Miracle-dz/UniFAR-FTUs huggingface dataset:
Organization of Escherichia coli O157 O Antigen Gene Cluster and Identification of Its Specific Genes

ABSTRACT The O157:H7 clone of Escherichia coli, which causes major, often prolonged outbreaks of gastroenteritis with hemolytic-uremic syndrome (HUS) such as those in Japan, Scotland, and the United States recently, is thought to be resident normally in cattle or other domestic animals. This clone is of major significance for public health and the food industry. We have developed a fast method for sequencing a given O antigen gene cluster and applied it to O157. The O157 O antigen gene cluster is 14 kb in length, comprising 12 genes and a remnant H-repeat unit. Based on sequence similarity, we have identified all the necessary O antigen genes, including five sugar biosynthetic pathway genes, four transferase genes, the O unit flippase gene, and the O antigen polymerase gene. By PCR testing against all 166 E. coli O serogroups and a range of gram-negative bacterial strains, including some that cross-react serologically with E. coli O157 antisera, we have found that certain O antigen genes are highly specific to O157 E. coli. This work provides the basis for a sensitive test for rapid detection of O157 E. coli. This is important both for decisions on patient care, since early treatment may reduce the risk of life-threatening complications, and for detection of sources of contamination. The method for fast sequencing of O antigen gene clusters plus an ability to predict which genes will be O antigen specific will enable PCR tests to be developed as needed for other clones of E. coli or, once flanking genes are identified, clones of any gram-negative bacterium.
Transcultural communication and ethnic comparisons in the experience of services.

The General Medical Council (GMC) emphasises putting patients at the centre of practice and good communication skills are essential for clinical practice to be patient-centred.1 Reflecting this, three out of the GMC's 15 ‘duties of a doctor’ specifically relate to communication: namely to listen to patients and respect their views; give patients information in a way they can understand and respect the rights of patients to be fully involved in decisions about their care.2 There has been a concurrent increased interest in patient evaluations of both practitioners and services. Patient evaluations of GPs form one component of mandatory ‘GP appraisal’. Surveys asking patients about their experience and satisfaction are increasingly used to evaluate services. A number of different measures of patient satisfaction and service experience have been developed.3,4 These cover factors seem to be core features of quality of primary care, such as access, technical skills, communication, interpersonal care, patient-centredness, continuity and trust. While overall levels of satisfaction are high, a number of studies have reported less positive experiences and lower satisfaction with primary care services among those from ethnic minorities.3,5 In the Journal this month Ogden and Jain's study of patients' experiences found that Vietnamese patients reported more positive experiences of services than either white or black patients.6 The positive findings of the study should be seen in the context in which the study took place. The study setting was a single general practice, which was sufficiently interested in the service they were providing to ethnic minorities to take on a research project in this area. The authors point out that the practice served …
Scanning laser vibrometry imaging of fatigue cracks via nonlinear ultrasonic guided wave scattering and mode conversion

This paper presents the Scanning Laser Vibrometry (SLV) imaging of fatigue cracks by taking advantage of the nonlinear ultrasonic guided wave scattering and mode conversion phenomena. The investigation starts with the numerical modeling using the Local Interaction Simulation Approach (LISA) to demonstrate the distinctive scattering and mode conversion features at rough fatigue cracks. During the wave crack interactions, nonlinear higher harmonics are generated from Contact Acoustic Nonlinearity (CAN). In addition, the microscale rough crack surface condition may introduce mode conversion between the symmetric and antisymmetric Lamb modes. After the theoretical analysis, SLV experiments are conducted on an aluminum plate, where fatigue cracks are nucleated from a rivet hole. The damage imaging scheme utilizes the post-processing techniques via Fast Fourier Transform (FFT), frequency domain filtering, and Inverse Fast Fourier Transform (IFFT) to eliminate the linear wave field, leaving only the scattered higher harmonics in the images. In this way, the fatigue cracks can be distinguished from structural features such as rivet holes and stiffeners. This paper finishes with summary, concluding remarks, and suggestions for future work.
OFDM Vector Signal Generation Based on Optical Carrier Suppression

We propose a novel method to generate photonic quadrature-phase-shift-keying (QPSK) orthogonal frequency division multiplexing (OFDM) vector signal using only one Mach-Zehnder modulator, in which the OFDM signal is phase precoded and amplitude precoded according to the square-law characteristic of the photodetector. We theoretically analyze and experimentally demonstrate that this concept of the generation of the QPSK OFDM vector signal can be employed in our system architecture based on our proposed scheme. The results show that the bit-error ratios of the transmission system are less than the forward-error-correction threshold of 3.8 × 10-3. By this scheme, we simplify the configuration and reduce the cost of the OFDM transmission system.
A volumetric integral equation formulation for magnetic induction tomography

In magnetic induction tomography of biological tissue, an alternating magnetic field is used to induce eddy currents inside tissues, which in turn generate a secondary magnetic field. This perturbation of the field depends on the dielectric properties of the tissue and, through resolution of the inverse problem, a map of these properties can be reconstructed. Current state-of-art methods either rely on the quasi-static and low conductivity approximations or are based on differential solvers or surface integral equations. A formulation based on volumetric integral equations offers clear advantages such as a better accuracy than the approximative methods, a smaller solution domain than differential solvers and a better conditionning than surface integral methods. The aim of this paper is to formulate the eddy current problem in terms of a volume integral equation and to show its validity.
Children's adoption of self-reward patterns: incentive level and method of transmission.

This study investigated the effects of incentive level and method of transmission on children's adoption of a self-reward standard. A 2 X 2 X 3 factorial design with 2 incentive levels, sex of subjects, and 3 modes of training was employed. As predicted, high incentive resulted in greater rule violation than did low incentive when subjects performed alone. Further, as anticipated, modeling and direct training procedures both proved to be effective. A hypothesized "patterning" of rule deviations in the modeling and direct training groups was also found.
Tarantula Hemocyanin Shows Phenoloxidase Activity*

An enzyme generally catalyzes one well defined reaction with high specificity and efficiency. We report here in contrast that the copper protein hemocyanin of the tarantulaEurypelma californicum exhibits two different functions. These occur at the same active site. While hemocyanin usually is an oxygen carrier, its function can be transformed totally to monophenoloxidase and o-diphenoloxidase activity after limited proteolysis with trypsin or chymotrypsin.N-acetyldopamine (NADA) is more effectively oxidized thanl-dopa or dopamine. This irreversible functional switch of tarantula hemocyanin function is limited to the two subunitsb and c of its seven subunit types. A conserved phenylalanine in the hemocyanin molecule acts as a placeholder for other substrates that are phenylalanine derivatives. The proteolytic cleavage removes an N-terminal fragment, including the critical phenylalanine residue, which opens an entrance for substrates. Therefore no new arrangement of the active site, with its two copper atoms and the μ − η2:η2 bound O2 molecule, is necessary to develop the catalytic function.
Singing modulates mood, stress, cortisol, cytokine and neuropeptide activity in cancer patients and carers

There is growing evidence that psychosocial interventions can have psychological benefits for people affected by cancer, including improved symptoms of mental health and wellbeing and optimised immune responses. However, despite growing numbers of music interventions, particularly singing, in cancer care, there is less research into their impact. We carried out a multicentre single-arm preliminary study to assess the impact of singing on mood, stress and immune response in three populations affected by cancer: carers (n = 72), bereaved carers (n = 66) and patients (n = 55). Participants were excluded if pregnant or if they were currently being treated with chemotherapy, radiotherapy or oral immunosuppressive drugs. Participants were regular participants in five choirs across South Wales and took part in one hour of group singing. Before and after singing, visual analogue mood scales, stress scales and saliva samples testing for cortisol, beta-endorphin, oxytocin and ten cytokines were taken. Across all five centres and in all four participant groups, singing was associated with significant reductions in negative affect and increases in positive affect (p < .01) alongside significant increases in cytokines including GM-CSF, IL17, IL2, IL4 and sIL-2rα (all p < .01). In addition, singing was associated with reductions in cortisol, beta-endorphin and oxytocin levels. This study provides preliminary evidence that singing improves mood state and modulates components of the immune system. Further work is needed to ascertain how this differs for more specific patient groups and whether repeat exposure could lead to meaningful, longitudinal effects.
Parallel chamber calorimetric concept

A new type of a calorimetric measurement system concept for drives measurements based on open- and balance-type calorimeter is introduced and practically verified. The calorimetric concept with two parallel chambers is used to obtain the losses of the commercial frequency converter. The main advantage of this concept is the measurement rate of different operating points compared to the standard open- and balance-type calorimeter, because the main and balance test are carried out at the same time.
Identifying ad-hoc synchronization for enhanced race detection

Parallel programs contain a surprising number of ad-hoc synchronization operations. Ad-hoc synchronization operations are loops that busy-wait on condition variables. Current race detectors produce unnecessary warnings (false positives) when ad-hoc synchronization is used. False positives are also generated when programmers use synchronization primitives that are unknown to race detectors, for instance when programmers switch libraries. These shortcomings may result in an overwhelming number of false positives, dissuading programmers from using race detectors. This paper shows that ad-hoc synchronization operations can be detected automatically. The method requires no user intervention such as annotations and has been implemented in the race detector Helgrind+. Evaluation results on various benchmarks confirm that Helgrind+ is aware of all synchronizations in programs, reliably reports true races, and produces few false alarms. A surprising result is that with the new technique, Helgrind+ can analyze synchronization libraries, so special knowledge about these libraries is not needed in the detector.
Underlying reasons associated with hospital readmission following surgery in the United States.

IMPORTANCE Financial penalties for readmission have been expanded beyond medical conditions to include surgical procedures. Hospitals are working to reduce readmissions; however, little is known about the reasons for surgical readmission. OBJECTIVE To characterize the reasons, timing, and factors associated with unplanned postoperative readmissions. DESIGN, SETTING, AND PARTICIPANTS Patients undergoing surgery at one of 346 continuously enrolled US hospitals participating in the American College of Surgeons National Surgical Quality Improvement Program (ACS NSQIP) between January 1, 2012, and December 31, 2012, had clinically abstracted information examined. Readmission rates and reasons (ascertained by clinical data abstractors at each hospital) were assessed for all surgical procedures and for 6 representative operations: bariatric procedures, colectomy or proctectomy, hysterectomy, total hip or knee arthroplasty, ventral hernia repair, and lower extremity vascular bypass. MAIN OUTCOMES AND MEASURES Unplanned 30-day readmission and reason for readmission. RESULTS The unplanned readmission rate for the 498,875 operations was 5.7%. For the individual procedures, the readmission rate ranged from 3.8% for hysterectomy to 14.9% for lower extremity vascular bypass. The most common reason for unplanned readmission was surgical site infection (SSI) overall (19.5%) and also after colectomy or proctectomy (25.8%), ventral hernia repair (26.5%), hysterectomy (28.8%), arthroplasty (18.8%), and lower extremity vascular bypass (36.4%). Obstruction or ileus was the most common reason for readmission after bariatric surgery (24.5%) and the second most common reason overall (10.3%), after colectomy or proctectomy (18.1%), ventral hernia repair (16.7%), and hysterectomy (13.4%). Only 2.3% of patients were readmitted for the same complication they had experienced during their index hospitalization. Only 3.3% of patients readmitted for SSIs had experienced an SSI during their index hospitalization. There was no time pattern for readmission, and early (≤7 days postdischarge) and late (>7 days postdischarge) readmissions were associated with the same 3 most common reasons: SSI, ileus or obstruction, and bleeding. Patient comorbidities, index surgical admission complications, non-home discharge (hazard ratio [HR], 1.40 [95% CI, 1.35-1.46]), teaching hospital status (HR, 1.14 [95% CI 1.07-1.21]), and higher surgical volume (HR, 1.15 [95% CI, 1.07-1.25]) were associated with a higher risk of hospital readmission. CONCLUSIONS AND RELEVANCE Readmissions after surgery were associated with new postdischarge complications related to the procedure and not exacerbation of prior index hospitalization complications, suggesting that readmissions after surgery are a measure of postdischarge complications. These data should be considered when developing quality indicators and any policies penalizing hospitals for surgical readmission.
An Object-oriented Foundation for Desktop Computing

Integration based on low-level interoperability of autonomous software components causes a number of problems which hurt both user productivity and performance. In this paper, we propose an object-oriented foundation for architecturing next-generation desktop computing systems which should reduce, if not eliminate, these problems. This foundation provides extensible, protected and transparent management of distributed persistent objects. We use the example of next-generation hypermedia systems to illustrate our design choices. We also report on our computing environment prototype which implements solutions to some of the issues facing this foundation.
ACTIVE RESOURCES ALLOCATION FOR CLOUD VIRTUAL ENVIRONMENTS USING EASJSA

Cloud computing allows business customers to scale up and down their resource usage based on needs. Many of the touted gains in the cloud model come from resource multiplexing through virtualization technology. This project presents a system that uses virtualization technology to allocate data center resources dynamically based on application demands and support green computing by optimizing the number of servers in use. The existing system is "skewness" model introduced to measure the unevenness in the multidimensional resource utilization of a server. By minimizing skewness, we can combine different types of workloads nicely and improve the overall utilization of server resources. It develops a set of heuristics that prevent overload in the system effectively while saving energy used. In addition, this paper proposes an Enhanced Adaptive Scoring Job Scheduling Algorithm (EASJSA) for the cloud environment. Compared to other methods, it can decrease the completion time of submitted jobs, which may compose of computing-intensive jobs and data-intensive jobs.
There's the rub: a novel ubiquitin-like modification linked to cell cycle regulation.

Covalent attachment of the polypeptide ubiquitin to intracellular proteins is achieved through an intricate and highly conserved enzymatic pathway that is beginning to be understood in some detail (for review, see Wilkinson 1995; Hochstrasser 1996; Pickart 1997). Ubiquitin is joined reversibly to proteins by an isopeptide linkage of the carboxy-terminal carboxyl group of ubiquitin to lysine side chains of the acceptor proteins (Fig. 1). In the majority of cases examined, the modified protein, particularly when it is attached to multiple ubiquitin molecules, is targeted to a large, abundant intracellular protease called the proteasome, which degrades the substrate into small peptides but allows recycling of the ubiquitin moieties. Over the past few years, it has emerged that eukaryotes also express a set of ubiquitin-like proteins (Ubls) that are significantly diverged from ubiquitin itself yet are also ligated to other proteins (Haas and Siepmann 1997; Johnson and Hochstrasser 1997). The reactions involving these variants appear to have much in common with those of ubiquitin, but the Ubls have novel regulatory functions not necessarily linked to proteolysis. In this issue, Lammer et al. describe an unexpected connection between a Ubl called Rub1 (related to ubiquitin 1) from the yeast Saccharomyces cerevisiae and a ubiquitin–protein ligase complex that is critical for progression from G1 to S phase in the cell cycle. In this commentary, I will discuss these new results together with recent related developments on the mechanisms and functions of Ubl–protein ligation.
Gefitinib and erlotinib in metastatic non-small cell lung cancer: a meta-analysis of toxicity and efficacy of randomized clinical trials.

BACKGROUND Tyrosine kinase inhibitors (TKIs) targeting the epidermal growth factor receptor (EGFR) have been evaluated in patients with metastatic and advanced non-small cell lung cancer (NSCLC). The U.S. Food and Drug Administration initially granted accelerated approval to gefitinib but subsequently rescinded the authorization. Erlotinib and afatinib are similar compounds approved for the treatment of metastatic NSCLC. The objective of this study was to compare the efficacy and toxicity of erlotinib, gefitinib, and afatinib in NSCLC. METHODS We tabulated efficacy variables including overall response rate (ORR), progression-free survival (PFS), and overall survival (OS) and quantitated toxicities and rates of dose reductions and discontinuation. Summary odds ratios were calculated using random and fixed-effects models. An odds ratio was the summary measure used for pooling of studies. RESULTS We examined 28 studies including three randomized trials with afatinib. Clinical toxicities, including pruritus, rash, anorexia, diarrhea, nausea, fatigue, mucositis, paronychia, and anemia, were similar between erlotinib and gefitinib, although some statistical differences were observed. Afatinib treatment resulted in more diarrhea, rash, and paronychia compared with erlotinib and gefitinib. Regarding efficacy, similar outcomes were recorded for ORR, PFS, or OS in the total population and in specific subgroups of patients between erlotinib and gefitinib. All three TKIs demonstrated higher ORRs in first line in tumors harboring EGFR mutations. CONCLUSION Gefitinib has similar activity and toxicity compared with erlotinib and offers a valuable alternative to patients with NSCLC. Afatinib has similar efficacy compared with erlotinib and gefitinib in first-line treatment of tumors harboring EGFR mutations but may be associated with more toxicity, although further studies are needed. Gefitinib deserves consideration for U.S. marketing as a primary treatment for EGFR-mutant NSCLC.
Learning Bayesian Network Structure using LP Relaxations

We propose to solve the combinatorial problem of nding the highest scoring Bayesian network structure from data. This structure learning problem can be viewed as an inference problem where the variables specify the choice of parents for each node in the graph. The key combinatorial diculty arises from the global constraint that the graph structure has to be acyclic. We cast the structure learning problem as a linear program over the polytope dened by valid acyclic structures. In relaxing this problem, we maintain an outer bound approximation to the polytope and iteratively tighten it by searching over a new class of valid constraints. If an integral solution is found, it is guaranteed to be the optimal Bayesian network. When the relaxation is not tight, the fast dual algorithms we develop remain useful in combination with a branch and bound method. Empirical results suggest that the method is competitive or faster than alternative exact methods based on dynamic programming.
A 12 Gb/s 0.9 mW/Gb/s Wide-Bandwidth Injection-Type CDR in 28 nm CMOS With Reference-Free Frequency Capture

A wide band, low power, injection-locked oscillator (ILO)-type clock and data recovery (CDR) with high jitter tolerance is implemented in 28 nm CMOS. A robust phase and frequency detection algorithm independently controls ILO free running frequency and clock phase without an external time reference. A wide capture range of -25/+15% enables reference-free frequency acquisition. Jitter tolerance is 0.56 UI at 300 MHz and 1 UI at 120 MHz, with 2 UI locking time after optional calibration. The CDR operates from 1 to 12 Gbps, consuming 11 mW from 0.9 V supply at 12 Gbps for a power efficiency of 0.9 mW/Gbps. A comparison with published results shows a substantial improvement on the trend of wide CDR bandwidth coupled to degraded power efficiency.
Low speed maneuvering flight of the rose-breasted cockatoo (Eolophus roseicapillus). I. Kinematic and neuromuscular control of turning

SUMMARY Maneuvering flight has long been recognized as an important component of the natural behavior of many bird species, but has been the subject of little experimental work. Here we examine the kinematics and neuromuscular control of turning flight in the rose-breasted cockatoo Eolophus roseicapillus (N=6), testing predictions of maneuvering flight and control based on aerodynamic theory and prior kinematic and neuromuscular studies. Six cockatoos were trained to navigate between two perches placed in an L-shaped flight corridor, making a 90° turn midway through each flight. Flights were recorded with three synchronized high-speed video cameras placed outside the corridor, allowing a three-dimensional reconstruction of wing and body kinematics through the turn. We simultaneously collected electromyography recordings from bilateral implants in the pectoralis, supracoracoideus, biceps brachii and extensor metacarpi radialis muscles. The cockatoos maneuvered using flapping, banked turns with an average turn radius of 0.92 m. The mean rate of change in heading during a complete wingbeat varied through the turn and was significantly correlated to roll angle at mid-downstroke. Changes in roll angle were found to include both within-wingbeat and among-wingbeat components that bear no direct relationship to one another. Within-wingbeat changes in roll were dominated by the inertial effects while among-wingbeat changes in roll were likely the result of both inertial and aerodynamic effects.