Miracle-dz/UniFAR-FTUs huggingface dataset:
Location of Peptidases Outside and Inside the Membrane of Streptococcus cremoris

Peptidase activity determinations involving native cells of Streptococcus cremoris and completely disrupted cell preparations, as well as experiments concerned with peptidase activity distribution among cell fractions obtained by a damage-restrictive removal of the cell wall and release of intracellular material, suggest the presence of peptidases with distinguishable locations. Alanyl, leucyl, and prolyl aminopeptidase activities are most likely located in the cell wall-membrane interface, showing no detectable association with the membrane. Lysyl aminopeptidase is present not only in this location, but also as an intracellular enzyme. Endopeptidase activity and glutamate aminopeptidase activity appear to be weakly associated with the membrane. The locations of these two peptidase activities, unlike those of the former aminopeptidase activities, impose a restriction on their expression. Results of experiments concerned with permeabilization of the membrane and findings regarding an effect of the local environment of the enzymes on their pH activity profiles are evaluated and considered as being indicative of the proposed location. The possible implications of these findings with respect to protein utilization during growth of the organism in milk are discussed.
Biofield perception: a series of pilot studies with cultured human cells.

BACKGROUND Energy medicine (EM) practitioners often claim to be able to perceive an energetic field associated with the body and to be able to use this skill to diagnose illness and guide treatment strategies. If a biofield associated with cells growing in culture is perceptible to EM practitioners, such an in vitro model would be a useful resource for investigating biofield perception that would provide some unique advantages over clinical models. OBJECTIVE To evaluate whether EM practitioners can perceive the presence of cultured human cells without visual cues. DESIGN Three randomized double-blinded pilot studies were used to evaluate the ability of participants to distinguish a flask containing cancer cells growing in culture medium from a flask containing either culture medium or sterile water. Each study consisted of six independent experiments: three with EM practitioners and three with non-practitioners. The number of independent trials for each experiment was estimated by statistical power analyses of the design. Practitioners' feedback from the first two studies was used to revise the protocol for the subsequent studies, with the intent to eliminate potential problems in making this distinction. Labeled flasks ("cells" and "no-cells") were added to serve as references for comparison in the second study and the number of experimental trials was reduced in the third study. SUBJECTS Eight experienced EM practitioners and nine non-practitioners (laboratory personnel with no EM training). SETTING A basic science laboratory and office at an academic medical center. OUTCOME MEASURES In the first 2 studies, we determined the number of correct determinations in a series of 34 trials. In the third study, we determined the number of correct determinations in a series of 10 trials. RESULTS All participants performed at the level expected by chance. CONCLUSION While preliminary and inconclusive, these pilot studies found no evidence that EM practitioners can perceive a biofield associated with cancer cells growing in culture.
A Specific Angiographic View of Left Coronary Artery Bifurcation in the Left Main Percutaneous Coronary Intervention Era.

OBJECTIVES We propose a right lateral (90-120° RAO) with 30° cranial angiographic view to expose the bifurcation of the left main coronary artery (LMCA) when previously used routine projections were inefficient at clearly showing this region. BACKGROUND Little has been published in the medical literature regarding angiographic projections dedicated to special anatomies. METHODS A total of 84 patients were subjected to the proposed projections. A reproducibility study, conducted with the participation of 2 independent observers, judged the effectiveness of the proposed projection. The Prevalence and Bias Adjusted Kappa (PABAK) index, with a 95% confidence interval (CI), was used to demonstrate the intensity of intra/inter-observer agreement. RESULTS The proposed projection was efficient in 79% of the angiograms, with agreement of 0.76 (0.6-0.9; P ≤ 0.001). The origins and the proximal segments of: the anterior descending coronary artery were exposed in 89% of the angiograms, agreement of 0.86 (0.7-1.0; P ≤ 0.001); the circumflex artery were exposed in 83% of the angiograms, with agreement of 0.72 (0.5-1.0; P ≤ 0.001); and the intermediate branch, when present, were exposed in 89% of the angiograms, agreement of 0.79 (0.6-1.0; P ≤ 0.001). CONCLUSION The right lateral (90-120° RAO) with 30° cranial projection is effective, safe, and reproducible. In special situations where routine projections fail, this proposed projection can reveal important details of the anatomy of the bifurcation of the LMCA during conventional coronary angiography or be the working projection during coronary angioplasty. (J Interven Cardiol 2016;29:293-299).
A measurement study of diskless workstation traffic on an Ethernet

The traffic on a 10-Mb/s Ethernet local-area network that connects diskless workstations to file servers in a university environment is analyzed. The traffic is substantially heavier than has been recorded in previous studies; measured over 1-s intervals, it frequently exceeds 30% of the network bandwidth. The distribution of packet lengths and the patterns of packet interarrival times are interpreted for the three protocols that carry significant traffic: the transmission control protocol (character traffic), the network disk protocol (paging traffic), and the network file system protocol (remote file access traffic). The two latter protocols account for 68% of the packets and 94% of the data bytes on the network. File access to a remote file server generates bursts of traffic that can last several seconds and that demand bandwidths on the order of 120 kB/s, or about 10% of the Ethernet bandwidth. >
Comparability of Neuropsychological Test Profiles in Patients with Chronic Substance Abuse and Mild Traumatic Brain Injury

The purpose of this study was to compare 104 patients with acute uncomplicated mild traumatic brain injury (MTBI) to a sample of 104 patients from an inpatient substance abuse program to determine whether these patients could be differentiated by their pattern of relative cognitive strengths and weaknesses. Patients were matched on age, education, and gender. Eight cognitive measures were used that included tests of attention, memory, and processing speed. There were no statistically significant differences between the two groups on any of the cognitive measures. Using a two-step cluster analysis procedure (i.e., hierarchical and k-means analyses), seven common profiles were identified. There was no significant difference in the proportions of patients from the MTBI or substance abuse group in each of the seven profiles. These results show that patients with uncomplicated MTBIs could not be reliably differentiated from patients with substance abuse problems on these cognitive measures. This is of particular concern for clinicians evaluating the neuropsychological effects of MTBI in individuals with a comorbid history of substance abuse.
Sistemática filogenética e evolução cromossômica em espécies amazônicas de Aspredinidae (Ostariophysi, Siluriformes)

A familia Aspredinidae, ordem Siluriformes, e composta por um grupo de peixes neotropicais, popularmente conhecidos como bagres banjo ou rabeca. Possui distribuicao restrita a America do Sul, tendo na bacia amazonica, importantes grupos de especies endemicas. No presente trabalho, foram realizadas analises citogeneticas e moleculares em especies desta familia, com objetivo de compreender os processos evolutivos envolvidos na diversificacao destes pequenos bagres, a fim de inferir no status taxonomico. Foram disponibilizadas caracterizacoes cromossomicas ineditas de Amaralia hypsiura, Bunocephalus cf. aloikae, B. amaurus, B. coracoideus, B. aff coracoideus, B. verrucosus e Platystacus cotylephorus. Os dados cromossomicos, com mapeamento de DNAr 5S e distribuicao da heterocromatina constitutiva revelaram um sistema de cromossomos sexuais inedito do tipo X 1 X 1 X 2 X 2 /X 1 Y 1 X 2 Y 2 em uma populacao de B. coracoideus. E caracterizacao cariotipica de P. cotylephorus revelou um segundo caso em Siluriformes de sistema sexual XX/XO. A analise de um filograma com quatro populacoes de Bunocephalus coracoideus, com base em uma regiao do mitogenoma, revelou clados com diversidade genetica, que corroboraram os dados de distribuicao geografica e variacao cariotipica, sugerindo a existencia de Unidades Evolutivas Significativas bem suportadas, formando um complexo de especies, em processo de especiacao alopatrica e simpatrica. Ainda, os dados cromossomicos permitiram a percepcao de uma tendencia a reducao do numero diploide na evolucao cromossomica da familia em relacao ao cariotipo ancestral dos Siluriformes, conservando um cariotipo com maioria de cromossomos de dois bracos. E, posteriormente, por rearranjos cromossomicos do tipo inversoes pericentricas e fissoes, o numero diploide de algumas especies teria aumentado e a morfologia cariotipica se modificado para cromossomos de um braco, sendo este uma sinapomorfia na familia. A diversidade cariotipica, tanto no numero diploide como na morfologia dos cromossomos em Aspredinidae e muito parecida as encontradas nas familias do clado asiatico Sisoroidea (Amblycipitidae, Akysidae, Sisoridae e Erethistidae), sugerindo que essas familias sofreram as diferentes pressoes seletivas para formacao dos cariotipos ou uma historia natural em comum. Assim, corroborando com a proposta de Aspredinidae e Sisoroidea serem grupos-irmaos, sugerida por Ferraris (1989), de Pinna (1998), Britto (2002), Diogo et al. (2004) e Cardoso (2010).
Construction of 3D FDTD schemes with frequency-dependent operator coefficients

Aiming at the minimization of numerical dispersion effects in finite-difference time-domain (FDTD) simulations, we investigate the potential of introducing frequency-dependent coefficients in the approximations of differential operators. The proposed methodology exploits some previous results on optimized finite-differences, but initially avoids the necessity for selecting a specific optimization point. Herein, the operators' coefficient formulae are approximated by a low-order polynomial, which is transformed into a finite-difference counterpart using the Helmholtz equation. This modifies the initial spatial stencil and improves performance over all frequencies, which can be further controlled with the least-squares method, leading to various new FDTD schemes of augmented reliability.
The Histone Demethylase JMJD1C Regulates CAMKK2-AMPK Signaling to Participate in Cardiac Hypertrophy

The roles of the histone demethylase JMJD1C in cardiac hypertrophy remain unknown. JMJD1C was overexpressed in hypertrophic hearts of humans and mice, whereas the histone methylation was reduced. Jmjd1c knockdown repressed the angiotensin II (Ang II)-mediated increase in cardiomyocyte size and overexpression of hypertrophic genes in cardiomyocytes. By contrast, JMJD1C overexpression promoted the hypertrophic response of cardiomyocytes. Our further molecular mechanism study revealed that JMJD1C regulated AMP-dependent kinase (AMPK) in cardiomyocytes. JMJD1C did not influence LKB1 but repressed Camkk2 expression in cardiomyocytes. Inhibition of CAMKK2 with STO609 blocked the effects of JMJD1C on AMPK. AMPK knockdown blocked the inhibitory functions of JMJD1C knockdown on Ang II-induced hypertrophic response, whereas metformin reduced the functions of JMJD1C and repressed the hypertrophic response in cardiomyocytes.
On the analysis of the bifurcation sets of equilibrium points in parameter space

This paper addresses the problems of characterizing and estimating the bifurcation sets of equilibrium points in multi-parameter space of a class of nonlinear dynamical systems. Specifically, we investigate the sets of parameters that lead to saddle-node bifurcations and Hopf bifurcations at an equilibrium point of interest. First, a characterization of these sets is provided in terms of the zeros of some functions. Second, this characterization is exploited to estimate such sets through convex programming for the case of polynomial dynamical systems. In particular, two conditions are proposed for establishing whether a sublevel set of a given polynomial does not contain parameters that lead to bifurcations. By using these conditions, the largest of such sublevel sets can be estimated by solving an eigenvalue problem. Some numerical examples illustrate the proposed results.
Finding synonyms and other semantically-similar terms from coselection data

Clickthrough data has been proposed for numerous uses, and this paper describes how a special form of clickthough data, coselection data, can form non-ambiguous clusters that can then be used to detect semantic similarity between query terms. This semantic similarity assessment can be applied to distinct terms in the same language, giving rise to synonyms, or in different languages, indicating possible translations. It can determine alternative names or descriptors for items which do not occur in traditional thesauri, such as phrases, proper nouns or technical terms. The semantic similarity is calculated without any use of external reference materials and without any analysis of content.
A method for ontology and knowledge-base assisted text mining for diabetes discussion forum

Social media offers researchers vast amount of unstructured text as a source to discover hidden knowledge and insights. However, social media poses new challenges to text mining and knowledge discovery due to its short length, temporal nature and informal language. In order to identify the main requirements for analysing unstructured text in social media, this research takes a case study of a large discussion forum in the diabetes domain. It then reviews and evaluates existing text mining methods for the requirements to analyse such a domain. Using domain background knowledge to bridge the semantic gap in traditional text mining methods was identified as a key requirement for analysing text in discussion forums. Existing ontology engineering methodologies encounter difficulties in deriving suitable domain knowledge with the appropriate breadth and depth in domain-specific concepts with a rich relationships structure. These limitations usually originate from a reliance on human domain experts. This research developed a novel semantic text mining method. It can identify the concepts and topics being discussed, the strength of the relationships between them and then display the emergent knowledge from a discussion forum. The derived method has a modular design that consists of three main components: The Ontology building Process, Semantic Annotation and Topic Identification, and Visualisation Tools. The ontology building process generates domain ontology quickly with little need for domain experts. The topic identification component utilises a hybrid system of domain ontology and a general knowledge base for text enrichment and annotation, while the visualisation methods of dynamic tag clouds and cooccurrence network for pattern discovery enable a flexible visualisation of these results and can help uncover hidden knowledge. Application of the derived text mining method within the case study helped identify trending topics in the forum and how they change over time. The derived method performed better in semantic annotation of the text compared to the other systems evaluated. The new text mining method appears to be “generalisable” to other domains than diabetes. Future study needs to confirm this ability and to evaluate its applicability to other types of social media text sources.
Taxing Political Life: Reevaluating the Relationship between Voluntary Association Membership, Political Engagement, and the State

Previous research has shown that participation in voluntary associations, including those labeled nonpolitical, increases political participation. Using data gathered from 2,517 interviews for the American Citizen Participation Study, we complicate this understanding by exploring the relationship between voluntary association involvement and political activity in a more nuanced manner–separating association involvements according to the level of exposure to political dialogue and information, even within organizations typically considered apolitical. We find that the extent to which association involvement predicts political participation is dependent upon the level of political activity that transpires within these otherwise nonpolitical organizations. In order for participation in voluntary associations to lead to increases in political participation, participants must have exposure to political discourse. It is not the generic act of participation that supports political life but rather the opportunity to engage with politics that serves as an impetus for political activity. In light of this, we offer a critical exploration of existing federal tax policies governing nonprofit organizations.
Isolation and characterization of sporulation‐specific promoters in the yeast Saccharomyces cerevisiae

A library of random yeast genomic DNA:lacZ fusions has been constructed using an episomal yeast‐Escherichia coli shuttle vector (pCS1). Plasmid pCS1 requires insertion of a promoter and an inframe ATG codon upstream of its resident truncated lacZ gene to regulate expression in yeast. Yeast genomic DNA fragments of 4–6 kb were generated by partial digestion with Sau3A and ligated into the unique BamHI site of plasmid pCS1 to generate a library of 5 × 104 individual E. coli transformants. This library was screened to identify promoter‐lacZ fusions that were expressed uniquely during sporulation. Of 342 yeast transformants that exhibited β‐galactosidase activity, two were found to express the lacZ gene in a sporulation‐specific manner.
Metabolic engineering of Escherichia coli W3110 to produce L‐malate

A four‐carbon dicarboxylic acid L‐malate has recently attracted attention due to its potential applications in the fields of medicine and agriculture. In this study, Escherichia coli W3110 was engineered and optimized for L‐malate production via one‐step L‐malate synthesis pathway. First, deletion of the genes encoding lactate dehydrogenase (ldhA), pyruvate oxidase (poxB), pyruvate formate lyase (pflB), phosphotransacetylase (pta), and acetate kinase A (ackA) in pta‐ackA pathway led to accumulate 20.9 g/L pyruvate. Then, overexpression of NADP+‐dependent malic enzyme C490S mutant in this multi‐deletion mutant resulted in the direct conversion of pyruvate into L‐malate (3.62 g/L). Next, deletion of the genes responsible for succinate biosynthesis further enhanced L‐malate production up to 7.78 g/L. Finally, L‐malate production was elevated to 21.65 g/L with the L‐malate yield to 0.36 g/g in a 5 L bioreactor by overexpressing the pos5 gene encoding NADH kinase in the engineered E. coli F0931 strain. This study demonstrates the potential utility of one‐step pathway for efficient L‐malate production. Biotechnol. Bioeng. 2017;114: 656–664. © 2016 Wiley Periodicals, Inc.
A cellular, molecular, and pharmacological basis for appendage regeneration in mice

In this study, Leung et al. used a model of mouse ear regeneration to identify novel mechanisms regulating mammalian tissue regeneration. Mice lacking p21 fully regenerate injured ears without discernable scarring, and, using this model, the authors demonstrate that stromal-derived factor-1 (Sdf1) and Cxcr4-expressing leukocytes are important regulators of mammalian appendage regeneration.
Adjuvant trastuzumab in early breast cancer.

The benefit derived from the use of adjuvant systemic therapy either as cytotoxic chemotherapy or endocrine treatment was progressively defined over three decades of intensive and laborious clinical research [1]. The extensive research effort clearly established that women derived not only a sizeable advantage in term of reduced relapses and deaths, but also that such benefit was durable and persistent over time [2, 3]. In 2005 an unprecedented success has brought in a large subgroup of women with HER2 expressing early breast cancer the benefit deriving from one of the first targeted new drugs, the humanized monoclonal antibody trastuzumab (Herceptin ). In view that palliation rather than cure is still the achievable goal of the therapeutic intervention in advanced disease, the addition of trastuzumab to the list of interventions contributing to cure women with early breast cancer is a major achievement.
Metronidazole resistance: A predictor of failure of Helicobacter pylori eradication by triple therapy

Triple therapy (bismuth and two antibiotics) will eradicate Helicobacter pylori infection in 70–90% of subjects. Treatment failure has been attributed to patient compliance and antimicrobial drug resistance. The aim of this study was to examine factors influencing the eradication of H. pylori following triple therapy. Thirty seven subjects with H. pylori cultured from antral biopsies were treated with colloidal bismuth subcitrate (120 mg qid for 2 weeks), metronidazole (400 mg tid for 1 week) and amoxycillin (500 mg tid for 1 week). Pretreatment isolates of H. pylori were tested for metronidazole susceptibility by agar dilution according to the National Committee for Clinical Laboratory Standards guidelines. Factors including age, sex, clinical diagnosis and metronidazole resistance were evaluated in relation to H. pylori. The overall metronidazole resistance was 32%. Metronidazole resistant strains were more frequent in females, with a resistance rate of 54%. Helicobacter pylori eradication occurred in 68% of patients with a metronidazole susceptible stain and only 17% of patients with a metronidazole resistant strain (P < 0.03). Helicobacter pylori eradication is dependent upon susceptibility to metronidazole. This data would support the role for routine metronidazole susceptibility testing using appropriate standardized methods when triple therapy is to be considered.
An agent server for the next generation of Web applications

We expect that the next generation of Web applications will provide services based on information about individual users, and will be integrated with e-mail notification services. However, existing approaches are not adequate for developing such applications. We therefore provide a framework and running environment, named Caribbean. The framework is based on a concept of multi-agent systems. Modules, namely agents, are partitioned in accordance with the roles of participants. The authors first explain the type of applications for which Caribbean is intended by describing two examples that were developed. Then, they introduce the Caribbean framework. Finally, they discuss the benefits of the framework for application developers.