Miracle-dz/UniFAR-FTUs huggingface dataset:
PI3K-dependent ERK is involved in GM-CSF-mediated activation of progenitor cells in a neovascularisation model

The current study investigated the effects of the granulocyte-macrophage colony-stimulating factor (GM-CSF) on rat endothelial progenitor cell (EPC) biology. EPCs were isolated from rat bone marrow and experiments were carried out to determine the dose- and time-dependent effects of GM-CSF on angiogenesis, proliferation, viability, migration and vasculogenesis. EPCs were cocultured with rat cardiac microvascular endothelial cells (CMECs) to determine the effect of GMCSF on EPC angiogenesis in vitro. EPC proliferation and viability, migration, and vasculogenesis were measured by the respective application of the method of transcription and translation (MTT) assay, the Transwell chamber assay and the Matrigel assay. GM-CSF treatment stimulated EPC angiogenesis, proliferation, viability, migration and tubule formation in a dose- and timedependent manner. Furthermore, GM-CSF treatment led to the upregulation of integrinβ2, vascular endothelial growth factor (VEGF) and p-extracellular signal-regulated kinase (p-ERK) 1/2 levels in EPCs. Moreover, two different phosphatidylinositol 3-kinase (PI3K) inhibitors (LY294002 and Wortmannin) partially inhibited the GM-CSF-mediated increase in p-ERK1/2 levels in EPCs. The ERK inhibitor, FR180204, dramatically inhibited GM-CSF-mediated stimulation of EPC proliferation, migration and vasculogenesis. Taken together, the results of the current study provide evidence that a PI3K-dependent ERK signalling pathway is, at least, partially responsible for the GM-CSFmediated effects on EPC function.
Sources of age determination errors for sablefish (Anoplopoma fimbria)

This study was undertaken to resolve problems in age determina­ tion of sablefish (Anoplopoma fimbria). Aging of this species has been ham­ pered by poor agreement (averaging less than 45%) among age readers and by differences in assigned ages of as much as 15 years. Otoliths from fish that had been injected with oxytetracycline (OTC) and that had been at liberty for known durations were used to determine why age determinations were so difficult and to help determine the correct aging procedure. All fish were sampled from Oregon southwards, which represents the southern part of their range. The otoliths were examined with the aid of image processing. Some fish showed little or no growth on the otolith after eight months at liberty, whereas otoliths from other fish grew substantially. Some fish lay down two prominent hyaline zones within a single year, one in the summer and one in the winter. We classified the otoliths by morphological type and found that certain types are more likely to lay down multiple hyaline zones and other types are likely to lay down little or no zones. This finding suggests that some improvement could be achieved by detailed knowledge of the growth char­ acteristics of the different types. This study suggests that it may not be possible to obtain reliable ages from sablefish otoliths. At the very least, more studies will be required to understand the growth of sablefish otoliths. Manuscript approved for publication 14 July 2003 by Scientific Editor. Manuscript received 20 October 2003 at NMFS Scientific Publications Office. Fish Bull. 102:127–141 (2004). Sources of age determination errors for sablefish (Anoplopoma fimbria)*
Diatom sinkings speeds: Improved predictions and insight from a modified Stokes' law

Accurately predicting the size‐dependant sinking rate of diatoms is necessary to fully understand the cycling of oceanic carbon and silicon. Stokes' law predicts that sinking velocity should be proportional to the square of a diatom's radius (a scaling exponent of 2), which does not agree with empirically measured sinking speeds (scaling exponents of 1.2‐1.6). We offer an alternative model for sinking speed that separately accounts for the different densities of a diatom's frustule (its siliceous cell armor) and its cytoplasm. The ratio of frustule to cytoplasm volume changes with size and, thereby, affects the scaling relationship between velocity and radius. The resulting model predicts a scaling exponent between 1 and 2 depending on the size and shape of the diatom, more accurately predicting the upper bound of measured sinking speeds and offering an analytical formula for the prediction of the maximum sinking speed of diatoms.
Mating compatibility and phylogeography in Pleurotus tuberregium

Genetic relationships were investigated among several populations of Pleurotus tuberregium from Nigeria, Papua New Guinea and New Caledonia. Intrastock mating compatibility studies using progeny from two collections demonstrated a tetrapolar mating system for P. tuberregium. Interstock matings among the geographically distinct populations were compatible. All isolates were found to be intersterile with tester strains of other Pleurotus species, showing that P. tuberregium represents a unique intersterility group in Pleurotus. Nucleotide sequences of the ITS region of the rDNA gene were determined for 30 isolates and used to infer phylogenetic structure of populations. Phylogenetic analysis shows that African and Australasian-Pacific isolates form at least two distinct evolutionary lineages. Higher genetic divergence was observed among ITS sequences from the Australasian-Pacific region than among African isolates, which suggests a possible origin of P. tuberregium in the Australasian-Pacific region.
Global transcriptional regulation by cell-free supernatant of Salmonella Typhimurium peptide transporter mutant leads to inhibition of intra-species biofilm initiation

Salmonella is a genus of widely spread Gram negative, facultative anaerobic bacteria, which is known to cause ¼th of the diarrhoeal morbidity and mortality globally. It causes typhoid fever and gastroenteritis by gaining access to the host gut through contaminated food and water. Salmonella utilizes its biofilm lifestyle to strongly resist antibiotics and persist in the host. Although the biofilm removal or dispersal have been studied widely, the inhibition of initiation Salmonella biofilm has not been studied much. This study was conducted to determine the anti-biofilm property of the cell-free supernatant obtained from a carbon-starvation inducible proline peptide transporter mutant (ΔyjiY) strain. Our study shows that Salmonella ΔyjiY culture supernatant inhibits biofilm initiation by regulating biofilm associated transcriptional network. This work demonstrates that highly abundant proteases like ecotin, HslV and GrpE cleave the protein aggregates, whereas global transcription regulators H-NS, FlgM regulate expression of SPIs and flagellar genes. Relatively low abundance of flavoredoxin, glutaredoxin, thiol peroxidase etc. leads to accumulation of ROS within the biofilm, and subsequent toxicity. This work further suggests that targeting these oxidative stress relieving proteins might be a good druggable choice to reduce Salmonella biofilm.
Neuropsychophysiological Measures of Alcohol Dependence: Can We Use EEG in the Clinical Assessment?

Addiction management is complex, and it requires a bio-psycho-social perspective, that ought to consider the multiple etiological and developmental factors. Because of this, a large amount of resources has been allocated to assess the vulnerability to dependence, i.e., to identify the processes underlying the transition from substance use to dependence, as well as its course, in order to determine the key points in its prevention, treatment, and recovery. Consequently, knowledge \from neuroscience must be taken into account, which is why different initiatives have emerged with this objective, such as the “Research Domain Criteria” (RDoC), and the “Addiction Neuroclinical Assessment” (ANA). Particularly, neuropsychophysiological measures could be used as markers of cognitive and behavioral attributes or traits in alcohol dependence, and even trace clinical change. In this way, the aim of this narrative review is to provide an overview following ANA clinical framework, to the most robust findings in neuropsychophysiological changes in alcohol dependence, that underlie the main cognitive domains implicated in addiction: incentive salience, negative emotionality, and executive functioning. The most consistent results have been found in event-related potential (ERP) analysis, especially in the P3 component, that could show a wide clinical utility, mainly for the executive functions. The review also shows the usefulness of other components, implicated in affective and substance-related processing (P1, N1, or the late positive potential LPP), as well as event-related oscillations, such as theta power, with a possible use as vulnerability or clinical marker in alcohol dependence. Finally, new tools emerging from psychophysiology research, based on functional connectivity or brain graph analysis could help toward a better understanding of altered circuits in alcohol dependence, as well as communication efficiency and effort during mental operations. This review concludes with an examination of these tools as possible markers in the clinical field and discusses methodological differences, the need for more replicability studies and incipient lines of work. It also uses consistent findings in psychophysiology to draw possible treatment targets and cognitive profiles in alcohol dependence.
Predicting primer and panel off-target rate in QIAseq targeted DNA panels using convolutional neural networks

In QIAseq targeted DNA panels, synthetic primers (short single-strand DNA sequences) are used for target enrichment via complementary DNA binding. Off-target priming could occur in this process when a primer binds to some loci where the DNA sequences are identical or very similar to the target template. These off-target DNA segments go through the rest of the workflow, wasting sequencing resources in unwanted regions. Off-target cannot be avoided if some segments of the target region are repetitive throughout the genome, nor can it be quantified until after sequencing. But if off-target rates can be prospectively predicted, scientists can make informed decisions about investment on high off-target panels. We developed pordle (predicting off-target rate with deep learning and epcr07), a convolutional neural network (CNN) model to predict off-target binding events of a given primer. The neural network was trained using 10 QIAseq DNA panels with 29,274 unique primers and then tested on an independent QIAseq panel with 7,576 primers. The model predicted a 10.5% off-target rate for the test panel, a -0.1% bias from the true value of 10.6%. The model successfully selected the better primer (in terms of off-target rate) for 89.2% of 3,835 pairs of close-by primers in the test panel whose off-target rates differ by at least 10%. The order-preserving property may help panel developers select the optimal primer from a group of candidates, which is a common task in panel design.
A murine model with aspects of clinical relevance for the study of antibiotic-induced endotoxin release in septic hosts

A murine model which utilizes a burn to increase susceptibility to sepsis is presented. The model is inexpensive, highly reproducible, versatile, easy to use, and clinically relevant to many aspects of a Gram-negative sepsis which develops over time from a localized focus of infection. Additionally, studies of LPS-intoxication in mice with the same burn indicate that the animals show increased sensitivity to endotoxin without having to be exposed to exogenous sensitizing chemicals. Hence, this burned mouse model of sepsis might provide a sensitive, clinically relevant model for the study of antibiotic-induced endotoxin release from Gram-negative bacteria in septic hosts.
Response of Tabanidae (Diptera) Species to Malaise Traps Baited with 1-octan-3-ol and 4-methylphenol

Natural and synthetic attractants have been widely used for controlling horse fly populations. Relative responses of horse fly species to different attractants may vary under the different environmental conditions in different geographical areas. Many studies reported that, octanol and methylphenol are effective attractants for horse fly species and when they were combined with phenolic compounds together, their attractant effect increased. In this study we examine the effectiveness of Malaise traps baited with octenol and methylphenol on tabanids species in the province of Eskisehir, Catacik Forests and Hekim Mountain in Turkey. As a result, a total of 3045, 1428 and 626 specimens were caught with the trap baited with octanol, methylphenol and the control trap, respectively. The results of this study are compared and evaluated with the results of previous studies performed with natural and synthetic attractants in different geographical regions. The results obtained demonstrated that, octanol and methylphenol can be used effectively for controlling horse flies in this part of Turkey.
Medicinal plants: a re-emerging health aid

Interest in medicinal plants as a re-emerging health aid has been fuelled by the rising costs of prescription drugs in the maintenance of personal health and well-being, and the bioprospecting of new plant-derived drugs. Several issues as well as a range of interests and activities in a number of countries are dealt with. Based on current research and financial investments, medicinal plants will, seemingly, continue to play an important role as an health aid.
Deterrents extracted from the leaves of Ginkgo biloba: effects on feeding and contact chemoreceptors

Powdered dried ginkgo tree leaves were subjected to various chemical extractions and successive extracts were monitored for antifeedant activity against larvae of Pieris brassicae. Many fractions moderately inhibited food intake, and some were deterrent at levels as low as 25–50 ppm. Some behaviourally highly active fractions were tested electrophysiologically for neural responses in the maxillary taste sensilla. These extracts appeared to stimulate deterrent receptors. There were distinct differences in responses between Pieris brassicae and P. rapae. Ginkgolide A, B, and C each strongly stimulated deterrent receptors in P. rapae, which corresponds with the observation (Matsumoto & Sei, 1987) that these compounds are effective antifeedants for this species. No toxic effects were observed in insects after feeding for 24 h on diets containing ginkgo extracts.
When Should a Retailer Create an Exciting Store Environment?

Addressing inconsistent results in the literature, the conceptual framework that the authors develop proposes that the consumer's motivational orientation moderates the effect of the arousal produced by a store environment on the pleasantness of the environment. Two experiments support the framework. When consumers have a recreational motivational orientation, high arousal has a positive effect on pleasantness, but when consumers have a task-oriented motivational orientation, high arousal decreases pleasantness. In addition, high arousal increases consumer intentions to visit and make purchases in the store for recreationally oriented consumers, but it has a negative impact on shopping behavior for task-oriented consumers. Pleasantness mediates the effect of arousal on shopping behavior.
The T Cell Receptor Repertoire in Neuropsychiatric Systemic Lupus Erythematosus

Objective: In systemic lupus erythematosus (SLE), widespread T cell infiltration into target organs contributes to inflammation and organ damage. Autoreactive T cells become aberrantly activated in this disease due to dysfunctional T cell receptor signaling that lowers the activation threshold. Characterizing the T cell repertoire can provide further insight into the specific homing and proliferation of these T cells into lupus target organs. In the spontaneous lupus model, MRL/lpr, the TCR repertoire has not been fully elucidated, especially for T cells infiltrating the brain. Our aim was to investigate and compare the TCR repertoire between MRL/lpr mice and its congenic controls, MRL/MpJ, and within MRL/lpr tissues. Methods: Spleen, salivary gland, and brain choroid plexus were isolated from female MRL/lpr mice and MRL/MpJ mice. The TCRβ CDR3 region was analyzed by multiplex PCRs and sequencing. Results: Significant differences were seen not only between the MRL/lpr and MRL/MpJ spleens, but also between MRL/lpr tissues. The TCR repertoire in MRL/lpr choroid plexus tissues had significantly increased clonality and sequence homology compared to MRL/lpr spleen and salivary gland. The consensus sequence, CASSQDWGGYEQYFF, was identified in the MRL/lpr choroid plexus repertoire. Conclusions: The TCR repertoire in lupus prone mice is not uniform between target organs, and suggests that T cells are specifically recruited into the choroid plexus of MRL/lpr mice. Further studies are needed to determine the antigen specificities for these infiltrating T cells in target organs of lupus mice, and their possible contribution to the pathogenesis of neuropsychiatric disease and other lupus manifestations.
Modeling collaterally sensitive drug cycles: shaping heterogeneity to allow adaptive therapy

In previous work, we focused on the optimal therapeutic strategy with a pair of drugs which are collaterally sensitive to each other, that is, a situation in which evolution of resistance to one drug induces sensitivity to the other, and vice versa. [1] Here, we have extended this exploration to the optimal strategy with a collaterally sensitive drug sequence of an arbitrary length, N(≥ 2). To explore this, we have developed a dynamical model of sequential drug therapies with N drugs. In this model, tumor cells are classified as one of N subpopulations represented as {Ri|i = 1,2,…, N}. Each subpopulation, Ri, is resistant to ‘Drug i’ and each subpopulation, Ri–1 (or RN, if i = 1), is sensitive to it, so that Ri increases under ‘Drug i’ as it is resistant to it, and after drug-switching, decreases under ‘Drug i + 1’ as it is sensitive to that drug(s). Similar to our previous work examining optimal therapy with two drugs, we found that there is an initial period of time in which the tumor is ‘shaped’ into a specific makeup of each subpopulation, at which time all the drugs are equally effective . After this shaping period, all the drugs are quickly switched with duration relative to their efficacy in order to maintain each subpopulation, consistent with the ideas underlying adaptive therapy. [2, 3]Additionally, we have developed methodologies to administer the optimal regimen under clinical or experimental situations in which no drug parameters and limited information of trackable populations data (all the subpopulations or only total population) are known. The therapy simulation based on these methodologies showed consistency with the theoretical effect of optimal therapy.
Enfriamiento artificial y tasa de concepción de vaquillas holstein con estrés térmico

espanolLas altas temperaturas afectan la reproduccion del ganado bovino reduciendo la intensidad del estro y la fertilidad. Basado en lo anterior el objetivo del estudio fue evaluar los efectos de la inseminacion artificial (IA) a tiempo fijo mas un periodo corto de enfriamiento ambiental sobre la tasa de concepcion y respuesta fisiologica de vaquillas bajo estres calorico. Noventa vaquillas Holstein fueron distribuidas aleatoriamente en uno de los siguientes tratamientos: Un tratamiento testigo (T1) con deteccion visual de estro e IA manana-tarde (n= 30); un segundo tratamiento (T2) bajo un protocolo de IA a tiempo fijo (n= 30) y un tercer tratamiento (T3) con el mismo protocolo de IA de T2 mas un periodo de enfriamiento ambiental (ventilacion y aspersion) de las vaquillas 11 d antes y 21 d despues de la IA (n= 30). El experimento se dividio en dos periodos: el primero del 25 de junio al 26 de julio; el segundo del 15 de agosto al 16 de septiembre. En el primer periodo las vaquillas en T3 tuvieron una temperatura rectal (39,35°C) mas baja (p EnglishThe objective of this study was to evaluate the effect of a timed artificial insemination protocol plus a period of artificial cooling on conception rate and physiologic response of heifers under heat stress. Ninety Holstein heifers were randomly allotted into one of three treatments: A control treatment (T1) with visual heat detection and insemination morning-evening (n= 30), a second treatment (T2) under a timed artificial insemination protocol and a third treatment (T3) with the same protocol than T2 plus an artificial cooling period beginning 11 d before and ending 21 d after inse-mination. The experiment was divided in two pe-riods: the first period was from June 25 to July 26, and the second one from August 15 to September 16. In period 1, heifers in T3 had a lower (p
Diminishing effects of mechanical loading over time during rat Achilles tendon healing

Mechanical loading affects tendon healing and recovery. However, our understanding about how physical loading affects recovery of viscoelastic functions, collagen production and tissue organisation is limited. The objective of this study was to investigate how different magnitudes of loading affects biomechanical and collagen properties of healing Achilles tendons over time. Achilles tendon from female Sprague Dawley rats were cut transversely and divided into two groups; normal loading (control) and reduced loading by Botox (unloading). The rats were sacrificed at 1, 2- and 4-weeks post-injury and mechanical testing (creep test and load to failure), small angle x-ray scattering (SAXS) and histological analysis were performed. The effect of unloading was primarily seen at the early time points, with inferior mechanical and collagen properties (SAXS), and reduced histological maturation of the tissue in unloaded compared to loaded tendons. However, by 4 weeks no differences remained. SAXS and histology revealed heterogeneous tissue maturation with more mature tissue at the peripheral region compared to the center of the callus. Thus, mechanical loading advances Achilles tendon biomechanical and collagen properties earlier compared to unloaded tendons, and the spatial variation in tissue maturation and collagen organization across the callus suggests important regional (mechano-) biological activities that require more investigation.
Effect of Polychlorinated Biphenyls (PCB's) on Survival and Reproduction of Daphnia, Gammarus, and Tanytarsus

Abstract Continuous-flow and static bioassays were conducted at 18 C, with survival and reproduction as measures of relative toxicity of eight PCB's, Aroclor 1221 (A-1221), A-1232, A-1242, A-1248, A-1254, A-1260, A-1262, and A-1268. Three PCB-mixture bioassays were also conducted. Aroclor 1248 was the most toxic to Daphnia magna of the eight Aroclors tested in static tests; the 3-wk LC50 was 25 μg/liter. Aroclor 1254 was the most toxic PCB to Daphnia under continuous-flow conditions with a 3-wk LC50 of 1.3 μg/liter. Ninety-six-hr LC50 values for A-1242, and A-1248 on Gammarus pseudolimnaeus in continuous-flow tests were 73 and 20 μg/liter. Survival after 60 days was 52% at 8.7 μg/liter 1242 and 53% at 5.1 μg/liter A-1248. Reproduction and survival of young were good at 2.8 μg/liter A-1242 and 2.2 μg/liter A-1248. The midge Tanytarsus dissimilis, in continuous-flow tests, did not emerge in abundance above 5.1 μg/liter A-1248 or 3.5 μg/liter A-1254. The 3-wk LC50 for Aroclor 1254 was 0.65 μg/liter for larva.