Miracle-dz/UniFAR-FTUs huggingface dataset:
Prevalence and Molecular Characterization of Pertactin-Deficient Bordetella pertussis in the United States

ABSTRACT Pertussis has shown a striking resurgence in the United States, with a return to record numbers of reported cases as last observed in the 1950s. Bordetella pertussis isolates lacking pertactin, a key antigen component of the acellular pertussis vaccine, have been observed, suggesting that B. pertussis is losing pertactin in response to vaccine immunity. Screening of 1,300 isolates from outbreak and surveillance studies (historical isolates collected from 1935 up to 2009, isolates from the 2010 California pertussis outbreak, U.S. isolates from routine surveillance between 2010-2012, and isolates from the 2012 Washington pertussis outbreak) by conventional PCR and later by Western blotting and prn sequencing analyses ultimately identified 306 pertactin-deficient isolates. Of these pertactin-deficient strains, 276 were identified as having an IS481 in the prn gene (prnIS481 positive). The first prnIS481-positive isolate was found in 1994, and the next prnIS481-positive isolates were not detected until 2010. The prevalence of pertactin-deficient isolates increased substantially to more than 50% of collected isolates in 2012. Sequence analysis of pertactin-deficient isolates revealed various types of mutations in the prn gene, including two deletions, single nucleotide substitutions resulting in a stop codon, an inversion in the promoter, and a single nucleotide insertion resulting in a frameshift mutation. All but one mutation type were found in prn2 alleles. CDC 013 was a predominant pulsed-field gel electrophoresis (PFGE) profile in the pertactin-positive isolates (203/994) but was found in only 5% (16/306) of the pertactin-deficient isolates. Interestingly, PFGE profiles CDC 002 and CDC 237 represented 55% (167/306) of the identified pertactin-deficient isolates. These results indicate that there has been a recent dramatic increase in pertactin-deficient B. pertussis isolates throughout the United States.
Uterine sarcomas: then and now.

OBJECTIVE The purpose of this article is to provide an updated review of uterine sarcomas. The traditionally described neoplasms are reviewed as well as several recently characterized entities in terms of their imaging and clinical aspects. We attempt to provide a longitudinal imaging overview, from initial presentation to follow-up. Imaging features are also described of response to traditional therapeutic agents and newer targeted agents. CONCLUSION A greater understanding of the pathogenesis has improved our ability to image and treat uterine sarcomas, both at initial staging and on follow-up. Targeted therapy is assuming an increasingly important role in the management of these lesions. It is imperative for radiologists to be aware of response characteristics and potential complications of these agents as well as conventional chemotherapeutic agents.
[Syringocele of the Cowper's gland. Report of 2 cases diagnosed in adulthood].

OBJECTIVE To describe two cases of symptomatic syringocele diagnosed in adult patients. METHODS/RESULTS Two cases of symptomatic syringocele diagnosed in adult patients that both consulted for obstructive voiding syndrome, are described. Diagnosis was made by retrograde urethrography. An incision extending to the outlet of the syringocele was performed in both cases. Good results were achieved and the symptoms remitted. CONCLUSIONS Syringocele is the cystic dilatation of Cowper's gland. It is generally congenital and a majority of the symptomatic cases (urinary infection, obstruction or hematuria) are diagnosed in childhood. The diagnosis is based on the findings of retrograde urethrography and urethroscopy. Treatment is by urethroscopic incision or marsupialization of the syringocele. Some cases may require open surgery via the perineal approach.
Security Monitoring of DNS traffic

The Domain Name System (DNS) is a critical part of the Internet. This paper analyzes methods for passive DNS replication and describes the replication setup at the University of Auckland. Analysis of the replicated DNS traffic showed great dependency of collaborative anti-spam tools on the DNS. These tools also put a great burden on the DNS. This paper discusses analyzed anomalies in the replicated DNS traffic: typo squatter and fast flux domains, private IP address space leaks and non recommended characters in DNS names. Future applications of passive DNS replication are also discussed.
Luteinizing hormone-releasing hormone agonist triptorelin in combination with cytotoxic chemotherapy in patients with advanced ovarian carcinoma. A prospective double blind randomized trial. Decapeptyl Ovarian Cancer Study Group.

BACKGROUND Several lines of evidence suggest that the proliferation of ovarian carcinoma might be stimulated by gonadotrophins. A number of Phase I/Phase II clinical trials have reported that the suppression of endogenous luteinizing hormone and follicle-stimulating hormone secretion by luteinizing hormone-releasing hormone (LHRH) analogs induced objective remissions and/or disease stabilization in 10-30% of patients with advanced refractory ovarian carcinoma. The current study was performed to evaluate whether the addition of LHRH agonist treatment to standard platinum-based chemotherapy could prolong survival of patients with surgically treated Stage III or IV epithelial ovarian carcinoma. METHODS One hundred and thirty-five patients with Stage III or IV epithelial ovarian carcinoma participated in this prospective randomized double blind trial. After cytoreductive surgery, 69 patients received monthly injections of a depot preparation of the LHRH agonist [D-Trp6] LHRH (triptorelin, 3.75 mg) and 66 patients received placebo until their deaths or termination of trial, respectively. All patients were treated with a standard platinum-based chemotherapy, and, if necessary, with second- or third-line cytotoxic regimens. RESULTS Endogenous gonadotrophins were reliably suppressed in patients treated with triptorelin. However, their progression free and overall survival were not significantly different from that of patients receiving placebo injections (statistical power > 80% for a difference between both groups of > or = 20%). CONCLUSIONS The results of this trial suggest that the suppression of endogenous gonadotrophins by conventional doses of an LHRH agonist produces no relevant beneficial effects in patients with advanced ovarian carcinoma who receive standard surgical cytoreduction and cytotoxic chemotherapy.
Gamification: an Emerging Trend

This study presents the results of an archival analysis which highlights that gamification is an emerging research trend. The archival analysis (conducted for the period 2008-2015) of the gamification literature published in top tier research outlets resulted in the retrieval of 99 articles, of which only 35 were relevant. This study identifies (i) the common themes, (ii) the context explored, and (iii) the gamification element examined. We observe that most research was conducted in the educational and organizational context. The periodic analysis of publications indicates a growing interest in this research domain. Overwhelmingly the results from this archival analysis highlights that research on gamification is at its infancy. Therefore the need and opportunity to investigate this phenomenon is of profound importance.
The presence of English and Spanish dyslexia in the Web

In this study we present a lower bound of the prevalence of dyslexia in the Web for English and Spanish. On the basis of analysis of corpora written by dyslexic people, we propose a classification of the different kinds of dyslexic errors. A representative data set of dyslexic words is used to calculate this lower bound in web pages containing English and Spanish dyslexic errors. We also present an analysis of dyslexic errors in major Internet domains, social media sites, and throughout English- and Spanish-speaking countries. To show the independence of our estimations from the presence of other kinds of errors, we compare them with the overall lexical quality of the Web and with the error rate of noncorrected corpora. The presence of dyslexic errors in the Web motivates work in web accessibility for dyslexic users.
The structure of the membrane protein squalene-hopene cyclase at 2.0 A resolution.

Squalene cyclases catalyze a cationic cyclization cascade, which is homologous to a key step in cholesterol biosynthesis. The structure of the enzyme from Alicyclobacillus acidocaldarius has been determined in a new crystal form at 2.0 A resolution (1 A=0.1 nm) and refined to an R-factor of 15.3 % (Rfree=18.7 %). The structure indicates how the initial protonation and the final deprotonation of squalene occur and how the transient carbocations are stabilized. The pathways of the flexible educt squalene from the membrane interior to the active center cavity and of the rigid fused-ring product hopene in the reverse direction are discussed. The enzyme contains eight so-called QW-sequence repeats that fortify the alpha/alpha-barrels by an intricate interaction network. They are unique to the known triterpene cyclases and are presumed to shield these enzymes against the released enthalpy of the highly exergonic catalyzed reaction. The enzyme is a monotopic membrane protein, the membrane-binding interactions of which are described and compared with those of two prostaglandin-H2 synthase isoenzymes, the only other structurally characterized proteins of this type. In the crystals the membrane-binding regions face each other, suggesting a micelle-type detergent structure between them.
Stochastic resonance in thermally activated reactions: Application to biological ion channels.

At the molecular level many thermally activated reactions can be viewed as Poisson trains of events whose instantaneous rates are defined by the reaction activation barrier height and an effective collision frequency. When the barrier height depends on an external parameter, variation in this parameter induces variation in the event rate. Extending our previous work, we offer a detailed theoretical analysis of signal transduction properties of these reactions considering the external parameter as an input signal and the train of resulting events as an output signal. The addition of noise to the system input facilitates signal transduction in two ways. First, for a linear relationship between the barrier height and the external parameter the output signal power grows exponentially with the mean square fluctuation of the noise. Second, for noise of a sufficiently high bandwidth, its addition increases output signal quality measured as the signal-to-noise ratio (SNR). The output SNR reaches a maximum at optimal noise intensity defined by the reaction sensitivity to the external parameter, reaction initial rate, and the noise bandwidth. We apply this theory to ion channels of excitable biological membranes. Based on classical results of Hodgkin and Huxley we show that open/closed transitions of voltage-gated ion channels can be treated as thermally activated reactions whose activation barriers change linearly with applied transmembrane voltage. As an experimental example we discuss our recent results obtained with polypeptide alamethicin incorporated into planar lipid bilayers. (c) 1998 American Institute of Physics.
An Overview of Statistical Methods for the Classification and Retrieval of Patient Events

Abstract: Statistical methods that can support text retrieval are becoming an increasing focus of medical informatics activities. We overview our adaptation of existing knowlege sources to create pseudo-documents for concept based latent semantic indexing. Experience demonstrated this tack of limited practical value, since retrieval performance was invariably unsatisfactory. We discovered this was due in part to the introduction of a vocabulary gap between the queries and the cases we sought to retrieve. In part to address this problem, and to avail our large body of humanly coded text as a knowledge source, we developed a least squares fit alternative for the computer assisted indexing and retrieval of biomedical texts. This technique demonstrates equivalent or superior retrieval performance when compared to all other textual retrieval techniques. It does not depend upon elaborate knowledge bases, lexicons, or thesauri. It is a promising technique for classifying and retrieving the large volumes of clinical text.
Visual Perception Based Engagement Awareness for Multiparty Human-Robot Interaction

Computational systems for human–robot interaction (HRI) could benefit from visual perceptions of social cues that are commonly employed in human–human interactions. However, existing systems focus on one or two cues for attention or intention estimation. This research investigates how social robots may exploit a wide spectrum of visual cues for multiparty interactions. It is proposed that the vision system for social cue perception should be supported by two dimensions of functionality, namely, vision functionality and cognitive functionality. A vision-based system is proposed for a robot receptionist to embrace both functionalities for multiparty interactions. The module of vision functionality consists of a suite of methods that computationally recognize potential visual cues related to social behavior understanding. The performance of the models is validated by the ground truth annotation dataset. The module of cognitive functionality consists of two computational models that (1) quantify users’ attention saliency and engagement intentions, and (2) facilitate engagement-aware behaviors for the robot to adjust its direction of attention and manage the conversational floor. The performance of the robot’s engagement-aware behaviors is evaluated in a multiparty dialog scenario. The results show that the robot’s engagement-aware behavior based on visual perceptions significantly improve the effectiveness of communication and positively affect user experience.
Questioning four preconceived ideas on immunotherapy of clinical type 1 diabetes: lessons from recent CD3 antibody trials.

Patients presenting type 1 diabetes (T1D) are currently treated with insulin substitutive therapy that is remarkably successful. The treatment has, however, two major limitations that cannot be underestimated due to the major problems and/or discomfort they create, particularly in the numerous patients with unstable metabolic control or insufficient compliance to treatment. The first limitation is degenerative complications that remain an important concern even if their frequency has been dramatically reduced in patients with good metabolic control. The second is the worrisome daily constraints and risks (especially hypoglycemia) linked to regular insulin administration. Several alternatives to palliative insulin therapy have been proposed: pancreas or islet transplantation, β-cell regeneration and immunotherapy. The last strategy, which is in many regards the most straightforward and does not expose patients to the hazards and complications of cell therapy and transplantation, was initiated in the 1980s using cyclosporin in patients presenting new-onset T1D [1-3]. Successful remission of disease was obtained with very limited side effects. When the drug was administered at reasonable doses, neither chronic nephrotoxicity nor infections were observed [1-5]. Thus, ten years after cyclosporin treatment, patients from the French study showed perfectly normal renal function as assessed by creatinine and paraaminohypuric (PAH) acid clearance [5]. It remains true, though, that cyclosporin did not restore self-tolerance to islet autoantigens. Diabetes returned rapidly after cessation of treatment, indicating that indefinite treatment was needed to maintain the therapeutic effect, hardly an acceptable strategy in young subjects because of the long-term risk of overimmunosuppression (infections and tumors). These results justified the intensive search for alternative approaches aimed at inducing and/or restoring self-tolerance addressed by a large number of laboratories using the NOD mouse as a preclinical model [6]. Four misleading concepts emerged from these efforts: 1. tolerance induction requires the administration of β-cell antigens, the potential targets of autoimmune aggression, 2. results obtained in animal models (NOD mouse and BB rat) are not predictive of efficacy in human T1D, 3. at the time of established (even recently diagnosed) diabetes, too many β-cells are already destroyed to allow any room for effective and long-standing metabolic reconstitution, a statement which oriented investigators towards prevention trials in subjects at high risk of developing the disease, 4. to be successful, trials should use the combination of several agents because of the unlikelihood of having a significant effect with a single agent. The aim of this brief review, based on the results we recently obtained in a phase II randomized trial using a CD3-specific antibody [7], is to question all these four preconceived ideas.
The cardiovascular responses of the freshwater turtle Trachemys scripta to warming and cooling

SUMMARY Seven freshwater turtles Trachemys scripta were instrumented with flow probes and cannulated for blood pressure measurements. The turtles were warmed from 24 to 34°C, and cooled down to 24°C, with and without atropine. Animals exhibited a hysteresis of heart rate and blood flow to both the pulmonary and systemic circulations, which was not cholinergically mediated. Blood pressure remained constant during both warming and cooling, while systemic resistance decreased during heating and increased during cooling, indicating a barostatic response. There was a large right-to-left (R–L) shunt during warming and cooling in untreated animals, which remained relatively constant. Atropinisation resulted in a large L–R shunt, which decreased during warming and increased during cooling. Nevertheless, heating rates were the same in untreated and atropinised animals, and cooling rates were significantly longer in atropinised animals, indicating that shunt patterns contribute little to heat exchange.
Determination of rubella virus‐specific cell‐mediated immunity using IFNγ‐ELISpot

Immunity to rubella virus (RV) is conventionally determined by measuring specific immunoglobulin G (IgG). However, several individuals may be considered immune despite undetectable antibody levels. In the present study RV‐specific interferon‐gamma (IFNγ)‐ELISpot and rubella‐IgG‐ELISA were compared in 75 young adults aged between 20 and 30 years. In a subgroup, not only rubella‐like particles (RLP), but also HPV77 rubella vaccine derived antigen was used in IFNγ‐ELISpot. The results from both, ELISA and ELISpot were independent of previous encounter to RV (vaccination, exanthematous disease, or childhood infection). There was no difference between RLP and RV vaccine antigen in IFNγ‐ELISpot response, and there was no correlation between IFNγ‐ELISpot and RV‐specific IgG levels. IFNγ‐producing cells were found in 78.7% of all tested persons, and 83.8% of them were positive in ELISA. In almost all individuals seronegative for RV antibody, IFNγ‐producing cells were detected. Considering both humoral and cell‐mediated immune responses, a positive RV immune reaction was seen in 98.6%. The results indicate that the IFNγ‐ELISpot can provide valuable additional information in seronegative individuals. J. Med. Virol. 82:335–340, 2010. © 2009 Wiley‐Liss, Inc.
Calcium-Dependent Regulation of Rab3 in Short-Term Plasticity

The Rab3 proteins are monomeric GTP-binding proteins associated with secretory vesicles. In their active GTP-bound state, Rab3 proteins are involved in the regulation of hormone secretion and neurotransmitter release. This action is thought to involve specific effectors, including two Ca2+-binding proteins, Rabphilin and Rim. Rab3 acts late in the exocytotic process, in a cell domain in which the intracellular Ca2+ concentration is susceptible to rapid changes. Therefore, we examined the possible Ca2+-dependency of the regulatory action of GTP-bound Rab3 and wild-type Rab3 on neuroexocytosis at identified cholinergic synapses in Aplysia californica. The effects of recombinant GTPase-deficient Aplysia-Rab3 (apRab3-Q80L) or wild-type apRab3 were studied on evoked acetylcholine release. Intraneuronal application of apRab3-Q80L in identified neurons of the buccal ganglion of Aplysia led to inhibition of neurotransmission; wild-type apRab3 was less effective. Intracellular chelation of Ca2+ ions by EGTA greatly potentiated the inhibitory action of apRab3-Q80L. Train and paired-pulse facilitation, two Ca2+-dependent forms of short-term plasticity induced by a rise in intraterminal Ca2+concentration, were increased after injection of apRab3-Q80L. This result suggests that the inhibition exerted by GTP-bound Rab3 on neuroexocytosis is reduced during transient augmentations of intracellular Ca2+ concentration. Therefore, a Ca2+-dependent modulation of GTP-bound Rab3 function may contribute to short-term plasticity.
Fit for purpose? Pattern cutting and seams in wearables development

This paper describes how a group of practitioners and researchers are working across disciplines at Nottingham Trent University in the area of Technical Textiles. It introduces strands of ongoing enquiry centred around the development and application of stretch sensors on the body, focusing on how textile and fashion knowledge are being reflexively revealed in the collaborative development of seamful wearable concepts, and on the tensions between design philosophies as revealed by definitions of purpose. We discuss the current research direction of the Aeolia project, which seeks to exploit the literal gaps found in pattern cutting for fitted stretch garments towards experiential forms and potential interactions. Normative goals of fitness for purpose and seamlessness are interrogated and the potential for more integrated design processes, which may at first appear ‘upside down’, is discussed.
A Novel Lightness Localization Algorithm Based on Anchor Nodes Equilateral Triangle Layout in WSNs

Localization, which determines the geographical locations of sensors, is a crucial issue in wireless sensor networks. In this paper, we propose a novel lightweight equilateral triangle localization algorithm (LETLA) that accurately localizes sensors and minimizes the power consumption. In the LETLA, the approximate coordinates substituted for the real coordinates of the unknown node, and the corresponding optimization problem is formulated to minimize the estimation error. With the sequences that represent the ranking of distances from the anchors to the unknown node, a simple and robust technique is developed to quickly and efficiently estimate a region containing the approximate coordinates, and a condition under which the approximate error can be minimized is given. This condition employs a new geometric construct of anchor layout called equilateral triangle diagrams. Extensive simulations show that the LETLA performs better than other state-of-the-art approaches in terms of energy consumption with the same localization precision.