Miracle-dz/UniFAR-FTUs huggingface dataset:
Visualization of left atrial appendage and assessment of its function by transthoracic second harmonic imaging and contrast-enhanced pulsed Doppler.

BACKGROUND Low flow velocity within the left atrial appendage, as assessed by transoesophageal echocardiography, is a predictor of thromboembolism and of a low success rate of cardioversion of atrial fibrillation. However, the semi-invasive nature does limit its serial application as a screening technique. METHODS AND RESULTS We investigated the value of transthoracic second harmonic echocardiography and pulsed Doppler at baseline and after intravenous contrast injection to visualize the left atrial appendage and assess blood flow velocities within its cavity. We studied 51 consecutive patients undergoing transoesophageal echocardiography. After transoesophageal echocardiography, transthoracic second harmonic imaging was performed and the left atrial appendage was visualized in 46 patients. Interpretable pulsed Doppler tracings of left atrial appendage flow were obtained at baseline in 39 patients and in 45 patients during Levovist administration. The correlations between peak emptying velocity of left atrial appendage as measured by transoesophageal echocardiography and by transthoracic standard and contrast-enhanced Doppler were 0.81 and 0.91, respectively. The agreement between transoesophageal echocardiography and transthoracic contrast-enhanced pulsed Doppler echocardiography in classifying left atrial appendage flow velocity patterns was 93%. Left atrial appendage thrombus was detected by transthoracic second harmonic imaging in only one of the eight patients shown by transoesophageal echocardiography to have a thrombus. However, all but one of the patients with left atrial appendage thrombus and/or spontaneous echocardiographic contrast at transoesophageal echocardiography had <30cm/s left atrial appendage flow velocity by transthoracic Doppler. CONCLUSIONS This study shows that left atrial appendage can be visualized by transthoracic second harmonic imaging and that the flow velocity within its cavity is reliably measured by pulsed Doppler in a substantial fraction of patients. Contrast enhancement improves the feasibility and the accuracy of transthoracic evaluation of left atrial appendage flow velocity. The practical value of these results in predicting thromboembolic risk and success of cardioversion of atrial fibrillation needs to be proved by prospective studies.
The Short Pet in Pediatrics

Background The peritoneal equilibration test (PET) is a 4-hour procedure that is recommended to be performed in children receiving peritoneal dialysis to assist in prescription management. While a shortened version of the PET has been used in adults and reliably characterizes peritoneal membrane transport capacity, no similar experience with children has been reported. Methods Retrospective evaluation of 2-hour and 4-hour PET data obtained from 20 children receiving chronic peritoneal dialysis in a single center. Characterization of membrane transport capacity was based on evaluation of serum and dialysate samples used to determine the dialysate-to-plasma ratio (D/P) of creatinine and the ratio of dialysate glucose to baseline dialysate glucose (D/D0). Patient values were compared to pediatric reference data. Results In all 20 patients, characterization of peritoneal membrane transport capacity using 2-hour D/P and D/D0 results was identical to that determined using 4-hour data for the same solute. While the creatinine- and glucose-based characterization was discrepant in 14 of 20 patients, in only 1 case was the discrepancy of more than a single transport category. Conclusion These results support the accuracy of a short PET in children, a procedure that should prove beneficial in terms of patient and staff time.
Prediction of scour depth at piers with debris accumulation effects using linear genetic programming

Abstract Exact evaluation of scour depth around piers under debris accumulation is crucial for the safe design of pier structures. Experimental studies on scouring around pier bridges with debris accumulation have been conducted to estimate the maximum scour depth using various empirical relationships. However, due to the oversimplification of a complex process, the proposed relationships have not always been able to accurately predict the pier scour depth. This research proposes linear genetic programming (LGP) approach as an extension of the genetic programming to predict the scour depth around bridge piers. Among the artificial intelligence techniques, LGP and locally weighted linear regression (LWLR) models have not been used to predict the scour depth at bridge piers. Literature experimental data were collected and used to develop the models. The performance of the LGP method was compared with gene-expression programming, LWLR, multilinear regression and empirical equations using rigorous statistical criteria. The correlation coefficient (R) and the root mean squared error (RMSE) were (R = 0.962, RMSE =0.31) and (R = 0.885, RMSE =0.542) for the LGP and LWLR, respectively. The results demonstrated the superiority of the LGP method for increasing the accuracy of the predicted scour depth in comparison with the other models.
Simple High-Performance Liquid Chromatographic Method for Determination of Ciprofloxacin in Human Plasma

Arapid, simple and sensitive high-performance liquid chromatography method was developed for determination of ciprofloxacin in plasma by means of ultraviolet detection. Ofloxacin was used as an internal standard and separation carried on a Novapak C18 column using a mobile phase of 0.01 M phosphate buffer (pH =2.6): methanol (82:18 v/v). Extraction of drug was performed from plasma by liquid-liquid extraction and the average recovery was 78.2% The assay is precise, with inter-assay coefficient of variation of 6.70 % at 0.25-8 kg/ml (n=3). Using UVdetection at 277 nm the detection limit for ciprofloxacin was 20 ng/ml of plasma and the mean extraction recovery was 78.2 %. Short elution time, using UVdetector and usage of ofloxacin as internal standard are advantages of this method
Mechanisms for Complex Chromosomal Insertions

Chromosomal insertions are genomic rearrangements with a chromosome segment inserted into a non-homologous chromosome or a non-adjacent locus on the same chromosome or the other homologue, constituting ~2% of nonrecurrent copy-number gains. Little is known about the molecular mechanisms of their formation. We identified 16 individuals with complex insertions among 56,000 individuals tested at Baylor Genetics using clinical array comparative genomic hybridization (aCGH) and fluorescence in situ hybridization (FISH). Custom high-density aCGH was performed on 10 individuals with available DNA, and breakpoint junctions were fine-mapped at nucleotide resolution by long-range PCR and DNA sequencing in 6 individuals to glean insights into potential mechanisms of formation. We observed microhomologies and templated insertions at the breakpoint junctions, resembling the breakpoint junction signatures found in complex genomic rearrangements generated by replication-based mechanism(s) with iterative template switches. In addition, we analyzed 5 families with apparently balanced insertion in one parent detected by FISH analysis and found that 3 parents had additional small copy-number variants (CNVs) at one or both sides of the inserting fragments as well as at the inserted sites. We propose that replicative repair can result in interchromosomal complex insertions generated through chromothripsis-like chromoanasynthesis involving two or three chromosomes, and cause a significant fraction of apparently balanced insertions harboring small flanking CNVs.
Bacteriophage HP2 of Haemophilus influenzae

ABSTRACT Temperate bacteriophages effect chromosomal evolution of their bacterial hosts, mediating rearrangements and the acquisition of novel genes from other taxa. Although the Haemophilus influenzae genome shows evidence of past phage-mediated lateral transfer, the phages presumed responsible have not been identified. To date, six different H. influenzae phages are known; of these, only the HP1/S2 group, which lyosogenizes exclusively Rd strains (which were originally encapsulated serotype d), is well characterized. Phages in this group are genetically very similar, with a highly conserved set of genes. Because the majority of H. influenzae strains are nonencapsulated (nontypeable), it is important to characterize phages infecting this larger, genetically more diverse group of respiratory pathogens. We have identified and sequenced HP2, a bacteriophage of nontypeable H. influenzae. Although related to the fully sequenced HP1 (and even more so to the partially sequenced S2) and similar in genetic organization, HP2 has a few novel genes and differs in host range; HP2 will not infect or lysogenize Rd strains. Genomic comparisons between HP1/S2 and HP2 suggest recent divergence, with new genes completely replacing old ones at certain loci. Sequence comparisons suggest that H. influenzae phages evolve by recombinational exchange of genes with each other, with cryptic prophages, and with the host chromosome.
Linguistic Metadata Augmented Classifiers at the CLEF 2017 Task for Early Detection of Depression

Methods for automatic early detection of depressed individuals based on written texts can help in research of this disorder and especially offer better assistance to those affected. FHDO Biomedical Computer Science Group (BCSG) has submitted results obtained from five models for the CLEF 2017 eRisk task for early detection of depression that are described in this paper. All models utilize linguistic meta information extracted from the texts of each evaluated user and combine them with classifiers based on Bag of Words (BoW) models, Paragraph Vector, Latent Semantic Analysis (LSA), and Recurrent Neural Networks (RNN) using Long Short Term Memory (LSTM). BCSG has achieved top performance according to ERDE5 and F1 score for this task.
Initial viral decay to assess the relative antiretroviral potency of protease inhibitor-sparing, nonnucleoside reverse transcriptase inhibitor-sparing, and nucleoside reverse transcriptase inhibitor-sparing regimens for first-line therapy of HIV infection

Objectives:To evaluate the effects of sex and initial antiretroviral regimen on decay of HIV-RNA and virologic outcome. Methods:We conducted a viral dynamics substudy of A5142, a trial comparing lopinavir (LPV)/ritonavir with efavirenz (LPV/EFV) versus LPV and two nucleoside reverse transcriptase inhibitor (NRTI) (LPV) versus EFV and two NRTI (EFV) in antiretroviral (ARV)-naive individuals. HIV-RNA was measured at days 2, 10, and 14 in the substudy and at weeks 1, 4, and 8 in A5142 participants. Two-phase viral decay was estimated in the substudy with biexponential mixed-effects modeling and compared using Wilcoxon tests. Week 1 HIV-RNA change was assessed as a predictor of virologic failure (HIV-RNA above 50 or 200 copies/ml) at weeks 24–96 using logistic regression. Results:Sixty-eight individuals were enrolled in the substudy (median HIV-RNA 4.9 log10 copies/ml). Median rates of phase 1 viral decay by treatment were 0.61(EFV/LPV), 0.53(LPV), and 0.63(EFV) per day. Phase 1 decay was significantly faster for EFV than LPV (P = 0.023); other comparisons were not significant (P > 0.11). Viral decay did not differ by sex (P = 0.10). Week 1 HIV-RNA change, calculated in 571 participants of A5142, was greater for the EFV (median −1.47 log10 copies/ml) than either the LPV/EFV or LPV groups (−1.21 and −1.16 log10 copies/ml, respectively; P < 0.001). Week 1 HIV-RNA change was associated with virologic failure above 50 copies/ ml at weeks 24 and 48 (P < 0.018), but not above 200 copies/ml at these time points or for any value at week 96. Conclusion:Phase 1 decay was faster for EFV than LPV or LPV/EFV. Week 1 HIV-RNA change predicted virologic outcome up to week 48, but not at week 96.
Prognostic Role of Apoptotic, Bcl-2, c-erbB-2 and p53 Tumor Markers in Salivary Gland Malignancies

Objective: The clinical characteristics and survival probability rate of 36 patients with salivary gland malignancies and 10 patients with benign salivary tumors were summarized in relation to the immunohistological analysis of the tumor, apoptotic-related markers and apoptosis rate. The expression of the markers examined – Bcl-2, c-erbB-2, p53 – was detected in paraffin sections of the tumors by the streptavidin-biotin peroxidase method following heat-induced antigen retrieval, and the apoptosis rate was determined by the TUNEL method. Results: The overall 5-year survival probability was 61% for patients with malignant tumors and 100% for those with benign tumors. The survival probability of patients over 60 at diagnosis was significantly lower than that of younger patients. Patients whose malignant tumors were larger than 2 cm at diagnosis had worse survival than those with smaller tumors. The survival probability of patients whose malignant tumors were located in the submandibular glands was significantly lower than that of patients whose malignancies were located in the parotid and minor salivary glands. The survival probability of patients who demonstrated positive staining for c-erbB- 2 or TUNEL was lower than for those with negative staining. Gender, the existence of concomitant non-salivary malignancies and ethnic origin had no significant impact on survival. Conclusions: Our results demonstrated significant positive staining in the salivary tumorigenic tissue but not in the surrounding non-tumorigenic tissue examined for TUNEL, c-erbB-2, Bcl-2 and p53, pointing to a biological role for all four markers in the tumorigenic process which is yet to be elucidated. Significant reduction in survival was related to the specific location of the tumor in the submandibular gland, its size and older age of patient. Survival was also found to be significantly reduced when positive staining was demonstrated in the tumor tissue for TUNEL or c-erbB-2, more so for concomitant positive staining of both markers. Clinically, the most important result of the current study is that the survival rate of the patients examined with salivary tumors larger than 2 cm, with positive staining for both TUNEL and c-erbB-2, was 0 (p = 0.0001)!
Permanental Polynomials of the Smaller Fullerenes

Using a general computer code developed previously, permanental polynomials were computed for all fullerenes C< or =36. Mathematical properties of the coefficients and zeroes were investigated. For a given isomer series of constant n, the n/2 independent zeroes appear to consist of a set of 10 that are nearly constant within the series and a set of n/2-10 that differ greatly with structure.
Power Stabilization With Double Transmitting Coils and T-Type Compensation Network for Dynamic Wireless Charging of EV

Power fluctuation caused by the movement of the receiver has always been a difficult problem for the development of dynamic wireless charging of electric vehicles (EVs). A segmented dynamic wireless charging system (DWCS) based on double transmitting coils and T-type compensation network is presented in this paper to restrain the power fluctuation. Cross-coupling effects are removed by adding switches in series with the transmitting coils. A genetic algorithm based multiobject optimization for the power fluctuation factor (PFF) and the reactive component is used to design the parameters of the T-type network. Simulations show that the optimization of the T-type network is not limited to a certain structure of the transmitter and receiver coils but can minimize the PFF for different values of the gap between the transmitting coils. Experiments for separated and overlapped transmitting coils show that the proposed double-transmitting-coil power supply scheme T-type network can maintain the power fluctuation less than 6% of the average output power with the dc–dc efficiency above 85%.
Clinically significant Coagulase Negative Staphylococci and their antibiotic resistance pattern in a tertiary care hospital.

OBJECTIVES To identify various species of coagulase negative staphylococci involved in neonatal septicaemia and determine their antimicrobial resistance pattern. METHODS The prospective descriptive study was carried out from January 2012 to October 2013, at Umm Al-Qura University, Makkah, Saudi Arabia, and comprised clinical isolates of coagulase negative staphylococci recovered from the blood of neonates at Maternity and Children Hospital, Makkah.The identification of species and antibiotic sensitivity for each isolate was done using Microscan Walk Away system. RESULTS Of the 190 clinical isolates S. epidermidis was the most common species found 144(75.8%). The overall drug resistance among the species ranged from 1.6% to 99.5% to all the drugs tested, except to vancomycin and linezolid which were 100% sensitive.The highest drug resistance was exhibited by penicillin 189 (99.5%), ampicillin 188 (99%), oxacillin 178 (93.6%) and augmentin 177 (93%). The minimum drug resistance was shown by synercid 4 (2.2%) and daptomycin 3 (1.6%). All species were 100% resistant to penicillin and ampicillin, except S. hyicus and one isolate of S. hominis-homin which was sensitive to ampicillin. CONCLUSION High rates of antibiotic resistance was seen among coagulase negative staphylococci to commonly-used antibiotics and majority of them were methicillin-resistant. The newer drugs tested can be used as an alternative.
Primary Healthcare Data Management Practice and Associated Factors: The Case of Health Extension Workers in Northwest Ethiopia

Collecting quality and timely healthcare data is crucial to improve health service performance. This study aimed at assessing data management practice and associated factors among health extension workers in East Gojjam zone, Northwest Ethiopia. An institution based cross-sectional study was conducted in 2014 among 302 health extension workers. Data were collected using a self-administered questionnaire and analyzed using SPSS version 20. The study objectives were described by descriptive statistics, and factors in data management were identified by multivariable logistic regression analysis. A total of 302 health extension workers participated in the study. About 47.4% and 53.3% of respondents had good data management knowledge and practice, respectively. Inaccessibility of transportation, communication services, reference materials, and data collection/reporting formats were the mentioned challenges. Workload, data management knowledge, supervision, urban residence, reference materials access and clarity of formats were positively associated with better data management practice (p <0.05). Based on this study, the data management practice of health extension workers was low. Factors for low data management practice were organizational and technical related. Addressing knowledge gaps through professional development and improving supportive supervision are crucial to solve the problem.
Dissecting structure–function interactions in acute optic neuritis to investigate neuroplasticity

Structural MRI, electrophysiology, and functional MRI (fMRI) elucidate different aspects of damage and repair in demyelinating diseases. We combined them to investigate why patients with optic neuritis (ON) exhibit a wide variation in severity of acute visual loss, with the following objectives: (1) To determine how structural and electrophysiological changes in the anterior and posterior visual pathways contribute to acute visual loss. (2) To combine these data with fMRI, to investigate whether cortical activity modulates visual acuity. The visual system of 28 patients with acute unilateral ON was assessed. Linear regression modeling was used to identify parameters associated with acute visual loss, and to determine whether fMRI activity was associated with vision, after accounting for structural and electrophysiological predictors, age, and gender. Optic nerve lesion length and visual evoked potential (VEP) amplitude were associated with visual loss. Bilateral activation in the extra‐striate occipital cortex correlated directly with vision, after adjusting for optic nerve lesion length, VEP amplitude, and demographic characteristics. These data suggest that acute visual loss is associated with the extent of inflammation and conduction block in the optic nerve, but not with pathology in the optic radiations or occipital cortex. The association of better vision with greater fMRI responses, after accounting for factors which reduce afferent input, suggests a role for adaptive neuroplasticity within the association cortex of the dorsal stream of higher visual processing. Longitudinal studies will clarify whether different extra‐striate cortical regions play a role in adaptive plasticity in the acute and chronic stages of injury. Hum Brain Mapp, 2010. © 2009 Wiley‐Liss, Inc.
L'epilepsie du lobe temporal chez le rat : role des structures cles et du systeme gabaergique dans l'epileptogenese

L'hypothese avancee pour expliquer l'apparition de l'epilepsie du lobe temporal (elt) est la suivante : une agression initiale induit des lesions cerebrales responsables de la mise en place d'un circuit epileptique. Cependant, l'etendue des lesions varie et le role des structures lesees n'est pas determine. Le but de mon travail de these consistait en l'identification des structures cerebrales necessaires a la mise en place du circuit epileptique. A savoir, quelle est l'etendue minimale des lesions necessaire pour induire les series de reorganisations responsables de l'epilepsie ? quelles reorganisations sont directement liees a l'apparition des crises ? nous avons choisi de travailler sur le modele d'elt induite par l'injection de lithium et de pilocarpine. Ce modele animal reproduit les caracteristiques de l'elt humaine. L'agression initiale est produite par l'etat de mal (em). Une phase de reorganisations caracterisee par l'absence de crises et l'apparition de lesions suit l'em et enfin, l'epilepsie chronique est caracterisee par la presence de crises spontanees qui surviennent chez 100% des animaux. Dans une premiere serie d'experiences, nous avons tente de proteger le cerveau des dommages induits par un em. La premiere strategie visait a augmenter chroniquement la concentration de gaba intracerebral apres l'em. La deuxieme strategie visait a sensibiliser les structures cerebrales par l'administration de crises breves repetees. Les lesions induites par l'em ont ete quantifiees six jours apres l'em. L'apparition des crises recurrentes ainsi que la duree de la periode silencieuse ont ete determinees jusqu'a six mois apres l'em. Dans une deuxieme serie d'experiences, nous avons effectue des marquages immunohistochimiques afin de visualiser les interneurones de l'hippocampe et les reorganisations qui prennent place apres un em. Nos resultats suggerent le role preponderant de la formation hippocampique dans l'epileptogenese. Le cortex entorhinal pourrait jouer le role de generateur dans la formation des activites responsables des reorganisations par l'intermediaire du hile lese apres l'em. De plus, l'apparition de cellules dans le hile des animaux epileptiques semble conforter le role de cette structure dans l'epileptogenese. La confirmation du role de ces deux structures dans l'epileptogenese pourrait donner de nouvelles perspectives dans la comprehension et le traitement de l'elt.