Miracle-dz/UniFAR-FTUs huggingface dataset:
Knowledge of cardiopulmonary resuscitation of clinicians at a South African tertiary hospital

Abstract Objectives: The objectives of this study were to assess clinicians' knowledge about evaluating possible cardiac arrest patients and recognising cardiac arrest, to assess clinicians' knowledge about appropriate decisions and actions during cardiopulmonary resuscitation (CPR), and to determine which advanced life support courses had been undertaken and whether they were still valid. Design: This was a descriptive, cross-sectional survey. Setting and subjects: The subjects were doctors who worked in clinical disciplines at a South African tertiary hospital. Using convenience sampling, doctors from each clinical discipline were invited to participate. Those who consented were included, until a sample of 100 was obtained. Outcome measures: A self-administered, closed-ended questionnaire that was based on the course content of the American Heart Association (AHA) Basic Life Support (BLS) course was used. The minimum score of 84%, benchmarked against the AHA BLS course, was used to define adequate knowledge. Results: One hundred doctors participated. None of the participants showed adequate knowledge. The mean total score was 35.1% (95% CI: 31.7; 38.6). The mean adult CPR score was 40.6% (95% CI: 37.4; 45.6). The mean paediatric CPR score was 36.6% (95% CI: 37.0; 41.6). Conclusion: The participants' knowledge of resuscitation was poor. This raises considerable concern about the effectiveness of the CPR that is performed. This study highlights the need for adequate training of clinicians in the skill of resuscitation and the importance of developing appropriate CPR training programmes that are accessible, innovative and inexpensive.
Conformational dynamics of stem II of the U2 snRNA

The spliceosome undergoes dramatic changes in both small nuclear RNA (snRNA) composition and structure during assembly and pre-mRNA splicing. It has been previously proposed that the U2 snRNA adopts two conformations within the stem II region: stem IIa or stem IIc. Dynamic rearrangement of stem IIa into IIc and vice versa is necessary for proper progression of the spliceosome through assembly and catalysis. How this conformational transition is regulated is unclear; although, proteins such as Cus2p and the helicase Prp5p have been implicated in this process. We have used single-molecule Förster resonance energy transfer (smFRET) to study U2 stem II toggling between stem IIa and IIc. Structural interconversion of the RNA was spontaneous and did not require the presence of a helicase; however, both Mg2+ and Cus2p promote formation of stem IIa. Destabilization of stem IIa by a G53A mutation in the RNA promotes stem IIc formation and inhibits conformational switching of the RNA by both Mg2+ and Cus2p. Transitioning to stem IIa can be restored using Cus2p mutations that suppress G53A phenotypes in vivo. We propose that during spliceosome assembly, Cus2p and Mg2+ may work together to promote stem IIa formation. During catalysis the spliceosome could then toggle stem II with the aid of Mg2+ or with the use of functionally equivalent protein interactions. As noted in previous studies, the Mg2+ toggling we observe parallels previous observations of U2/U6 and Prp8p RNase H domain Mg2+-dependent conformational changes. Together these data suggest that multiple components of the spliceosome may have evolved to switch between conformations corresponding to open or closed active sites with the aid of metal and protein cofactors.
Predicting bacteremia by procalcitonin levels in patients evaluated for sepsis in the emergency department

Evaluation of: Riedel S, Melendez JH, An AT, Rosenbaum JE, Zenilman JM. Procalcitonin as a marker for the detection of bacteremia and sepsis in the emergency department. Am. J. Clin. Pathol. 135(2), 182–189 (2011). In a recent report, Riedel et al. proposed a procalcitonin cutoff of 0.1 ng/ml to rule out bacteremia in adult patients presenting to the emergency department with systemic infections. Procalcitonin levels were higher in patients with true bacteremia than in patients with negative blood cultures or bacteremia due to possible contaminants. For prediction of bacteremia, a procalcitonin level of 0.1 ng/ml had an excellent negative predictive value of 96.3%, and a good sensitivity of 75%, specificity of 70.6% and area under the curve of 0.73, but poor positive predictive value of 12.8%. Based on the results in this study, we propose that a procalcitonin value of 0.1 ng/ml or less could be used to rule out bacteremia (NPV: 96.3%).
Is it feasible to use the supratrochlear artery for inducing intra-arterial fibrinolysis in cases of central retinal artery occlusion? An anatomical investigation

Background In order to investigate a possible alternative approach for catheterizing the ophthalmic artery, the detailed anatomy of the intraorbital arteries was examined in eight half-heads.Results The supratrochlear artery was found beneath or at the lateral border of the superior oblique muscle. In six cases the supratrochlear artery was the largest branch of the ophthalmic artery, continuing in the same direction as the latter vessel. In the other two orbits it branched off from the parent vessel at angles of 900 and 1150. In five orbits, the ophthalmic artery divided distally into the supratrochlear and supraorbital arteries, the angles between the two measuring 25o, 300, 400, 400 and 6o. In one case the supraorbital followed a course at right-angles to the supratrochlear, and in two cases it was absent.The mean intraorbital length of the vessels was as follows: supratrochlear: 3.94 cm (1.8 to 6.4 cm); ophthalmic: 3.13 cm (2.1 to 4.3 cm); supraorbital: 3.06 cm (2.1 to 3.8 cm). The following mean exter.
Canonicalizing Open Knowledge Bases

Open information extraction approaches have led to the creation of large knowledge bases from the Web. The problem with such methods is that their entities and relations are not canonicalized, leading to redundant and ambiguous facts. For example, they may store {Barack Obama, was born, Honolulu and {Obama, place of birth, Honolulu}. In this paper, we present an approach based on machine learning methods that can canonicalize such Open IE triples, by clustering synonymous names and phrases. We also provide a detailed discussion about the different signals, features and design choices that influence the quality of synonym resolution for noun phrases in Open IE KBs, thus shedding light on the middle ground between "open" and "closed" information extraction systems.
Chemical footprinting reveals conformational changes of 18S and 28S rRNAs at different steps of translation termination on the human ribosome

Translation termination in eukaryotes is mediated by release factors: eRF1, which is responsible for stop codon recognition and peptidyl-tRNA hydrolysis, and GTPase eRF3, which stimulates peptide release. Here, we have utilized ribose-specific probes to investigate accessibility of rRNA backbone in complexes formed by association of mRNA- and tRNA-bound human ribosomes with eRF1•eRF3•GMPPNP, eRF1•eRF3•GTP, or eRF1 alone as compared with complexes where the A site is vacant or occupied by tRNA. Our data show which rRNA ribose moieties are protected from attack by the probes in the complexes with release factors and reveal the rRNA regions increasing their accessibility to the probes after the factors bind. These regions in 28S rRNA are helices 43 and 44 in the GTPase associated center, the apical loop of helix 71, and helices 89, 92, and 94 as well as 18S rRNA helices 18 and 34. Additionally, the obtained data suggest that eRF3 neither interacts with the rRNA ribose-phosphate backbone nor dissociates from the complex after GTP hydrolysis. Taken together, our findings provide new information on architecture of the eRF1 binding site on mammalian ribosome at various translation termination steps and on conformational rearrangements induced by binding of the release factors.
Barriers to Conducting Multicenter Nursing Research

Introduction: The move towards evidence-based nursing practice requires active participation by nurses at all levels along the continuum of care. Despite this fact, nursing involvement in multicenter research is limited. This not only limits the generalizability of findings, but hinders collaborative and interdisciplinary research networking between hospitals. Reasons for single site nursing research barriers have been explored. Yet, knowledge of the barriers nurses face when they seek to engage in multicenter research activities is limited. Methods: A core group of experienced nurse researchers sought to initiate a multicenter observational research study of intracranial pressure monitoring. This article uses a case series approach to highlight the challenges encountered throughout the process. Results: Barriers to multicenter nursing research were identified and categorized by theme. Conclusions: Institutional changes are suggested to support the participation of clinical nurses in research and recommendations are made for future study.
EFFECT OF CHRONIC ORAL ADMINISTRATION OF CHLOROQUINE ON THE WEIGHT OF THE HEART IN WISTAR RATS

The effect of chronic oral administration of chloroquine, an antimalarial and antirheumatic drug on the histology of the heart in Wistar rats was investigated. Ten Wistar rats were randomly grouped into two, control and treated. The treated group rats were administered 20mg/kg body wt, weekly of chloroquine for 4 weeks while the control group rats were given distilled water for 4 weeks. On day 29 of the experiment, the rats were weighed and sacrificed. The hearts were carefully dissected out and quickly fixed in 10% formal saline for routine histological study after H&E method. The histological findings indicated that the treated sections of the hearts showed moderate hypertrophy of the cardiomyocytes when compared with the control. Thus, our result suggests that though chloroquine may be a widely used antimalarial and antirheumatic drug, its chronic administration may result in cardiotoxicity. Therefore, it is recommended that the drug be prescribed with caution in patients with cardiac abnormality, such as cardiomyopathy and further studies to corroborate this observation should be carried.
Using in-cell SHAPE-Seq and simulations to probe structure–function design principles of RNA transcriptional regulators

Antisense RNA-mediated transcriptional regulators are powerful tools for controlling gene expression and creating synthetic gene networks. RNA transcriptional repressors derived from natural mechanisms called attenuators are particularly versatile, though their mechanistic complexity has made them difficult to engineer. Here we identify a new structure–function design principle for attenuators that enables the forward engineering of new RNA transcriptional repressors. Using in-cell SHAPE-Seq to characterize the structures of attenuator variants within Escherichia coli, we show that attenuator hairpins that facilitate interaction with antisense RNAs require interior loops for proper function. Molecular dynamics simulations of these attenuator variants suggest these interior loops impart structural flexibility. We further observe hairpin flexibility in the cellular structures of natural RNA mechanisms that use antisense RNA interactions to repress translation, confirming earlier results from in vitro studies. Finally, we design new transcriptional attenuators in silico using an interior loop as a structural requirement and show that they function as desired in vivo. This work establishes interior loops as an important structural element for designing synthetic RNA gene regulators. We anticipate that the coupling of experimental measurement of cellular RNA structure and function with computational modeling will enable rapid discovery of structure–function design principles for a diverse array of natural and synthetic RNA regulators.
Pharmaceutical systematics: Description and preliminary investigation of an alternative method for structuring drug information

Objectives: To identify the 30 most common adverse drug events or reactions (ADE/ADRs) within the top 200 medications: (1) by raw incidence, (2) weighted by prescription volume, (3) and weighted by retail dollars. Methods: The Pharmacy Times Top 200 Medications (as ranked by prescription volume) was utilized to identify the top 200 medications in 2008. The ADE/ADRs for each medication were obtained from Facts and Comparisons, Micromedex, and Lexi-Comp and entered into a database. These ADE/ADRs were compiled and summed, identifying the number of times each appeared. These then were ranked to identify the 30 most common ADE/ADRs. The actual prescription volume and total retail dollars for each medication were obtained and listed next to each medication’s ADE/ADR. The incidence of each ADE/ADR then was weighted by actual prescription volume and retail dollars to determine the top 30 most common ADE/ADRs. Results: Initial evaluation resulted in 9829 individual ADE/ADRs and summed into 1477 distinct ADE/ADRs, after adjusting for interchangeable terminology. Examples of the 30 most common ADE/ADRs (raw incidence) included: dizziness/vertigo, headache, nausea, vomiting, and diarrhea/loose stools. The list remained the same after weighting by actual prescription volume. After weighting by retail dollars, the order of ADE/ADRs changed slightly. Conclusion: Knowledge of ADE/ADRs is important for pharmacists in all healthcare settings. Consolidating ADE/ADRs for medications may enable pharmacists to recall the most common side effects and aid in earlier identification of ADE/ADRs, which may positively impact patient safety across practice settings.
Malignant Neoplasms of the Anal Canal

Background: Malignant neoplasms of the anal canal are rare accounting for approximately 4% of all colorectal malignancies. Objectives: The present study aimed to report the clinicopathological characteristics and treatment outcomes of 41 cases with malignant neoplasms of the anal canal. Patients and Methods: Between 1999 and 2012, 41 consecutive patients were diagnosed with primary malignant neoplasm of the anal canal which were treated and followed up at Namazi hospital. Only primary malignant tumors arising from the anal canal were included. Patients with secondary anal canal involvement from rectal or perianal skin cancers and metastatic tumors were excluded. Results: There were 22 women and 19 men, age ranging from 33 to 83 years, with a median age of 57 years at diagnosis. Sixteen patients (39%) had localized disease, 21 (51%) had regional disease, and 4 (10%) had metastatic disease at diagnosis. Squamous cell carcinoma (61%) was the most frequent histologic subtype, followed by adenocarcinoma (27%), malignant melanoma (10%), and gastrointestinal stromal tumor (2%). After a median follow-up of 51 (11-169) months for surviving patients, 22 patients were alive and without disease, three were alive with disease, and 19 patients died due to the disease. Histological subtype (P = 001), and stage of disease (P = 0.002) were prognostic factors for overall survival. The 5-year local control, disease-free, and overall survival rates for all patients were 63.9%, 53%, and 59.4% respectively. Conclusions: This study indicated that squamous cell carcinoma, adenocarcinoma, and malignant melanoma are the most frequent malignant neoplasms in the anal canal. Histological subtype and disease stage are the most important prognostic factors for overall survival in this region.
Rolling Stock Rescheduling in Passenger Railways: Applications in short-term planning and in disruption management

Modern society is highly dependent on a reliable railway system for workforce mobility and easy access to the cities. However, the daily operations of a large passenger railway system are subject to unexpected disruptions such as rolling stock breakdowns or malfunctioning infrastructure. In a disrupted situation, the railway operator must adapt the timetable, rolling stock and crew to the modified conditions. This adaptation of resource allocations requires the solution of complex combinatorial problems in very short time and thus represents a major challenge for the involved dispatchers. This thesis will develop models and solution methods for the rescheduling of the rolling stock during disruptions. The models incorporate service aspects (such as seat capacity), efficiency aspects (such as number of kilometers driven by the rolling stock), and process related aspects (such as the need for night-time relocation of rolling stock). The thesis contains applications of the developed models in three different contexts. First, the thesis presents a framework for applying the rescheduling models in the highly uncertain environment of railway disruption management, and demonstrates the trade-off between computation time and solution quality. Second, the rolling stock rescheduling models are embedded in a simulation framework to account for the dynamic passenger behavior during disruptions. This framework allows us to significantly decrease the delays experienced by passengers. Third, the thesis applies the rescheduling models to real-life planning problems from the short-term planning department of the Netherlands Railways. The models lead to a considerable speed-up of the process and significant savings.
m6aViewer: software for the detection, analysis, and visualization of N6-methyladenosine peaks from m6A-seq/ME-RIP sequencing data

Recent methods for transcriptome-wide N6-methyladenosine (m6A) profiling have facilitated investigations into the RNA methylome and established m6A as a dynamic modification that has critical regulatory roles in gene expression and may play a role in human disease. However, bioinformatics resources available for the analysis of m6A sequencing data are still limited. Here, we describe m6aViewer—a cross-platform application for analysis and visualization of m6A peaks from sequencing data. m6aViewer implements a novel m6A peak-calling algorithm that identifies high-confidence methylated residues with more precision than previously described approaches. The application enables data analysis through a graphical user interface, and thus, in contrast to other currently available tools, does not require the user to be skilled in computer programming. m6aViewer and test data can be downloaded here: http://dna2.leeds. ac.uk/m6a.
Two modes of targeting transposable elements by piRNA pathway in human testis

PIWI proteins and their partner small RNAs, termed piRNAs, are known to control transposable elements (TEs) in the germline. Here, we provide evidence that in humans this control is exerted in two different modes. On the one hand, production of piRNAs specifically targeting evolutionarily youngest TEs (L1HS, L1PA2-L1PA6, LTR12C, SVA) is present both at prenatal and postnatal stages of spermatogenesis and is performed without involvement of piRNA clusters. On the other hand, at postnatal stages, piRNAs deriving from pachytene clusters target "older" TEs and thus complement cluster-independent piRNA production to achieve relevant targeting of virtually all TEs expressed in postnatal testis. We also find that converging transcription of antisense-oriented genes contributes to the origin of genic postnatal prepachytene clusters. Finally, while a fraction of pachytene piRNAs was previously shown to arise from long intergenic noncoding RNAs (lincRNAs, i.e., pachytene piRNA cluster primary transcripts), we ascertain that these are a specific set of lincRNAs that both possess distinguishing epigenetic features and are expressed exclusively in testis.
Ligand recognition and helical stacking formation are intimately linked in the SAM-I riboswitch regulatory mechanism

Riboswitches are noncoding mRNA elements that control gene expression by altering their structure upon metabolite binding. Although riboswitch crystal structures provide detailed information about RNA–ligand interactions, little knowledge has been gathered to understand how riboswitches modulate gene expression. Here, we study the molecular recognition mechanism of the S-adenosylmethionine SAM-I riboswitch by characterizing the formation of a helical stacking interaction involving the ligand-binding process. We show that ligand binding is intimately linked to the formation of the helical stacking, which is dependent on the presence of three conserved purine residues that are flanked by stacked helices. We also find that these residues are important for the formation of a crucial long-range base pair formed upon SAM binding. Together, our results lend strong support to a critical role for helical stacking in the folding pathway and suggest a particularly important function in the formation of the long-range base pair.
Mechanism and emergency management of blast eye/orbital injuries

Nonconventional combat is ever-present around the world. In recent years, there has been an unprecedented increase in suicides, homicides and insurgents using improvised explosive devices such as improvised explosive devices, land mines, rocket-propelled grenades (RPG-7 to -29), thermobaric ‘enhanced-blast explosives’ and explosive-formed projectiles. All of these devices have been shown to dramatically increase eye/orbital injuries. The pathophysiology, biophysics and mechanism of primary and secondary blast-wave front effects are primary causative factors of war-induced eye injuries. This review aims to reappraise eye/orbit blast injuries, thus helping in their management and protection. Blast ocular orbital trauma includes rupture of the globe, serous retinitis, hyphema, corneoscleral lacerations, penetrating eyeball, traumatic cataracts and injury of the optic nerve, nasal–orbital–ethmoidal injuries, brain injury, maxillofacial crushed middle-third fractures and associated multisystem injuries. If the eye is significantly damaged as a result of an initial blast wave, such that it cannot be properly repaired, primary enucleation may be a reasonable option. Another instance where enucleation is possible is if a patient with a significant injury cannot obtain adequate follow-up and be monitored for signs of sympathetic ophthalmia, or in instances where other injuries prevent the patient from actively participating in the decision to save or enucleate an eye in the first 14 days after injury; as in associated head injury. Wearing a visor can protect against eye/orbital damage caused by foreign body penetration and will provide reasonable protection against blast induced eye/orbital injuries.
Unusual presentation of a case of fallopian tube carcinoma

Background: Primary fallopian tube carcinoma (PFTC) accounts only for <1% of all female genital cancers. The diagnosis of PFTC is rarely considered preoperatively and is usually first appreciated at the time of operation or by a pathologist. Case Presentation: Here we are presenting a case report of 45 years old lady with fallopian tube carcinoma, who presented to us with features of advanced ovarian malignancy. FNAC from tumor showed epithelial malignancy and she received neo-adjuvant chemotherapy followed by staging laparotomy and interval debulking surgery. She developed a non-healing ulcer at FNAC site which was excised during laparotomy. On laparotomy, 200cc ascitic fluid was drained. Uterus, right ovary and tube appeared normal. Left side tube showed growth of 3cm x 2cm. Total abdominal hysterectomy, bilateral salpingo-oophorectomy and infracolic omentectomy was done. Histopathological examination revealed left side poorly differentiated primary fallopian tube carcinoma. Uterus and right tube with ovary were free of tumor. She was advised to get 3 cycle of chemotherapy postoperatively. Conclusion: In our patient, FNAC gave a positive diagnosis of malignancy and we were able to operate her malignancy properly following chemotherapy.