Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of Clarithromycin Resistance Among Iranian Helicobacter pylori Isolates by E-Test and Real-Time Polymerase Chain Reaction Methods

Background Helicobacter pylori is an important pathogen of human gastric mucosa. Antibiotic resistance, especially resistance to clarithromycin is a major factor for treatment failure of H. pylori infections. The main mechanism of clarithromycin resistance in these bacteria is related to point mutations in three different locations of 23S rRNA gene. Objectives The aims of this study were to evaluate the resistance rate to clarithromycin among local H. pylori isolates by the E-test method and to determine the profile of point mutation in 23S rRNA by real-time polymerase chain reaction (PCR) method. Patients and Methods Eighty biopsy samples were collected from dyspeptic patients by endoscopy during 2011 - 2012. All samples were homogenized immediately and cultured on supplemented brucella blood agar and incubated under microaerophilic conditions. Further biochemical tests and ureC gene PCR was done for H. pylori confirmation. The H. pylori OC1096 strain was used as the control strain, simultaneously. Frequency of clarithromycin resistance was determined by the E-test method based on the clinical and laboratory standard institute (CLSI) standards. Point mutation profile was determined by real-time PCR and further analysis of melting curve, amplicon sequencing was done continuously. Results From 80 biopsy samples, 20 positive H. pylori isolates were detected and confirmed by biochemical tests and PCR method. Overall, 21.7% of the H. pylori isolates, showed clarithromycin resistance phenotype by use of the E-test. Also, the minimal inhibitory concentration of clarithromycin was determined as ≥ 0.5 mg/L by the E-test method. Only point mutation in the location of A2143G with melting temperature of 54.7°C was observed in all resistant isolates. Conclusions This study showed that the frequency of H. pylori clarithromycin resistance in Iran is relatively high. Since clarithromycin is not commonly used in Iran for H. pylori eradication, the high rate of resistance could be related to cross-reactivity between other macrolides. Therefore, macrolide antibiotics must be prescribed with precaution in any case of treatment other than H. pylori infections. All resistant isolates showed A2143G mutation in 23S rRNA as the dominant pattern of point mutation at least in Tehran H. pylori isolates.
Acceptability of Using Electronic Vending Machines to Deliver Oral Rapid HIV Self-Testing Kits: A Qualitative Study

Introduction Rates of unrecognized HIV infection are significantly higher among Latino and Black men who have sex with men (MSM). Policy makers have proposed that HIV self-testing kits and new methods for delivering self-testing could improve testing uptake among minority MSM. This study sought to conduct qualitative assessments with MSM of color to determine the acceptability of using electronic vending machines to dispense HIV self-testing kits. Materials and Methods African American and Latino MSM were recruited using a participant pool from an existing HIV prevention trial on Facebook. If participants expressed interest in using a vending machine to receive an HIV self-testing kit, they were emailed a 4-digit personal identification number (PIN) code to retrieve the test from the machine. We followed up with those who had tested to assess their willingness to participate in an interview about their experience. Results Twelve kits were dispensed and 8 interviews were conducted. In general, participants expressed that the vending machine was an acceptable HIV test delivery method due to its novelty and convenience. Discussion Acceptability of this delivery model for HIV testing kits was closely associated with three main factors: credibility, confidentiality, and convenience. Future research is needed to address issues, such as user-induced errors and costs, before scaling up the dispensing method.
Capsule anchoring in Bacillus anthracis occurs by a transpeptidation reaction that is inhibited by capsidin

Bacillus anthracis, the causative agent of anthrax, is a dangerous biological weapon, as spores derived from drug‐resistant strains cause infections for which antibiotic therapy is no longer effective. We sought to develop an anti‐infective therapy for anthrax and targeted CapD, an enzyme that cleaves poly‐γ‐d‐glutamate capsule and generates amide bonds with peptidoglycan cross‐bridges to deposit capsular material into the envelope of B. anthracis. In agreement with the model that capsule confers protection from phagocytic clearance, B. anthracis capD variants failed to deposit capsule into the envelope and displayed defects in anthrax pathogenesis. By screening chemical libraries, we identified the CapD inhibitor capsidin, 4‐[(4‐bromophenyl)thio]‐3‐(diacetylamino)benzoic acid), which covalently modifies the active‐site threonine of the transpeptidase. Capsidin treatment blocked capsular assembly by B. anthracis and enabled phagocytic killing of non‐encapsulated vegetative forms.
Automatic indexing of scanned documents: a layout-based approach

Archiving official written documents such as invoices, reminders and account statements in business and private area gets more and more important. Creating appropriate index entries for document archives like sender's name, creation date or document number is a tedious manual work. We present a novel approach to handle automatic indexing of documents based on generic positional extraction of index terms. For this purpose we apply the knowledge of document templates stored in a common full text search index to find index positions that were successfully extracted in the past.
Free Vibrations of Curved Sandwich Beams with a Transversely Flexible Core

A high-order model for free vibrations of singly curved sandwich beams is presented. The model takes into account the transverse flexibility of the sandwich core while the faces of the sandwich are treated as thin beams. Linear equations of motion as well as the natural boundary conditions are derived. Verification of the model is performed for straight beams via a number of asymptotic cases. For the straight and curved sandwich beams, it is shown that there exist four eigenmodes. Their nature is clarified, and simple theoretical estimations for the eigenfrequencies are obtained. A numerical analysis of free vibration of the simply supported beams is carried out. Effects of design parameters of the sandwich constituents on the eigenmodes and their appropriate frequencies are investigated. The developed model may find its use in the context of various applications of curved sandwich members in the high-performance vehicles.
Neurofibromin regulates corticostriatal inhibitory networks during working memory performance

Neurofibromatosis type I (NF1) is one of the most common single-gene causes of learning disabilities. Here, we use behavioral working memory probes and electrophysiological studies in a mouse model of NF1 (Nf1 heterozygous null mutants; Nf1+/−) to demonstrate that (i) Neurofibromin regulates prefrontal and striatal inhibitory networks, specifically activity-dependent GABA release and (ii) is required for working memory performance, with inhibition-dependent working memory deficits seen in Nf1+/− mice. We find that increased inhibition in medial prefrontal cortex (mPFC) is sufficient to alter persistent activity in a biophysical model of an mPFC microcircuit, suggesting a possible mechanism for Nf1+/− working memory deficits. Accordingly, working memory assays applied during functional MRI (fMRI) studies in human subjects with NF1 reveal hypoactivation of corticostriatal networks, which is associated with impaired working memory performance. Collectively, these integrative mouse and human studies reveal molecular and cellular mechanisms contributing to working memory deficits in NF1.
Analysis of Gradient Descent Methods With Nondiminishing Bounded Errors

The main aim of this paper is to provide an analysis of gradient descent (<inline-formula><tex-math notation="LaTeX"> $\text{GD}$</tex-math></inline-formula>) algorithms with gradient errors that do not necessarily vanish, asymptotically. In particular, sufficient conditions are presented for both stability (almost sure boundedness of the iterates) and convergence of <inline-formula><tex-math notation="LaTeX">$\text{GD}$</tex-math></inline-formula> with bounded (possibly) nondiminishing gradient errors. In addition to ensuring stability, such an algorithm is shown to converge to a small neighborhood of the minimum set, which depends on the gradient errors. It is worth noting that the main result of this paper can be used to show that <inline-formula><tex-math notation="LaTeX">$\text{GD}$</tex-math> </inline-formula> with asymptotically vanishing errors indeed converges to the minimum set. The results presented herein are not only more general when compared to previous results, but our analysis of <italic><inline-formula> <tex-math notation="LaTeX">$\text{GD}$</tex-math></inline-formula> with errors</italic> is new to the literature to the best of our knowledge. Our work extends the contributions of Mangasarian and Solodov, Bertsekas and Tsitsiklis, and Tadić and Doucet. Using our framework, a simple yet effective implementation of <inline-formula> <tex-math notation="LaTeX">$\text{GD}$</tex-math></inline-formula> using simultaneous perturbation stochastic approximations, with constant sensitivity parameters, is presented. Another important improvement over many previous results is that there are no “additional” restrictions imposed on the step sizes. In machine learning applications where step sizes are related to learning rates, our assumptions, unlike those of other papers, do not affect these learning rates. Finally, we present experimental results to validate our theory.
Results from a Semi-Supervised Feature Learning Competition

We present results from a recent large-scale semi-supervised feature learning competition, which attracted twenty-nine teams and 238 total submissions. The learning task was drawn from a real world task in malicious url classification. This was a large scale binary classification task, with a sparse feature space of one million features, and training data sets of 50,000 labeled examples and one million unlabeled examples. Participants were to learn a method of projecting the given high dimensional training and test data into a space of no more than 100 features that would be useful for supervised prediction. We expected to find that the best performing methods would make extensive use of the unlabeled data in addition to the labeled training data, and that the best methods would utilize deep learning or other sophisticated feature learning approaches. Surprisingly, relatively straight-forward supervised learning approaches using random forests out-performed all other submitted methods. Submissions using deep learning were explicitly sought out, but were under-represented in the final results.
A thrombospondin in the anthozoan Nematostella vectensis is associated with the nervous system and upregulated during regeneration

Summary Thrombospondins are multimeric extracellular matrix glycoproteins that play important roles in development, synaptogenesis and wound healing in mammals. We previously identified four putative thrombospondins in the genome of the starlet sea anemone Nematostella vectensis. This study presents the first analysis of these thrombospondins, with the goals of understanding fundamental roles of thrombospondins in the Eumetazoa. Reverse transcriptase PCR showed that each of the N. vectensis thrombospondins (Nv85341, Nv22035, Nv168100 and Nv30790) is transcribed. Three of the four thrombospondins include an RGD or KGD motif in their thrombospondin type 3 repeats at sites equivalent to mammalian thrombospondins, suggesting ancient roles as RGD integrin ligands. Phylogenetic analysis based on the C-terminal regions demonstrated a high level of sequence diversity between N. vectensis thrombospondins. A full-length cDNA sequence was obtained for Nv168100 (NvTSP168100), which has an unusual domain organization. Immunohistochemistry with an antibody to NvTSP168100 revealed labeling of neuron-like cells in the mesoglea of the retractor muscles and the pharynx. In situ hybridization and quantitative PCR showed that NvTSP168100 is upregulated during regeneration. Immunohistochemistry of the area of regeneration identified strong immunostaining of the glycocalyx, the carbohydrate-rich matrix coating the epidermis, and electron microscopy identified changes in glycocalyx organization during regeneration. Thus, N. vectensis thrombospondins share structural features with thrombospondins from mammals and may have roles in the nervous system and in matrix reorganization during regeneration.
Does Vasopressin Contribute to Salt‐Induced Hypertension in the Dahl Strain?

SUMMARY A humoral factor has been Implicated in Dahl salt-sensitive genetically hypertensive rats. The goal of this study was to evaluate the pressor role of vasopressin (AVP) in Dahl rats. Salt-sensitive (S) and resistant (R) rats were fed either high (8%) or low (0.4%) NaCI diets for 6 to 8 weeks. Blood pressure was elevated in S rats fed high salt diets (p < 0.05). Plasma AVP increased with high salt diet in both groups (p < 0.05), but was higher in S than R rats (2.0 ± 0J and 1.3 ± 0.2 j/U/ml respectively, mean ± SE, (p < 0.05). With low salt diet, plasma AVP did not differ significantly in S and R rats (1.0 ± 0.2 and 0.7 ± 0.2 μU/ml respectively). Pressor responses to intravenous injection of AVP were greater in S than R rats (p < 0.05), but this difference was also observed with pressor responses to norepinephrine (S > R, p < 0.05); there was no difference in pressor responses to AVP in S rats fed high vs low salt diet. Injection of 50 ng of d(CH,), VDAVP, which selectively inhibits vasoconstrictor effects of AVP, failed to lower blood pressure in S and R rats fed high or low salt diets despite the fact that this dose decreased pressor responses to 8 mil of AVP more than 90%. Although plasma AVP and vasopressor responses to AVP and NE are slightly elevated in S rats fed high salt, results with d(CH,), VDA VP suggest that vasoconstrictor effects of AVP do not play an important role in the maintenance of hypertension in Dahl S rats.
MODIS-Based Estimation of Terrestrial Latent Heat Flux over North America Using Three Machine Learning Algorithms

Terrestrial latent heat flux (LE) is a key component of the global terrestrial water, energy, and carbon exchanges. Accurate estimation of LE from moderate resolution imaging spectroradiometer (MODIS) data remains a major challenge. In this study, we estimated the daily LE for different plant functional types (PFTs) across North America using three machine learning algorithms: artificial neural network (ANN); support vector machines (SVM); and, multivariate adaptive regression spline (MARS) driven by MODIS and Modern Era Retrospective Analysis for Research and Applications (MERRA) meteorology data. These three predictive algorithms, which were trained and validated using observed LE over the period 2000–2007, all proved to be accurate. However, ANN outperformed the other two algorithms for the majority of the tested configurations for most PFTs and was the only method that arrived at 80% precision for LE estimation. We also applied three machine learning algorithms for MODIS data and MERRA meteorology to map the average annual terrestrial LE of North America during 2002–2004 using a spatial resolution of 0.05°, which proved to be useful for estimating the long-term LE over North America.
A Characterization of the Entropies of Multidimensional Shifts of Finite Type

We show that the values of entropies of multidimensional shifts of finite type (SFTs) are characterized by a certain computation-theoretic property: a real number $h\geq 0$ is the entropy of such an SFT if and only if it is right recursively enumerable, i.e. there is a computable sequence of rational numbers converging to $h$ from above. The same characterization holds for the entropies of sofic shifts. On the other hand, the entropy of an irreducible SFT is computable.
Prediction of Antisense Oligonucleotide Efficacy Using Local and Global Structure Information with Support Vector Machines

Designing antisense oligonucleotides with high efficacy is of great interest both for its usefulness to the study of gene regulation and for its potential therapeutic effects. The high cost associated with experimental approaches has motivated the development of computational methods to assist in their design. Essentially, these computational methods rely on various sequential and structural features to differentiate the high efficacy antisense oligonucleotides from the low efficacy. By far, however, most of the features used are either local motifs present in primary sequences or in secondary structures. We proposed a novel approach to profiling antisense oligonucleotides and the target RNA to reflect some of the global structural features such as hairpin structures. Such profiles are then utilized for classification and prediction of high efficacy oligonucleotides using support vector machines. The method was tested on a set of 348 antisense oligonucleotides of 19 RNA targets with known activity. The performance was evaluated by cross validation and ROC scores. It was shown that the prediction accuracy was significantly enhanced
Intravitreal bevacizumab as an adjunctive therapy before diabetic vitrectomy

Purpose To evaluate the effect of intravitreal injection of Avastin, bevacizumab (IVA) on diabetic vitrectomy and on the postoperative course. Methods Thirty patients undergoing diabetic vitrectomy were distributed to standard vitrectomy (group 1) or vitrectomy with preoperative IVA (group 2). Bevacizumab was injected 5 to 7 days before surgery. Patients of both groups were matched as much as possible according to surgical indication and preoperative visual acuity. Main outcome measures were the feasibility of surgery and the postoperative complications. Feasibility of surgery was evaluated through recording surgical time, intraoperative bleeding, use of endodiathermy, relaxing retinotomies, use of perfluorocarbon liquid (PFCL) and silicone oil tamponade. Results Follow up ranged between 7 and 18 months. There was significant reduction of mean surgical time, bleeding frequency, and diathermy use in group 2 compared to group 1. The rate of PFCL use and relaxing retinotomies were less in group 2 in comparison to group 1. Gas or air was used in 80% of patients in group 2 while silicone oil represented 60% of group 1. Postoperative visual acuity improvement was highly significant in both groups but the difference in both groups was not statistically significant. Vision improved in 87% in group 2 and 80% in group 1. Primary anatomical attachment was achieved in 90.3% in group 2 and 86.6% in group 1. Rate of subsequent surgeries and persistent cataract were higher in group 1. Postoperative bleeding was reported in 26.6% of cases in group 1 and none in group 2. In group 2, no complications related to avastin injection or progression of traction were reported during the preoperative period. Conclusion Preoperative IVA was helpful in achieving the surgical and anatomical goals by reducing the time of surgery, the intraoperative and postoperative bleeding, and the use of silicone oil with subsequent reduction of second surgery.
Standardized care plans in Swedish health care: their quality and the extent to which they are used.

OBJECTIVES To investigate the quality of standardized care plans and the extent to which they are used within Swedish in-hospital somatic care. Further, to examine the quality of the knowledge summaries on which existing standardized care plans were supposed to be based. DESIGN Submitted documents were reviewed with study-specific protocols. SETTING A national survey, based on a structured selection of Swedish hospitals. PARTICIPANTS A total of 25 Swedish hospitals participated, and were asked to submit all documents in use that were labelled standardized care plan. RESULTS Only 4% (34 out of 782) of the reviewed documents fulfilled the criteria for being a standardized care plan. None of the 34 knowledge summaries (an accompanying document with a compilation of scientific facts and reliable experience) was evidence-based. CONCLUSIONS There is a lack of knowledge regarding what a standardized care plan is, and how such a document should emanate from evidence-based knowledge. Our results raise the question of how recent developments in research are used to create standardized care plans for the best possible care. In the process of developing standardized care plans it is important to acknowledge that staff who develop these plans need scientific training and experience. Standardized care plans are in the early stages of development, and at this stage it seems appropriate to initiate a discussion regarding possible cooperation at national level when developing standardized care plans for certain large groups of patients suffering from specific diseases, or undergoing the same treatment.
Series damper actuator: a novel force/torque control actuator

A novel force/torque control actuator called series damper actuator (SDA) is proposed, modeled and analyzed. Compared to conventional force/torque control schemes and series elastic actuator (SEA), SDA has good output force/torque fidelity, low output impedance and large force/torque range. Furthermore, varying damping coefficient endows the SDA with more advantages and makes the system more versatile. An experimental SDA system is developed, in which a magnetorheological (MR) fluid damper is employed as the series damper. The experimental results show that SDA system is an effective force/torque control actuator.
Relationship Between Iron and Erythropoiesis

In recent years there has been important advancement in our knowledge of iron metabolism regulation that also has implications for understanding the physiopathology of some human disorders like beta-thalassemia and other iron overload diseases. In fact, progressive iron overload is the most salient and ultimately fatal complication of beta-thalassemia. Iron deposition occurs in visceral organs (mainly in the heart, liver and endocrine glands), causing tissue damage and ultimately organ dysfunction and failure. Both transfusional iron overload and excess gastrointestinal absorption are contributory. Paradoxically, excess gastrointestinal iron absorption persists despite massive increases in total body iron load. However, little is known about the relationship among ineffective erythropoiesis, the role of iron-regulatory genes, and tissue iron distribution in beta-thalassemia. The focus of this chapter is an update about iron homeostasis and erythroid differentiation with a particular attention to the molecular mechanisms of iron homeostasis deregulation in thalassemia and to the GDF15-BMP-Hepcidin-Ferroportin regulatory pathway in order to understand the contribution to iron overload. The chapter describes evidences for these relationships and discusses how recent discoveries on iron metabolism and erythropoiesis could lead to new therapeutic strategies and better clinical care of these diseases, thereby yielding a much better quality of life for the patients.