Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of MagPix Assays and Enzyme-Linked Immunosorbent Assay for Detection of Hemorrhagic Fever Viruses

ABSTRACT Viral hemorrhagic fevers, because of their high mortality rates, the lack of medical countermeasures, and their potential use as instruments of bioterrorism, pose a significant threat to the developed and the developing areas of the world. The key to preventing the spread of these diseases is early and accurate detection. For decades, the gold-standard immunoassay for hemorrhagic fever detection has been the enzyme-linked immunosorbent assay (ELISA); however, newer technologies are emerging with increased sensitivities. One such technology is the Luminex MagPix platform using xMAP microspheres. Here, we compare the MagPix platform with a traditional ELISA for IgM and antigen detection of infections from Lassa and Ebola viruses (LASV and EBOV, respectively). For IgM detection in nonhuman primate samples, the MagPix platform was 5 and 25 times more sensitive in detecting LASV and EBOV, respectively, compared to that with ELISA. For antigen detection in buffer, the MagPix platform was 25 and 2.5 times more sensitive in detecting lower levels of LASV and EBOV, respectively. In both IgM and antigen detection assays, the MagPix platform demonstrated excellent reproducibility at the lower limit of detection (LLOD). These findings demonstrate that the MagPix platform is a viable diagnostic replacement for the ELISA for viral hemorrhagic fevers.
pSCAN: Fast and exact structural graph clustering

In this paper, we study the problem of structural graph clustering, a fundamental problem in managing and analyzing graph data. Given a large graph G = (V, E), structural graph clustering is to assign vertices in V to clusters and to identify the sets of hub vertices and outlier vertices as well, such that vertices in the same cluster are densely connected to each other while vertices in different clusters are loosely connected to each other. Firstly, we prove that the existing SCAN approach is worst-case optimal. Nevertheless, it is still not scalable to large graphs due to exhaustively computing structural similarity for every pair of adjacent vertices. Secondly, we make three observations about structural graph clustering, which present opportunities for further optimization. Based on these observations, in this paper we develop a new two-step paradigm for scalable structural graph clustering. Thirdly, following this paradigm, we present a new approach aiming to reduce the number of structural similarity computations. Moreover, we propose optimization techniques to speed up checking whether two vertices are structure-similar to each other. Finally, we conduct extensive performance studies on large real and synthetic graphs, which demonstrate that our new approach outperforms the state-of-the-art approaches by over one order of magnitude. Noticeably, for the twitter graph with 1 billion edges, our approach takes 25 minutes while the state-of-the-art approach cannot finish even after 24 hours.
What the work of nurses really looks like: Identifying factors influencing the work of nurses in hospital

Aim: The aim of this study was to gain deeper understanding of the work of nurses and shed light on the factors influencing their work in acute care. Professional nursing care makes a difference to patient outcomes. Therefore it is important to identify potential improvements in nurses’ work to make better use of their knowledge and time for the benefit of patient safety. Method: Participants were 8 registered nurses (RNs) and 10 practical nurses (PNs) in one university hospital, observed during their work. Rich multilayer real-time quantitative data were collected with qualitative field notes on nurses’ work, factors influencing their work, movements and time. Following each shift, participants were interviewed by observers. Data were entered onto a handheld computer during. Data collection took place in 2008 and data analysis in 2009-2010. Results: Nursing work was characterized by frequent shifting of attention, interruptions, operational failures, multitasking and constant movements which influenced their work. On average, RNs and PNs encountered influencing factors 4.2 and 2.0 times per hour, respectively, the most common one being face-to-face communication initiated by a co-worker. However, participants described their shifts as quiet and manageable, and without interruptions and delays. Conclusions: Study findings provide a picture of the complex interplay of nurses’ work, influencing factors and movements, with frequent attention shifting in chronological order. Participants were interrupted within an interruption leading to layers of interruptions, adding to the complexity of their work. Study findings demonstrate the importance of approaching and measuring nursing work as a complex phenomenon.
The I222V Neuraminidase Mutation Has a Compensatory Role in Replication of an Oseltamivir-Resistant Influenza Virus A/H3N2 E119V Mutant

ABSTRACT Oseltamivir-resistant A/H3N2 influenza isolates with or without the E119V and I222V neuraminidase (NA) mutations were recovered from an immunocompromised patient. Based on plaque size, yield assays, and NA activity, the impaired viral fitness of the E119V mutant was partially restored by the I222V NA mutation.
RNA (E6 and E7) Assays versus DNA (E6 and E7) Assays for Risk Evaluation for Women Infected with Human Papillomavirus

ABSTRACT In the majority of cases, high-risk human papillomavirus (HR HPV) infections regress spontaneously, with only a small percentage progressing to high-grade lesions. Current screening methods are based on DNA detection. An alternative would be to monitor expression of the E6 and E7 viral oncogenes continuously expressed by malignant phenotypes. In the work reported in this paper, we compared the two methods for a group of women with high-risk HPV infections. Cervical specimens from 400 women, previously found to be HPV DNA positive, were analyzed for HPV DNA by a liquid hybridization assay and typed by multiplex PCR (for types 16, 18, 31, and 33). Identification of HR HPV E6 and E7 RNA transcripts was performed using real-time reverse transcription-PCR and nucleic acid sequence-based amplification assays. Results were compared with concurrent cytological data. HR HPVs were found in 61.2% of patients. The most common genotype was HPV type 16 (HPV-16) (47.1%), followed by HPV-18, HPV-31, and HPV-33. Nine percent of cases involved other genotypes. Among 223 HPV DNA-positive samples, only 118 were positive in the RNA test. Among HPV DNA-positive patients with normal cytology, we detected E6 and E7 RNA transcripts in two cases (18.2%). The rate of detection increased gradually with the grade of the observed lesions, rising from 20% for patients with atypical squamous cells of undetermined significance to 48.1% for women with low-grade squamous intraepithelial lesions and 86.3% for those with high-grade squamous intraepithelial lesions. These results suggest that testing for HPV E6 and E7 transcripts could be a useful tool for screening and patient management, providing more accurate predictions of risk than those obtained by DNA testing.
Joint replacement in 131 painful osteoarthritic and post-traumatic distal interphalangeal joints

This study reports the results of Swanson replacement of 131 DIP joints for painful osteoarthritis and two for ongoing pain after injury. Thirty-seven arthroplasties (28 patients) were carried out with extensor tendon division and repair, and postoperative immobilization for 8 weeks. Ninety-four (60 patients) were then carried out without tendon division, allowing immediate mobilization. At assessment after a mean period of 57 months, the mean postoperative range of movement was 39°, and the mean extensor lag was 11°, with significant improvement of both in both operative groups. The severity of pain improved significantly following surgery. All but one patient were satisfied with the cosmetic result of replacement. The overall complication rate was 7/131(5%). Three joints developed cellulitis and one developed osteomyelitis, requiring subsequent fusion. Two joints had subsequent fusions because of persistent lateral instability and marked ulnar deviation and one had a persistent mallet-type deformity, corrected by tendon shortening.
The Frequency of Different Clinical Presentation of Appendicitis, Complications and Prognosis in Elderly

Background: The classic symptoms of acute appendicitis are seldom seen in the elderly patient and the diagnosis is particularly easy to miss in this group. Therefore complications are more common as a result of delayed diagnosis. The aim of this study was to identify prognosis, complications and factors associated with perforation in elderly patients with acute appendicitis. Materials and Methods: This is a retrospective (descriptive-analytic) study which was conducted from August 2011 until October 2013 in Tehran. A sample of 76 available patients with suspected acute appendicitis ‐who had been admitted to Rasoul-e-Akram and firoozgar hospital were recruited to participate in this study. Patients’ demographic data, symptoms, complications and their blood samples for CRP and Leukocyte count were collected and sent to the laboratory for analysis. Statistical analysis was carried out
Performance Characteristics of the Cepheid Xpert vanA Assay for Rapid Identification of Patients at High Risk for Carriage of Vancomycin-Resistant Enterococci

ABSTRACT We compared the performance characteristics of culture and the Cepheid Xpert vanA assay for routine surveillance of vancomycin-resistant enterococci (VRE) from rectal swabs in patients at high risk for VRE carriage. The Cepheid Xpert vanA assay had a limit of detection of 100 CFU/ml and correctly detected 101 well-characterized clinical VRE isolates with no cross-reactivity in 27 non-VRE and related culture isolates. The clinical sensitivity, specificity, positive predictive value, and negative predictive value of the Xpert vanA PCR assay were 100%, 96.9%, 91.3%, and 100%, respectively, when tested on 300 consecutively collected rectal swabs. This assay provides excellent predictive values for prompt identification of VRE-colonized patients in hospitals with relatively high rates of VRE carriage.
Evaluation of the New Vitek 2 ANC Card for Identification of Medically Relevant Anaerobic Bacteria

ABSTRACT Of 261 anaerobic clinical isolates tested with the new Vitek 2 ANC card, 257 (98.5%) were correctly identified at the genus level. Among the 251 strains for which identification at the species level is possible with regard to the ANC database, 217 (86.5%) were correctly identified at the species level. Two strains (0.8%) were not identified, and eight were misidentified (3.1%). Of the 21 strains (8.1%) with low-level discrimination results, 14 were correctly identified at the species level by using the recommended additional tests. This system is a satisfactory new automated tool for the rapid identification of most anaerobic bacteria isolated in clinical laboratories.
Serotype and Genotype Replacement among Macrolide-Resistant Invasive Pneumococci in Adults: Mechanisms of Resistance and Association with Different Transposons

ABSTRACT The aim of this study was to analyze trends in adult invasive pneumococcal disease (IPD) due to macrolide-resistant strains and to study the evolution of serotypes, genotypes, and macrolide-resistant determinants of strains collected in a prospective study between 1999 and 2007 in Barcelona, Spain. IPD due to macrolide-resistant strains of serotypes included in the 7-valent conjugate vaccine (PCV7) decreased from 2.16/100,000 (pre-PCV7 period, 1999 to 2001) to 0.80/100,000 (late-PCV7 period, 2005 to 2007) (P = 0.001), whereas IPD due to macrolide-resistant strains of non-PCV7 serotypes increased from 1.08/100,000 to 2.83/100,000 (P < 0.001). These changes were related to a fall of clones of PCV7 serotypes (ST81 [P < 0.05], ST90, ST315, and ST17) and an increase in new clones of serotypes 19A and 24F (ST230) and 33F (ST717) in the late-PCV7 period. The most common phenotype was MLSB (90.9%), related to the erm(B) gene. The frequent association between MLSB phenotype and tetracycline resistance [tet(M) gene], was related to transposons of the Tn916-family such as Tn6002 or Tn3872. In conclusion, overall adult IPD rates due to macrolide-resistant pneumococci stabilized between 1999 and 2007 in Barcelona. The decrease in macrolide-resistant PCV7 pneumococci was balanced by the increase in macrolide-resistant non-PCV7 pneumococci.
Cognitive Effects Of Anti-Epileptic Drugs In Nigerians With Epilepsy

Background Epilepsy is particularly highly prevalent in developing African countries and has been associated with cognitive disturbances, but more importantly is the contribution of the anti-epileptic drugs (AEDs). Objective This study aimed at comparing the effects of AEDs on the cognitive functions of Nigerian epileptic patients. Methods This is a prospective study of 55 consecutive patients with epilepsy, aged 14 years and above, over a two year period (October 2000 to October 2002), recruited from the Neurology Clinic of the University Teaching Hospital, Benin City, Nigeria. Anti-epileptic treatment with either carbamazepine (19 patients), phenytoin (18 patients), or phenobarbitone (18 patients) which was randomly assigned constituted the interventional measure. Cognitive testing, using the Iron Psychology (FePsy) a computerized neuro-psychological test battery, measured the visual and auditory reaction times, the continuous performance test and the recognition memory test to assess the mental speed, attention and memory respectively. Results The effect of the individual drug on cognitive performance revealed significant impairment of mental speed (p 0.05). Carbamazepine did not significantly affect the verbal (Words section) memory scores (p>0.05) implying better performance in tasks of verbal memory (p Introduction La prevalence de l\'epilepsie est elevee en Afrique de meme que les troubles cognitifs associes a l\'utilisation des antiepileptiques (AEDs). But Le but de l\'etude est de comparer les effets des AEDs sur les fonctions cognitives d\'une population epileptique nigeriane. Methodes L\'etude prospective, randomizee, concerne 55 patients epileptiques âges de 14 ans et plus, etudies sur une periode de 2 ans (octobre 2000 a octobre 2002) et recrutes dans le service de neurologie du CHU de Benin City. Le traitement etait soit la carbamazepine, (19 patients) soit la phenitoine (18 patients), soit du phenobarbital (18 patients) Les tests cognitifs utilisant le Iron Psychology (FePsy), tests psychologiques, ont mesure les temps de reaction auditif et visuels, les tests de performance de la memoire mentale, de l\'attention et de la memoire. Resultats Chacun des medicaments a entraine une perturbation de la vivacite mentale (p 0.05). La carbamazepine n\'a pas affecte de maniere significative la memoire verbale (mots) (p > 0.05). Tous les autres antiepileptiques ont reduit les capacites d\'attention des patients ( p Keywords : Africa, Anti-epileptic drugs, Epilepsy, Memory, Mental speed, Nigeria, Afrique, Antiepileptiques, Epilepsie, Memoire. Nigeria, Tests psychologiques African Journal of Neurological Sciences Vol. 24 (1) 2005: pp. 18-24
Pattern of Circulation of Norovirus GII Strains during Natural Infection

ABSTRACT Norovirus (NoV) is considered a major cause of nonbacterial gastroenteritis among people of all ages worldwide, but the natural course of infection is incompletely known. In this study, the pattern of circulation of NoVs was studied among 146 children and 137 adults in a small community in southwestern Cameroon. The participants provided monthly fecal samples during a year. NoV RNA was detected in at least one sample from 82 (29%) of the participants. The partial VP1 region could be sequenced in 36 NoV GII-positive samples. Three different genotypes were identified (GII.1, GII.4, and GII.17), with each genotype circulating within 2 to 3 months and reappearing after a relapse period of 2 to 3 months. Most infections occurred once, and 2 episodes at most within a year were detected. No difference in the frequency of NoV infection between children and adults was recorded. The same genotype was detected for a maximum of 2 consecutive months in 3 children only, suggesting that a less than 30-day duration of viral shedding in natural infection was common. Reinfection within a year with the same genotype was not observed, consistent with short-term homotypic immune protection. The study revealed that NoV strains are circulating with a limited duration of viral shedding both in the individuals and the population as part of their natural infection. The results also provide evidence of cross-protective immunity of limited duration between genotypes of the same genogroup.
Dupuytren’s disease in a rock climber with an unaffected identical twin

There is strong evidence of an inherited susceptibility to Dupuytren’s disease. Identical twins are a useful tool for studying diseases with genetic influences. Very few reports have been published on identical twins with Dupuytren’s disease and only two are in English (Couch, 1938; Lyall, 1993). We report identical twins, of which only one has developed Dupuytren’s disease, and we hypothesize that rock climbing might have been the environmental trigger in this case. Twin 1 is a secondary school teacher who started high-intensity climbing at the age of 22. A few months later, a first nodule appeared in his left palm. Now, aged 34, he has two in the left hand and one in the right hand. He is a high-level climber who climbs up to 7c+ routes on the French scale and goes climbing 4–5 times a week. His twin brother, Twin 2, is a psychologist who runs marathons and has no nodules (Figure 1). They have no family history of Dupuytren’s disease and no serious illnesses. Twin 1 is a moderate drinker (8 units per week) and Twin 2 has a dust mite allergy and asthma. Many risk factors have been proposed for Dupuytren’s disease, including the genetic influence. Hindocha et al. (2006) calculated a sibling recurrence risk ratio of 2.9. Factors that increase oxygen free radicals, such as alcohol, cigarettes and diabetes mellitus, and trauma including manual work, vibration exposure and overuse of the hand, which would include rock climbing, have been implicated. Couch (1938) reported a pair of twins with identical Dupuytren’s contractures. Lyall (1993) reported two pairs of identical twins of whom only one in each pair had the disease and suggested that the genetic background alone is not sufficient for onset of the disease and that an unknown environmental trigger must be present. Logan et al. (2005) found that rock climbing might be associated with an early onset of Dupuytren’s disease in male climbers owing to repeated microtrauma in the palmar area. The twins reported here are both healthy, with no serious illnesses and no apparent risk factors predisposing to Dupuytren’s disease, other than climbing in one twin. Alcohol consumption in Twin 1 is the only additional feature that might possibly have some minor influence of the appearance of Dupuytren’s disease, although he is only a moderate consumer of alcohol. It is noteworthy that the appearance of the first nodule coincided with the beginning of high-intensity climbing. Therefore, this case report tentatively suggests that repeated microtrauma has a determinant influence in the early manifestation of Dupuytren’s disease and supports the findings of Logan et al. (2005). The onset of the disease in the climber does not contradict the hypothesis of a genetic influence, since his brother might still contract the disease in the future.
Adapting classification rule induction to subgroup discovery

Rule learning is typically used for solving classification and prediction tasks. However learning of classification rules can be adapted also to subgroup discovery. This paper shows how this can be achieved by modifying the covering algorithm and the search heuristic, performing probabilistic classification of instances, and using an appropriate measure for evaluating the results of subgroup discovery. Experimental evaluation of the CN2-SD subgroup discovery algorithm on 17 UCI data sets demonstrates substantial reduction of the number of induced rules, increased rule coverage and rule significance, as well as slight improvements in terms of the area under the ROC curve.
Keeping Pace with Parvovirus B19 Genetic Variability: a Multiplex Genotype-Specific Quantitative PCR Assay

ABSTRACT Three genotypes have been identified within the parvovirus B19 species (B19V), and such genetic diversity may have significant implications for the development of molecular detection assays. In the present study, B19V genetic variability has been examined on a subset of genomic sequences available in the NCBI nucleotide database, and a quantitative PCR (qPCR) assay able to detect, differentiate, and quantify all viral variants has been established. The designed primers and probes have been used for the development of alternative detection formats, based on a combined use of intercalating dye and genotype-specific hydrolysis probes. The qPCR assay analytical performances have been determined on the 1st WHO International Reference Panel for Parvovirus B19 Genotypes. The developed qPCR protocols allow for the detection of genotypes 1 to 3 with equal accuracy, and with a limit of detection (LOD) of 200 IU/ml. A comparison of routine performance was carried out with respect to a previously established assay specifically validated on B19V genotype 1. For 130 clinical samples analyzed, 126 showed concordant results (31 positive and 97 negative), while 4 showed discordant results. Overall, the genotype-specific qPCR assay showed a sensitivity of 93.94% and a specificity of 97.94%, with an agreement rate of 96.92%. The proposed qPCR assay and the alternative protocols developed, each with robust performance, may allow choice with respect to operational systems and diagnostic requirements and might contribute to provide a more reliable diagnostic service and epidemiological surveillance of B19 virus.
The exploded hand syndrome: a report of five industrial injury cases

The term ‘exploded hand syndrome’ refers to a specific type of crush injury to the hand in which a high compressive force excessively flattens the hand leading to thenar muscle extrusion through burst lacerations. Out of 89 crushed hands seen over a period of seven years, only five had exploded hand syndrome. They were all male industrial workers ranging in age between 24 and 55 years. All patients had thenar muscle extrusion. Other concurrent injuries included fractures/dislocations, compartment syndrome, and ischaemia. All patients were treated by excision of the extruded intrinsic muscles, as well as primary management of concurrent injuries. All patients had functional assessment including: motor power and sensory testing, range of motion of hand joints, and the quick DASH score. Objective testing showed reduced sensibility in the thumb, reduced grip strength (mean 52% of contralateral hand), reduced pinch strength (mean of 27% of contralateral hand), reduced thumb opposition (the mean Kapandji Score was 5 out of 10), and deficits in the range of motion of the metacarpophalangeal and interphalangeal joints of the thumb. The quick DASH score ranged from 11 to 49 and only two patients were able to go back to regular manual work.