Miracle-dz/UniFAR-FTUs huggingface dataset:
The Population and Evolutionary Dynamics of Phage and Bacteria with CRISPR–Mediated Immunity

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), together with associated genes (cas), form the CRISPR–cas adaptive immune system, which can provide resistance to viruses and plasmids in bacteria and archaea. Here, we use mathematical models, population dynamic experiments, and DNA sequence analyses to investigate the host–phage interactions in a model CRISPR–cas system, Streptococcus thermophilus DGCC7710 and its virulent phage 2972. At the molecular level, the bacteriophage-immune mutant bacteria (BIMs) and CRISPR–escape mutant phage (CEMs) obtained in this study are consistent with those anticipated from an iterative model of this adaptive immune system: resistance by the addition of novel spacers and phage evasion of resistance by mutation in matching sequences or flanking motifs. While CRISPR BIMs were readily isolated and CEMs generated at high rates (frequencies in excess of 10−6), our population studies indicate that there is more to the dynamics of phage–host interactions and the establishment of a BIM–CEM arms race than predicted from existing assumptions about phage infection and CRISPR–cas immunity. Among the unanticipated observations are: (i) the invasion of phage into populations of BIMs resistant by the acquisition of one (but not two) spacers, (ii) the survival of sensitive bacteria despite the presence of high densities of phage, and (iii) the maintenance of phage-limited communities due to the failure of even two-spacer BIMs to become established in populations with wild-type bacteria and phage. We attribute (i) to incomplete resistance of single-spacer BIMs. Based on the results of additional modeling and experiments, we postulate that (ii) and (iii) can be attributed to the phage infection-associated production of enzymes or other compounds that induce phenotypic phage resistance in sensitive bacteria and kill resistant BIMs. We present evidence in support of these hypotheses and discuss the implications of these results for the ecology and (co)evolution of bacteria and phage.
Inactivation of 9q22.3 tumor suppressor genes predict outcome for patients with head and neck squamous cell carcinoma.

AIM This study examined the prognostic significance of candidate tumor suppressor genes (TSGs) PHD finger protein-2 (PHF2), Fanconi anaemia complementation group C (FANCC) and human homologue of Drosophila patched gene (PTCH1), in head and neck squamous cell carcinoma (HNSCC) treated primarily with surgery, or surgery followed by adjuvant radiotherapy. PATIENTS AND METHODS Eighty-four patients with HNSCC were followed-up for recurrence/death for up to five years after diagnosis. Molecular alterations (deletion/methylation) of TSGs and human papilloma virus (HPV) status were determined in previous studies of our group. Statistical analyses of correlation of genetic alterations with treatment response and survival were carried out. RESULTS Alterations of FANCC and PTCH1 were significantly associated with locoregional recurrence/death. In the surgery with adjuvant radiotherapy-group (n=56), patients showing alterations in FANCC and in PTCH1 were seven- and six-times, respectively, more likely to have locoregional recurrence compared to those with no alterations. In addition, the presence of alterations of both FANCC and PTCH1 had remarkable prognostic significance. CONCLUSION FANCC and PTCH1 alterations might be used as molecular markers for prognosis and to develop strategies for effective treatment planning.
Reporting false indications of startup analysis when diagnosing damper damages in synchronous motors

The analysis of the startup current has been recently revealed as an excellent informational source for the diagnosis of the rotor condition in electric motors. In induction machines, the analysis of such current may provide important advantages versus the classical method employed for rotor assessment (Motor Current Signature Analysis, MCSA), as the avoidance of eventual false indications obtained with the traditional approach or its suitability for any operating condition of the machine. In this context, the startup current analysis is increasingly employed to complement (or even to discard) the diagnostic conclusions obtained with MCSA. With regards to synchronous motors, the analysis of the startup current is also an interesting option to determine the condition of the damper cage. However, the investigation on this latter issue is still incipient and only circumscribed to particular geometries of the damper. The present paper analyses the suitability of the startup current analysis for assessing the condition of the damper cage in salient-pole synchronous motors. The interesting results show that, for these machines, due to the particular construction of the damper, false positive indications are obtained when relying on startup analysis. This important fact is of great interest to avoid false diagnostics in the field when assessing the condition of such elements.
Maternal nutritional status, C1 metabolism and offspring DNA methylation: a review of current evidence in human subjects

Evidence is growing for the long-term effects of environmental factors during early-life on later disease susceptibility. It is believed that epigenetic mechanisms (changes in gene function not mediated by DNA sequence alteration), particularly DNA methylation, play a role in these processes. This paper reviews the current state of knowledge of the involvement of C1 metabolism and methyl donors and cofactors in maternal diet-induced DNA methylation changes in utero as an epigenetic mechanism. Methyl groups for DNA methylation are mostly derived from the diet and supplied through C1 metabolism by way of choline, betaine, methionine or folate, with involvement of riboflavin and vitamins B6 and B12 as cofactors. Mouse models have shown that epigenetic features, for example DNA methylation, can be altered by periconceptional nutritional interventions such as folate supplementation, thereby changing offspring phenotype. Evidence of early nutrient-induced epigenetic change in human subjects is scant, but it is known that during pregnancy C1 metabolism has to cope with high fetal demands for folate and choline needed for neural tube closure and normal development. Retrospective studies investigating the effect of famine or season during pregnancy indicate that variation in early environmental exposure in utero leads to differences in DNA methylation of offspring. This may affect gene expression in the offspring. Further research is needed to examine the real impact of maternal nutrient availability on DNA methylation in the developing fetus.
3D Timeline: Reverse engineering of a part‐based provenance from consecutive 3D models

We present a novel tool for reverse engineering of modeling histories from consecutive 3D files based on a timeline abstraction. Although a timeline interface is commonly used in 3D modeling packages for animations, it has not been used on geometry manipulation before. Unlike previous visualization methods that require instrumentation of editing software, our approach does not rely on pre‐recorded editing instructions. Instead, each stand‐alone 3D file is treated as a keyframe of a construction flow from which the editing provenance is reverse engineered. We evaluate this tool on six complex 3D sequences created in a variety of modeling tools by different professional artists and conclude that it provides useful means of visualizing and understanding the editing history. A comparative user study suggests the tool is well suited for this purpose.
The Trajectory of Dispersal Research in Conservation Biology. Systematic Review

Dispersal knowledge is essential for conservation management, and demand is growing. But are we accumulating dispersal knowledge at a pace that can meet the demand? To answer this question we tested for changes in dispersal data collection and use over time. Our systematic review of 655 conservation-related publications compared five topics: climate change, habitat restoration, population viability analysis, land planning (systematic conservation planning) and invasive species. We analysed temporal changes in the: (i) questions asked by dispersal-related research; (ii) methods used to study dispersal; (iii) the quality of dispersal data; (iv) extent that dispersal knowledge is lacking, and; (v) likely consequences of limited dispersal knowledge. Research questions have changed little over time; the same problems examined in the 1990s are still being addressed. The most common methods used to study dispersal were occupancy data, expert opinion and modelling, which often provided indirect, low quality information about dispersal. Although use of genetics for estimating dispersal has increased, new ecological and genetic methods for measuring dispersal are not yet widely adopted. Almost half of the papers identified knowledge gaps related to dispersal. Limited dispersal knowledge often made it impossible to discover ecological processes or compromised conservation outcomes. The quality of dispersal data used in climate change research has increased since the 1990s. In comparison, restoration ecology inadequately addresses large-scale process, whilst the gap between knowledge accumulation and growth in applications may be increasing in land planning. To overcome apparent stagnation in collection and use of dispersal knowledge, researchers need to: (i) improve the quality of available data using new approaches; (ii) understand the complementarities of different methods and; (iii) define the value of different kinds of dispersal information for supporting management decisions. Ambitious, multi-disciplinary research programs studying many species are critical for advancing dispersal research.
Human-Readable Machine-Verifiable Proofs for Teaching Constructive Logic

A linear syntax for natural deduction proofs in first-order intuitionistic logic is presented, which has been an effective tool for teaching logic. The proof checking algorithm is also given, which is the core of the tutorial proof checker Tutch. This syntax is then extended to proofs on the assertion level which resemble single inferences one would make in a rigorous proof. The resulting language has only four constructs. Checking of these proofs is decidable, and an efficient algorithm is given.
SmartVenues: Recommending Popular and Personalised Venues in a City

We present SmartVenues, a system that recommends nearby venues to a user who visits or lives in a city. SmartVenues models the variation over time of each venue's level of attendance, and uses state-of-the-art time series forecasting algorithms to predict the future attendance of these venues. We use the predicted levels of attendance to infer the popularity of a venue at future points in time, and to provide the user with recommendations at different times of the day. If the users log in with their Facebook account, the recommendations are personalised using the pages they "like". In this demonstrator, we detail the architecture of the system and the data that we collect in real-time to be able to perform the predictions. We also present two different interfaces that build upon our system to display the recommendations: a web-based application and a mobile application.
Saturation throughput of IEEE 802.11e EDCA based on mean value analysis

The IEEE 802.11-based wireless LANs have been widely deployed for local area high-speed data access. The IEEE 802.11e amendment aims at providing QoS provisioning to support real-time multimedia traffic in WLANs. The enhanced distributed channel access (EDCA) is a QoS extension of the distributed coordination function (DCF) in IEEE 802.11a/b/g. In this paper, we propose an analytical model to evaluate the saturation throughput of the IEEE 802.11e EDCA. Our analytical model is based on the use of mean value analysis. We carry out extensive simulation study to validate the accuracy of the proposed model. Our scheme models accurately the effects of the change of contention window size and AIFS (arbitration inter-frame space). Our analytical model is applicable to real-time system tuning and on-line admission control algorithms which require a low computation complexity
Studying antecedents of emotional experiences in interactive contexts

This paper describes a research approach to the experimental study of emotional experiences and their connections to other components of user experience in human-technology interaction. We present a model of user experience that integrates interaction characteristics, instrumental and non-instrumental quality perceptions, emotional user reactions and overall judgments of system quality. An experiment is reported to illustrate the application of our approach. System properties of an interactive prototype were varied to produce versions of different usability and aesthetics which in turn led to different perceptions of instrumental and non-instrumental qualities. The results indicate that both quality aspects significantly influence emotional reactions with respect to subjective feelings, facial expressions and physiological responses. These findings are consistent with the users' overall judgments of the systems and show that the perception of both, instrumental and non-instrumental qualities influences the appraisal of interactive systems.
R 25 Mutually Coupled Ring Oscillators for Large Array Time-of-Flight Imagers

Time-of-flight (TOF) image sensors require high levels of accuracy and precision on time quantization, typically through a Time-to-Digital Converters (TDCs). Achieving such performance, while keeping power consumption low, is not trivial, even more for large arrays. Although offsets (from asymmetry, overall speed variation, IR-drop induced variations, etc.) can be calibrated and corrected, varying offsets are harder to compensate for. In this paper, we present a simple and robust method for synchronization that drastically reduces process-voltagetemperature (PVT) variations, while providing noise filtering to reduce accumulated jitter. An 8 x 8 array of ring oscillators (RO), serving as many TDCs, is implemented. About 18 dB better phase noise and 14 dB better jitter is obtained, under 200 μW/GHz power efficiency and better than 100 ps resolution. Index Terms — ring oscillators, coupled-oscillators, brusselator, time-to-digital converter, TDC, LIDAR, time-offlight, TOF, noise reduction.
Hybrid procedure in a patient with symptomatic thoraco-abdominal aneurysm and prior abdominal aortic reconstruction – case report

Open repair of thoracoabdominal aortic aneurysm is connected with high mortality and morbidity. On the other hand, endovascular treatment of thoraco-abdominal aneurysms, which started 10 years ago, reduced perioperative mortality and morbidity. However, it results in a high level of late complications. It seems that an interesting solution to the problem is a hybrid procedure, which allows late complications to be reduced with acceptable levels of operative mortality and morbidity. This case report presents the use of a hybrid procedure in treatment of symptomatic thoraco-abdominal aneurysm in a patient with prior abdominal aortic reconstruction. In the first stage the patient underwent open revascularization of visceral vessels of the aorta. One week later a thoraco-abdominal stent-graft was implanted. The perioperative and postoperative period was uncomplicated. Two months after the second intervention the patient returned to work. Control imaging conducted 30 and 90 days after the procedure confirmed patency of all revascularized vessels and did not reveal any graft-related complications. The hybrid procedure seems to be an interesting alternative for open and endovascular repair of thoraco-abdominal aneurysms because it combines the advantages of open and endovascular repair. It also gives an opportunity to perform the procedure within a reasonable period of time from diagnosis of symptomatic thoraco-abdominal aneurysm.
Palliative Care of the Terminally Ill Drug Addict

Palliative care with terminally ill drug addicts is a major challenge for medical professionals to face. With growing problems of prescription drug abuse in this country, the problem is only going to continue to grow and be faced more often. To date, very little has been done focusing on this special population of end-of-life care patients. This review article attempts to explore the terminology and definitions for identifying addiction in the terminally ill as well as exploring management options for healthcare professionals. As with other opioid treated pain patients, relying on terms such as “physiological dependence” and “tolerance” is inappropriate for use in this population, who are likely to have been on opioids for extended periods of time requiring dose escalation for progressive disease. Thus, these terms have little utility for identifying problem patients. Rather, understanding the context of the drug abuse as it reflects on the concepts of use despite harm and the damage inflicted to the physical, psychological, or social make-up of the patient is necessary. Recommendations include careful monitoring and assessment of patients, utilizing multidisciplinary team approaches, encouraging participation in recovery programs, and utilization of pill counts and urine toxicology screenings as necessary. Implications for the field are discussed.
Kinetic spanners in Rd

We present a new (1+ε)-spanner for sets of n points in R<sup>d</sup>. Our spanner has size O(n/ε<sup>d-1</sup>) and maximum degree O(log<sup>d</sup> n). The main advantage of our spanner is that it can be maintained efficiently as the points move: Assuming the trajectories of the points can be described by bounded-degree polynomials, the number of topological changes to the spanner is O(n<sup>2</sup>/ε<sup>d-1</sup>), and using a supporting data structure of size O(n log<sup>d</sup>n) we can handle events in time O(log<sup>d+1</sup>n). Moreover, the spanner can be updated in time O(log n) if the flight plan of a point changes. This is the first kinetic spanner for points in R<sup>d</sup> whose performance does not depend on the spread of the point set.
Optimization Research on Processes I/O Performance in Container-level Virtualization

As representative of container-level virtualization, the core idea of OpenVZ group scheduling is fairness. System ensures CPU time is shared fairly among virtual containers and among processes belonging to the same container. Thus processes may not be scheduled immediately when awakened by I/O, affecting their responsiveness and I/O throughput. If breaking this kind of absolute fairness and permitting processes to deal with current burst I/O events by borrowing their future time temporarily, I/O performance will be improved. The approach also does not destroy system fairness in the long run. The paper analyses OpenVZ group scheduling and points out factors that affect I/O performance of processes in virtual containers. To solve these problems, we make two layers of optimization. In virtual container layer, we implement container preemption based on I/O by priority queue, in bottom layer, we still permit optimized processes to take precedence over other processes to use CPU in the case of continuous I/O, also maintaining original time mechanism and minimizing system modification. We evaluate network response time, network throughput, block I/O throughput, test results demonstrate at the scheduling cost of 2.9% processes’ I/O performance is ameliorated remarkably.
Dressing Field Control of Band Gap Reflection in a Homogeneous Atomic Medium

Dressing field control of band gap reflection is investigated in an inverse Y-type four-level atomic system. It is shown that when the dressing field is blocked, a band gap reflection with a maximum bandwidth and nearly ~90% reflectivity can be achieved for the detuning of the coupling field . When a weak dressing field is applied to the system (the intensity is much less than that of the coupling field), a narrowing top flat with ~86% reflectivity of the band gap reflection is observed in comparison with that in the first case. We also show that the band gap reflection can be dramatically suppressed due to the collapse of the stop band when a strong dressing field (the intensity is comparable with or larger than that of the coupling field) is employed. This control of photonic band gap reflection can be used in the applications of all-optical reflection mirrors and band optical filters.
A Hybrid Photoreceptor Expressing Both Rod and Cone Genes in a Mouse Model of Enhanced S-Cone Syndrome

Rod and cone photoreceptors subserve vision under dim and bright light conditions, respectively. The differences in their function are thought to stem from their different gene expression patterns, morphologies, and synaptic connectivities. In this study, we have examined the photoreceptor cells of the retinal degeneration 7 (rd7) mutant mouse, a model for the human enhanced S-cone syndrome (ESCS). This mutant carries a spontaneous deletion in the mouse ortholog of NR2E3, an orphan nuclear receptor transcription factor mutated in ESCS. Employing microarray and in situ hybridization analysis we have found that the rd7 retina contains a modestly increased number of S-opsin–expressing cells that ultrastructurally appear to be normal cones. Strikingly, the majority of the photoreceptors in the rd7 retina represent a morphologically hybrid cell type that expresses both rod- and cone-specific genes. In addition, in situ hybridization screening of genes shown to be up-regulated in the rd7 mutant retina by microarray identified ten new cone-specific or cone-enriched genes with a wide range of biochemical functions, including two genes specifically involved in glucose/glycogen metabolism. We suggest that the abnormal electroretinograms, slow retinal degeneration, and retinal dysmorphology seen in humans with ESCS may, in part, be attributable to the aberrant function of a hybrid photoreceptor cell type similar to that identified in this study. The functional diversity of the novel cone-specific genes identified here indicates molecular differences between rods and cones extending far beyond those previously discovered.
Laminar distribution of pheromone‐receptive neurons in rat vomeronasal epithelium

1 Responses of vomeronasal sensory neurons to urine excreted from rats, mice and hamsters were studied by the on‐cell patch clamp method in slices of sensory epithelium from female Wistar rats. 2 The urine excreted from male and female Wistar rats, male Donryu rats and male C57BL/6 mice induced relatively large responses, while urine from male Sprague‐Dawley rats and male Syrian hamsters induced small responses. 3 Of the 62 neurons responding to urine, 57 responded to only one of the urine preparations. 4 The sensory neurons that responded to the male Wistar urine were localized in the apical position of the epithelium where one type of GTP‐binding protein, Gi2α, is selectively expressed. The neurons in the basal position of the epithelium, which express Goα, responded to urine from the other animals. 5 This study demonstrates that sensory neurons responsive to different urinary pheromones are localized in a segregated layer in the rat vomeronasal sensory epithelium.