Miracle-dz/UniFAR-FTUs huggingface dataset:
Distribution of mutation frequencies among isolates from animal and human sources and genetic characterization of a Heidelberg hypermutator

Hypermutation is an important mechanism used by different subspecies to regulate genetic stability in adaptation to changing environments, including antimicrobial treatments and industrial processes. Strong hypermutator strains generally contain a mutation in genes of the methyl mismatch repair (MMR) system and have mutation frequencies up to 1000 fold higher than wild type strains. The objectives of this study were to determine the distribution of mutation frequencies from a collection of 209 strains, to genetically characterize a strong mutator, and to study MMR mutated protein-DNA binding interactions. Only one strain of Heidelberg was determined to have a hypermutator phenotype by virtue of its high mutation rate. Sequencing of genes of the MMR system showed a 12bp deletion in the S gene was present. The MMR mutated protein-DNA binding interactions were studied by bioanalysis, using the available crystal structure of a similar MutS protein from . This analysis showed the small deletion in the MutS was localized within the core domain. A retardation assay with MutS from hypermutable and wild type strains showed this mutation has no effect on MutS DNA binding. A better understanding of the genetic mechanisms of hypermutation will help to anticipate the behavior of hypermutator strains in various conditions.
THE EFFECT OF RACE AND SEX ON PHYSICIANS’ RECOMMENDATIONS FOR CARDIAC CATHETERIZATION

A BSTRACT Background Epidemiologic studies have reported differences in the use of cardiovascular procedures according to the race and sex of the patient. Whether the differences stem from differences in the recommendations of physicians remains uncertain. Methods We developed a computerized survey instrument to assess physicians’ recommendations for managing chest pain. Actors portrayed patients with particular characteristics in scripted interviews about their symptoms. A total of 720 physicians at two national meetings of organizations of primary care physicians participated in the survey. Each physician viewed a recorded interview and was given other data about a hypothetical patient. He or she then made recommendations about that patient’s care. We used multivariate logistic-regression analysis to assess the effects of the race and sex of the patients on treatment recommendations, while controlling for the physicians’ assessment of the probability of coronary artery disease as well as for the age of the patient, the level of coronary risk, the type of chest pain, and the results of an exercise stress test. Results The physicians’ mean (±SD) estimates of the probability of coronary artery disease were lower for women (probability, 64.1±19.3 percent, vs. 69.2±18.2 percent for men; P<0.001), younger patients (63.8±19.5 percent for patients who were 55 years old, vs. 69.5±17.9 percent for patients who were 70 years old; P<0.001), and patients with nonanginal pain (58.3±19.0 percent, vs. 64.4±18.3 percent for patients with possible angina and 77.1±14.0 percent for those with definite angina; P<0.001). Logistic-regression analysis indicated that women (odds ratio, 0.60; 95 percent confidence interval, 0.4 to 0.9; P=0.02) and blacks (odds ratio, 0.60; 95 percent confidence interval, 0.4 to 0.9; P=0.02) were less likely to be referred for cardiac catheterization than men and whites, respectively. Analysis of race–sex interactions showed that black women were significantly less likely to be referred for catheterization than white men (odds ratio, 0.4; 95 percent confidence interval, 0.2 to 0.7; P=0.004). Conclusions Our findings suggest that the race and sex of a patient independently influence how physicians manage chest pain. (N Engl J Med 1999; 340:618-26.)
Secrecy Rate Analysis of Open-Loop Analog Collaborative Beamforming Under Position Estimation Error of Virtual Antenna Array

As the importance to guarantee confidentiality against security attacks by eavesdroppers has attracted significant attention, there has been much effort to enhance the security performance through cooperative beamforming (CB) in the context of physical layer security (PLS). In particular, analog CB (ACB), which requires vastly lower overhead compared to digital CB, can provide significantly higher secrecy rate compared to the PLS methods with co-located array. In this letter, we focus on ACB with open-loop architecture that requires low complexity, and consider phase offsets across multiple virtual antenna array (VAA) elements for ACB, which are caused by position estimation error of VAA. We investigate the impact of the phase offsets in ACB in terms of the secrecy throughput loss.
Reactive Execution in a Command , Planning and Control Environment

The primary contributions of the research have been 1) a charac^rised model of rational behaviour 2) an inter-agent communication language (IACL) for adapting rational Denaviuui , causal structure to predict execution time behaviour and 3) Jhe ^e °fjaus reasoning ^bout ,0 rm:nt totasks failure'related to tasks, and tasks with temper^ extent i^raTwith lielasic sll of capabilities to provide a robust model for competent and rational situated behaviour. DTXC QUALITY INSPECTED 8
Commissioning of the European XFEL

The European X-ray Free-Electron Laser (EUROPEAN XFEL) in Hamburg, Northern Germany, was built to produce X-rays in the range from 0.25 up to 25 keV out of three undulators that can be operated simultaneously with up to 27,000 pulses per second. The EUROPEAN XFEL is driven by a 17.5 GeV superconducting linac. This linac is the worldwide largest installation based on superconducting radio-frequency acceleration, using the so-called TESLA technology which was developed for the superconducting version of an international electron posi-tron linear collider. The construction of the European XFEL has been finished at the end of 2016 and commissioning has been started. Meanwhile the entire facility, driving 3 Free-Electron-Lasers in the hard and soft X-ray regime, is in operation. This contribution will report on commissioning and the transition to user operation.
Development of introgression lines of AA genome Oryza species, O. glaberrima, O. rufipogon, and O. nivara, in the genetic background of O. sativa L. cv. Taichung 65

To evaluate and utilize potentially valuable quantitative trait loci or genes of wild relatives in the genetic background of domesticated crop species, chromosome segment substitution lines (CSSLs) are a valuable tool. CSSLs can be constructed through the exchange of chromosome segments of AA genome species of the genus Oryza with cultivated rice, Oryza sativa L. Here we report the development of three sets of CSSLs carrying segments of AA genome species closely related to Oryza sativa—O. glaberrima (IRGC 103777 from Mali), O. rufipogon (W1962 from China), and O. nivara (IRGC 105715 from Cambodia)—in the genetic background of ssp. japonica cultivar Taichung 65 through the use of 101 to 121 simple-sequence-repeat markers in whole-genome genotyping and marker-assisted selection. The materials are available via the National Bioresource Project (Rice) Oryzabase Web page.
Entropy-Based Segregation Indices

Recent research has shown that two entropy-based segregation indices possess an appealing mixture of basic and subsidiary but useful properties. It would appear that the only fundamental difference between the mutual information or M index, and the entropy information or H index, is that the second is a normalized version of the first. This paper introduces another normalized index in that family, the H* index, which captures segregation as the tendency of racial groups to have different distributions across schools. More importantly, the paper shows that applied researchers may do better using the M index than using either H or H* in two circumstances: (1) if they are interested in the decomposability of the measurement of segregation, and (2) if they are interested in a margin-free measurement of segregation changes. The shortcomings of the H and H* indices are illustrated below by means of numerical examples, as well as with school segregation data by ethnic group in the U.S. public school system between 1989 and 2005.
Analytical Approaches to Load Modulation Power Amplifier Design

In future mobile communication networks, there will be a shift toward higher carrier frequencies and highly integrated multiple antenna systems. The system performance will largely depend on the available radio frequency (RF) hardware. As such, RF power amplifiers (PAs) with improved performance, e.g. energy efficiency, are needed. Active load modulation (ALM) is one of the most common PA efficiency enhancement techniques. Unfortunately, different ALM techniques come at the cost of degrading other PA attributes. Through investigation of new ALM design techniques, the overall objective of this thesis is to improve upon different attributes and performance trade-offs in ALM PAs for future wireless systems. The working principle of ALM PAs is determined by both how the individual transistors are operated and how their outputs are combined. In the first part of the thesis, an analytical approach, where the output combiner is assumed to be an arbitrary black-box, is applied to the Doherty PA. The fundamental interaction between the main and auxiliary transistors is analyzed and generalized. New solutions with improved performance are identified, such as higher gain and an improved efficiency-linearity trade-off. This approach also introduces improved integration possibilities, which are demonstrated by a transmitter where the antenna acts as both the radiator and the Doherty combiner. Additionally, the analytical approach is applied to an isolated two-way power divider. This unlocks many new possibilities, such as improved integration and layout flexibility. In the second part, one embodiment of the emerging ALM architecture, the load modulated balanced amplifier (LMBA), is proposed: the RF-input Doherty-like LMBA. Design equations are derived and the fundamental operation is studied. This variant presents several advantages over other known architectures, such as higher gain and device periphery scaling of the different transistors. The third part proposes a new measurement-based ALM PA design procedure, which emulates the full behavior of the transistors in any ALM architecture using active load-pull measurements. This method can predict the intricate behavior in ALM PAs and it gives measurement-based insights into the internal operation of the circuit already at the design stage. This facilitates the design for optimal ALM PA performance. The thesis contributes with several promising techniques for reducing performance trade-offs and improving the overall performance of ALM PAs. Therefore, the results will contribute to the development of more energy efficient and high capacity wireless services in the future.
Parallel‐series connected rectenna array using frequency selective surface (FSS) for power harvesting applications at 5.8 GHz

This article presents a frequency selective surface (FSS) and rectenna array in parallel‐series connection to harvest power of wireless power systems. To improve the basic antenna parameters, a frequency selective surface was mounted on the reverse side of the substrate. According to the results, the proposed method showed significant improvement in comparison to other methods in both single and rectenna array. Moreover, the conversion efficiency of the presented technique was increased to 76%. The output voltage of 4.5 and 9 V and the current of 60 and 120 mA were resulted for 5 and 10 rectenna units, respectively. The proposed arrays can be expanded to large scale integrated array without any significant degradation in conversion efficiency.
Posttraumatic psychopathology and the pace of the epigenetic clock: a longitudinal investigation

Abstract Background Posttraumatic stress disorder (PTSD) and stress/trauma exposure are cross-sectionally associated with advanced DNA methylation age relative to chronological age. However, longitudinal inquiry and examination of associations between advanced DNA methylation age and a broader range of psychiatric disorders is lacking. The aim of this study was to examine if PTSD, depression, generalized anxiety, and alcohol-use disorders predicted acceleration of DNA methylation age over time (i.e. an increasing pace, or rate of advancement, of the epigenetic clock). Methods Genome-wide DNA methylation and a comprehensive set of psychiatric symptoms and diagnoses were assessed in 179 Iraq/Afghanistan war veterans who completed two assessments over the course of approximately 2 years. Two DNA methylation age indices (Horvath and Hannum), each a weighted index of an array of genome-wide DNA methylation probes, were quantified. The pace of the epigenetic clock was operationalized as change in DNA methylation age as a function of time between assessments. Results Analyses revealed that alcohol-use disorders (p = 0.001) and PTSD avoidance and numbing symptoms (p = 0.02) at Time 1 were associated with an increasing pace of the epigenetic clock over time, per the Horvath (but not the Hannum) index of cellular aging. Conclusions This is the first study to suggest that posttraumatic psychopathology is longitudinally associated with a quickened pace of the epigenetic clock. Results raise the possibility that accelerated cellular aging is a common biological consequence of stress-related psychopathology, which carries implications for identifying mechanisms of stress-related cellular aging and developing interventions to slow its pace.
Characterization of McDonald's intermediate part of the Central nucleus of the amygdala in the rat

The actual organization of the central nucleus of the amygdala (CEA) in the rat is mostly based on cytoarchitecture and the distribution of several cell types, as described by McDonald in 1982. Four divisions were identified by this author. However, since this original work, one of these divisions, the intermediate part, has not been consistently recognized based on Nissl‐stained material. In the present study, we observed that a compact condensation of retrogradely labeled cells is found in the CEA after fluorogold injection in the anterior region of the tuberal lateral hypothalamic area (LHA) in the rat. We then searched for neurochemical markers of this cell condensation and found that it is quite specifically labeled for calbindin (Cb), but also contains calretinin (Cr), tyrosine hydroxylase (TH) and methionine‐enkephalin (Met‐Enk) immunohistochemical signals. These neurochemical features are specific to this cell group which, therefore, is distinct from the other parts of the CEA. We then performed cholera toxin injections in the mouse LHA to identify this cell group in this species. We found that neurons exist in the medial and rostral CEAl that project into the LHA but they have a less tight organization than in the rat.
Protocol-independent brain MRI segmentation method

We present a segmentation method that combines the robust, accurate, and efficient techniques of fuzzy connectedness with standardized MRI intensities and fast algorithms. The result is a general segmentation framework that more efficiently utilizes the user input (for recognition) and the power of computer (for delineation). This same method has been applied to segment brain tissues from a variety of MRI protocols. Images were corrected for inhomogeneity and standardized to yield tissue-specific intensity values. All parameters for the fuzzy affinity relations were fixed for a specific input protocol. Scale-based fuzzy affinity was used to better capture fine structures. Brain tissues were segmented as 3D fuzzy-connected objects by using relative fuzzy connectedness. The user can specify seed points in about a minute and tracking the 3D fuzzy-connected objects takes about 20 seconds per object. All other computations were performed before any user interaction took place. Segmentation of brain tissues as 3D fuzzy-connected objects from MRI data is feasible at interactive speeds. Utilizing the robust fuzzy connectedness principles and fast algorithms, it is possible to interactively select fuzzy affinity, seed point, and threshold parameters and perform efficient, precise, and accurate segmentations.
Lateral Semicircular Canal Pressures During Cochlear Implant Electrode Insertion: a Possible Mechanism for Postoperative Vestibular Loss.

HYPOTHESIS Insertion of cochlear implant electrodes generates transient pressure spikes within the vestibular labyrinth equivalent to high-intensity acoustic stimuli. BACKGROUND Though cochlear implant (CI) surgery is regarded as having low risk of impacting the vestibular system, several studies have documented changes in vestibular function after implantation. The mechanism of these changes is not understood. We have previously established that large, potentially damaging pressure transients can be generated in the cochlea during electrode insertion, but whether pressure transients occur within the vestibular labyrinth has yet to be determined. Here, we quantify the exposure of the vestibular system to potentially damaging pressure transients during CI surgery. METHODS Five human cadaveric heads were prepared with an extended facial recess and implanted sequentially with eight different CI electrode styles via a round window approach. Fiber-optic sensors measured intralabyrinthine pressures in scala vestibuli, scala tympani, and the lateral semicircular canal during insertions. RESULTS Electrode insertion produced a range of high-intensity pressure spikes simultaneously in the cochlea and lateral semicircular canal with all electrodes tested. Pressure transients recorded were found to be significantly higher in the vestibular labyrinth than the cochlea and occurred at peak levels known to cause acoustic trauma. CONCLUSION Insertion of CI electrodes can produce transients in intralabyrinthine fluid pressure levels equivalent to high-intensity, impulsive acoustic stimuli. Results from this investigation affirm the importance of atraumatic surgical techniques and suggest that in addition to the cochlea, the vestibular system is potentially exposed to damaging fluid pressure waves during cochlear implantation.
Techniques for Efficiently Handling Power Surges in Fuel Cell Powered Data Centers: Modeling, Analysis, Results

Fuel cells are a promising power source for future data centers, offering high energy efficiency, low greenhouse gas emissions, and high reliability. However, due to mechanical limitations related to fuel delivery, fuel cells are slow to adjust to sudden increases in data center power demands, which can result in temporary power shortfalls. To mitigate the impact of power shortfalls, prior work has proposed to either perform power capping by throttling the servers, or to leverage energy storage devices (ESDs) that can temporarily provide enough power to make up for the shortfall while the fuel cells ramp up power generation. Both approaches have disadvantages: power capping conservatively limits server performance and can lead to service level agreement (SLA) violations, while ESD-only solutions must significantly overprovision the energy storage device capacity to tolerate the shortfalls caused by the worst-case (i.e., largest) power surges, which greatly increases the total cost of ownership (TCO). We propose SizeCap, the first ESD sizing framework for fuel cell powered data centers, which coordinates ESD sizing with power capping to enable a cost-effective solution to power shortfalls in data centers. SizeCap sizes the ESD just large enough to cover the majority of power surges, but not the worst-case surges that occur infrequently, to greatly reduce TCO. It then uses the smaller capacity ESD in conjunction with power capping to cover the power shortfalls caused by the worst-case power surges. As part of our new flexible framework, we propose multiple power capping policies with different degrees of awareness of fuel cell and workload behavior, and evaluate their impact on workload performance and ESD size. Using traces from Microsoft's production data center systems, we demonstrate that SizeCap significantly reduces the ESD size without violating any SLAs.
Sensor fault management techniques for wireless smart sensor networks in structural health monitoring

Faulty sensor data often occur in structural health monitoring (SHM) systems using wireless smart sensor networks (WSSN). Serious sensor faults in the raw data may negatively affect SHM analysis and subsequent informed decisions. This issue is more critical for WSSN running decentralized data acquisition, because raw data are not transmitted back, and hence, data quality assessment can be extremely difficult for users. Therefore, developing efficient techniques to autonomously detect, identify, and recover sensor faults is essential. In the vibration data collected from the Jindo Bridge, some data sets are corrupted with sensor faults, which can be categorized as one of three types: drift, spikes, and bias. Accordingly, this paper presents a three‐stage strategy to address this problem in WSSN. First, a distributed similarity test is employed to detect sensor faults; this test is based on the similarity of the power spectral density of the data among sensors within a cluster of nodes. Second, an artificial neural network model is trained to identify the types of sensor faults. Third, sensor data are recovered from the identified faults by applying a correction function or replacing faulty data with estimated values. Subsequently, numerical analysis is performed using a set of field measurements collected from the Jindo Bridge. Decentralized system identification is conducted using the original data and data recovered using the proposed strategy. The three‐stage strategy is shown to successfully detect, identify, and recover sensor faults, which improves the results of system identification. Finally, the benefits and limitations of this strategy are discussed.
Postgenomic Approaches and Bioinformatics Tools to Advance the Development of Vaccines against Bacteria of the Burkholderia cepacia Complex

Bacteria of the Burkholderia cepacia complex (Bcc) remain an important cause of morbidity and mortality among patients suffering from cystic fibrosis. Eradication of these pathogens by antimicrobial therapy often fails, highlighting the need to develop novel strategies to eradicate infections. Vaccines are attractive since they can confer protection to particularly vulnerable patients, as is the case of cystic fibrosis patients. Several studies have identified specific virulence factors and proteins as potential subunit vaccine candidates. So far, no vaccine is available to protect from Bcc infections. In the present work, we review the most promising postgenomic approaches and selected web tools available to speed up the identification of immunogenic proteins with the potential of conferring protection against Bcc infections.
Superradiance of Rydberg atoms in thermal vapour cells

In this thesis the investigation of superradiance in a thermal vapour of caesium atoms is reported. The atoms are continuously pumped to the Rydberg state with principal quantum number n = 32 via a two-photon excitation scheme. The superradiance is indirectly observed via the investigation of the optical fluorescence. It was observed that superradiance exhibits a threshold behaviour under continuous pumping. The threshold behaviour was studied for varying ground state density, Rabi frequency and excitation volume. It was shown that under certain conditions it is possible to influence the superradiant dynamics via the variation of the excitation volume. In order to describe the measurements a simple theoretical model was developed.