Miracle-dz/UniFAR-FTUs huggingface dataset:
ExonHunter: a comprehensive approach to gene finding

MOTIVATION We present ExonHunter, a new and comprehensive gene finding system that outperforms existing systems and features several new ideas and approaches. Our system combines numerous sources of information (genomic sequences, expressed sequence tags and protein databases of related species) into a gene finder based on a hidden Markov model in a novel and systematic way. In our framework, various sources of information are expressed as partial probabilistic statements about positions in the sequence and their annotation. We then combine these into the final prediction via a quadratic programming method, which we show to be an extension of existing methods. Allowing only partial statements is key to our transparent handling of missing information and coping with the heterogeneous character of individual sources of information. In addition, we give a new method for modeling the length distribution of intergenic regions in hidden Markov models. RESULTS On a commonly used test set, ExonHunter performs significantly better than the existing gene finders ROSETTA, SLAM and TWINSCAN, with more than two-thirds of genes predicted completely correctly. AVAILABILITY Supplementary material available at http://www.bioinformatics. uwaterloo.ca/supplements/05eh/
OF THE EXPERIMENTAL ANALYSIS OF BEHAVIOR THREE VERSIONS OF THE ADDITIVE THEORIES OF BEHAVIORAL CONTRAST

The additive theories of behavioral contrast state that contrast will occur only when two types of responses interact during multiple schedules. Three more specific versions of the theories may be defined according to how they distinguish these two types of responses. A strong version physically distinguishes them. A second version distinguishes them according to the theoretical processes which control them. A weak version distinguishes them on the basis of the environmental relations which control them. Only the weak version of the theories is currently testable. The weak theory should be tested by establishing each of the two environmental relations independently and then combining them to assess their effect on behavior. Because this test is not usually performed, many of the results which have been taken to support or contradict the additive theories are actually ambiguous.
Using webinars to extend the reach of soil learning in New South Wales: A first look

Increasingly knowledge is shared using new web‐based channels. The use of these channels is relatively new in the realm of soil science. However, they may prove to be very useful for connecting time‐poor, geographically dispersed audiences in an efficient and cost‐effective way. There has been limited study of this form of knowledge sharing for natural science (let alone soil science). In New South Wales (NSW), Australia, the NSW Department of Primary Industries (NSW DPI) has coordinated the Soil Network of Knowledge (SNoK) monthly webinar over 3 years, with over 40 webinars targeting an audience of next users of soil information. Aggregated data collected from these webinars indicated that the majority of information is used for professional development by participants. Whether this will eventually lead to on‐ground practice change because of the improved professional and technical knowledge of participants is still a moot point and will require further investigation over time. The information collected on attendance and participation showed that webinars are a good way to connect with some target audiences such as other government bodies that have a historical relationship with NSW DPI. However, other target audiences that NSW DPI has always found difficulty in engaging, such as private advisers, require more active overtures to drive participation. The growing subscriber base is encouraging.
Pretreatment Neutrophil to Lymphocyte Ratio as a Prognostic Predictor of Urologic Tumors

AbstractThe relationship between inflammation and tumor development and progression has been recognized in recent decades. NLR is an easily reproducible and widely used inflammatory response marker. The prognostic value of NLR for urologic tumors has been reported in succession. Here, we perform a systematic review and meta-analysis to summarize the association between the NLR and prognosis of urologic tumors.We conducted a computerized search of PubMed, Embase, and ISI Web of Knowledge to identify clinical studies that had evaluated the association between the pretreatment NLR and prognosis in urologic tumors. Prognostic outcomes included overall survival (OS), cancer-specific survival (CSS), recurrence-free survival (RFS), progression-free survival (PFS), and metastasis-free survival (MFS). We extracted and synthesized corresponding hazard ratios (HRs) and confidence intervals (CIs) using Review Manager 5.3 and STATA 13.We identified 34 retrospective cohort studies and conducted the meta-analysis. The results showed that all OS, CSS, RFS, PFS, and MFS risks were significantly different between patients with an elevated NLR and those with a low NLR in various urologic tumors. A high NLR portended poor prognosis. However, no significance was observed for CSS in patients with renal cell carcinoma (HR = 1.38, 95% CI: 0.96–1.99). Our meta-analysis suggests that NLR could be a prognostic predictor for urologic tumors. Patients with a high NLR were deemed to have a poor prognosis.
Extended abstract: A quantitative discourse analysis of first-year engineering student reflections: A pilot study of a service learning communication assignment

Service learning is a growing area of pedagogical study in both technical communication and engineering education. The focus of this pilot study is to discover if service learning within a technical communication classroom is a way of teaching students empathy for public welfare. Because empathy is the capacity and ability to recognize emotions in others, this pilot study focusses on identifying emotional language used by students in their reflections to see to whom it is associated.
An exploration of crowdsourcing citation screening for systematic reviews

Systematic reviews are increasingly used to inform health care decisions, but are expensive to produce. We explore the use of crowdsourcing (distributing tasks to untrained workers via the web) to reduce the cost of screening citations. We used Amazon Mechanical Turk as our platform and 4 previously conducted systematic reviews as examples. For each citation, workers answered 4 or 5 questions that were equivalent to the eligibility criteria. We aggregated responses from multiple workers into an overall decision to include or exclude the citation using 1 of 9 algorithms and compared the performance of these algorithms to the corresponding decisions of trained experts. The most inclusive algorithm (designating a citation as relevant if any worker did) identified 95% to 99% of the citations that were ultimately included in the reviews while excluding 68% to 82% of irrelevant citations. Other algorithms increased the fraction of irrelevant articles excluded at some cost to the inclusion of relevant studies. Crowdworkers completed screening in 4 to 17 days, costing $460 to $2220, a cost reduction of up to 88% compared to trained experts. Crowdsourcing may represent a useful approach to reducing the cost of identifying literature for systematic reviews.
Source Localization of Triphasic Waves: Implications for the Pathophysiological Mechanism

To investigate the current source location from the electroencephalograms (EEGs) of 12 patients who showed typical triphasic waves attributable to various causes, using the combination of a dipole source model and a distributed source model. The triphasic waves were explained by a single main dipole in 10 of the 12 patients, and 2 patients had two dipoles responsible for the triphasic waves. All the main dipoles had a radial orientation with respect to the frontal pole. The current density of the triphasic waves was distributed mainly in the bilateral medial frontal regions along the cingulate cortices. These findings suggest that current sources located in the medial frontal area are crucial for generating triphasic waves. The source localization may be useful for elucidating the pathophysiologic mechanism of generalized non-epileptic EEG activities, such as triphasic waves.
Palliative Care among Heart Failure Patients in Primary Care: A Comparison to Cancer Patients Using English Family Practice Data

Introduction Patients with heart failure have a significant symptom burden and other palliative care needs often over a longer period than patients with cancer. It is acknowledged that this need may be unmet but by how much has not been quantified in primary care data at the population level. Methods This was the first use of Clinical Practice Research Datalink, the world's largest primary care database to explore recognition of the need for palliative care. Heart failure and cancer patients who had died in 2009 aged 18 or over and had at least one year of primary care records were identified. A palliative approach to care among patients with heart failure was compared to that among patients with cancer using entry onto a palliative care register as a marker for a palliative approach to care. Results Among patients with heart failure, 7% (234/3 122) were entered on the palliative care register compared to 48% (3 669/7 608) of cancer patients. Of heart failure patients on the palliative care register, 29% (69/234) were entered onto the register within a week of their death. Conclusions This confirms that the stark inequity in recognition of palliative care needs for people with heart failure in a large primary care dataset. We recommend a move away from prognosis based criteria for palliative care towards a patient centred approach, with assessment of and attention to palliative needs including advance care planning throughout the disease trajectory.
Retina Superior Retinal Gene Transfer and Biodistribution Profile of Subretinal Versus Intravitreal Delivery of AAV 8 in Nonhuman Primates

Immanuel P. Seitz, Stylianos Michalakis, Barbara Wilhelm, Felix F. Reichel, G. Alex Ochakovski, Eberhart Zrenner, Marius Ueffing, Martin Biel, Bernd Wissinger, Karl U. Bartz-Schmidt, Tobias Peters, and M. Dominik Fischer; for the RD-CURE Consortium University Eye Hospital, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany Center for Integrated Protein Science Munich (CIPSM) at the Department of Pharmacy–Center for Drug Research, LudwigMaximilians-Universität München, Munich, Germany STZ Eyetrial at the Centre for Ophthalmology, University of Tübingen, Tübingen, Germany Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
Integrated medicines management - can routine implementation improve quality?

RATIONALE, AIMS AND OBJECTIVES Previous service development work in the area of integrated medicines management (IMM) has demonstrated clear quality improvements in a targeted group of patients within a hospital in Northern Ireland. In order to determine whether this programme could be transferable to routine practice and thereby assess its generalizability, research has been carried out to quantify the health care benefits of incorporating the concept of IMM as routine clinical practice. METHOD The IMM programme of care was delivered to all eligible patients (subject to inclusion criteria) across two hospital sites in Northern Ireland during normal pharmacy opening hours. All patients were followed up for a period of 12 months from their time of hospital admission. All patient data were collected using the custom-designed Electronic Pharmacist Intervention Clinical System at each stage of their hospital journey, that is, admission, inpatient stay and discharge. RESULTS Patients who received the IMM service benefited from a reduced length of hospital stay on their reference admission (1.42 days; P = 0.020) as well as a reduced length of stay during the first rehospitalization (5.86 days; P = 0.013). There was also a trend of a reduced number of readmissions and a longer time to readmission during the 12-month follow-up period. Potential significant opportunity cost savings were demonstrated as well as a significant improvement in medication appropriateness (discharge vs. reference admission). CONCLUSIONS The IMM programme of care has proven to be transferable to routine hospital care within two hospitals in Northern Ireland. It is anticipated that this current research will further inform the development of IMM as routine clinical practice across Northern Ireland and beyond.
Gender Differences in Emotion Regulation: An fMRI Study of Cognitive Reappraisal

Despite strong popular conceptions of gender differences in emotionality and striking gender differences in the prevalence of disorders thought to involve emotion dysregulation, the literature on the neural bases of emotion regulation is nearly silent regarding gender differences (Gross, 2007; Ochsner & Gross, in press). The purpose of the present study was to address this gap in the literature. Using functional magnetic resonance imaging, we asked male and female participants to use a cognitive emotion regulation strategy (reappraisal) to down-regulate their emotional responses to negatively valenced pictures. Behaviorally, men and women evidenced comparable decreases in negative emotion experience. Neurally, however, gender differences emerged. Compared with women, men showed (a) lesser increases in prefrontal regions that are associated with reappraisal, (b) greater decreases in the amygdala, which is associated with emotional responding, and (c) lesser engagement of ventral striatal regions, which are associated with reward processing. We consider two non-competing explanations for these differences. First, men may expend less effort when using cognitive regulation, perhaps due to greater use of automatic emotion regulation. Second, women may use positive emotions in the service of reappraising negative emotions to a greater degree. We then consider the implications of gender differences in emotion regulation for understanding gender differences in emotional processing in general, and gender differences in affective disorders.
Significant Differences in the Development of Acquired Resistance to the MDM2 Inhibitor SAR405838 between In Vitro and In Vivo Drug Treatment

SAR405838 is a potent and specific MDM2 inhibitor currently being evaluated in Phase I clinical trials for the treatment of human cancer. Using the SJSA-1 osteosarcoma cell line which harbors an amplified MDM2 gene and wild-type p53, we have investigated the acquired resistance mechanisms both in vitro and in vivo to SAR405838. Treatment of SJSA-1 cells with SAR405838 in vitro leads to dose-dependent cell growth inhibition, cell cycle arrest and robust apoptosis. However, prolonged treatment of SJSA-1 cells in vitro with SAR405838 results in profound acquired resistance to the drug. Analysis of in vitro-derived resistant cell lines showed that p53 is mutated in the DNA binding domain and can no longer be activated by SAR405838. Treatment of the parental SJSA-1 xenograft tumors with SAR405838 in mice yields rapid tumor regression but the tumors eventually regrow. Culturing the regrown tumors established a number of sublines, which showed only modest (3–5 times) loss of sensitivity to SAR405838 in vitro. Sequencing of the p53 showed that it retains its wild-type status in these in vivo sublines, with the exception of one subline, which harbors a single heterozygous C176F p53 mutation. Using xenograft models of two in vivo derived sublines, which has either wild-type p53 or p53 containing a single heterozygous C176F mutation, we showed that while SAR405838 effectively achieves partial tumor regression in these models, it no longer induces complete tumor regression and tumors resume growth once the treatment is stopped. Harvesting and culturing tumors obtained from a prolonged treatment with SAR405838 in mice established additional in vivo sublines, which all contain a single heterozygous C176F mutation with no additional p53 mutation detected. Interestingly, SAR405838 can still effectively activate p53 in all sublines containing a single heterozygous C176F mutation, with a moderately reduced potency as compared to that in the parental cell line. Consistently, SAR405838 is 3–5 times less effective in all the in vivo derived sublines containing a single heterozygous C176F p53 mutation than in the SJSA-1 parental cell line in assays of cell growth and apoptosis. Computational modeling suggested that a p53 tetramer containing two wild-type p53 molecules and two C176F mutated molecules can maintain the structural stability and interactions with DNA by formation of additional hydrophobic and cation-π interactions which compensate for the loss of sulphur-zinc coordination. Our data thus show that SJSA-1 tumor cells acquire very different levels of resistance in vitro and in vivo to the MDM2 inhibitor SAR405838. Our present study may have a significant implication for the investigation of resistant mechanisms for other classes of anticancer drugs.
A New Approach for Diagnosis of Diabetes and Prediction of Cancer Using ANFIS

The multi factorial, chronic, severe diseases like diabetes and cancer have complex relationship. When the glucose level of the body goes to abnormal level, it will lead to Blindness, Heart disease, Kidney failure and also Cancer. Epidemiological studies have proved that several cancer types are possible in patients having diabetes. Many researchers proposed methods to diagnose diabetes and cancer. To improve the classification accuracy and to achieve better efficiency a new approach like Adaptive Neuro Fuzzy Inference System (ANFIS) is proposed.
Effects of Intra-Arterial Octreotide on Pancreatic Texture: A Randomized Controlled Trial

Background and Aims: Octreotide is suggested to harden the pancreas, thus facilitating the construction of a pancreatic anastomosis and lowering the risk of postoperative fistula. We tested the hypothesis that intra-arterial application of octreotide in the gastroduodenal artery during pancreatectomy may increase pancreatic hardness. Material and Methods: A single-center, prospective, double-blinded, randomized controlled trial with parallel assignment was conducted. Patients planned for a pancreatoduodenectomy or a total pancreatectomy, who had a palpatory and durometer proven (<40 Shore units) soft pancreas, were assigned to receive intraoperatively either 5 mL 500µg octreotide or 5 mL 0.9% saline solution as a bolus injection in the gastroduodenal artery. Pancreatic hardness was measured before, early, and late after intervention. The investigator performing the durometer measurements and pathologist were masked to group assignment. The primary outcome was increased pancreatic hardness. Analysis was by intention to treat. This trial is registered at http://www.clinicaltrials. gov (ID NCT01400100). Results: A total of 12 patients received octreotide and 13 received saline solution. Pancreatic hardness marginally increased in the octreotide group: 0.67 ± 2.3 Shore units, whereas it decreased in the control group: −2.15 ± 2.7 Shore units. The difference was statistically significant, p = 0.029 (95% confidence interval = −4.87 to −0.77). Histology did not find any correlate for this clinically irrelevant hardening effect. Conclusions: A single bolus application of octreotide did not deliver a clinically relevant increase in pancreatic hardness. Future studies on the hardening effect of octreotide should employ repeated or continuous preoperative administration of this drug.
1700V Bi-Mode Insulated Gate Transistor (BIGT) on Thin Wafer Technology

An advanced Reverse Conducting (RC) IGBT concept referred to as the Bi-mode Insulated Gate Transistor (BIGT) has been previously documented mainly for high voltage devices rated at 3300V. In this paper, we report on the progress made to implement the new technology for lower voltage classes rated below 2000V which would require complex thin wafer processing for the design realization. The paper covers mainly the process challenges met to introduce the BIGT into the lower voltage class and present the latest test results of the first thin wafer 1700V/150A prototype BIGT in both IGBT and diode mode of operation.
User Education in Automated Driving: Owner's Manual and Interactive Tutorial Support Mental Model Formation and Human-Automation Interaction

Automated driving systems (ADS) and a combination of these with advanced driver assistance systems (ADAS) will soon be available to a large consumer population. Apart from testing automated driving features and human–machine interfaces (HMI), the development and evaluation of training for interacting with driving automation has been largely neglected. The present work outlines the conceptual development of two possible approaches of user education which are the owner’s manual and an interactive tutorial. These approaches are investigated by comparing them to a baseline consisting of generic information about the system function. Using a between-subjects design, N = 24 participants complete one training prior to interacting with the ADS HMI in a driving simulator. Results show that both the owner’s manual and an interactive tutorial led to an increased understanding of driving automation systems as well as an increased interaction performance. This work contributes to method development for the evaluation of ADS by proposing two alternative approaches of user education and their implications for both application in realistic settings and HMI testing.
Posterior dislocation of the humeral head in infancy associated with obstetrical paralysis. A case report.

Posterior dislocation of the humeral head in infancy is rare. Although originally believed to be a congenital condition that developed in litero, this disorder most often has been associated with brachial plexus palsy secondary to birth traumats4o. Since it was first reported in 1888. few posterior dislocations of the humeral head in infancy have been described4s4ss. To our the first year of life, and the condition was treated with an early open reduction in both patients.
Nominal v. Real Wage Rigidities in New Keynesian Models with Hiring Costs: A Bayesian Evaluation

The introduction of labor market frictions into the New Keynesian DSGE model solves some of the main drawbacks of the baseline framework. In this paper we show that this extended model, by assuming real wage rigidities, fails to replicate the correct wage dynamics and the observed negative conditional correlation between supply shocks and employment, known as â€œproductivity employment puzzleâ€ . We then show that these empirical limitations can be overcome by a model incorporating nominal wage rigidities in addition to price rigidities and hiring costs. Adopting a Bayesian perspective, we estimate the dynamic properties of the model with real wage rigidities and confront them with those of the model with nominal wage rigidities, concluding that there is decisive evidence in favor of the latter.
Influence of laser irradiation on endogenous hyaluronan in rabbit iris and aqueous humor.

PURPOSE To monitor changes of endogenous hyaluronan in the iris tissue and aqueous humor after an isolated trauma to the iris by argon laser irradiation of the anterior surface of the iris. METHODS Iris and aqueous hyaluronan concentrations in rabbit were measured with a radiometric assay at different time points after laser irradiation. RESULTS Total hyaluronan content in iris tissue increased 3-fold to a peak concentration of 71-72 microg/g at 1 and 2 days after laser treatment. Aqueous hyaluronan increased to a maximum of about 1.6 microg/ml at 2 h and 12 h after laser irradiation of the iris. CONCLUSIONS The iris tissue responds with increased hyluronan synthesis to an isolated iris argon laser irradiation and it seems to be the most important source of aqueous hyaluronan.