Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of epidermal growth factor receptor and phosphatase and tensin homologue gene expression on the inhibition of U87MG glioblastoma cell proliferation induced by protein kinase inhibitors

The aim of the present study was to analyse the antiproliferative effects and mechanisms of action of protein kinase inhibitors (PKIs) in human glioblastoma multiforme (GBM) cells with different epidermal growth factor receptor (EGFR) and phosphatase and tensin homologue (PTEN) status. The GBM cell models were established by transfection of plasmids carrying wild‐type EGFR, mutated EGFRvIII or PTEN and clonal selection in U87MG cells. Phosphatidylinositol 3‐kinase (PI3‐K)/AKT pathway‐focused gene profiles were examined by real‐time polymerase chain reaction‐based assays, protein expression was evaluated by western blotting and the antiproliferative effects of PKI treatment were determined by the 3‐(4,5‐dimethyl‐2 thiazoyl)‐2,5‐diphenyl‐2H‐tetrazolium bromide (MTT) assay in GBM cells. The cell model with intact PTEN and low EGFR levels was the most sensitive to treatment with the EGFR inhibitor erlotinib, whereas the model with EGFRvIII was the most resistant to treatment with the mitogen‐activated protein kinase kinase inhibitor U0126. The dual PI3‐K and mammalian target of rapamycin (mTOR) inhibitor PI103 had the most potent antiproliferative effects against all GBM cells tested. Following simultaneous stimulation of AKT and extracellular signal‐regulated kinase, rapamycin concentrations > 0.5 nmol/L failed to exhibit a further growth inhibitory effect. Concurrent inhibition of mTOR and ribosomal protein s6 activity may underlie the inhibition of GBM proliferation by PKI. In conclusion, overexpression of EGFR or EGFRvIII, accompanied by a loss of PTEN, contributed to the activation of multiple intracellular signalling pathways in GBM cells. Rigorous examination of biomarkers in tumour tissues before and after treatment may be necessary to determine the efficacy of PKI therapy in patients with GBM.
Ursolic Acid Inhibits Proliferation and Induces Apoptosis of Cancer Cells In Vitro and In Vivo

The aims of the study are to explore the effect of ursolic acid (UA) on the growth of gastric cancer cell line BGC-803 and hepatocellular cancer cell H22 xenograft and to understand the mechanism. UA inhibits growth of BGC-803 cells in vitro in dose-dependent and time-dependent manner. Treated with UA in vivo, tumor cells can be arrested to G0/G1 stage. The apoptotic rate was significantly increased in tumor cells treated with UA both in vitro and in vivo. DNA fragmentation was found in BGC-803 cells exposed to UA. UA activated caspase-3, -8, and -9 and down regulated expression of Bcl-2 in BGC-803 cells. The expression of caspase-3 and -8 was elevated in tumor cells from xenograft treated with UA. 18F-FLT PET-CT imaging confirmed tumor model and UA effectiveness. Our results indicated that UA inhibits growth of tumor cells both in vitro and in vivo by decreasing proliferation of cells and inducing apoptosis.
Influence of water quality on enteric virus concentration by microporous filter methods

Four enteric viruses, poliovirus type 1, echovirus type 1, reovirus type 3, and simian adenovirus SV-11, were concentrated from seeded 1.3-liter volumes of raw, finished, and granular activated carbon-treated waters by adsorption to 47-mm-diameter (17 cm2), electropositive ( Virosorb 1MDS ) filters at pH 7.5 or electronegative ( Filterite ) filters at pH 3.5 with and without 5 mM added MgCl2, followed by elution with 0.3% beef extract in 50 mM glycine at pH 9.5. Removal of particulates from raw and finished waters by 0.2-micron prefiltration before virus addition and pH adjustment had little effect on virus concentration efficiencies. Soluble organic compounds reduced virus adsorption efficiencies from both raw and finished waters compared with granular activated carbon-treated water, but the extent of interference varied with virus type and adsorption conditions. For electropositive 1MDS filters, organic interference was similar with all virus types. For Filterite filters, organic interference was evident with poliovirus and echovirus, but could be overcome by adding MgCl2. Reovirus and SV-11 were not adversely affected by organics during adsorption to Filterite filters. Elution of reovirus and adenovirus was inefficient compared with that of poliovirus and echovirus. None of the three adsorption schemes ( 1MDS at pH 7.5 and Filterite with and without 5 mM MgCl2 at pH 3.5) could be judged superior for all viruses and water types tested.
Recurrence of stuttering after callosal infarction : a case report

We report a year (cid:15) old right (cid:15) handed male in whom developmental stuttering had almost been cured previously who suffered a recurrence after callosal infarction. The patient’s stuttering was much more severe than he had ever experienced. Investigation of his speech revealed the following results. (cid:19) (cid:11) The main feature of his stuttering was repetition of sounds and syllables (cid:14823) preparation (hesitation or preparatory movement of the articulatory organs before starting to speak) and breaks (inappropriate pauses within a word or a phrase) were also observed. (cid:20) (cid:11) His stuttering was associat-ed with secondary phenomena such as tongue clicking and facial grimacing. (cid:21) (cid:11) His stuttering demonstrated no adaptation benefit and no benefits from repetition or choral reading (cid:14823) it also exhibited no masking effect. (cid:22) (cid:11) His stuttering showed consistency effect, and disappeared during singing. These results suggest that the stuttering of this patient might have characteristics of both developmental and acquired stuttering, which in turn may suggest that after callosal infarction, acquired stuttering occurs in addition to a recurrence of developmental stuttering. Comparison of the lesion sites of the patient with those of reported patients who had acquired stuttering after callosal infarction suggested that the trunk of the corpus callosum might play some role in integrating the function of speech production in the left and right hemispheres.
Understanding Partitions and the \ No Partition "

The paper discusses partitions in asynchronous message-passing systems. In such systems slow processes and slow links can lead to virtual partitions that are indistinguishable from real ones. This raises the following question: what is a \partition" in an asyn-chronous system? To overcome the impossibility of detecting crashed processes in an asynchronous system, our system model incorporates a failure suspector to detect (possibly erroneously) process failures. Based on failure suspicions we give a deenition of partitions that accounts for real partitions as well as virtual ones. We show that under certain assumptions about the process behavior, any incorrect failure suspicion inevitably partitions the system. We then show how to interpret the \absence of partition" assumption.
Towards an Environmental Psychology of Workspace: How People are Affected by Environments for Work

Abstract Inquiry into how people experience environmental conditions at work is a growing area of study. Until the 1980s, there was insufficient research on ‘workspaces’—and on office environments in particular—to warrant review. Since that time, the range and number of studies of workspace have burgeoned. This paper will identify and review the main themes and findings of this area of research with the objective of defining basic parameters and prevailing theories of the environmental psychology of workspace. These will generate questions and directions for future research.
An Antifungal Role of Hydrogen Sulfide on the Postharvest Pathogens Aspergillus niger and Penicillium italicum

In this research, the antifungal role of hydrogen sulfide (H2S) on the postharvest pathogens Aspergillus niger and Penicillium italicum growing on fruits and under culture conditions on defined media was investigated. Our results show that H2S, released by sodium hydrosulfide (NaHS) effectively reduced the postharvest decay of fruits induced by A. niger and P. italicum. Furthermore, H2S inhibited spore germination, germ tube elongation, mycelial growth, and produced abnormal mycelial contractions when the fungi were grown on defined media in Petri plates. Further studies showed that H2S could cause an increase in intracellular reactive oxygen species (ROS) in A. niger. In accordance with this observation we show that enzyme activities and the expression of superoxide dismutase (SOD) and catalase (CAT) genes in A. niger treated with H2S were lower than those in control. Moreover, H2S also significantly inhibited the growth of Saccharomyces cerevisiae, Rhizopus oryzae, the human pathogen Candida albicans, and several food-borne bacteria. We also found that short time exposure of H2S showed a microbicidal role rather than just inhibiting the growth of microbes. Taken together, this study suggests the potential value of H2S in reducing postharvest loss and food spoilage caused by microbe propagation.
Some comments on the notion of ‘functional variability’ in stone‐tool assemblages

Abstract This paper examines some of the difficulties encountered in attempting to interpret stone‐tool assemblages in terms of ‘functional variability’ — i.e. by reference to variations in the economic and technological activities undertaken by a single human group. An exclusively ‘functional’ interpretation of Mousterian industries in South‐West France would be open to serious objections from several points of view — chronological, typological, economic and others. Recent studies of Mousterian assemblages in the Near East and northern Spain by means of ‘factor analysis’ are interesting from a methodological viewpoint, but provide little positive support for the functional interpretations of these industries which are offered. It is suggested that evidence for functional variability in Palaeolithic and Mesolithic industries may in fact be much less conspicuous than some writers have imagined. Finally, attention is drawn to the difficulty of adequately ‘testing’ hypotheses concerning this kind of patterni.
Pharmacokinetic and pharmacodynamic end points with anti-VEGFR: the more it hurts, the more it works?

For the past decade, an increasing number of publications and international meeting abstracts have suggested a relationship between the occurrence of specific toxicities and the anti-tumour activity of molecular targeted agents. Indeed, these agents are supposed to be targeted against specific kinases and signal transducers in cancer cells and their micro-environment, but their targets are also expressed in normal tissues, leading to a broad range of clinical and biological toxicities. In particular, hypertension has been suggested as a potential surrogate marker for the activity of anti-vascular endothelial growth factor (VEGF) agents bevacizumab, sunitinib, sorafenib and axitinib [1]. A majority of previously published studies found a relationship between blood pressure (BP) elevation (with various thresholds) and treatment activity (based on response rate, progression-free survival or overall survival) [2–8]. Theoretically, five hypotheses may account for these results, but also for the contradictory results of large cohort analyses [9]:
A Feasibility Study for Body Surface Cardiac Propagation Maps of Humans from Laplacian Moments of Activation

In this feasibility study, Laplacian electrocardiograms were utilized to generate body surface moment-of-activation (MOA) maps. The data were obtained with Laplacian sensors from humans. Inverse distance interpolation was applied to improve the image quality. For normal subjects, the MOA maps showed certain common features. A partial activation cycle of atrial flutter was mapped and is presented. Further studies must be conducted to determine the diagnostic potential of such patterns based on a larger number of subjects.
Hepatic autophagy mediates endoplasmic reticulum stress–induced degradation of misfolded apolipoprotein B

Induction of endoplasmic reticulum (ER) stress was previously shown to impair hepatic apolipoprotein B100 (apoB) production by enhancing cotranslational and posttranslational degradation of newly synthesized apoB. Here, we report the involvement of autophagy in ER stress–induced degradation of apoB and provide evidence for a significant role of autophagy in regulating apoB biogenesis in primary hepatocyte systems. Induction of ER stress following short‐term glucosamine treatment of McA‐RH7777 cells resulted in significantly increased colocalization of apoB with green fluorescent protein–microtubule‐associated protein 1 light chain 3 (GFP‐LC3), referred to as apoB‐GFP‐LC3 puncta, in a dose‐dependent manner. Colocalization with this autophagic marker correlated positively with the reduction in newly synthesized apoB100. Treatment of McA‐RH7777 cells with 4‐phenyl butyric acid, a chemical ER stress inhibitor, prevented glucosamine‐ and tunicamycin‐induced increases in GRP78 and phosphorylated eIF2α, rescued newly synthesized [35S]‐labeled apoB100, and substantially blocked the colocalization of apoB with GFP‐LC3. Autophagic apoB degradation was also observed in primary rat and hamster hepatocytes at basal conditions as well as upon the induction of ER stress. In contrast, this pathway was inactive in HepG2 cells under ER stress conditions, unless proteasomal degradation was blocked with N‐acetyl‐leucinyl‐leucinyl‐norleucinal and the medium was supplemented with oleate. Transient transfection of McA‐RH7777 cells with a wild‐type protein kinase R–like ER kinase (PERK) complementary DNA resulted in dramatic induction of apoB autophagy. In contrast, transfection with a kinase inactive mutant PERK gave rise to reduced apoB autophagy, suggesting that apoB autophagy may occur via a PERK signaling–dependent mechanism. Conclusion: Taken together, these data suggest that induction of ER stress leads to markedly enhanced apoB autophagy in a PERK‐dependent pathway, which can be blocked with the chemical chaperone 4‐phenyl butyric acid. ApoB autophagy rather than proteasomal degradation may be a more pertinent physiological mechanism regulating hepatic lipoprotein production in primary hepatocytes. (HEPATOLOGY 2011;)
From Query to Usable Code: An Analysis of Stack Overflow Code Snippets

Enriched by natural language texts, Stack Overflow code snippets arean invaluable code-centric knowledge base of small units ofsource code. Besides being useful for software developers, theseannotated snippets can potentially serve as the basis for automatedtools that provide working code solutions to specific natural languagequeries. With the goal of developing automated tools with the Stack Overflowsnippets and surrounding text, this paper investigates the followingquestions: (1) How usable are the Stack Overflow code snippets? and(2) When using text search engines for matching on the naturallanguage questions and answers around the snippets, what percentage ofthe top results contain usable code snippets? A total of 3M code snippets are analyzed across four languages: C\#,Java, JavaScript, and Python. Python and JavaScript proved to be thelanguages for which the most code snippets are usable. Conversely,Java and C\# proved to be the languages with the lowest usabilityrate. Further qualitative analysis on usable Python snippets showsthe characteristics of the answers that solve the original question. Finally,we use Google search to investigate the alignment ofusability and the natural language annotations around code snippets, andexplore how to make snippets in Stack Overflow anadequate base for future automatic program generation.
Comparison of results for intradermal testing between clinically normal horses and horses affected with recurrent airway obstruction.

OBJECTIVE To evaluate differences in response to ID injection of histamine, phytohemagglutinin (PHA), and Aspergillus organisms between clinically normal horses and horses with recurrent airway obstruction (RAO). ANIMALS 5 healthy adult horses and 5 adult horses with RAO. PROCEDURE Intradermal testing (IDT) was performed on the neck with 2 positive control substances (histamine and PHA) and a mixture comprising 5 Aspergillus species. Four concentrations of each test substance plus a negative control substance were used. Equal volumes (0.1 mL) of each test substance were prepared to yield 15 syringes ([4 concentrations of each test substance plus 1 negative control substance] times 3 test substances) for each side of each horse (ie, 30 syringes/horse). Intradermal injections were administered; diameter of wheals was recorded 0.5, 4, and 24 hours after injection. RESULTS Hypersensitive responses to ID injection of histamine were detected 0.5 hours after injection, and a delay in wheal formation after ID injection of Aspergillus mixture 24 hours after injection was detected in RAO-affected horses but was not observed in clinically normal horses. No differences were detected between the 2 groups after ID injection of PHA. CONCLUSIONS AND CLINICAL RELEVANCE RAO-affected horses are hypersensitive to histamine, suggesting that RAO is associated with a heightened vascular response to histamine. Higher concentrations of Aspergillus mixture may be needed to detect horses that are sensitive to this group of antigens. Wheal reactions to Aspergillus may be a delayed response, suggesting that IDT results should be evaluated 0.5, 4, and 24 hours after ID injection.
Localization of Cell Division Protein FtsK to theEscherichia coli Septum and Identification of a Potential N-Terminal Targeting Domain

ABSTRACT Escherichia coli cell division protein FtsK is a homolog of Bacillus subtilis SpoIIIE and appears to act late in the septation process. To determine whether FtsK localizes to the septum, we fused three N-terminal segments of FtsK to green fluorescent protein (GFP) and expressed them in E. colicells. All three segments were sufficient to target GFP to the septum, suggesting that as little as the first 15% of the protein is a septum-targeting domain. Localized fluorescence was detectable only in cells containing a visible midcell constriction, suggesting that FtsK targeting normally occurs only at a late stage of septation. The largest two FtsK-GFP fusions were able at least partially to complement the ftsK44 mutation in trans, suggesting that the N- and C-terminal domains are functionally separable. However, overproduction of FtsK-GFP resulted in a late-septation phenotype similar to that of ftsK44, with fluorescent dots localized at the blocked septa, suggesting that high levels of the N-terminal domain may still localize but also inhibit FtsK activity. Interestingly, under these conditions fluorescence was also sometimes localized as bands at potential division sites, suggesting that FtsK-GFP is capable of targeting very early. In addition, FtsK-GFP localized to potential division sites in cephalexin-induced andftsI mutant filaments, further supporting the idea that FtsK-GFP can target early, perhaps by recognizing FtsZ directly. This hypothesis was supported by the failure of FtsK-GFP to localize inftsZ mutant filaments. In ftsK44 mutant filaments, FtsA and FtsZ were usually localized to potential division sites between the blocked septa. When the ftsK44 mutation was incorporated into the FtsK-GFP fusions, localization to midcell ranged between very weak and undetectable, suggesting that the FtsK44 mutant protein is defective in targeting the septum.
Hormonal and Sex Impact on the Epidemiology of Canine Lymphoma

The Surveillance Epidemiology and End Results data demonstrate that the risk of non-Hodgkin lymphoma is lower for women, but that the incidence increases after fifty years of age, at which menopause is regularly reached, suggesting that female hormones may be protective for NHL. This study examines the influence of sex on lymphoma risk in a relevant large animal model. Records for dogs in the Veterinary Medical Database were analyzed from 1964 to 2002. Risk ratios were calculated to evaluate associations between sex, neutering status, and lymphoma occurrence. A total of 14,573 cases and 1,157,342 controls were identified. Intact females had a significantly lower risk of developing lymphoma, Odds Ratio 0.69 (0.63–0.74) with a P < . 001. We conclude that there is a sex effect on NHL risk in dogs similar to humans. We hypothesize that the hormone levels of intact females lower the risk of NHL. The possibility of a protective role of endogenous estrogens in the etiology of NHL should be investigated.
Evidence of Recombination in Intrapatient Populations of Hepatitis C Virus

Hepatitis C virus (HCV) is a major cause of liver disease worldwide and a potential cause of substantial morbidity and mortality in the future. HCV is characterized by a high level of genetic heterogeneity. Although homologous recombination has been demonstrated in many members of the family Flaviviridae, to which HCV belongs, there are only a few studies reporting recombination on natural populations of HCV, suggesting that these events are rare in vivo. Furthermore, these few studies have focused on recombination between different HCV genotypes/subtypes but there are no reports on the extent of intra-genotype or intra-subtype recombination between viral strains infecting the same patient. Given the important implications of recombination for RNA virus evolution, our aim in this study has been to assess the existence and eventually the frequency of intragenic recombination on HCV. For this, we retrospectively have analyzed two regions of the HCV genome (NS5A and E1-E2) in samples from two different groups: (i) patients infected only with HCV (either treated with interferon plus ribavirin or treatment naïve), and (ii) HCV-HIV co-infected patients (with and without treatment against HIV). The complete data set comprised 17712 sequences from 136 serum samples derived from 111 patients. Recombination analyses were performed using 6 different methods implemented in the program RDP3. Recombination events were considered when detected by at least 3 of the 6 methods used and were identified in 10.7% of the amplified samples, distributed throughout all the groups described and the two genomic regions studied. The resulting recombination events were further verified by detailed phylogenetic analyses. The complete experimental procedure was applied to an artificial mixture of relatively closely viral populations and the ensuing analyses failed to reveal artifactual recombination. From these results we conclude that recombination should be considered as a potentially relevant mechanism generating genetic variation in HCV and with important implications for the treatment of this infection.
Effectiveness of a teleaudiology approach to hearing aid fitting

This research was conducted to evaluate the efficacy of an online speech perception test (SPT) for the measurement of hearing and hearing aid fitting in comparison with conventional methods. Phase 1 was performed with 88 people to evaluate the SPT for the detection of significant hearing loss. The SPT had high sensitivity (94%) and high selectivity (98%). In Phase 2, phonetic stimulus–response matrices derived from the SPT results for 408 people were used to calculate “Infograms™. ” At every frequency, there was a highly significant correlation (p < 0.001) between hearing thresholds derived from the Infogram and conventional audiograms. In Phase 3, initial hearing aid fittings were derived from conventional audiograms and Infograms for two groups of hearing impaired people. Unaided and aided SPTs were used to measure the perceptual benefit of the aids for the two groups. The mean increases between unaided and aided SPT scores were 19.6%, and 22.2% (n = 517, 484; t = 2.2; p < 0.05) for hearing aids fitted using conventional audiograms and Infograms respectively. The research provided evidence that the SPT is a highly effective tool for the detection and measurement of hearing loss and hearing aid fitting. Use of the SPT reduces the costs and increases the effectiveness of hearing aid fitting, thereby enabling a sustainable teleaudiology business model.