Miracle-dz/UniFAR-FTUs huggingface dataset:
Left lateral intercostal region versus subxiphoid position for pleural drain during elective coronary artery bypass graft surgery: randomized clinical trial

ABSTRACT BACKGROUND: The pleural drain insertion site after coronary artery bypass graft (CABG) surgery may alter lung function, especially respiratory muscle strength. The main objective of this study was to compare the effectiveness and safety of use of the left lateral intercostal region versus the subxiphoid position for pleural drainage during elective CABG surgery using extracorporeal circulation (ECC). DESIGN AND SETTING: Randomized trial conducted in a tertiary-level hospital in Porto Alegre, Brazil. METHODS: 48 patients were assigned to group 1 (pleural drain in the left lateral intercostal region) or group 2 (pleural drain in the subxiphoid position). Respiratory muscle strength was measured in terms of maximal inspiratory pressure (MIP) and maximal expiratory pressure (MEP), in cmH2O, by means of manovacuometry preoperatively, 24 and 72 hours after drain removal and before discharge from hospital. Painand dyspnea scales, presence of infections, pleural effusion and atelectasis, duration of drain use, drainage volumes and surgical reinterventions were also evaluated. RESULTS: After adjustments, there were no significant differences between the groups at the end of the study (before discharge), in predicted percentages either for MIP (delta group 1: -17.21% versus delta group 2: -22.26%; P = 0.09) or for MEP (delta group 1: -9.38% versus delta group 2: -13.13%; P = 0.17). Therewere no differences between the groups in relation to other outcomes. CONCLUSION: There was no difference in maximal respiratory pressures in relation to the pleural drain insertion site among patients who underwent CABG surgery using ECC. TRIAL REGISTRATION: ReBEc V1111.1159. 4447.
Development and interlaboratory evaluation of a NIST Reference Material RM 8366 for EGFR and MET gene copy number measurements

Abstract Background The National Institute of Standards and Technology (NIST) Reference Material RM 8366 was developed to improve the quality of gene copy measurements of EGFR (epidermal growth factor receptor) and MET (proto-oncogene, receptor tyrosine kinase), important targets for cancer diagnostics and treatment. The reference material is composed of genomic DNA prepared from six human cancer cell lines with different levels of amplification of the target genes. Methods The reference values for the ratios of the EGFR and MET gene copy numbers to the copy numbers of reference genes were measured using digital PCR. The digital PCR measurements were confirmed by two additional laboratories. The samples were also characterized using Next Generation Sequencing (NGS) methods including whole genome sequencing (WGS) at three levels of coverage (approximately 1 ×, 5 × and greater than 30 ×), whole exome sequencing (WES), and two different pan-cancer gene panels. The WES data were analyzed using three different bioinformatic algorithms. Results The certified values (digital PCR) for EGFR and MET were in good agreement (within 20%) with the values obtained from the different NGS methods and algorithms for five of the six components; one component had lower NGS values. Conclusions This study shows that NIST RM 8366 is a valuable reference material to evaluate the performance of assays that assess EGFR and MET gene copy number measurements.
Accuracy of consumer-level and research-grade activity trackers in ambulatory settings in older adults

Wrist-worn activity trackers have experienced a tremendous growth lately and studies on the accuracy of mainstream trackers used by older adults are needed. This study explores the performance of six trackers (Fitbit Charge2, Garmin VivoSmart HR+, Philips Health Watch, Withings Pulse Ox, ActiGraph GT9X-BT, Omron HJ-72OITC) for estimating: steps, travelled distance, and heart-rate measurements for a cohort of older adults. Eighteen older adults completed a structured protocol involving walking tasks, simulated household activities, and sedentary activities. Less standardized activities were also included, such as: dusting, using a walking aid, or playing cards, in order to simulate real-life scenarios. Wrist-mounted and chest/waist-mounted devices were used. Gold-standards included treadmill, ECG-based chest strap, direct observation or video recording according to the activity and parameter. Every tracker showed a decreasing accuracy with slower walking speed, which resulted in a significant step under-counting. A large mean absolute percentage error (MAPE) was found for every monitor at slower walking speeds with the lowest reported MAPE at 2 km/h being 7.78%, increasing to 20.88% at 1.5 km/h, and 44.53% at 1 km/h. During household activities, the MAPE climbing up/down-stairs ranged from 8.38–19.3% and 10.06–19.01% (dominant and non-dominant arm), respectively. Waist-worn devices showed a more uniform performance. However, unstructured activities (e.g. dusting, playing cards), and using a walking aid represent a challenge for all wrist-worn trackers as evidenced by large MAPE (> 57.66% for dusting, > 67.32% when using a walking aid). Poor performance in travelled distance estimation was also evident during walking at low speeds and climbing up/down-stairs (MAPE > 71.44% and > 48.3%, respectively). Regarding heart-rate measurement, there was no significant difference (p-values > 0.05) in accuracy between trackers placed on the dominant or non-dominant arm. Concordant with existing literature, while the mean error was limited (between -3.57 bpm and 4.21 bpm), a single heart-rate measurement could be underestimated up to 30 beats-per-minute. This study showed a number of limitations of consumer-level wrist-based activity trackers for older adults. Therefore caution is required when used, in healthcare or in research settings, to measure activity in older adults.
Pheromone Source Location by Flying Moths: A Supplementary Non-Anemotactic Mechanism

After the wind was stopped in an insect flight tunnel, male oriental fruit moths continued to fly in zigzag fashion along a stationary pheromone plume. Their lateral excursions from the time-averaged pheromone plume were no greater without wind than in wind of 38 centimeters per second. When the pheromone plume was removed and the wind stopped, males initiated wider track reversals when they reached the pheromone-free area in still air than they had made while in the pheromone plume. This non-anemotactic mechanism of maintaining plume contact—possibly a special kind of klinotaxis—when coupled with the orthokinetic retinal velocity of apparent ground pattern motion, allowed males to reach the pheromone source area from 1 to 2 meters away without wind.
A new normalization for Nanostring nCounter gene expression data

Abstract The Nanostring nCounter gene expression assay uses molecular barcodes and single molecule imaging to detect and count hundreds of unique transcripts in a single reaction. These counts need to be normalized to adjust for the amount of sample, variations in assay efficiency and other factors. Most users adopt the normalization approach described in the nSolver analysis software, which involves background correction based on the observed values of negative control probes, a within-sample normalization using the observed values of positive control probes and normalization across samples using reference (housekeeping) genes. Here we present a new normalization method, Removing Unwanted Variation-III (RUV-III), which makes vital use of technical replicates and suitable control genes. We also propose an approach using pseudo-replicates when technical replicates are not available. The effectiveness of RUV-III is illustrated on four different datasets. We also offer suggestions on the design and analysis of studies involving this technology.
“Mercedes-Benz Sign” on CSF Cytology

Cryptococcus meningitis is a potentially lethal disease, and cerebrospinal fluid cytology is crucial in establishing diagnosis. We report a novel and interesting morphological sign of Cryptococcus neoformansin CSF cytology resembling the logo of Mercedes-Benz. The sign is highly suggestive of Cryptococcus infection and is a strong indicator for more specific tests and timely treatment.
The Cumulative Prevalence of Termination of Parental Rights for U.S. Children, 2000–2016

Recent research has used synthetic cohort life tables to show that having a Child Protective Services investigation, experiencing confirmed maltreatment, and being placed in foster care are more common for American children than would be expected based on daily or annual rates for these events. In this article, we extend this literature by using synthetic cohort life tables and data from the Adoption and Foster Care Analysis and Reporting System to generate the first cumulative prevalence estimates of termination of parental rights. The results provide support for four conclusions. First, according to the 2016 estimate, 1 in 100 U.S. children will experience the termination of parental rights by age 18. Second, the risk of experiencing this event is highest in the first few years of life. Third, risks are highest for Native American and African American children. Nearly 3.0% of Native American children and around 1.5% of African American children will ever experience this event. Finally, there is dramatic variation across states in the risk of experiencing this event and in racial/ethnic inequality in this risk. Taken together, these findings suggest that parental rights termination, which involves the permanent loss of access to children for parents, is far more common than often thought.
Free-Space Time Domain Position Insensitive Technique for Simultaneous Measurement of Complex Permittivity and Thickness of Lossy Dielectric Samples

A novel time domain measurement technique is proposed to facilitate the simultaneous measurement of electrical properties (complex relative permittivity) and geometrical parameters (thickness) of the material under test (MUT). The overall process is noninvasive and noncontacting, which uses the measured scattering data of the MUT in the equivalent time domain or spatial domain. The effective time domain scattering data are employed to detect the primary and secondary peaks of the overall reflection and transmission coefficients. To this end, a novel algorithm is proposed to obtain the complex permittivity and thickness of the MUT in terms of extracted reflection and transmission power peaks. From the practical point of view, the main advantage of the proposed scheme is that one avoids the complicated calibration procedure normally required to define the reference plane. For increasing the accuracy of the overall reconstruction process, an automated optimization procedure based on parameter sensitivity analysis is proposed, which uses standard time gating procedure to implement the corresponding direct problem. The proposed technique is validated by extracting the relative permittivity, the dielectric loss (effective conductivity), and the thickness of various standard materials, such as polyethylene, Plexiglas, PVC, mortar, nylon, and so on, and comparing the extracted data with their values available in the literature.
Improving quality of adaptive video by traffic prediction with (F)ARIMA models

During the past years, adaptive video based on hypertext transfer protocol HTTP has become very popular. Streaming of the adaptive video relies heavily on an estimation of end-to-end network throughput, which can be challenging especially in mobile networks, where the capacity highly fluctuates. In this work, we propose to predict the network throughput using its past measurements. As the analysis shows, the network throughput forms a long range-dependent process, thus, for the throughput prediction we apply fractional ARIMA (FARIMA) model. Our approach does not require any modifications to the network infrastructure or the TCP stack. The predictions are performed for data traces obtained from measurements of throughput of a real mobile network. As the experiment shows, the obtained traffic model is able to enhance the performance of an adaptive streaming algorithm. Compared to the throughput predictors employed in contemporary systems dedicated to adaptive video streaming, the proposed technique obtains better results when taking into account effectiveness of network capacity utilisation and stability of video play-out.
Blood pressure at age 40 predicts carotid atherosclerosis two decades later: data from the Akershus Cardiac Examination 1950 Study.

OBJECTIVE We assessed the impact of a single time-point measurement of SBP, DBP and pulse pressure at the age of 40, on carotid plaque burden, echolucent plaques and carotid intima-media thickness late midlife. METHODS Individuals participating in two separate studies, 23 years apart, defined our cohort (n = 2714). 'The Age 40 Program', a nationwide Norwegian cardiovascular screening survey, performed 1985-1999, assessed cardiovascular risk factors and lifestyle variables at age 40. 'The ACE 1950 Study', a population-based cohort study on individuals born in 1950, performed 2012-2015, included ultrasound examinations of the carotid arteries. Blood pressure (BP) determinants of carotid atherosclerosis were assessed by regression models adjusted for cardiovascular risk factors at age 40, and late midlife BP. RESULTS The participants, 50.3% women, had a mean age of 40 (SD 0.3) years in the first study, and 64 (SD 0.6) years in the second. At age 40, mean SBP was 128 (SD 14) mmHg, mean DBP was 78 (SD 10) mmHg and mean pulse pressure was 50 (SD 9) mmHg. SBP and DBP at age 40 predicted carotid plaque burden in late midlife. Only DBP predicted echolucent plaques, and none of the BP components predicted carotid intima-media thickness. CONCLUSION A single time-point measurement of SBP and DBP at age 40 is associated with carotid plaque burden late midlife, also after adjustment for other cardiovascular risk factors at age 40, and of late midlife BP. Our findings emphasize the strong association between BP and atherosclerosis.
Crocin protects against dexamethasone-induced osteoblast apoptosis by inhibiting the ROS/Ca2+-mediated mitochondrial pathway

Osteoblast apoptosis has been identified as an important event in the development of glucocorticoid (GC)-induced osteoporosis and osteonecrosis of the femoral head. Crocin, a bioactive ingredient of saffron, has been demonstrated to induce antiapoptotic effects on numerous types of cell in vitro; however, the effects of crocin on the dexamethasone (Dex)-induced apoptosis of osteoblasts remain unclear. In the present study, the protective effects of crocin during Dex-induced apoptosis of MC3T3-E1 osteoblasts, and the underlying mechanisms, were investigated. MTT and Annexin V-FITC/PI flow cytometry assays were performed to evaluate the viability and apoptosis of cells, respectively. The mitochondrial transmembrane potential, reactive oxygen species (ROS), intracellular Ca2+ levels and apoptosis-associated protein expression were assessed via flow cytometry, fluorescence microscopy and western blotting. It was demonstrated that crocin pretreatment inhibited Dex-induced apoptosis of osteoblasts in a dose-dependent manner. Crocin reversed Dex-induced decreases in the mitochondrial transmembrane potential, and increases in ROS and intracellular Ca2+ levels. Furthermore, crocin upregulated the expression levels of B-cell lymphoma-2 (Bcl-2) and mitochondrial cytochrome c (Cyt C), and downregulated those of cleaved caspase-9, cleaved caspase-3, Bcl-2-associated X protein and cytoplasmic Cyt C. N-acetylcysteine, a ROS inhibitor, and 1,2-bis(2-aminophenoxy)ethane-N,N,N′,N′-tetraacetic acid, a calcium chelator, attenuated Dex-induced osteoblast apoptosis, whereas H2O2 and ionomycin, a calcium ionophore that increases intracellular calcium levels, reversed the antiapoptotic effects of crocin on Dex-treated osteoblasts. These results indicated that crocin may protect osteoblasts from Dex-induced apoptosis by inhibiting the ROS/Ca2+-mediated mitochondrial pathway, thus suggesting that crocin has potential value as a treatment for GC-induced bone diseases.
DNA double-strand break repair pathway choice - from basic biology to clinical exploitation

ABSTRACT Mutations in genes encoding components of the DNA damage response (DDR) are among the most frequent aberrations in human tumors. Moreover, a large array of human syndromes is caused by mutations in genes involved in DDR pathways. Among others, homologous recombination repair (HR) of DNA double-strand breaks (DSB) is frequently affected by disabling mutations. While impaired HR is clearly promoting tumorigenesis, it is also associated with an actionable sensitivity against PARP inhibitors. PARP inhibitors have recently received FDA approval for the treatment of breast- and ovarian cancer. However, as with all molecularly targeted agents, acquired resistance limits its use. Both pharmaco-genomic approaches and the study of human genome instability syndromes have led to a profound understanding of PARP inhibitor resistance. These experiments have revealed new insights into the molecular mechanisms that drive mammalian DSB repair. Here, we review recent discoveries in the field and provide a clinical perspective.
Functional Balance of the Hemagglutinin and Neuraminidase Activities Accompanies the Emergence of the 2009 H1N1 Influenza Pandemic

ABSTRACT The 2009 H1N1 influenza pandemic is the first human pandemic in decades and was of swine origin. Although swine are believed to be an intermediate host in the emergence of new human influenza viruses, there is still little known about the host barriers that keep swine influenza viruses from entering the human population. We surveyed swine progenitors and human viruses from the 2009 pandemic and measured the activities of the hemagglutinin (HA) and neuraminidase (NA), which are the two viral surface proteins that interact with host glycan receptors. A functional balance of these two activities (HA binding and NA cleavage) is found in human viruses but not in the swine progenitors. The human 2009 H1N1 pandemic virus exhibited both low HA avidity for glycan receptors as a result of mutations near the receptor binding site and weak NA enzymatic activity. Thus, a functional match between the hemagglutinin and neuraminidase appears to be necessary for efficient transmission between humans and may be an indicator of the pandemic potential of zoonotic viruses.
Symmetric Key Cryptography Using Random Key Generator

In the present work we have introduced a new symmetric key cryptographic method for encrypting as well as decrypting any file such as binary file, text file or any other file. In our method we have modified the idea of Play fair method into a new platform where we can encrypt or decrypt any file. We have introduced a new randomization method for generating the randomized key matrix to encrypt plain text file and to decrypt cipher text file. We have also introduced a new algorithm for encrypting the plain text multiple times. Our method is totally dependent on the random text_key which is to be supplied by the user. The maximum length of the text_key can be of 16 characters long and it may contain any character(ASCII code 0 to 255). We have developed an algorithm to calculate the randomization number and the encryption number from the given text_key. The size of the encryption key matrix is 16x16 and the total number of matrices can be formed from 16 x 16 is 256! which is quite large and hence if someone applies the brute force method then he/she has to give trail for 256! times which is quite absurd. Moreover the multiple encryption method makes the system further secured. We propose that our method could be appropriate in sensor network where the massive computation is not possible but the security of data is important at the same time.
Immunogenicity and Safety of a Quadrivalent Meningococcal ACWY-tetanus Toxoid Conjugate Vaccine 6 Years After MenC Priming as Toddlers.

BACKGROUND We assessed immunogenicity, antibody persistence and safety of the meningococcal serogroups A, C, W and Y-tetanus toxoid (TT) conjugate vaccine (MenACWY-TT) in children primed as toddlers with MenC vaccine. METHODS This open, multicenter extension study enrolled children 84-95 months of age who had received one dose of the combined Haemophilus influenzae type b (Hib)-MenC-TT conjugate vaccine (HibMenC group) or Hib-TT and monovalent MenC (MCC)-CRM197 vaccines (Hib+MCC group) at 12-18 months of age, in the primary study. All participants received one dose of MenACWY-TT. We assessed immunogenicity against MenA, MenC, MenW and MenY at 1 month and 2 years postvaccination by serum bactericidal assay using baby rabbit complement (rSBA). Safety and reactogenicity were evaluated. RESULTS Six years post-MenC vaccination, <20% of children retained rSBA-MenC titers ≥1:8. At 1 month post-MenACWY-TT vaccination, vaccine response rates against all serogroups were high for both groups with ≥97.1% of children having rSBA ≥1:8. Two years postvaccination, ≥63.6% of children retained rSBA-MenA ≥1:8, and ≥87.9% for other serogroups. Geometric mean titers for all serogroups declined at 2 years post-MenACWY-TT vaccination, but remained ≥13 times higher than prevaccination levels. For both groups, pain (≤58.5%), redness (≤51.4%) and fatigue (≤27.0%) were the most frequently reported adverse events. No serious adverse events were reported. CONCLUSIONS One dose of MenACWY-TT boosts protection against MenC in primed children, is safe and extends protection against MenA, MenW and MenY. Immunogenicity and safety were comparable in infants vaccinated with conjugated vaccine (HibMenC-TT) or the separate vaccines (Hib-TT and MCC-CRM197).
Fractionated stereotactic radiosurgery for the treatment of meningiomas.

BACKGROUND Although the vast majority of meningiomas are not malignant, their location within the cranial vault often leads to the development of symptoms. Traditional therapy has included observation, surgical resection, radiation therapy or a multimodality approach. The objective of this study is to review the outcomes in patients with meningioma treated at our institution using stereotactic radiosurgery. MATERIALS AND METHODS A total of 73 patients (median age of 59, 15 male and 58 female) with meningioma (median volume of 5.54 cc) underwent Cyber Knife TM stereotactic radiosurgery at our institution. Sixty patients had WHO grade 1 meningioma, eleven patients had WHO grade 2 meningioma, and two patients had WHO grade 3 meningioma. Treatment consisted of a median dose of 17.5 Gy (range, 6 - 27 Gy) delivered over a median of three fractions (range: 1 - 5). The patients were followed by clinical examination as well as serial imaging with magnetic resonance imaging (MRI). RESULTS The median follow-up was 16.1 months (range, 1.5 - 98.0). Follow-up MRI was available in all 73 patients. Local failure was documented in 11 cases. Actuarial local control at one year was 95, 71, and 0% for WHO grade 1, WHO grade 2, and WHO grade 3, respectively. There was no acute grade 3 or greater toxicity and only one episode of late grade 3 toxicity. A subjective improvement in the existing, tumor-related symptoms was noted in 60% of the patients. CONCLUSION Stereotactic radiosurgery is a safe and effective treatment for meningioma. Tumor-related symptoms often improve after treatment.