Miracle-dz/UniFAR-FTUs huggingface dataset:
Alginate synthesis by Pseudomonas aeruginosa: a key pathogenic factor in chronic pulmonary infections of cystic fibrosis patients

Pulmonary infection by mucoid, alginate-producing Pseudomonas aeruginosa is the leading cause of mortality among patients suffering from cystic fibrosis. Alginate-producing P. aeruginosa is uniquely associated with the environment of the cystic fibrosis-affected lung, where alginate is believed to increase resistance to both the host immune system and antibiotic therapy. Recent evidence indicates that P. aeruginosa is most resistant to antibiotics when the infecting cells are present as a biofilm, as they appear to be in the lungs of cystic fibrosis patients. Inhibition of the protective alginate barrier with nontoxic compounds targeted against alginate biosynthetic and regulatory proteins may prove useful in eradicating P. aeruginosa from this environment. Our research has dealt with elucidating the biosynthetic pathway and regulatory mechanism(s) responsible for alginate synthesis by P. aeruginosa. This review summarizes reports on the role of alginate in cystic fibrosis-associated pulmonary infections caused by P. aeruginosa and provides details about the biosynthesis and regulation of this exopolysaccharide.
Targeting cancer cells by using an antireceptor antibody-photosensitizer fusion protein

Antibody-photosensitizer chemical conjugates are used successfully to kill cancer cells in photodynamic therapy. However, chemical conjugation of photosensitizers presents several limitations, such as poor reproducibility, aggregation, and free photosensitizer impurities. Here, we report a fully genetically encoded immunophotosensitizer, consisting of a specific anti-p185HER-2-ECD antibody fragment 4D5scFv fused with the phototoxic fluorescent protein KillerRed. Both parts of the recombinant protein preserved their functional properties: high affinity to antigen and light activation of sensitizer. 4D5scFv-KillerRed showed fine targeting properties and efficiently killed p185HER-2-ECD-expressing cancer cells upon light irradiation. It also showed a remarkable additive effect with the commonly used antitumor agent cisplatin, further demonstrating the potential of the approach.
Performance Comparison of Routing Protocols Based on Different Models in Mobile Adhoc Network

The main characteristics of Mobile Adhoc NETwork (MANET) are no infrastructure, no centralized administration and self configuring networks. The primary motivation of MANET deployment is to increase portability, flexibility and mobility but, mobility causes an unpredictable change in topology and makes routing more difficult. Efficient dynamic routing is a research challenge in such networks. In this paper we have evaluated the performance of three protocols namely AODV (Adhoc On demand Distance Vector routing), DSR (Dynamic Source Routing) reactive routing protocol and DSDV(Destination Sequenced Distance Vector) routing which is a proactive routing protocol on the basis of packet delivery ratio and normalized routing overhead using NS 2 simulator. Four different models are created by changing few parameters of traffic generator file and scenario file like pause time, speed of mobile nodes, network size and number of maximum connections and the results demonstrate that the difference in the mechanism of routing protocols lead to specific performance variation. The selection of an efficient routing protocol thus depends on different parameters of the MANET.
Exercise in cardiac rehabilitation

A patient asks for your help with fatigue, which she has been experiencing for the past several weeks. She says she is having increasing difficulty carrying out her daily responsibilities, lacks motivation and energy, and is irritable and discouraged. She reports trouble sleeping, is often late to her scheduled responsibilities, is not performing as well as previously in her job and other roles, and has had several minor injuries and mild headache and back pain. If you are a family doctor or general practitioner, you would suspect that this woman has a major depressive disorder (MDD), although the likelihood that a depressed patient would actually present her symptoms in such a clear and obvious fashion is extraordinarily low. However, if you are a sports doctor and the patient is a competitive athlete, you may label her as being burned out, overtrained or stale, depending on your personal nomenclature for this problem. You may carry out a routine battery of laboratory tests, often including measuring a variety of immunological, hormonal, and haematological variables, consult with the athlete's coach about a modified training schedule, and suggest the athlete consider a trial of rest which may even include cessation of all training and competition. On the other hand, …
Predictors of Prescription Filling After Visits to the Pediatric Emergency Department

Objective The study’s objective was to describe readily identifiable predictors of filling medication prescriptions after discharge from the pediatric emergency department (PED). Methods The study was a prospective cohort study of caregivers of children aged 0 to 17 years, discharged from the PED of an urban safety net hospital with a medication prescription. Prescription filling was confirmed by direct contact with pharmacies. Logistic regression was used to estimate the association between baseline characteristics and prescription filling. Results Overall, 36 (32%) of 111 families did not fill their children’s prescriptions. We found no association between any predictors of interest and prescription filling. In the patient attributes domain, neither English as one’s nondominant language (adjusted odds ratio [aOR], 0.72; 95% confidence interval [CI], 0.25–2.10) nor low health literacy (aOR, 0.78; 95% CI, 0.17–3.62) was associated with prescription filling. In the patient-provider interaction domain, poor physician-family communication (aOR, 1.52; 95% CI, 0.50–4.61), lack of trust in the medical provider (aOR, 0.68; 95% CI, 0.24–1.77), and caregiver disagreement with the treatment plan (aOR, 0.81; 95% CI, 0.14–4.92) had no association with prescription filling. In the patient–health system interaction domain, concern that the prescription would be unaffordable (aOR, 1.30; 95% CI, 0.48–3.53) and lack of an identified primary care physician for the child (aOR, 0.29; 95% CI, 0.08–1.04) were not associated with filling the prescriptions. Conclusions Among a low-income urban population, approximately one third of families do not fill prescriptions for their children after discharge from the PED. We were unable to predict which families would fill prescriptions and which would not.
TwiMed: Twitter and PubMed Comparable Corpus of Drugs, Diseases, Symptoms, and Their Relations

Background Work on pharmacovigilance systems using texts from PubMed and Twitter typically target at different elements and use different annotation guidelines resulting in a scenario where there is no comparable set of documents from both Twitter and PubMed annotated in the same manner. Objective This study aimed to provide a comparable corpus of texts from PubMed and Twitter that can be used to study drug reports from these two sources of information, allowing researchers in the area of pharmacovigilance using natural language processing (NLP) to perform experiments to better understand the similarities and differences between drug reports in Twitter and PubMed. Methods We produced a corpus comprising 1000 tweets and 1000 PubMed sentences selected using the same strategy and annotated at entity level by the same experts (pharmacists) using the same set of guidelines. Results The resulting corpus, annotated by two pharmacists, comprises semantically correct annotations for a set of drugs, diseases, and symptoms. This corpus contains the annotations for 3144 entities, 2749 relations, and 5003 attributes. Conclusions We present a corpus that is unique in its characteristics as this is the first corpus for pharmacovigilance curated from Twitter messages and PubMed sentences using the same data selection and annotation strategies. We believe this corpus will be of particular interest for researchers willing to compare results from pharmacovigilance systems (eg, classifiers and named entity recognition systems) when using data from Twitter and from PubMed. We hope that given the comprehensive set of drug names and the annotated entities and relations, this corpus becomes a standard resource to compare results from different pharmacovigilance studies in the area of NLP.
Managing faecal incontinence

Simple measures in primary care are often effective F aecal incontinence is a major problem. A recent systematic review of theliterature shows a prevalence of 11-15% in the community.1 These figures have to be interpreted with caution because the relevant studiesare hampered by possible under-reporting and, more importantly, by a lack of a consensus definition. Incontinence of flatus, liquid stool, or solid stool that has an impact on quality of life is a practical definition,2 and here we summarise the management of this heterogeneous condition mostly from a primary care perspective but including possible surgical interventions. Faecal incontinence has many causes and varies in severity from minor faecal soiling to frank incontinence of solid stool. When a patient presents with this symptom we need to establish the degree of debility and obtain an obstetric history.3 Inspection of the anal canal and digital rectal examination is essential. Anal skin tags associated with haemorrhoids can hinder adequate toilet, and poor …
Exploiting the natural dynamics of compliant joint robots for cyclic motions

Due to the significant flexibility arising as a result of the incorporation of passive compliance into traditional rigid actuators, that enables the excitation of sizeable resonance movements, the generation of highly dynamic motions using such systems has been studied in the literature; however, a majority of these methods are limited to single actuators. This work presents a novel scheme employing the natural dynamics of compliant joint robots in order to perform cyclic motions. The use of the system's natural dynamics can therefore result in the execution of robot movements that consume a slight amount of energy as compared to the energy they generate, provided that the motion trajectory is on the limit cycle manifold. The energy efficiency advantages during such cyclic motions, which have rarely been studied in the literature, are also discussed. The proposed scheme, which is based on modal decoupling of the system's natural dynamics, is finally evaluated in simulation in order to investigate the energy-efficiency of different modal motions, as well as the effect of various joint stiffness levels.
Antivascular Actions of Microtubule-Binding Drugs

Microtubule-binding drugs (MBD) are widely used in cancer chemotherapy and also have clinically relevant antiangiogenic and vascular-disrupting properties. These antivascular actions are due in part to direct effects on endothelial cells, and all MBDs (both microtubule-stabilizing and microtubule-destabilizing) inhibit endothelial cell proliferation, migration, and tube formation in vitro, actions that are thought to correspond to therapeutic antiangiogenic actions. In addition, the microtubule-destabilizing agents cause prominent changes in endothelial cell morphology, an action associated with rapid vascular collapse in vivo. The effects on endothelial cells occur in vitro at low drug concentrations, which do not affect microtubule gross morphology, do not cause microtubule bundling or microtubule loss and do not induce cell cycle arrest, apoptosis, or cell death. Rather, it has been hypothesized that, at low concentrations, MBDs produce more subtle effects on microtubule dynamics, block critical cell signaling pathways, and prevent the microtubules from properly interacting with transient subcellular assemblies (focal adhesions and adherens junctions) whose subsequent stabilization and/or maturation are required for cell motility and cell-cell interactions. This review will focus on recent studies to define the molecular mechanisms for the antivascular actions of the MBDs, information that could be useful in the identification or design of agents whose actions more selectively target the tumor vasculature.
Trace-element analysis in clinical chemistry.

Present knowledge of human bodily contents and concentrations in blood, urine, and hair of 11 essential trace elements and 17-22 nonessential inert or toxic trace elements is reviewed and summarized. Analyses of trace elements are applicable as diagnostic aids and indices for therapy in a number of clinical conditions. Techniques are not difficult, and analyses will probably become more or less routine for many diseases in which primary or secondary abnormalities are manifest. Trace elements play fundamental roles in human metabolism.
RELIC – A bioinformatics server for combinatorial peptide analysis and identification of protein‐ligand interaction sites

Phage display technology provides a versatile tool for exploring the interactions between proteins, peptides and small molecule ligands. Quantitative analysis of peptide population sequence diversity and bias patterns has the power to significantly enhance the impact of these methods [1, 2]. We have developed a suite of computational tools for the analysis of peptide populations and made them accessible by integrating fifteen software programs for the analysis of combinatorial peptide sequences into the REceptor LIgand Contacts (RELIC) relational database and web‐server. These programs have been developed for the analysis of statistical properties of peptide populations; identification of weak consensus sequences within these populations; and the comparison of these peptide sequences to those of naturally occurring proteins. RELIC is particularly suited to the analysis of peptide populations affinity selected with a small molecule ligand such as a drug or metabolite. Within this functional context, the ability to identify potential small molecule binding proteins using combinatorial peptide screening will accelerate as more ligands are screened and more genome sequences become available. The broader impact of this work is the addition of a novel means of analyzing peptide populations to the phage display community.
Coordinated compliance review: Guidebook for the English language learner coordinator

This project was designed to guide the English Language Learner Coordinator of an elementary school with the appropriate steps that must be taken to be compliant with the State of California policies related to providing English Language Learners with equitable educational programs. Individual school districts receive funding under Titles I and III from the State of California in order to provide services to their English Language learner (ELL) population. The ELL program is only one of the many categorical programs for which Local Educational Agencies, (LEAs) or school districts, can receive funding. Other programs include adult education, child development, educational equity, gifted and talented education, improving teacher quality state grants, migrant education, and physical education among others. The Adelanto School District is one of such districts that receive funding from the State of California to provide services to their ELL population. As such, they are mandated to comply with the State's Coordinated Compliance Review (CCR) requirements. The Goal of this project is to provide English Language Learners' Coordinators with a handbook on how to
3D facial mesh detection using geometric saliency of surface

This paper proposes a 3D facial mesh detection algorithm based on the geometric saliency of surface. Specifically, the geometric saliency of each vertex on 3D triangle mesh is measured by the combination of Gaussian-weighted curvature and spin-image correlation. Salient vertices with similar properties are clustered into regions on the saliency map, and represented as nodes by the graph model. To detect a 3D facial mesh, initialization and registration steps are applied to match each triangle in the graph model with a reference graph, corresponding to a 3D reference facial mesh. Furthermore, the match error between the graph model of the testing 3D mesh and the reference facial mesh is computed to classify face and non-face meshes. Experimental results demonstrate that the proposed algorithm is effective to detect 3D facial meshes and robust to facial expressions and geometric noises.
Models of germ cell development and their application for toxicity studies

Germ cells are unique in their ability to transfer genetic information and traits from generation to generation. As such, the proper development of germ cells and the integrity of their genome are paramount to the health of organisms and the survival of species. Germ cells are also exquisitely sensitive to environmental influences although the testing of germ cell toxicity, especially in females, has proven particularly challenging. In this review, we first describe the remarkable odyssey of germ cells in mammals, with an emphasis on the female germline, from their initial specification early during embryogenesis to the generation of mature gametes in adults. We also describe the current methods used in germ cell toxicity testing and their limitations in examining the complex features of mammalian germ cell development. To bypass these challenges, we propose the use of alternative model systems such as Saccharomyces cerevisiae, Drosophila melanogaster, Caenorhabditis elegans, and in vitro germ cell methods that have distinct advantages over traditional toxicity models. We discuss the benefits and limitations of each approach, their application to germ cell toxicity studies, and the need for computational approaches to maximize the usefulness of these models. Together, the inclusion of these alternative germ cell toxicity models will be invaluable for the examination of stages not easily accessible in mammals as well as the large scale, high‐throughput investigation of germ cell toxicity. Environ. Mol. Mutagen. 56:637–649, 2015. © 2015 Wiley Periodicals, Inc.
Direct Measurement of Coherent Coupling in a MoSe2/WSe2 Heterostructure

We use multidimensional coherent spectroscopy to identify interlayer coherent coupling between excitons in a M<inf>o</inf>Se<inf>2/</inf>WSe<inf>2</inf> heterostructure, which brings us towards the goal of resolving energy transfer processes in transition metal dichalcogenide heterostructures. © 2019 The Author(s)
Emergency Medicine Physicians’ and Pediatricians’ Use of Computed Tomography in the Evaluation of Pediatric Patients With Abdominal Pain Without Trauma in a Community Hospital

There is a paucity of data regarding emergency department (ED) provider type and computed tomography (CT) scan use in the evaluation of pediatric patients with abdominal pain without trauma. The purpose of this retrospective single community hospital study was to determine if there was a difference in CT use between emergency medicine physicians (EMPs) and pediatricians (PEDs) in all patients younger than 18 years with abdominal pain without trauma who presented to the ED during the study period. The study included 165 patients. EMPs saw 83 patients and used CT in 31 compared with PEDs who saw 82 patients and used CT in 12 (P = .002). EMPs used CT significantly more frequently than PEDs in the designated sample. Economic pressures may cause changes in ED provider type in community and rural hospitals and this study shows that ED provider type may affect medical decision making, including CT use.
Detection of processing model basic elements in intellectual analysis of flexible processes through business process intelligence

The problem of constructing flexible process models is very urgent nowadays. The structure of flexible processes may be changed either at configuration or runtime stages. Therefore, the flexible process model can be further adapted to the specific implementation conditions in static and dynamic modes. The process model can be constructed by traditional methods, involving domain experts, and by process mining techniques as well. Process mining technique is used for process modeling based on their execution recorded in event logs. The current work is based on the idea of constructing a flexible process model by process mining techniques using algebra of finite predicates (AFP) and logical networks. AFP is intended to formalize the logical processes and represents the discrete unit to describe arbitrary finite relations. Solving AFP equations is implemented by logical networks that convert algebraic equations into a binary system. The proposed approach represents augmentation of a consecutive model at the stage of log analysis for various executions of the process. Identification of different elements is performed by logical networks.
Distance Measures for Uncertain Linear Systems: A General Theory

In this paper, we propose a generic notion of distance between systems that can be used to measure discrepancy between open-loop systems in a feedback sense under several uncertainty structures. When the uncertainty structure is chosen to be four-block (or equivalently, normalized coprime factor) uncertainty, then this generic distance measure reduces to the well-known nu-gap metric. Associated with this generic distance notion, we also define a generic stability margin notion that allows us to give the distance measure a feedback interpretation by deriving generic robust stability and robust performance results. The proposed distance notion and the corresponding results exploit a powerful generalization of the small-gain theorem which handles perturbations in RfrL infin, rather than only in RfrH infin. When the uncertainty structure is fixed to one of the standard structures (e.g., additive, multiplicative, inverse multiplicative, coprime factor, four-block or any mixtures of the above), we give a step-by-step procedure (based on model validation ideas) that shows how the generic notion of distance and the correspondingly generic winding number conditions can be reduced to simple formulae. This work provides a unified framework that captures and embeds previous results in this area and also completes the picture by showing how other results of a similar nature can be obtained from the same framework. The techniques used involve only basic linear algebra, so they also provide a simplification of previous advanced proofs. Furthermore, the various distance measures so created can be used for non-conservative model embedding into the smallest uncertain family. An illustrative example is also given that demonstrates the superior qualities, above the nu-gap metric, of a particular distance measure obtained from this work in situations where the plant is lightly-damped. All systems considered in this paper are linear time-invariant.