LLukas22/scidocs huggingface dataset:
Probabilistic visual search for masses within mammography images using deep learning

We developed a deep learning-based visual search system for the task of automated search and localization of masses in whole mammography images. The system consists of two modules: a classification engine and a localization engine. It first classifies mammograms as containing a mass or no mass using a deep learning classifier, and then localizes the mass(es) within the image using a regional probabilistic approach based on a deep learning network. We obtained 85% accuracy for the task of identifying images that contain a mass, and we were able to localize 85% of the masses at an average of 0.9 false positives per image. Our system has the advantages of being able to work with an entire mammography image as input without the need for image segmentation or other pre-processing steps, such as cropping or tiling the image, and it is based on deep learning with unsupervised feature discovery, so it does not require pre-defined and hand-crafted image features.
Successful immune tolerance induction to enzyme replacement therapy in CRIM-negative infantile Pompe disease

Purpose:Infantile Pompe disease resulting from a deficiency of lysosomal acid α-glucosidase (GAA) requires enzyme replacement therapy (ERT) with recombinant human GAA (rhGAA). Cross-reactive immunologic material negative (CRIM-negative) Pompe patients develop high-titer antibody to the rhGAA and do poorly. We describe successful tolerance induction in CRIM-negative patients.Methods:Two CRIM-negative patients with preexisting anti-GAA antibodies were treated therapeutically with rituximab, methotrexate, and gammaglobulins. Two additional CRIM-negative patients were treated prophylactically with a short course of rituximab and methotrexate, in parallel with initiating rhGAA.Results:In both patients treated therapeutically, anti-rhGAA was eliminated after 3 and 19 months. All four patients are immune tolerant to rhGAA, off immune therapy, showing B-cell recovery while continuing to receive ERT at ages 36 and 56 months (therapeutic) and 18 and 35 months (prophylactic). All patients show clinical response to ERT, in stark contrast to the rapid deterioration of their nontolerized CRIM-negative counterparts.Conclusion:The combination of rituximab with methotrexate ± intravenous gammaglobulins (IVIG) is an option for tolerance induction of CRIM-negative Pompe to ERT when instituted in the naïve setting or following antibody development. It should be considered in other conditions in which antibody response to the therapeutic protein elicits robust antibody response that interferes with product efficacy.Genet Med 2012:14(1):135–142
ARTTag: aesthetic fiducial markers based on circle pairs

In this paper, we present ARTTag, an aesthetic fiducial marker system, of which the design development can be performed with any color, texture, shape, or other features as long as circle pairs are integrated. By utilizing the projective properties of circular features, ARTTag is appropriate for detection, identification, and camera-based registration in augmented reality (AR) applications.
Efficient Access Mechanisms for Tabled Logic Programs

Abstract The use of tabling in logic programming allows bottom-up evaluation to be incorporated in a top-down framework, combining advantages of both. At the engine level, tabling also introduces issues not present in pure top-down evaluation, due to the need for subgoals and answers to access tables during resolution. This article describes the design, implementation, and experimental evaluation of data structures and algorithms for high-performance table access. Our approach uses tries as the basis for tables. Tries, a variant of discrimination nets, provide complete discrimination for terms, and permit a lookup and possible insertion to be performed in a single pass through a term. In addition, a novel technique of substitution factoring is proposed. When substitution factoring is used, the access cost for answers is proportional to the size of the answer substitution, rather than to the size of the answer itself. Answer tries can be implemented both as interpreted structures and as compiled WAM-like code. When they are compiled, the speed of computing substitutions through answer tries is competitive with the speed of unit facts compiled or asserted as WAM code. Because answer tries can also be created an order of magnitude more quickly than asserted code, they form a promising alternative for representing certain types of dynamic code, even in Prolog systems without tabling.
Cost-effectiveness of switching to insulin degludec from other basal insulins: evidence from Swedish real-world data.

OBJECTIVES
Health economic analysis from a healthcare and societal point of view was conducted to assess the cost-effectiveness of insulin degludec (IDeg) after switching from other basal insulins in people with type 1 diabetes.


MATERIAL AND METHODS
This was a prospective, open-label, single arm, observational follow-up from August 2013 to October 2015 of 476 consecutive patients at Danderyd Hospital (Stockholm, Sweden) who switched to IDeg from other basal insulins (99% basal insulin analogs). The IMS CORE Diabetes Model (CDM) was used to predict the cost-effectiveness of life-long treatment with IDeg vs. other basal insulins, based on a Swedish setting.


RESULTS
Mean (SD) duration of follow-up was 21.7 (6.0) weeks. Mean HbA1c decreased by 2.7 mmol/mol, mean basal insulin dose decreased by 13.1% (p < .0001), and mean bolus insulin dose decreased by 7.5% (p < .0001) after switching. Frequencies of non-severe daytime hypoglycemia and non-severe nocturnal hypoglycemia decreased by 12% (p = .0127) and 53% (p < .0001) respectively and severe hypoglycemia was reduced by 62% (p = .0225). The CDM predicted a gain in life expectancy of 0.33 years, a discounted gain in quality-adjusted life-years (QALYs) of 0.54, and lower estimated direct lifetime healthcare costs of SEK 22,757 for patients switching to IDeg. The incremental cost-effectiveness ratio (ICER) showed IDeg as dominant (i.e. higher effectiveness with a lower cost). Sensitivity analyses confirmed the results.


CONCLUSION
Based on this prospective, real-world, follow-up and using the CDM, it was estimated that switching to IDeg from other basal insulins translated into QALY gains including improved life expectancy and health-related quality of life, as well as dominant ICER, meaning cost-savings for the healthcare system. However, the study is limited by its observational design. Extrapolation into the future is only estimated since the actual treatment effect cannot be projected with certainty.
Ex vivo evaluation of the effectiveness of bleaching agents on the shade alteration of blood-stained teeth.

AIM
To evaluate ex vivo effectiveness of the three formulations of bleaching materials for intracoronal bleaching of root filled teeth using the walking bleach technique.


METHODOLOGY
Extracted premolar teeth were stained artificially with human blood. After biomechanical preparation, the root canals were filled and a 3-mm thick intermediate base of zinc phosphate cement was placed at the level of the cementoenamel junction. The teeth were divided into four groups (n = 12): C (control, without bleaching material), A1 (sodium perborate + distilled water), A2 (sodium perborate + 10% carbamide peroxide) and A3 (sodium perborate + 35% carbamide peroxide). The bleaching materials were changed at 7 and 14 days. Evaluation of shade was undertaken with aid of the VITA Easyshadetrade mark (DeltaE*ab) and was performed after tooth staining and at 7, 14 and 21 days after bleaching, based on the CIELAB system. Data were analysed by anova for repeated measurements, Tukey and Dunnett tests (alpha = 0.05).


RESULTS
The Tukey test revealed that group A1 (10.58 +/- 4.83 DeltaE*ab) was statistically different from the others (A2, 19.57 +/- 4.72 DeltaE*ab and A3, 17.58 +/- 3.33 DeltaE*ab), which were not different from each other. At 7 days: A1 was significantly different from A2; at 14 and 21 days: A2 and A3 were significantly better than A1; the Dunnett test revealed that the control group was different from A1, A2 and A3 at all periods (P < 0.05).


CONCLUSION
Sodium perborate associated with both 10% and 35% carbamide peroxide was more effective than when associated with distilled water.
Childhood osteomyelitis-incidence and differentiation from other acute onset musculoskeletal features in a population-based study

BACKGROUND
Osteomyelitis can be difficult to diagnose and there has previously not been a prospective approach to identify all children in a defined geographic area. The aim of this study was to assess the annual incidence of osteomyelitis in children, describe the patient and disease characteristics in those with acute (< 14 days disease duration) and subacute osteomyelitis (> or = 14 days disease duration), and differentiate osteomyelitis patients from those with other acute onset musculoskeletal features.


METHODS
In a population-based Norwegian study physicians were asked to refer all children with suspected osteomyelitis. Children with osteomyelitis received follow-up at six weeks, six months and thereafter as long as clinically needed.


RESULTS
The total annual incidence rate of osteomyelitis was 13 per 100,000 (acute osteomyelitis 8 and subacute osteomyelitis 5 per 100,000). The incidence was higher in patients under the age of 3 than in older children (OR 2.9, 95%: CI 2.3-3.7). The incidence of non-vertebral osteomyelitis was higher than the incidence of vertebral osteomyelitis (10 vs. 3 per 100 000; p = .002). Vertebral osteomyelitis was more frequent in girls than in boys (OR 7.0, 95%: CI 3.3-14.7). ESR > or = 40 mm/hr had the highest positive predictive laboratory value to identify osteomyelitis patients at 26% and MRI had a positive predictive value of 85%. Long-bone infection was found in 16 (43%) patients. ESR, CRP, white blood cell count, neutrophils and platelet count were higher for patients with acute osteomyelitis than for patients with subacute osteomyelitis. Subacute findings on MRI and doctor's delay were more common in subacute osteomyelitis than in acute osteomyelitis patients. Blood culture was positive in 26% of the acute osteomyelitis patients and was negative in all the subacute osteomyelitis patients.


CONCLUSION
The annual incidence of osteomyelitis in Norway remains high. ESR values and MRI scan may help to identify osteomyelitis patients and differentiate acute and subacute osteomyelitis.
Obstacle Detection and Collision Avoidance Using Ultrasonic Distance Sensors for an Autonomous Quadrocopter

A simple approach for obstacle detection and collision avoidance of an autonomous flying quadrocopter using low-cost ultrasonic sensors and simple data fusion is presented here. The approach has been implemented and tested in a self-developed quadrocopter (Figure 1) and its evaluation shows the general realizability as well as the drawbacks of this approach. The presented approach is intended to be used as part of the AQopterI8 project at the department of Aerospace Information Technology (University of Würzburg), which aims to develop an autonomous flying quadrocopter for indoor application. Figure 1: AQopterI8
The impact of a self-management patient education program for patients with chronic heart failure undergoing inpatient cardiac rehabilitation.

OBJECTIVE
To evaluate a patient-centred self-management educational group program for patients with chronic systolic heart failure as compared to usual care education during inpatient cardiac rehabilitation.


METHODS
A multicentre cluster randomized controlled trial of 475 patients was conducted. In the intervention condition, patients received the new self-management educational group program whereas in the control condition, patients received a short lecture-based educational program (usual care). The primary outcome was patients' self-reported self-management competence. Secondary outcomes included self-management health behaviour, health-related quality of life, and treatment satisfaction. Patients completed self-reported outcome measures at admission, discharge, and after 6 and 12 months.


RESULTS
There was a significant small between-group intervention effect on certain dimension of patients' self-management competence (self-monitoring and insight) in short term (p<0.05). Furthermore, significant small effects were observed for treatment satisfaction at discharge as well as symptom monitoring after 6 months (p<0.05) and by trend on symptom monitoring and physical activity after 12 months.


CONCLUSIONS
The patient-centred self-management program might be more effective in certain self-management outcomes than a usual care education in both short-term and long-term periods.


PRACTICE IMPLICATIONS
Therefore, such programs may be considered for dissemination within cardiac rehabilitation.
Evaluation of a Rapid Molecular Drug-Susceptibility Test for Tuberculosis.

BACKGROUND
Fluoroquinolones and second-line injectable drugs are the backbone of treatment regimens for multidrug-resistant tuberculosis, and resistance to these drugs defines extensively drug-resistant tuberculosis. We assessed the accuracy of an automated, cartridge-based molecular assay for the detection, directly from sputum specimens, of Mycobacterium tuberculosis with resistance to fluoroquinolones, aminoglycosides, and isoniazid.


METHODS
We conducted a prospective diagnostic accuracy study to compare the investigational assay against phenotypic drug-susceptibility testing and DNA sequencing among adults in China and South Korea who had symptoms of tuberculosis. The Xpert MTB/RIF assay and sputum culture were performed. M. tuberculosis isolates underwent phenotypic drug-susceptibility testing and DNA sequencing of the genes katG, gyrA, gyrB, and rrs and of the eis and inhA promoter regions.


RESULTS
Among the 308 participants who were culture-positive for M. tuberculosis, when phenotypic drug-susceptibility testing was used as the reference standard, the sensitivities of the investigational assay for detecting resistance were 83.3% for isoniazid (95% confidence interval [CI], 77.1 to 88.5), 88.4% for ofloxacin (95% CI, 80.2 to 94.1), 87.6% for moxifloxacin at a critical concentration of 0.5 μg per milliliter (95% CI, 79.0 to 93.7), 96.2% for moxifloxacin at a critical concentration of 2.0 μg per milliliter (95% CI, 87.0 to 99.5), 71.4% for kanamycin (95% CI, 56.7 to 83.4), and 70.7% for amikacin (95% CI, 54.5 to 83.9). The specificity of the assay for the detection of phenotypic resistance was 94.3% or greater for all drugs except moxifloxacin at a critical concentration of 2.0 μg per milliliter (specificity, 84.0% [95% CI, 78.9 to 88.3]). When DNA sequencing was used as the reference standard, the sensitivities of the investigational assay for detecting mutations associated with resistance were 98.1% for isoniazid (95% CI, 94.4 to 99.6), 95.8% for fluoroquinolones (95% CI, 89.6 to 98.8), 92.7% for kanamycin (95% CI, 80.1 to 98.5), and 96.8% for amikacin (95% CI, 83.3 to 99.9), and the specificity for all drugs was 99.6% (95% CI, 97.9 to 100) or greater.


CONCLUSIONS
This investigational assay accurately detected M. tuberculosis mutations associated with resistance to isoniazid, fluoroquinolones, and aminoglycosides and holds promise as a rapid point-of-care test to guide therapeutic decisions for patients with tuberculosis. (Funded by the National Institute of Allergy and Infectious Diseases, National Institutes of Health, and the Ministry of Science and Technology of China; ClinicalTrials.gov number, NCT02251327 .).
Flexible metal-oxide devices made by room-temperature photochemical activation of sol–gel films

Amorphous metal-oxide semiconductors have emerged as potential replacements for organic and silicon materials in thin-film electronics. The high carrier mobility in the amorphous state, and excellent large-area uniformity, have extended their applications to active-matrix electronics, including displays, sensor arrays and X-ray detectors. Moreover, their solution processability and optical transparency have opened new horizons for low-cost printable and transparent electronics on plastic substrates. But metal-oxide formation by the sol–gel route requires an annealing step at relatively high temperature, which has prevented the incorporation of these materials with the polymer substrates used in high-performance flexible electronics. Here we report a general method for forming high-performance and operationally stable metal-oxide semiconductors at room temperature, by deep-ultraviolet photochemical activation of sol–gel films. Deep-ultraviolet irradiation induces efficient condensation and densification of oxide semiconducting films by photochemical activation at low temperature. This photochemical activation is applicable to numerous metal-oxide semiconductors, and the performance (in terms of transistor mobility and operational stability) of thin-film transistors fabricated by this route compares favourably with that of thin-film transistors based on thermally annealed materials. The field-effect mobilities of the photo-activated metal-oxide semiconductors are as high as 14 and 7 cm2 V−1 s−1 (with an Al2O3 gate insulator) on glass and polymer substrates, respectively; and seven-stage ring oscillators fabricated on polymer substrates operate with an oscillation frequency of more than 340 kHz, corresponding to a propagation delay of less than 210 nanoseconds per stage.
Talactoferrin alfa versus placebo in patients with refractory advanced non-small-cell lung cancer (FORTIS-M trial).

BACKGROUND
Talactoferrin alfa is an oral dendritic cell (DC)-mediated immunotherapy (DCMI). We tested whether talactoferrin was superior to placebo in advanced non-small-cell lung cancer (NSCLC).


PATIENTS AND METHODS
An FORTIS-M trial was an international, multicenter, randomized, double-blind comparison of talactoferrin (1.5 g p.o. BID) versus placebo BID, in patients with stage IIIB/IV NSCLC whose disease had failed two or more prior regimens. Treatment was administered for a maximum of five 14-week cycles. The primary efficacy end point was overall survival (OS); secondary end points included 6- and 12-month survival, progression-free survival (PFS), and disease control rate (DCR).


RESULTS
Seven hundred and forty-two patients were randomly assigned (2:1) to talactoferrin (497) or placebo (245). The median OS in the intent-to-treat (ITT) population was 7.66 months in the placebo arm and 7.49 months in the talactoferrin arm [hazard ratio (HR), 1.04; 95% CI, 0.873-1.24; P = 0.6602]. The 6-month survival rates were 59.9% (95% CI, 53.4% to 65.8%) and 55.7% (95% CI, 51.1% to 59.9%), respectively. The 12-month survival rates were 32.2% (95% CI, 26.3% to 38.2%) and 30.9% (95% CI, 26.8% to 35%), respectively. The median PFS rates were 1.64 months and 1.68 months, respectively (HR, 0.99; 95% CI, 0.835-1.16; P = 0.8073). The DCRs were 38.4 and 37.6%, respectively [stratified odds ratio (OR), 0.96; 95% CI, 0.698-1.33; P = 0.8336]. The safety profiles were comparable between arms.


CONCLUSIONS
There was no improvement in efficacy with talactoferrin alfa in patients with advanced NSCLC whose disease had failed two or more previous regimens.
The Diabetes Quality Improvement Project: moving science into health policy to gain an edge on the diabetes epidemic.

BACKGROUND — As the worldwide diabetes epidemic continues to unfold, some experts have asked whether the war against it is being lost (1–3). In the U.S., blindness, kidney failure, amputations, and cardiovascular disease resulting from diabetes not only markedly reduce quality and length of life but also cost nearly $100 billion annually (4–7). Fortunately, a vast body of research has clearly established that several effective treatments and practices may substantially reduce or prevent this burden (8– 19). These interventions, if broadly implemented, can allow us to use our health efforts and resources more effectively and efficiently to minimize the diabetes burden. Judging from the scant data available, however, the level of care currently delivered to populations with diabetes often may not produce the possible health-related gains (20,21). To assess more completely the level of diabetes care delivered in the U.S., we need standardized uniform performance measures that can assess quality of care accurately and reliably. These measures will enhance uptake of research into practice and may ultimately improve diabetes care and clinical outcomes. In the early to mid1990s, many organizations developed performance measures for diabetes care, but the result was that providers were often required to collect and report many different, sometimes conflicting, measures, depending on their care delivery system. It was recognized that a national consensus on measures could enhance this process and provide a method for assessing care within and across health care settings while providing a meaningful mechanism for quality improvement (QI). In this review, we describe the Diabetes Quality Improvement Project (DQIP), which has developed and implemented a comprehensive set of national measures for evaluation and QI.
THE BASIC ELEMENTS OF ARGUMENT STRUCTURE

The term “argument structure” is used here to refer to the syntactic configuration projected by a lexical item. It is the system of structural relations holding between heads (nuclei) and arguments linked to them in the roster of syntactic properties listed for individual items in the lexicon. While a lexical entry is much more than this, of course, argument structure in the sense intended here is precisely this and nothing more.
Clinical and embryologic aspects of penile duplication and associated anomalies.

OBJECTIVES
To report 2 cases of penile duplication and review the literature in an attempt to categorize the associated anomalies in relation to the degree of penile duplication. Embryologic considerations of this rare anomaly are also reviewed.


METHODS
We report 2 distinct cases of diphallia. In the first case, true complete penile duplication was associated with multiple malformations, including a cloacal anomaly, colon and bladder duplication, a horseshoe kidney, a bifid scrotum with undescended testes, a hypoplastic right leg, and a ventricular septum defect. The second patient presented with true, complete diphallia and bladder and urethral duplication but an absence of other anomalies. The patients were individually treated according to the concomitant malformations. A review of published reports allowed a classification of associated anomalies in 77 cases of diphallia, according to the degree of penile duplication.


RESULTS
The first patient underwent a series of staged surgical repairs, including correction of the congenital heart anomaly, separation of the urogenital and gastrointestinal tract and resection of the duplicate terminal colon, excision of the smaller bladder and underdeveloped duplicate penis, bilateral orchiopexy, and hypospadias correction. The second patient underwent bladder fusion and excision of a urethrorectal fistula. Penile reconstruction was left for a later stage. An analysis of the cases available in published studies suggests that diphallia is often associated with a wide spectrum of anomalies that vary from severe malformations to less significant variations of human anatomy.


CONCLUSIONS
Penile duplication is a rare anomaly. Thorough investigations are mandatory in all cases to reveal underlying congenital malformations that are potentially life threatening and require immediate surgical correction. Treatment should always be individualized according to the degree of penile duplication and the extent of the concomitant anomalies.