposures. In both “responsive” strains, supplementation with 25 mM or 44 mM NaHCO3 significantly reduced β-lactam MICs to below the OXA susceptibility breakpoint (≤4 mg/liter) and resulted in bactericidal activity (≥3-log killing) in the model for both OXA and CFZ. In contrast, neither in vitro-defined nonresponsive MRSA strain showed significant sensitization in the SEV model to either β-lactam. At both NaHCO3 concentrations, the fractional time above MIC was >50% for both CFZ and OXA in the responsive MRSA strains. Also, in media containing RPMI plus 10% Luria-Bertani broth (proposed as a more host-mimicking microenvironment and containing 25 mM NaHCO3), both CFZ and OXA exhibited enhanced bactericidal activity against NaHCO3-responsive strains in the SEV model. Neither CFZ nor OXA exposures selected for emergence of high-level β-lactam-resistant mutants within SEVs. Thus, in this ex vivo model of endocarditis, in the presence of NaHCO3 supplementation, both CFZ and OXA are highly active against MRSA strains that demonstrate similar enhanced susceptibility in NaHCO3-supplemented media in vitro.
Exosomes and Friends: A General Overview on Reproduction

Nowadays, extracellular vesicles (EVs) as phospholipid bilayer enclosed vesicles are as popular as they have ever been. EVs are secreted by different cells and they target both tissues and/or cells in the body [1]. They play key roles in various aspects of biology, such as reproduction, as biomarkers of disease and as potent targets for therapeutic interposition [2]. Depending on their size, contents, biogenesis and function they have been classified as microvesicles, apoptotic bodies, ectosomes and exosomes [3].
Chemometrics on its way towards personalized health care

Nowadays, patients can be examined in unprecedented detail at molecular level. It is expected that this will allow for personalized health care, where diagnosis and treatment are catered towards the unique molecular characteristics of an individual patient. However, currently complexity and size of the data are a major obstacle for analysis. The main contributions of this thesis consist of a careful evaluation of current strategies to remove artefacts from data and the development of novel data analysis methods for personalized health care. These methods can be used to detect differences between groups of patients to obtain a better understanding of biomolecular processes, or to inspect individual patients and (with knowledge of the biological processes) diagnose a disease. The new models were successfully used to investigate effects of diets on metabolism of patients with metabolic syndrome. Additionally, the methods were used to inspect the health status of individual patients diagnosing several rare metabolic diseases.
Patologias de origen bacteriano en almejas cultivadas (tapes decussatus y t. Philippinarum)

En el presente estudio se han caracterizado dos patologias asociadas a procesos epizooticos de almejas cultivadas en la region suratlantica espanola: la enfermedad de la necrosis muscular, que afecto a los cultivos de almeja fina (tapes decussatus) en la provincia de cadiz, y la enfermedad del anillo marron (eam), que desde 1989 viene afectando a los cultivos de almeja japonesa (t.Philippinarum) en las costas de cadiz y huelva. Los estudios microbiologicos e histologicos realizados han permitido establecer el origen bacteriano de ambas patologias. Asi, el agente causal de la enfermedad de la necrosis muscular ha sido identificado como vibrio alginolyticus, mientras que el de la eam se ha incluido en la especia v. Splendidus. Por otra parte, se han desarrollado metodos de inmunodiagnosis, basados en la tecnica de inmunofluorescencia indirecta, del agente etiologico de la eam, que permiten la deteccion especifica del patogeno, tanto en muestras de agua intervalvar como en secciones histologicas de almejas infectadas, con y sin sintomatologia.
Weighing the cost: the impact of serial heatwaves on body mass in a small Australian passerine

Rising temperatures pose a grave risk to arid zone birds because they are already living close to their physiological limits and must balance water conservation against the need for evaporative cooling. We assess how extreme temperatures affect a wild population of small passerines by monitoring daily mass change in individual jacky winters Microeca fascinans (a small Australasian robin) across a series of severe heatwaves that afflicted southern Australia in the summer of 2018–2019. Daily maximum temperature and duration of heat exposure were negatively related to the birds’ ability to maintain body mass. At maximum temperatures ≥ 42°C, birds lost 2.0% of their body mass daily and at ≥ 45°C, 2.6%. Apparent mortality increased almost three‐fold, and all breeding birds abandoned their nests. Nevertheless, net daily mass loss was less than might be expected from laboratory‐based findings, presumably because wild jacky winters undertook behavioural thermoregulation. The birds also regained some mass between heatwave events and suffered no long‐term reduction in body condition.
Capacidad de reinicio de la meiosis de ovocitos provenientes de folículos de varios tamaños obtenidos de ovarios de camal

Se evaluó la capacidad de los ovocitos de folículos según su tamaño para reiniciar la meiosis. Los folículos se midieron y clasificaron como Grupo 1 (G1 <4 mm), Grupo 2 (G2 4-8 mm) y Grupo 3 (G3 >8 mm). La aspiración se realizó por grupo con una aguja 21G conectada a una bomba de vacío, con una presión de 65 mmHg. Los complejos cúmulos de ovocitos (COC) recuperados se clasificaron como adecuados y no adecuados para la producción de embriones in vitro, de acuerdo con las características del cúmulo y del citoplasma. Los COC elegibles e inadecuados se valoraron con la prueba de azul brillante de Cresilo (BCB) y se clasificaron en BCB+ y BCB-. La maduración in vitro (IVM) se llevó a cabo en microgotas, incubadas en una cámara de CO2 al 5%, 38.5 °C y 90% de humedad durante 24 horas. La progresión meiótica se determinó por extrusión del corpúsculo polar mediante epifluorescencia bajo un microscopio invertido. La morfometría de ovocitos se estableció mediante una cámara de alta definición (Excelis AU-600-HD) y un software (AmScope v.3.7). El porcentaje de recuperación de ovocitos fue mayor de 63%. Los folículos de G2 proporcionaron un mayor porcentaje de COC elegibles (65.7%), donde el 59% de este grupo se clasificó como BCB+. Los ovocitos aptos de G1 y G2 reanudaron la meiosis en un 75%. Además, se observó que los ovocitos después de IVM redujeron su diámetro. Se concluye que los ovocitos de folículos entre 4-8 mm (G2) proporcionan un mayor porcentaje de COC maduros; sin embargo, el 50% de folículos <4 mm (G1) son una fuente prometedora de ovocitos viables, por lo que deben usarse para la producción de embriones in vitro.
Effects of different growing media on growth of Cardopatium corymbosum (L.) Pers. (Asteraceae)

This study was conducted to determine the effect of different growing media on the growth of Cardopatium corymbosum (L.) Pers. The pot experiments were carried out with plants which are obtained from germination studies and from field and the effect of different applications on leaf number and leaf size was determined. The maximum leaf number change was observed at 200 ppm GA3 at 90 days and maximum leaf size change was observed in liquid nutrient medium at 60 days on plants which was obtained at germination experiment. The maximum leaf number change was determined in the application of 200 ppm GA3 at 60 days and the maximum change in the leaf size was determined in the field soil + 10% vermicompost experiment at 60 days on plants which was obtained from experiment field
In Vitro Study of Probiotics and their Antimicrobial Susceptibility on Common Pathogens

: Probiotics are viable bacteria or yeast having beneficial physiologic or therapeutic activities. They showed beneficial effects in several ailments like rota virus, diarrhea, and lactose intolerance, etc. and exhibited anticarcinogenic and immunomodulatory effects. In this study, we have successfully cultured and isolated two strains of probiotics. One of them is Lactobacillus casei, which was isolated from Yakult drink milk from local market of Agra. The other product is the sporlac from which the probiotic strain Lactobacillus sporogenesis was isolated. These two probiotics strains were then subjected to the study on antibiotic susceptibility and detecting the antagonistic activity of probiotic strains. Our results showed that the zone of inhibition was maximum when Lactobacillus casei was cultured under Chloroamphenicol (C30), while the zone of inhibition measured in Lactobacillus sporogenesis was found to be maximum with the antibiotic Levofloxacin (L5). Both strains showed the resistance to the antibiotic Ceftazidime CAZ30. On the other hand, for the antagonistic activity of Lactobacillus casei, the maximum zone of inhibition was observed in the presence of E. coli MTCC-1652 followed by Pseudomonas aeruginosa MTCC-103 and Staphylococcus aureus MTCC-740. As for Lactobacillus sporogenesis, the maximum zone of inhibition was produced against E.coli MTCC-1652 and equal zone of inhibition was observed against Pseudomonas aeruginosa MTCC-103 and Staphylococcus aureus. No zone was seen in the serial suspension for both strains. It is concluded that Lactobacillus sporogenesis produces better zone of inhibition than Lactobacillus casei against Pseudomonas aeruginosa MTCC-103 and Staphylococcus aureus MTCC-740 for some of serial suspension. Lactobacillus reuteri, e) Lactobacillus gasseri, f) Lactobacillus fermentum, g) Bifidobacterium bifidum, h) Bifidobacterium lactis, i) Enterococcus faecium, j) Bacillus subtilis, k) Bacillus cereus, l) Saccharomyces cerevisiae, m) Saccharomyces boulardii and n) Aspergillus oryzae. The antimicrobial attribute of probiotics is related to some active metabolites that is capable of inhibiting and having killing potential for pathogens. As probiotics ferment sugars and produces organic acids such as lactic acid and acetic acid. Thus, the mixture of organic acids has a powerful antimicrobial activity at low pH. In subsequent studies, it was shown that lactobacillus and bifidobacterium, also able to inhibit Helicobacter pylori growth through the release of bacteriocins or organic acid and decrease the ability of this pathogen to adhere to epithelial cells (Prince et al., 2012).
Deconstructing the structural conservation of distantly related bacterial nucleoid-associated proteins using functional chimeras

Nucleoid-associated proteins (NAPs) are DNA-binding proteins critical for the organization and function of the bacterial chromosome. A subclass of NAPs, including Caulobacter crescentus GapR and Escherichia coli H-NS, preferentially bind AT-rich regions of the nucleoid, but phylogenetic groups that encode GapR rarely encode H-NS. Here, utilizing genetic, biochemical, and biophysical studies of GapR in light of a recent DNA-bound crystal structure of GapR (Guo et al, 2018), we show that although evolutionarily distant, GapR and H-NS possess two regions that are structurally and functionally conserved. These regions are involved in self-association and DNA-binding, even though the two proteins oligomerize and regulate transcription differently. Functional analysis of GapR and H-NS protein chimeras identified structural elements present in H-NS but absent in GapR that rationalize differences in transcriptional regulation. In addition, we identified a sequence element unique to GapR that enables assembly into its tetrameric state. Using fluid-atomic force microscopy, we showed that GapR is capable of bridging DNA molecules in vitro. Together, these results demonstrate that two distantly related NAPs utilize evolutionarily conserved structural elements to serve specialized cellular roles via distinct mechanisms.
Investigating the Influence of the Brain-Derived Neurotrophic Factor Val66Met Single Nucleotide Polymorphism on Familiarity and Recollection Event-Related Potentials

The Val66Met single nucleotide polymorphism (SNP) has previously been reported to impact performance on recognition memory tasks. Whether the two subprocesses of recognition—familiarity and recollection—are differentially impacted by the Val66Met SNP remains unknown. Using event-related potentials (ERPs) recorded during a source memory task, we attempted to dissociate these two subprocesses. Behaviourally, we used participants’ scores on an item-recognition subtask as a measure of familiarity, and participants’ scores on a source-recognition subtask as a measure of recollection. Our findings reveal that Val/Val individuals outperform Met allele carriers on the item-but not the source-recognition task. Electrophysiologically, we were interested in the N400, an early frontal component previously linked to familiarity, and the late positive complex (LPC), a posterior component linked to recollection. We found evidence for Val/Val individuals having larger amplitudes of the LPC compared to Met allele carriers, and evidence for no difference in the N400 amplitudes of these groups. Based on the lack of dissociation between familiarity- and recollection-specific ERPs at the LPC time window, we argue that our behavioural and ERP results might reflect better item-recognition for Val/Val individuals compared to Met allele carriers. We further suggest that both these results reflect differences related to familiarity, rather than recollection.
Prevalencia de Giardia spp en roedores (Rattus spp) de un zoológico de Lima Metropolitana

El objetivo del estudio fue determinar la prevalencia de Giardia spp en roedores (Rattus rattus y Rattus norvegicus) capturados en un zoológico de Lima Metropolitana, así como la posible asociación entre la presencia del parásito con las variables especie, sexo y edad de las ratas. Se capturaron 127 roedores (Rattus spp) entre febrero de 2013 y agosto de 2016 mediante el uso de trampas de captura viva “Tomahawk”. La manipulación de los roedores y la recolección de las muestras cumplieron con los estándares de bioseguridad y normas de procesamiento de acuerdo con los protocolos del Centro de Enfermedades Infecciosas y Prevención de Atlanta (CDC). Muestras del intestino delgado y tracto digestivo posterior (ciego, colon y recto) fueron colectadas y conservadas con formol al 10%. Se utilizó la técnica de Ritchie modificado, considerándose como muestra positiva la presencia de alguna forma parasitaria de Giardia spp (trofozoito o quiste). La prevalencia de Giardia spp en los roedores fue 5.5 ± 0.04% (7/127), siendo de 2.1% en R. rattus (1/48) y 7.6% en R. norvergicus (6/79). No se encontró asociación significativa entre la frecuencia de Giardia spp y las variables especie, sexo y edad. Se reporta una baja prevalencia de Giardia spp en roedores capturados en el zoológico; sin embargo, podría existir un riesgo potencial de infección parasitaria para los concurrentes, principalmente niños y ancianos, así como animales y trabajadores de la institución.
The Impact of Edema and Fiber Crossing on Diffusion MRI Metrics: DBSI vs. Diffusion ODF

Purpose Diffusion tensor imaging (DTI) has been employed for over two decades to noninvasively quantify central nervous system (CNS) diseases/injuries. However, DTI is an inadequate simplification of diffusion modeling in the presence of co-existing inflammation, edema, and crossing nerve fibers. Methods We employed a tissue phantom using fixed mouse trigeminal nerves coated with various amounts of agarose gel to mimic crossing fibers in the presence of vasogenic edema. Diffusivity measures derived by DTI and diffusion basis spectrum imaging (DBSI) were compared at increasing levels of simulated edema and degrees of fiber crossing. Further, we assessed the ability of DBSI, diffusion kurtosis imaging (DKI), generalized q-sampling imaging (GQI), q-ball imaging (QBI), and neurite orientation dispersion and density imaging (NODDI) to resolve fiber crossing, in reference to the gold standard angles measured from structural images. Results DTI-computed diffusivities and fractional anisotropy (FA) were significantly confounded by gelmimicked edema and crossing fibers. Conversely, DBSI calculated accurate diffusivities of individual fibers regardless of the extent of simulated edema and degrees of fiber crossing angles. Additionaly, DBSI accurately and consistently estimated crossing angles in various conditions of gel-mimicked edema when comparing with gold standard (r2=0.92, p=1.9×10−9, bias=3.9°). Small crossing angles and edema sinficantly impact dODF, making DKI, GQI and QBI less accurate in detecting and estimating fibers corrsing angles. Lastly, we demonstrate DBSI’s superiority over DTI for recovering and delineating white matter tracts in peritumoral edema for preoperative planning of surgical resection. Conclusions DBSI is able to separate two crossing fibers and accurately recover their diffusivities in a complex environment characterized by increasing crossing angles and amounts of gel-mimicked edema. DBSI also indicated better angular resolution capability compared with DKI, QBI and GQI.
ANTIBIOTIC RESISTANCE PATTERN OF HELICOBACTER PYLORI IN PATIENTS WITH CHRONIC DYSPEPSIA IN NORTHEAST OF IRAN

Background and Objectives: Increasing Helicobacter pylori resistance to common antibiotics has created various treatment methods in different geographical areas. This study aimed at determining in vitro susceptibility of H. pylori to clarithromycin, metronidazole, amoxicillin and tetracycline, the four antibiotics commonly used in eradication therapies. Materials and Methods: Patients with chronic dyspepsia referred to our clinic for upper endoscopy were included. Patients with history of antibiotic or proton pump inhibitor consumption in recent two weeks prior to the endoscopy, and those with malignancy were excluded. Endoscopy samples were prepared for histology, rapid urease test, culture and antibiogram. Antibiotic resistance was evaluated with two methods; agar dilution and disc diffusion tests. Results: Among 185 patients, 124 cases (67%) were histologically positive. Sensitivity and specificity of culture, compared to the histology, was 66.1% and 100%, respectively. Reported resistance was 17.1 % for clarithromycin, 64.6% for metronidazole and 9.8% for amoxicillin. No resistance was observed for tetracycline. Resistance to metronidazole was more common in patients younger than 50 years (P=0.01). Sixty four percent of the specimens with resistance to clarithromycin showed co-resistance to metronidazole. Conclusion: According to high resistance to metroniazole in our study, especially in young patients, this drug is not recommended for H. pylori as the first line treatment in Iran. We suggest that in patients who failed to respond to clarithromycin, culturing and determining microbial susceptibility to other antibiotics be performed.
Hook size selectivity in the artisanal handline fishery of Shimoni fishing area, south coast, Kenya

Selectivity of five handline fishing hook sizes was determined following Holt’s 1963 model using data that was collected during January to June, 2016. A total of 966 fish specimens comprising of 65 species belonging to 23 families were sampled. Fish abundance was low for large sized hooks while catch rate was higher. Species diversity was higher during the northeast monsoon season and at the study sites of Mpunguti and Nyuli. However, species diversity decreased with increase in hook size. All hook sizes had a higher selection for mature Lethrinus borbonicus while hook size No. 8 selected immature Lethrinus lentjan . Hook sizes No. 9 and 10 selected mature L. lentjan and Lethrinus rubrioperculatus , hook size No. 15 selected immature L. lentjan , L. rubrioperculatus and Aprion virescens , while hook size No. 16 selected immature A. virescens and L. rubrioperculatus. Species similarity was higher for fish caught by hook sizes No. 16 and 15, and No. 8 and 9, while those captured by hook size No. 10 differed from those caught by other hook sizes. The larger hook size No. 8 is recommended for the sustainable exploitation species in the artisanal handline fishery in Shimoni fishing area. Future work needs to consider the effects of bait type and size and the stock status of the fish under exploitation.
Organic Acids and Nature Identical Compounds Can Increase the Activity of Conventional Antibiotics Against Clostridium Perfringens and Enterococcus Cecorum In Vitro

SUMMARY In a global context of increased antibiotic resistance, feed additives with enhanced antimicrobial properties are a useful and increasingly needed strategy. Organic acids (OA) and botanical molecules such as nature identical compounds (NIC) have been shown to be effective against bacterial infections based on their antimicrobial activity. The aim of this study was to evaluate whether the combination of OA or NIC with conventional antibiotics in poultry could increase antibiotic efficacy against Clostridium perfringens and Enterococcus cecorum. These organisms are the major poultry pathogens responsible for necrotic enteritis and bacterial chondronecrosis with osteomyelitis, respectively, and they have developed resistance to several antibiotics worldwide. A set of antimicrobial tests showed that both species had variable antibiotic sensitivity. Alternatively, OA and NIC were always effective in a dose-dependent manner, even when the antibiotics failed. For several strains, selected combinations of OA or NIC with antibiotics increased the bacterial sensitivity to antibiotics. Therefore, OA and NIC have potential to enhance the efficacy of conventional antibiotics against C. perfringens andE. cecorum.