Miracle-dz/UniFAR-FTUs huggingface dataset:
Preferential transmission in wild common shrews (Sorex araneus), heterozygous for Robertsonian rearrangements.

In Robertsonian heterozygotes for a particular arm combinaton equal transmission of the metacentric chromosome and two homologous acrocentrics would be expected. However, data from man and mouse suggest that this is not necessarily the case. In man, Boue (1979) and Hamerton (1970) provide evidence from prenatal diagnosis and family studies, respectively, that there is preferential transmission in favour of the 13q 14q Robertsonian metacentric over the acrocentric state in both male and female heterozygotes. By contrast, studies of spermatozoa from a 14q21q Robertsonian heterozygote man suggest preferential transmission in favour of the acrocentric chromosomes 14 and 21 (Balkan & Martin, 1983). In female laboratory mice there appears to be preferential transmission in favour of the acrocentric condition over a variety of feral-derived metacentrics (Gropp & Winking, 1981), while the Robertsonian metacentric (9-12) in female laboratory-bred, but feral-derived, Peruvian mice is apparently favoured over the acrocentric state (M. J. Harris, M. E. Wallace and E. P. Evans, personal communication).
Online Ordering of Overlapping Data Sources

Data integration systems offer a uniform interface for querying a large number of autonomous and heterogeneous data sources. Ideally, answers are returned as sources are queried and the answer list is updated as more answers arrive. Choosing a good ordering in which the sources are queried is critical for increasing the rate at which answers are returned. However, this problem is challenging since we often do not have complete or precise statistics of the sources, such as their coverage and overlap. It is further exacerbated in the Big Data era, which is witnessing two trends in Deep-Web data: first, obtaining a full coverage of data in a particular domain often requires extracting data from thousands of sources; second, there is often a big variation in overlap between different data sources. In this paper we present OASIS, an Online query Answering System for overlappIng Sources. OASIS has three key components for source ordering. First, the Overlap Estimation component estimates overlaps between sources according to available statistics under the Maximum Entropy principle. Second, the Source Ordering component orders the sources according to the new contribution they are expected to provide, and adjusts the ordering based on statistics collected during query answering. Third, the Statistics Enrichment component selects critical missing statistics to enrich at runtime. Experimental results on both real and synthetic data show high efficiency and scalability of our algorithm.
Effect of Blood Volume in Standard Anaerobic Blood Culture Bottles of the BacT/ALERT 3D System Used for the Detection of Pathogens and Time to Detection

Background Blood volume may profoundly affect the isolation of microorganisms in blood cultures. The effect of blood volume in standard anaerobic bottles of the BacT/ALERT 3D system was investigated. Methods Adult patients who visited the emergency department and referred for blood culture (n = 824) were enrolled from June to September 2013. Two sets of blood cultures were obtained from each patient. One set consisted of 5 mL that was collected in a standard aerobic bottle (SA5), 5 mL that was collected in a standard anaerobic bottle (SN5), and 10 mL that was collected in a standard anaerobic bottle (SN10). The growth of clinically significant pathogens and the time to detection (TTD) were compared between the SN5 and SN10 samples. Results Increasing the volume of blood collected from 5 to 10 mL yielded a 14.7% improvement in the isolation of microorganisms. There was a statistically significant difference in the isolation of pathogens (14 vs. 30, P = 0.023) between the SN5 and SN10 samples. Gram-positive microorganisms were detected earlier in the SN10 samples than the SN5 samples (P = 0.052). The mean TTD of all pathogens was 13.5 h for the SN5 samples and 12.9 h for the SN10 samples (P = 0.099). Conclusion Increased blood volume in the SN bottle yielded a significantly higher pathogen detection rate. However, there was no difference in the frequency of earlier detection or TTD between the SN5 and SN10 samples.
Role of herpesvirus as a cause of mononucleosis-like and febrile syndromes in Cuba, 2006-2009.

INTRODUCTION Herpesvirus infections are prevalent worldwide, but most run their course asymptomatically. Clinical presentations in symptomatic cases vary widely and include febrile and mononucleosis-like syndromes. In immunocompromised patients, herpetic infection can be lethal and routine laboratory tests are of little use. Use of novel techniques may provide important improvements in diagnosis and treatment of these patients. OBJECTIVE Investigate association between different herpesviruses and the etiology of mononucleosis and febrile syndromes in Cuban immunocompetent and immunocompromised patients. METHODS The study used multiplex nested polymerase chain reaction, enabling simultaneous detection of six herpesviruses--cytomegalovirus, herpes simplex (1 and 2), Epstein-Barr, varicella-zoster and human herpesvirus 6--to study 1157 samples (770 urine and 387 serum samples) from 1140 patients with mononucleosis-like syndrome or febrile syndrome, classified according to history of immunosuppressive disease. Samples were analyzed at the Laboratory for Sexually Transmitted Diseases (Virology) of the Pedro Kourí Tropical Medicine Institute from January 2006 through December 2009. SPSS statistical package was used and incidence rates calculated. RESULTS Of samples studied, 20.1% were positive for some herpesvirus. Higher risk of developing active herpesvirus infections was detected in samples from immunocompromised patients with febrile syndrome compared to those of immunocompetent ones (OR 2.02, CI 1.20-3.42, p=0.007). Cytomegalovirus was the most frequently found herpesvirus in both mononucleosis-like syndrome (60.4%) and febrile syndrome (63.6%) and in both children (69.2%) and adults (55.2%), followed by Epstein-Barr virus. Cytomegalovirus was detected in 68.9% of positive urine samples and in just 47.2% of serum samples. CONCLUSIONS This is the first Cuban study demonstrating the pathogenic role of herpesviruses, particularly cytomegalovirus, in patients with febrile or mononucleosis-like syndrome, in both immunocompetent and immunocompromised patients. Results highlight the importance of including molecular diagnosis of the herpesvirus family in investigating mononucleosis and febrile syndromes of unknown etiology and demonstrate that etiologic diagnosis would not have been feasible in many cases without the use of this diagnostic tool.
Analysis of Human Cytomegalovirus-Encoded SUMO Targets and Temporal Regulation of SUMOylation of the Immediate-Early Proteins IE1 and IE2 during Infection

Post-translational modification of proteins by members of the small ubiquitin-like modifier (SUMO) is involved in diverse cellular functions. Many viral proteins are SUMO targets and also interact with the cellular SUMOylation system. During human cytomegalovirus (HCMV) infection, the immediate-early (IE) proteins IE1 and IE2 are covalently modified by SUMO. IE2 SUMOylation promotes its transactivation activity, whereas the role of IE1 SUMOylation is not clear. We performed in silico, genome-wide analysis to identify possible SUMOylation sites in HCMV-encoded proteins and evaluated their modification using the E. coli SUMOylation system and in vitro assays. We found that only IE1 and IE2 are substantially modified by SUMO in E. coli, although US34A was also identified as a possible SUMO target in vitro. We also found that SUMOylation of IE1 and IE2 is temporally regulated during viral infection. Levels of SUMO-modified form of IE1 were increased during the early phase of infection, but decreased in the late phase when IE2 and its SUMO-modified forms were expressed at high levels. IE2 expression inhibited IE1 SUMOylation in cotransfection assays. As in IE2 SUMOylation, PIAS1, a SUMO E3 ligase, interacted with IE1 and enhanced IE1 SUMOylation. In in vitro assays, an IE2 fragment that lacked covalent and non-covalent SUMO attachment sites, but was sufficient for PIAS1 binding, effectively inhibited PIAS1-mediated SUMOylation of IE1, indicating that IE2 expression negatively regulates IE1 SUMOylation. We also found that the IE2-mediated downregulation of IE1 SUMOylation correlates with the IE1 activity to repress the promoter containing the interferon stimulated response elements. Taken together, our data demonstrate that IE1 and IE2 are the main viral SUMO targets in HCMV infection and that temporal regulation of their SUMOylation may be important in the progression of this infection.
Brain-computer interfaces for 1-D and 2-D cursor control: designs using volitional control of the EEG spectrum or steady-state visual evoked potentials

We have developed and tested two electroencephalogram (EEG)-based brain-computer interfaces (BCI) for users to control a cursor on a computer display. Our system uses an adaptive algorithm, based on kernel partial least squares classification (KPLS), to associate patterns in multichannel EEG frequency spectra with cursor controls. Our first BCI, Target Practice, is a system for one-dimensional device control, in which participants use biofeedback to learn voluntary control of their EEG spectra. Target Practice uses a KPLS classifier to map power spectra of 62-electrode EEG signals to rightward or leftward position of a moving cursor on a computer display. Three subjects learned to control motion of a cursor on a video display in multiple blocks of 60 trials over periods of up to six weeks. The best subject's average skill in correct selection of the cursor direction grew from 58% to 88% after 13 training sessions. Target Practice also implements online control of two artifact sources: 1) removal of ocular artifact by linear subtraction of wavelet-smoothed vertical and horizontal electrooculograms (EOG) signals, 2) control of muscle artifact by inhibition of BCI training during periods of relatively high power in the 40-64 Hz band. The second BCI, Think Pointer, is a system for two-dimensional cursor control. Steady-state visual evoked potentials (SSVEP) are triggered by four flickering checkerboard stimuli located in narrow strips at each edge of the display. The user attends to one of the four beacons to initiate motion in the desired direction. The SSVEP signals are recorded from 12 electrodes located over the occipital region. A KPLS classifier is individually calibrated to map multichannel frequency bands of the SSVEP signals to right-left or up-down motion of a cursor on a computer display. The display stops moving when the user attends to a central fixation point. As for Target Practice, Think Pointer also implements wavelet-based online removal of ocular artifact; however, in Think Pointer muscle artifact is controlled via adaptive normalization of the SSVEP. Training of the classifier requires about 3 min. We have tested our system in real-time operation in three human subjects. Across subjects and sessions, control accuracy ranged from 80% to 100% correct with lags of 1-5 s for movement initiation and turning. We have also developed a realistic demonstration of our system for control of a moving map display (http://ti.arc.nasa.gov/).
Concentrated runoff flow: implications for buffer design and water quality benefits.

Non-uniform or concentrated flow of surface runoff from agricultural fields can reduce the pollutant trapping effectiveness of buffer strips having constant width along a riparian zone or field margin. Effectiveness and cost-effectiveness might be improved by reconfiguring the buffer to be larger where more runoff flows and smaller where runoff is less. A GIS tool has been developed that accounts for non-uniform patterns of runoff flow which can be used for assessing performance of buffers and for designing them. This tool was used to assess the effect of nonuniform runoff on sediment trapping efficiency of constant-width buffer designs and to compare performance of constant-width and variable-size configurations. The tool is an ArcGIS extension based on the design model of Dosskey et al. (2011). It employs a digital elevation model (DEM) to divide the riparian area or field margin into many segments, determine contributing area and slope to each one and, then, design for a buffer area ratio that provides a specified level of trapping efficiency. The assessment procedure employs these same algorithms, but in a different order; first, determining the existing buffer area ratio and, then, calculating it's trapping efficiency. Results using this tool on a sample of fields in the Midwestern U.S. suggest that variable-size designs can be more than twice as effective per unit buffer area as conventional constant-width designs. Producing cost-effective designs and accurate performance assessments of buffers requires accounting for detailed spatial patterns of runoff flow from agricultural fields.
Barcoding rotifer biodiversity in Mediterranean ponds using diapausing egg banks

Abstract The biodiversity of Mediterranean freshwater bodies is among the most threatened worldwide; therefore, its accurate estimation is an urgent issue. However, traditional methods are likely to underestimate freshwater zooplankton biodiversity due to its high species seasonality and cryptic diversity. We test the value of applying DNA barcoding to diapausing egg banks, in combination with the creation of a reference collection of DNA barcodes using adult individual samples, to characterize rotifer communities. We use monogonont rotifers from two lakes in Doñana National Park and one from Ruidera Natural Park in Spain as models to create a reference collection of DNA barcodes for taxonomically diagnosed adult individuals sampled from the water column, to compare with the sequences obtained from individual eggs from the diapausing egg banks. We apply two different approaches to carry out DNA taxonomy analyses, the generalized mixed Yule coalescent method (GMYC) and the Automatic Barcode Gap Discovery (ABGD), to the obtained sequences and to publicly available rotifer sequences. We obtained a total of 210 new rotifer COI sequences from all three locations (151 diapausing eggs and 59 adults). Both GMYC and ABGD generated the same 35 operational taxonomic units (OTUs), revealing four potential cryptic species. Most sequences obtained from diapausing eggs (85%) clustered with sequences obtained from morphologically diagnosed adults. Our approach, based on a single sediment sample, retrieved estimates of rotifer biodiversity higher than or similar to those of previous studies based on a number of seasonal samples. This study shows that DNA barcoding of diapausing egg banks is an effective aid to characterize rotifer diversity in Mediterranean freshwater bodies.
Anterior Thalamic High Frequency Band Activity Is Coupled with Theta Oscillations at Rest

Cross-frequency coupling (CFC) between slow and fast brain rhythms, in the form of phase–amplitude coupling (PAC), is proposed to enable the coordination of neural oscillatory activity required for cognitive processing. PAC has been identified in the neocortex and mesial temporal regions, varying according to the cognitive task being performed and also at rest. PAC has also been observed in the anterior thalamic nucleus (ATN) during memory processing. The thalamus is active during the resting state and has been proposed to be involved in switching between task-free cognitive states such as rest, in which attention is internally-focused, and externally-focused cognitive states, in which an individual engages with environmental stimuli. It is unknown whether PAC is an ongoing phenomenon during the resting state in the ATN, which is modulated during different cognitive states, or whether it only arises during the performance of specific tasks. We analyzed electrophysiological recordings of ATN activity during rest from seven patients who received thalamic electrodes implanted for treatment of pharmacoresistant focal epilepsy. PAC was identified between theta (4–6 Hz) phase and high frequency band (80–150 Hz) amplitude during rest in all seven patients, which diminished during engagement in tasks involving an external focus of attention. The findings are consistent with the proposal that theta–gamma coupling in the ATN is an ongoing phenomenon, which is modulated by task performance.
Effects of a reward system on resident research productivity.

IMPORTANCE With the changing academic medical environment, nontraditional methods may need to be considered to foster research and scholarly activity during the otolaryngology residency experience. OBJECTIVE To evaluate the results of a reward system on resident research activity. DESIGN, SETTING, AND PARTICIPANTS Retrospective review of publications and approved institutional review board (IRB) projects between July 1, 1997, and June 30, 2011, among otolaryngology residents at a single otolaryngology residency program at the University of Missouri. INTERVENTION A resident reward system, which awards points for research efforts for each progressive step along the research path from project design to acceptance for publication, was implemented on July 1, 2004. Residents can convert points to a monetary amount to be used for academic enrichment. MAIN OUTCOMES AND MEASURES Publication rate and IRB approval rate were compared before and after institution of the reward system. Study design types that were published and study design types that received IRB approval were evaluated as well. We hypothesized that the reward system would increase research quantity and quality. RESULTS The mean publication output per resident per year increased from 0.13 (95% CI, 0.03-0.23) before commencement of the reward system to 0.43 (95% CI, 0.26-0.60) after implementation of the reward system (P = .004). Significantly more case reports were published compared with other study design types. The number of approved IRB projects before institution of the reward system was 0.47 (95% CI, 0.18-0.75) per resident per year. After instituting the reward system, this increased significantly to 1.29 (95% CI, 0.96-1.63) per resident per year (P = .007). Significant increases in IRB-approved case reports and retrospective clinical studies were noted. CONCLUSIONS AND RELEVANCE After implementation of a point-based reward system, resident research activity increased. The data suggest that this system may encourage resident research, although further refinement may be required to promote higher-quality research endeavors.
Clinical and Virological Aspects of Blood Donors Infected with Hepatitis B Virus Genotypes B and C

ABSTRACT Pathogenic and therapeutic differences among hepatitis B virus (HBV) genotypes have been documented. However, the association of virological characteristics with clinical differences among HBV genotypes remains unclear. We therefore studied the clinical and virological characteristics of Taiwanese volunteer blood donors infected with HBV genotypes B and C. HBV genotypes were determined in 300 candidate blood donors positive for HBV surface antigen (HBsAg), and sequences of the precore gene of the HBV genome were determined in 50 HBV e antigen (HBeAg)-positive and 50 HBeAg-negative blood donors. Of 300 HBsAg-positive blood donors, 10% had elevated serum aminotransferase levels and 27% were positive for HBeAg. HBV genotype distribution in 264 viremic carriers was as follows: B, 221 (83.7%); C, 39 (14.8%); F, 1 (0.4%); and mixed infection, 3 (1.1%). Blood donors with genotype C infection tended to have a higher frequency of HBeAg positivity and a higher serum HBV DNA level than those with genotype B infection. The frequency of precore stop codon mutation was significantly higher in HBeAg-negative blood donors than HBeAg-positive ones, irrespective of HBV genotypes. Meanwhile, only 5% of blood donors with genotype C infection had C-1858 strains. In conclusion, mixed infection of HBV genotypes indeed occurs, and genotype C has a higher serum HBV DNA level than genotype B. Precore stop codon mutation is common in HBeAg-negative HBV carriers, irrespective of HBV genotypes. In contrast, precore C-1858 strains are rarely identified in Taiwanese HBV genotype C.
Prolonged dynamic support from the Icelandic plume of the NE Atlantic margin

Sedimentary basins affected by hotspots often contain records of uplift and subsidence within coeval stratigraphic successions. The subsidence history can contain measurable perturbations in ancient palaeogeographies that can help constrain the duration of dynamic support. At c. 56 Ma the NE Atlantic experienced uplift related to the Iceland mantle plume. Within the Faroe–Shetland Basin, we document the stratigraphic record of subsidence following plume uplift, through integration of regional seismic datasets and well data. Subsidence following plume uplift is recorded by mapping the southward migration of palaeocoastlines throughout the early Eocene of the Faroe–Shetland Basin. We find that after initial uplift over 0.5 myr, subsidence was inhibited for 0.45 myr. Coeval with initiation of rifting in the North Atlantic, at 54.9 Ma, a c. 0.9 myr period of accelerated subsidence occurred, recorded by migration of the coastline by c. 80 km inland. We attribute these events to a prolonged period (2 myr) of dynamic support from the Iceland plume terminated by rapid loss of dynamic support coeval with rifting in the NE Atlantic at 54.9 Ma. Our results suggest that palaeogeographical analysis is a powerful tool in constraining the duration of dynamic support in basins affected by mantle plumes.
The Changing Character of Twenty-First-Century Precipitation over the Western United States in the Variable-Resolution CESM

AbstractThe changing characters of precipitation frequency and intensity have been comprehensively investigated from recent historical period to the end of the 21st century over the western United States. Variable-resolution Community Earth System Model (VR-CESM) ensemble simulations are applied with a fine grid resolution of ~0.25° over the study area. Simulations are forced with prescribed sea-surface temperatures, sea-ice extent and greenhouse gas concentrations from the representative concentration pathway (RCP) 8.5 scenario. VR-CESM is shown to be effective at accurately capturing the spatial patterns of the historical precipitation climatology. The results of VR-CESM output provide significantly regional details with crucial enhancement of precipitation representations over complex terrain. In the Intermountain West and Southwest U.S., we observe a statistically significant increase in mean precipitation and rainy days through mid-century, although this trend is tampered by end of century in respons.
Low energy FPGA interconnect design

We propose a new low energy FPGA interconnect fabric that is based on low energy switch blocks using Dynamic Threshold CMOS (DTMOS) based switches and an encoded-low swing (EL) technique. The presented case study illustrates that the encoded-low swing technique and Dual Threshold MOS based switches results in 41% energy reduction compared to the conventional technique using full swing signalling and NMOS pass transistor based switches. We also show through a theoretical analysis, that a certain timing budget can be met by the EL technique, using 11% more buffered switches, but still consuming 62% less energy than conventional techniques. Circuit simulations, taking also the transmitter and receiver complexity into account, are in line with the model results and indicate that a timing budget can be met at 30% less energy consumption. All our results are based on CMOS 0. 13μ process technology and are done using a transistor level simulator.