Miracle-dz/UniFAR-FTUs huggingface dataset:
Epithelial-to-mesenchymal transition leads to disease-stage differences in circulating tumor cell detection and metastasis in pre-clinical models of prostate cancer

Metastasis is the cause of most prostate cancer (PCa) deaths and has been associated with circulating tumor cells (CTCs). The presence of ≥5 CTCs/7.5mL of blood is a poor prognosis indicator in metastatic PCa when assessed by the CellSearch® system, the “gold standard” clinical platform. However, ~35% of metastatic PCa patients assessed by CellSearch® have undetectable CTCs. We hypothesize that this is due to epithelial-to-mesenchymal transition (EMT) and subsequent loss of necessary CTC detection markers, with important implications for PCa metastasis. Two pre-clinical assays were developed to assess human CTCs in xenograft models; one comparable to CellSearch® (EpCAM-based) and one detecting CTCs semi-independent of EMT status via combined staining with EpCAM/HLA (human leukocyte antigen). In vivo differences in CTC generation, kinetics, metastasis and EMT status were determined using 4 PCa models with progressive epithelial (LNCaP, LNCaP-C42B) to mesenchymal (PC-3, PC-3M) phenotypes. Assay validation demonstrated that the CellSearch®-based assay failed to detect a significant number (~40-50%) of mesenchymal CTCs. In vivo, PCa with an increasingly mesenchymal phenotype shed greater numbers of CTCs more quickly and with greater metastatic capacity than PCa with an epithelial phenotype. Notably, the CellSearch®-based assay captured the majority of CTCs shed during early-stage disease in vivo, and only after establishment of metastases were a significant number of undetectable CTCs present. This study provides important insight into the influence of EMT on CTC generation and subsequent metastasis, and highlights that novel technologies aimed at capturing mesenchymal CTCs may only be useful in the setting of advanced metastatic disease.
KNOWLEDGE-BASE AND ONLINE SELF-SERVICE

With a B2C orientation, this research focuses attention on knowledge-base (KB) capabilities and their relationships with customers‘ self-service experience in conjunction with repeat purchase intention. Using structural equation modeling, our analyses of experimental survey data show that both KB capabilities and self-service experience are significantly and positively related to purchase intention. Overall, this research makes two key contributions: (1) the concept of information search and relational marketing for decision-making is integrated into the study of KB; (2) it analyzes KB from a customer‘s perspective instead of the organizational perspective that characterizes prior work. Implications for future research are discussed.
Magnetic resonance imaging and vertebral artery dissection

Vocal cord abductor paralysis (VCAP) is considered a sign of a poor prognosis in neurodegenerative diseases, because severe laryngeal dysfunction by VCAP may result in acute airway obstruction and require emergency tracheotomy.1 Although VCAP is a cardinal feature in multiple system atrophy (MSA), it has not been reported in several types of spinocerebellar ataxia with dominant inheritance. We evaluated the movements of the vocal cords of seven patients with SCA1 by laryngofibroscopy. Seven unrelated patients with SCA1 who had the expanded CAG repeat of ataxin-1 were investigated. There were two men and five women ranging in age from 27 to 67 years old (mean 44.5 years). Spouses and other family members, in addition to the patients, were questioned about events of stridor, dyspnoea, and dysphagia. Vocal cord movement was examined by laryngofibroscopy and recorded during inspiration and phonation. The rating scale used to evaluate maximal abduction of the vocal …
The Maximum Degree of a Random Graph

Let 0 < p < 1, q = 1 − p and b be fixed and let G ∈ [Gscr ](n, p) be a graph on n vertices where each pair of vertices is joined independently with probability p. We show that the probability that every vertex of G has degree at most pn + b √npq is equal to (c + o(1))n, for c = c(b) the root of a certain equation. Surprisingly, c(0) = 0.6102 … is greater than ½ and c(b) is independent of p. To obtain these results we consider the complete graph on n vertices with weights on the edges. Taking these weights as independent normal N(p, pq) random variables gives a ‘continuous’ approximation to [Gscr ](n, p) whose degrees are much easier to analyse.
Mobile and accurate detection system for infection by the 2009 pandemic influenza A (H1N1) virus with a pocket‐warmer reverse‐transcriptase loop‐mediated isothermal amplification

The 2009 pandemic H1N1 influenza A virus spread quickly worldwide in 2009. Since most of the fatal cases were reported in developing countries, rapid and accurate diagnosis methods that are usable in poorly equipped laboratories are necessary. In this study, a mobile detection system for the 2009 H1N1 influenza A virus was developed using a reverse‐transcriptase loop‐mediated isothermal amplification (RT‐LAMP) kit with a disposable pocket‐warmer as a heating device (designated as pwRT‐LAMP). The pwRT‐LAMP can detect as few as 100 copies of the virus—which is nearly as sensitive as real‐time reverse‐transcription polymerase chain reaction (RT‐PCR)—and does not cross‐react with RNA of seasonal influenza viruses. To evaluate the usefulness of the pwRT‐LAMP system, nasal swab samples were collected from 56 patients with flu‐like symptoms and were tested. Real‐time RT‐PCR confirmed that the 2009 H1N1 influenza A virus was present in 27 of the 56 samples. Of these 27 positive samples, QuickVue Influenza A + B immunochromatography detected the virus in only 11 samples (11/27; 40.7%), whereas the pwRT‐LAMP system detected the virus in 26 of the 56 samples (26/27 of the positive samples; 96.3%). These findings indicate that the mobile pwRT‐LAMP system is an accurate diagnostic system for the 2009 H1N1 influenza A virus, and has great potential utility in diagnosing future influenza pandemics. J. Med. Virol. 83:568–573, 2011. © 2011 Wiley‐Liss, Inc.
Molecular Basis of β‐Thalassemia Mutations in Diyarbakir in the Southeastern Region of Turkey

b-Thalassemia (thal) is a common single gene disorder; it has been estimated that 3% of the world’s population (150 million people) carry a thalassemic gene. b-Thalassemia is an autosomal recessive disease characterized by a hypochromic, hemolytic anemia and dependence on blood transfusions to sustain life (1). Heterozygote carriers are essentially normal. They can usually be detected by screening red cell indices, that demonstrate a reduced mean corpuscular hemoglobin (Hb) value, and an elevated Hb A2 level (1). b-Thalassemia has a high frequency in the Mediterranean Basin, Africa, India, Southeast Asia, Iran, and Turkey. This disease is the most common genetic disorder in Turkey. Molecular cloning and DNA sequencing led to the identification of several mutations responsible for defect in the gene function (2). In the Turkish population, Professor Nazli Basak and her colleagues (Bogazici University, Istanbul, Turkey) have characterized more than 18 different mutations (3–5). The six most frequent alleles, accounting for about 70% of the cases, are IVS-1-110 (G! A), IVS-I-6 (T! C), the frameshift at codon (FSC) 8 ( AA), IVS-I-1 (G! A), 30 (T! A), and FSC 5 ( CT). We report here the results of a molecular screening carried out in a population from the southeastern region of Turkey, a region with an unknown incidence of thalassemia, by
The effect of piliation and exoproduct expression on the adherence of Pseudomonas aeruginosa to respiratory epithelial monolayers.

The adherence properties of Pseudomonas aeruginosa strains with known pilin DNA sequences were studied. A polar pilus clearly contributed to adherence, as 35S-labeled pilus-positive (Pil+) strains bound significantly more to bovine trachea epithelial monolayers than did pilus-negative (Pil-) mutants (P less than .05) and minimally more than hyperpiliated strains. A pil- mutant PAK/NP, constructed by gene replacement, demonstrated low levels of attachment (3.8% of the inoculum adherent compared with 7% for the wild-type strain PAK), suggesting that other adhesins are functional. The Pil-, flagellum-negative strain PAO1150.1 bound the least (0.3% of the inoculum adherent), confirming the importance of motility in the binding process. The pilin sequences of strains P1 and PA1244 were virtually identical, although P1 bound threefold more than did PA1244. P1 produced 10-fold more proteinase than did PA1244, and a proteinase-negative mutant of P1, isolated by transposon mutagenesis, had binding equivalent to that of PA1244. The adherence of PAO1 was increased 60% in the presence of bacterial supernatants from phosphate-limited cultures and correlated with phospholipase C activity in the supernatant. Thus, the expression of several Pseudomonas genes may be required to promote efficient binding to epithelial surfaces.
Computational intelligence in multiple sequence alignment

Purpose – Multiple sequence alignment (MSA) is one of essential bioinformatics methods for decoding cis‐regulatory elements in gene regulation, predicting structure and function of proteins and RNAs, reconstructing phylogenetic tree, and other common tasks in biomolecular sequence analysis. The purpose of this paper is to describe briefly the basic concepts and formulations of gapped MSA and un‐gapped motif discovery approaches, and then review computational intelligence (CI) applications in MSA and motif‐finding problems.Design/methodology/approach – This paper performs exhaustive literature review on the MSA and motif discovery using CI techniques.Findings – Although CI‐based MSA algorithms were developed nearly a decade ago, most recent CI effort seems attempted to tackle the NP‐complete motif discovery problem. Applications of various CI techniques to solve motif discovery problem, including neural networks, self‐organizing map, genetic algorithms, swarm intelligence and combinations thereof, are surv.
Antibiotic concentration in the serum of dogs and cats following a single oral dose of cephalexin

Six dogs and six cats were given a single oral tableted dose containing approximately 15 mg/kg bodyweight of the semisynthetic cephalosporin antibiotic, cephalexin. Three dogs and four cats were similarly dosed using a liquid preparation of the same antibiotic. At intervals after dosing, blood samples were taken and the level of antibiotic in the serum was determined by bioassay. After fitting the results to a mathematical model the calculated peak serum level of antibiotic was found to be about 15 micrograms/ml and to occur between one and two hours after dosing. Results agree with the performance of the antibiotic in human medicine.
Do Sigmoidal Acquisition Curves Indicate Conformity?

The potential for behaviours to spread via cultural transmission has profound implications for our understanding of social dynamics and evolution. Several studies have provided empirical evidence that local traditions can be maintained in animal populations via conformist learning (i.e. copying the majority). A conformist bias can be characterized by a sigmoidal relationship between a behavior’s prevalence in the population and an individual’s propensity to adopt that behavior. For this reason, the presence of conformist learning in a population is often inferred from a sigmoidal acquisition curve in which the overall rate of adoption for the behavior is taken as the dependent variable. However, the validity of sigmoidal acquisition curves as evidence for conformist learning has recently been challenged by models suggesting that such curves can arise via alternative learning rules that do not involve conformity. We review these models, and find that the proposed alternative learning mechanisms either rely on faulty or unrealistic assumptions, or apply only in very specific cases. We therefore recommend that sigmoidal acquisition curves continue to be taken as evidence for conformist learning. Our paper also highlights the importance of understanding the generative processes of a model, rather than only focusing solely on the patterns produced. By studying these processes, our analysis suggests that current practices by empiricists have provided robust evidence for conformist transmission in both humans and non-human animals.
Lack of mitochondrial DNA structure in Balkan donkey is consistent with a quick spread of the species after domestication.

A total of 132 mtDNA sequences from 10 Balkan donkey populations were analysed to ascertain their regional genetic structure and to contribute to the knowledge of the spreading of the species after domestication. The Balkan donkey sequences were compared with those from 40 Burkina Faso donkeys as an African outgroup to account for possible local Balkan scenarios. The 172 sequences gave 62 different haplotypes (55 in Balkan donkey). Virtually all the analysed populations had haplotypes assigned to either Clade 1 or Clade 2 even though the relative proportion of Clade 1 or 2 haplotypes differed across populations. Geographical maps constructed using factors computed via principal component analysis showed that the Balkan donkey populations are not spatially structured. AMOVA confirmed a lack of genetic structure in Balkan donkey mtDNA. Balkan populations were poorly differentiated (ΦST = 0.071). Differentiation between the Balkan donkey and the African outgroup also was low. The lack of correspondence between geographical areas and maternal genetic structure is consistent with the hypothesis suggesting a very quick spread of the species after domestication. The current research illustrates the difficulties to trace routes of expansion in donkey, as the species has no geographical structure.
Public awareness, concerns, and priorities about anthropogenic impacts on marine environments

Significance We report the results of a 10,106-person pan-European survey of public awareness, concerns, and priorities about marine anthropogenic impacts as a way to inform both science and policy initiatives in achieving marine sustainability. Results enable scientists and policymakers to understand how the public relates to the marine environment and how they frame impacts and can help make managerial, scientific, and policy priorities more responsive to public values. Numerous international bodies have advocated the development of strategies to achieve the sustainability of marine environments. Typically, such strategies are based on information from expert groups about causes of degradation and policy options to address them, but these strategies rarely take into account assessed information about public awareness, concerns, and priorities. Here we report the results of a pan-European survey of public perceptions about marine environmental impacts as a way to inform the formation of science and policy priorities. On the basis of 10,106 responses to an online survey from people in 10 European nations, spanning a diversity of socioeconomic and geographical areas, we examine the public’s informedness and concern regarding marine impacts, trust in different information sources, and priorities for policy and funding. Results show that the level of concern regarding marine impacts is closely associated with the level of informedness and that pollution and overfishing are two areas prioritized by the public for policy development. The level of trust varies greatly among different information sources and is highest for academics and scholarly publications but lower for government or industry scientists. Results suggest that the public perceives the immediacy of marine anthropogenic impacts and is highly concerned about ocean pollution, overfishing, and ocean acidification. Eliciting public awareness, concerns, and priorities can enable scientists and funders to understand how the public relates to marine environments, frame impacts, and align managerial and policy priorities with public demand.
Detection of a Point Mutation Associated with High-Level Isoniazid Resistance in Mycobacterium tuberculosis by Using Real-Time PCR Technology with 3′-Minor Groove Binder-DNA Probes

ABSTRACT Tuberculosis remains one of the leading infectious causes of death worldwide. The emergence of drug-resistant strains of Mycobacterium tuberculosis is a serious public health threat. Resistance to isoniazid (INH) is the most prevalent form of resistance in M. tuberculosis and is mainly caused by mutations in the catalase peroxidase gene (katG). Among high-level INH-resistant isolates (MIC ≥ 2), 89% are associated with a mutation at codon 315 of katG. There is a need to develop rapid diagnostic tests to permit appropriate antibiotic treatment and to improve clinical management. Therefore, a single-tube real-time PCR, using a novel kind of probe (3′-minor groove binder-DNA probe), was developed to detect either the wild-type or the mutant codon directly in Ziehl-Neelsen-positive sputum samples. The detection limit of the assay for purified DNA was 5 fg per well (one mycobacterial genome), and with spiked sputum samples, it was 20 copies per well, corresponding to 103 mycobacteria per ml of sputum. Sputum samples from 20 patients living in Kazakhstan or Moldova and infected with monodrug- or multidrug-resistant M. tuberculosis and 20 sputum samples from patients infected with INH-susceptible M. tuberculosis were tested. The sensitivities and specificities of the probes were 70 and 94% for the wild-type probe and 82 and 100% for the mutant probe. Binding to either probe was nonambiguous. This real-time PCR allows the rapid identification of a mutant katG allele and can easily be implemented in a clinical microbiology laboratory.
Effects of levodopa on regional cerebral metabolism and blood flow

Levodopa (l‐dopa) has been at the forefront of antiparkinsonian therapy for a half century. Recent advances in functional brain imaging have contributed substantially to the understanding of the effects of l‐dopa and other dopaminergic treatment on the activity of abnormal motor and cognitive brain circuits in Parkinson's disease patients. Progress has also been made in understanding the functional pathology of dyskinesias, a common side effect of l‐dopa treatment, at both regional and network levels. Here, we review these studies, focusing mainly on the new mechanistic insights provided by metabolic brain imaging and network analysis. © 2014 International Parkinson and Movement Disorder Society
Forty‐two years of peripheral nerve surgery

w h e n I started my surgical training in 195 1. surgery of peripheral nerves seemed to have reached a peak, that was hardly to be surpassed. The vast experience of World War I1 had been studied carefully in Great Britain, in Australia, and in the United States. However, many surgeons looked at the problem too optimistically. They did not really follow the cases, and they were pleased if any recovery could be detected after nerve repair, because they were convinced that with time the results would become better and would reach normal or nearly normal values. Sensibility was not regarded as important. It was the great merit of Eric Moberg to recognise the importance of sensibility and tactile gnosis. ’ He demonstrated that, except in children, useful sensibility did not return. This stimulated a whole generation of surgeons to think about the problem. Since then, many thiigs have changed, new techniques have been developed, and certainly an improvement has been achieved. In spite of this fact, many questions remain unanswered, and the results are far from being fully satisfactory. If I look back at the past 42 years, peripheral nerve surgery has run through three different phases, the mechanical phase, the biological phase, and the phase of neurotrophism.
A 9.0-kilobase-pair circular plasmid of Borrelia burgdorferi encodes an exported protein: evidence for expression only during infection

In this study, we report the cloning, sequencing, and molecular analysis of a gene located on a 9.0-kbp circular plasmid of virulent Borrelia burgdorferi B31 designated eppA (exported plasmid protein A). This gene encodes a precursor protein of 174 amino acids including a signal peptide of 20 amino acids and a type I signal peptidase cleavage site. The mature EppA protein of 154 amino acids has a calculated molecular weight of 17,972. Several lines of evidence suggest that eppA is not expressed by B. burgdorferi B31 during in vitro cultivation. Immunoblot analysis using hyperimmune rabbit antiserum to recombinant EppA (rEppA) did not detect the presence of EppA in B. burgdorferi B31 cultivated in vitro. Northern blot analysis using total RNA isolated from in vitro-cultivated virulent B. burgdorferi B31 failed to detect an eppA transcript. EppA was not detected in culture supernatants of virulent B. burgdorferi B31 in a sensitive antigen-capture enzyme-linked immunosorbent assay. In contrast, evidence for expression of eppA during infection was based on the observation that patients with Lyme disease as well as rabbits experimentally infected with B. burgdorferi B31 produced antibodies that recognized rEppA. Because the cellular location of EppA in B. burgdorferi cannot be determined in vivo because of very small numbers of organisms present in vertebrate infection, we examined the cellular location of rEppA expressed in Escherichia coli. In E. coli, rEppA is targeted to the outer membrane. In addition, purified E. coli outer membranes containing rEppA treated with chaotrophic agents did not result in rEppA release. These findings are consistent with the idea that EppA is not peripherally associated with the outer membrane of E. coli but rather has an integral outer membrane association.
Pain in neurosurgically treated patients: a prospective observational study.

OBJECT This is the first observational study to compare perioperative pain character and intensity in patients undergoing different types of elective neurosurgical procedures. METHODS A structured questionnaire was used to inquire about pain intensity, character, and management during the perioperative course, and the anticipated visual analogue scale (VAS) score in 649 patients during a 1-year period. The anticipated maximal postoperative VAS score was lower than the actual postoperative maximal VAS score and was independent of operation type and preoperative VAS score. Patients undergoing craniotomy experienced less pain than those undergoing spinal surgery. A majority of patients did not receive analgesic medication after surgery. Patients undergoing spinal surgery experienced higher preoperative VAS scores than those undergoing other neurosurgical treatments, with a shift from preoperative referred pain to postoperative local pain. After lumbar flavectomy, referred pain was greater than local pain. Patients with preoperative pain suffered significantly more postoperative pain than those without preoperative pain. In patients with postoperative surgery-related complications, VAS scores were higher than in those without complications. CONCLUSIONS Neurosurgical procedures cause more pain than anticipated. Anticipated pain intensity is independent of the operation type and preoperative pain intensity. Postcraniotomy on-demand analgesic medication is appropriate, if the nurses on the ward react quickly. Otherwise, patient-controlled analgesia might be an option. Other neurosurgical procedures require scheduled analgesic therapies. Spinal surgery requires intensive preoperative pain treatment; a shift in pain character from preoperative referred pain to postoperative local pain is expected. Patients with referred pain after lumbar flavectomy are prone to the most intense pain. Patients with preoperative pain experience more postoperative pain than those without preoperative pain and require more intensive pain management. Increased postoperative VAS scores are associated with surgery-related complications.