LLukas22/scidocs huggingface dataset:
Real-time scintillation array dosimetry for radiotherapy: the advantages of photomultiplier detectors.

PURPOSE
In this paper, a photomultiplier tube (PMT) array dosimetry system has been developed and tested for the real-time readout of multiple scintillation signals from fiber optic dosimeters. It provides array dosimetry with the advantages in sensitivity provided by a PMT, but without the need for a separate PMT for each detector element.


METHODS
The PMT array system consisted of a multianode PMT, a multichannel data acquisition system, housing and optic fiber connections suitable for clinical use. The reproducibility, channel uniformity, channel crosstalk, acquisition speed, and sensitivity of the PMT array were quantified using a constant light source. Its performance was compared to other readout systems used in scintillation dosimetry. An in vivo HDR brachytherapy treatment was used as an example of a clinical application of the dosimetry system to the measurement of dose at multiple sites in the rectum. The PMT array system was also tested in the pulsed beam of a linear accelerator to test its response speed and its application with two separate methods of Cerenkov background removal.


RESULTS
The PMT array dosimetry system was highly reproducible with a measurement uncertainty of 0.13% for a 10 s acquisition period. Optical crosstalk between neighboring channels was accounted for by omitting every second channel. A mathematical procedure was used to account for the crosstalk in next-neighbor channels. The speed and sensitivity of the PMT array system were found be superior to CCD cameras, allowing for measurement of more rapid changes in dose rate. This was further demonstrated by measuring the dose delivered by individual photon pulses of a linear accelerator beam.


CONCLUSIONS
The PMT array system has advantages over CCD camera-based systems for the readout of scintillation light. It provided a more sensitive, more accurate, and faster response to meet the demands of future developments in treatment delivery.
Provenance of early Palaeozoic sandstones, southeastern Australia, Part 1: vertical changes through the Bengal fan-type deposit

Abstract Ordovician strata of the Lachlan Fold Belt in southeastern Australia are dominated by a turbidite succession that in its undeformed state was comparable in size to the modern-day Bengal Fan. The ancient fan was derived from the northern part of the Cambrian Ross–Delamerian orogenic belt that formed at a convergent boundary between plates containing Gondwanaland and part of the palaeo-Pacific Ocean, respectively. Substrate to the submarine fan consisted of mafic volcanic rocks with an immature island arc affinity similar to the Eocene Izu–Mariana–Bonin system. Sandstone compositions, determined from several stratigraphically constrained sections, demonstrate a uniform framework composition dominated by monocrystalline quartz with less abundant feldspar, polycrystalline quartz, metamorphic rock fragments, sedimentary rock fragments and mica. These indicate derivation from a low-grade metamorphic terrain. Up-sequence variation is limited to decreasing feldspar and lithic fragments and increasing quartz, indicating increased weathering and lowering of topography, in the source terrain over time. 25% of counted sandstones in the Late Ordovician interval contain a small component of mafic–intermediate volcanic rock fragments that accompanied a change in palaeocurrent direction from eastwards to northwards. In the Early Silurian, the Ordovician sequence was disrupted by the formation of several major deformation zones. Between these zones, developed several deep-marine sedimentary basins that contain a continuous succession from the Ordovician into the Early Silurian. Early Silurian sandstone is similar in composition to underlying Early Ordovician rocks except that the feldspar component is generally absent. Early Silurian sandstone was derived from uplifted portions of the Ordovician sequence and includes texturally inverted types with sandstone containing a bimodal mixture of coarse well-rounded quartz and fine angular quartz.
Completeness Theorems, Incompleteness Theorems and Models of Arithmetic

Let & be a consistent extension of Peano arithmetic and let 6EJJ denote the set of TL°„ consequences of &. Employing incompleteness theorems to generate independent formulas and completeness theorems to construct models, we build nonstandard models of SP„+2 m which the standard integers are A°+1 -definable. We thus pinpoint induction axioms which are not provable in éE¡¡+2; in particular, we show that (parameter free) A?-induction is not provable in Primitive Recursive Arithmetic. Also, we give a solution of a problem of Gaifman on the existence of roots of diophantine equations in end extensions and answer questions about existentially complete models of 3^. Furthermore, it is shown that the proof of the Gödel Completeness Theorem cannot be formalized in 6E§ and that the MacDowell-Specker Theorem fails for all truncated theories (£¡¡. The completeness theorems of the title are the usual completeness and compactness theorems for the predicate calculus and strong variants of them which are obtained by virtue of the fact that the Henkin proof of the usual completeness theorem can be formalized in arithmetic. The incompleteness theorems are the Gödel theorems and the variants due to Rosser and Mostowski. Using model theoretic methods, Ryll-Nardzewski and also Rabin proved that (Peano) arithmetic was not finitely axiomatizable by showing that all finite subsystems of arithmetic have nonstandard models in which some induction axiom fails. On the other hand, using proof-theoretic methods, Mostowski and also Montague showed that in arithmetic one can prove the consistency of any finite subsystem of arithmetic, which again establishes nonfinite axiomatizability. In this paper we combine these techniques playing off the completeness theorems against the incompleteness theorems and construct nonstandard models of subsystems of arithmetic in which the standard integers and definable (§§3 and 6). The nonfinite axiomatizability results that we obtain in this way are optimal (from the point of view of quantifier complexity). We introduce the notion of representability of a theory in a model, cf. §2, which enables us to apply the incompleteness Received by the editors August 4, 1976. AMS (MOS) subject classifications (1970). Primary 02H05, 02H25, 02G15. (^Various results of this paper were announced in [Mc]. © American Mathematical Society 1978
Multi-Linear Probabilistic Energy Flow Analysis of Integrated Electrical and Natural-Gas Systems

The deep interdependence between electrical and gas systems entails a potential threat to the security (or reliability) of both systems. It is imperative to investigate the impacts of massive uncertainties on the overall secure and economical operation of both systems. In this paper, a probabilistic energy flow framework of integrated electrical and gas systems is initially proposed considering correlated varying energy demands and wind power. Three aspects of couplings between electrical and gas systems are considered: gas-fired generators, electric-driven compressors, and energy hubs integrated with power to gas (P2G) units. Furthermore, a multilinear method is specially designed to produce a deterministic energy flow solution for each sample generated by Monte Carlo simulation (MCS). Finally, test results have verified that the proposed multilinear MCS method prevails over the nonlinear MCS. In addition, P2G effectively benefits the operation of both electrical and gas networks.
Can Patients' Likelihood of Benefiting from Primary Chemotherapy for Breast Cancer Be Predicted Before Commencement of Treatment?

Purpose. Primary chemotherapy is commonly used in patients with breast cancer to downstage the primary tumour prior to surgery. There is a need to establish, prior to commencement of chemotherapy, predictors of clinical and pathological response, which may then be surrogate markers for patient survival and thus allow identification of patients who are most likely to benefit from such treatment. Patients and methods. A total of 104 patients with large and locally advanced breast cancers received an anthracycline/docetaxel-based regimen prior to surgery. Immunohistochemistry was carried out on pre-treatment core biopsies of the tumour to detect hormone receptors (oestrogen-ER; progesterone-PR), a proliferation marker (MIB-1), the oncoprotein Bcl-2, an extracellular matrix degradation enzyme (cathepsin D), p53, and an oestrogen associated protein (pS2). Both clinical and pathological response were assessed following completion of chemotherapy. Results. Patients whose tumours did not express oestrogen receptor (p= 0.02) or did not express Bcl-2 (p < 0.01) had a better pathological response in a univariate analysis. However, in a multivariate model, it was only the absence of detectable Bcl-2 protein that predicted a better pathological response (p= 0.001). Conclusions. This study has identified that patients whose breast cancers are most likely to experience the greatest degree of tumour destruction by primary chemotherapy do not express either oestrogen receptors or Bcl-2. This may have important implications in the selection of patients with breast cancer for primary chemotherapy who are most likely to gain a survival benefit.
Sentiment Analysis for Software Engineering: How Far Can We Go?

Sentiment analysis has been applied to various software engineering (SE) tasks, such as evaluating app reviews or analyzing developers' emotions in commit messages. Studies indicate that sentiment analysis tools provide unreliable results when used out-of-the-box, since they are not designed to process SE datasets. The silver bullet for a successful application of sentiment analysis tools to SE datasets might be their customization to the specific usage context.
 We describe our experience in building a software library recommender exploiting developers' opinions mined from Stack Overflow. To reach our goal, we retrained---on a set of 40k manually labeled sentences/words extracted from Stack Overflow---a state-of-the-art sentiment analysis tool exploiting deep learning. Despite such an effort- and time-consuming training process, the results were negative. We changed our focus and performed a thorough investigation of the accuracy of commonly used tools to identify the sentiment of SE related texts. Meanwhile, we also studied the impact of different datasets on tool performance. Our results should warn the research community about the strong limitations of current sentiment analysis tools.
A double blind community-based randomized trial of amoxicillin versus placebo for fast breathing pneumonia in children aged 2-59 months in Karachi, Pakistan (RETAPP)

BACKGROUND
Fast breathing pneumonia is characterized by tachypnoea in the absence of danger signs and is mostly viral in etiology. Current guidelines recommend antibiotic therapy for all children with fast breathing pneumonia in resource limited settings, presuming that most pneumonia is bacterial. High quality clinical trial evidence to challenge or support the continued use of antibiotics, as recommended by the World Health Organization is lacking.


METHODS/DESIGN
This is a randomized double blinded placebo-controlled non-inferiority trial using parallel assignment with 1:1 allocation ratio, to be conducted in low income squatter settlements of urban Karachi, Pakistan. Children 2-59 months old with fast breathing, without any WHO-defined danger signs and seeking care at the primary health care center are randomized to receive either three days of placebo or amoxicillin. From prior studies, a sample size of 2430 children is required over a period of 28 months. Primary outcome is the difference in cumulative treatment failure between the two groups, defined as a new clinical sign based on preset definitions indicating illness progression or mortality and confirmed by two independent primary health care physicians on day 0, 1, 2 or 3 of therapy. Secondary outcomes include relapse measured between days 5-14. Modified per protocol analysis comparing hazards of treatment failure with 95% confidence intervals in the placebo arm with hazards in the amoxicillin arm will be done.


DISCUSSION
This study will provide evidence to support or refute the use of antibiotics for fast breathing pneumonia paving a way for guideline change.


TRIAL REGISTRATION
Clinical Trials (NIH) Register NCT02372461.
A System for Ontology-Based Annotation of Biomedical Data

We present a system for ontology based annotation and indexing of biomedical data; the key functionality of this system is to provide a service that enables users to locate biomedical data resources related to particular ontology concepts. The system’s indexing workflow processes the text metadata of diverse resource elements such as gene expression data sets, descriptions of radiology images, clinical-trial reports, and PubMed article abstracts to annotate and index them with concepts from appropriate ontologies. The system enables researchers to search biomedical data sources using ontology concepts. What distinguishes this work from other biomedical search tools is:(i) the use of ontology semantics to expand the initial set of annotations automatically generated by a concept recognition tool; (ii) the unique ability to use almost all publicly available biomedical ontologies in the indexing workflow; (iii) the ability to provide the user with integrated results from different biomedical resource in one place. We discuss the system architecture as well as our experiences during its prototype implementation (http://www.bioontology.org/tools.html).
3-Dimensional prebent plate fixation in corrective osteotomy of malunited upper extremity fractures using a real-sized plastic bone model prepared by preoperative computer simulation.

PURPOSE
To assess the clinical outcome and accuracy of prebent plate fixation in corrective osteotomy for malunited upper extremity fractures using a plastic bone model manufactured by preoperative computer simulation.


METHODS
Nine consecutive patients underwent computed tomography (CT)-based 3-dimensional corrective osteotomy for malunited upper extremity fractures. There were 4 cubitus varus deformities, 1 cubitus valgus deformity, and 4 forearm diaphyseal malunions. We constructed a computer model of the affected bones using the CT data and simulated the 3-dimensional deformity correction on a computer. A real-sized plastic model of the corrected bone was manufactured by rapid prototyping. We used a metal plate, prebent to fit the plastic bone model, in the actual surgery. Patients were evaluated after an average follow-up of 22 months (range, 14-36 mo). We retrospectively collected radiographic and clinical data at the most recent follow-up and compared them with preoperative data. We also performed CT after surgery and evaluated the error in corrective osteotomy as the difference between preoperative simulation and postoperative bone model.


RESULTS
The range of forearm rotation and grip strength in patients with forearm malunions improved after corrective osteotomies of the radius and ulna. Wrist pain, which 2 patients with forearm malunion had experienced before surgery, disappeared or decreased substantially after surgery. Radiographic examination indicated that preoperative angular deformities were nearly nonexistent after all corrective osteotomies. Three-dimensional errors in the corrective osteotomy using a prebent plate, as evaluated by CT data, were less than 3 mm and 2°.


CONCLUSIONS
Prebent plate fixation in corrective osteotomy for malunited upper extremity fractures using a 3-dimensionally corrected, real-sized plastic bone model prepared by preoperative computer simulation is a precise and relatively easily performed technique that results in satisfactory clinical outcome.


TYPE OF STUDY/LEVEL OF EVIDENCE
Therapeutic IV.
Continuous Time Random Walks with Reactions Forcing and Trapping

One of the central results in Einstein’s theory of Brownian motion is that the mean square displacement of a randomly moving Brownian particle scales linearly with time. Over the past few decades sophisticated experiments and data collection in numerous biological, physical and financial systems have revealed anomalous sub-diffusion in which the mean square displacement grows slower than linearly with time. A major theoretical challenge has been to derive the appropriate evolution equation for the probability density function of sub-diffusion taking into account further complications from force fields and reactions. Here we present a derivation of the generalised master equation for an ensemble of particles undergoing reactions whilst being subject to an external force field. From this general equation we show reductions to a range of well known special cases, including the fractional reaction diffusion equation and the fractional Fokker-Planck equation.
Excellent outcomes among HIV+ children on ART, but unacceptably high pre-ART mortality and losses to follow-up: a cohort study from Cambodia

BACKGROUND
Although HIV program evaluations focusing on mortality on ART provide important evidence on treatment effectiveness, they do not asses overall HIV program performance because they exclude patients who are eligible but not started on ART for whatever reason. The objective of this study was to measure mortality that occurs both pre-ART and during ART among HIV-positive children enrolled in two HIV-programs in Cambodia.


METHODS
Retrospective cohort study on 1168 HIV-positive children <15 years old registered in two HIV-programs over a four-year period. Mortality rates were calculated for both children on treatment and children not started on ART.


RESULTS
Over half (53%) of children were 5 years or above and only 69(6%) were <18 months. Overall, 9% (105/1168) of children died since the set-up of the programs. By the end of the observation period, 66(14.5%) patients not on ART had died compared to 39(5.5%) of those under treatment, and 100(22%) who did not start ART were lost-to-follow-up compared to 13(2%) on ART. 66/105 (62.8%) of all in-program deaths occurred before starting ART, of which 56% (37/66) and 79% (52/66) occurred within 3 and 6 months of enrollment respectively. Mortality rate ratio between children not on ART and children on ART was 4.1 (95%CI: 2.7-6.2) (P < 0.001). The most common contributing cause of death in first 3 months of treatment and in first 3 months of program enrollment was tuberculosis. 41/52 (79%) children who died within 6 months of enrollment had met the ART eligibility criteria before death.


CONCLUSION
HIV-positive children experienced a high mortality and loss-to-follow-up rates before starting ART. These program outcomes may be improved by a more timely ART initiation. Measuring overall in-program mortality as opposed to only mortality on ART is recommended in order to more accurately evaluate pediatric HIV-programs performance.
Development and Implementation of the Balanced Scorecard for a Higher Educational Institution using Business Intelligence Tools

The objective of designing a strategy for an institution is to create more value and achieve its vision, with clear and coherent strategies, identifying the conditions in which they are currently, the sector in which they work and the different types of competences that generate, as well as the market in general where they perform, to create this type of conditions requires the availability of strategic information to verify the current conditions, to define the strategic line to follow according to internal and external factors, and in this way decide which methods to use to implement the development of a strategy in the organization. This research project was developed in an institution of higher education where the strategic processes were analyzed from different perspectives i.e. financial, customers, internal processes, and training and learning using business intelligence tools, such as Excel Power BI, Power Pivot, Power Query and a relational database for data repository; which helped having agile and effective information for the creation of the balanced scorecard, involving all levels of the organization and academic units; operating key performance indicators (KPI’s), for operational and strategic decisions. The results were obtained in form of boards of indicators designed to be visualized in the final view of the software constructed with previously described software tools. Keywords—Business intelligence; balanced scorecard; key performance indicators; BI Tools
Application of GeoGebra software into teaching mechanical engineering courses

Mechanics courses traditionally characterize with a rather low percentage of passing students. Dynamic mathematical packages like GeoGebra are widely used nowadays for teaching mathematics, but its interactive capabilities can be used for simulation of different physical phenomena. In this article few interactive applets for Static, Dynamic, Strength of Materials and Theory of Mechanisms and Machines courses, are presented. An experiment with comparison of the test results of two group of students after the exercise beam about internal forces, shows that group trained with GeoGebra applets have significantly higher mean result.
Monitoring Wind Turbine Vibration Based on SCADA Data

Three models for detecting abnormalities of wind turbine vibrations reflected in time domain are discussed. The models were derived from the supervisory control and data acquisition (SCADA) data collected at various wind turbines. The vibration of a wind turbine is characterized by two parameters, i.e., drivetrain and tower acceleration. An unsupervised data-mining algorithm, the k-means clustering algorithm, was applied to develop the first monitoring model. The other two monitoring models for detecting abnormal values of drivetrain and tower acceleration were developed by using the concept of a control chart. SCADA vibration data sampled at 10 s intervals reflects normal and faulty status of wind turbines. The performance of the three monitoring models for detecting abnormalities of wind turbines reflected in vibration data of time domain was validated with the SCADA industrial data. [DOI: 10.1115/1.4005753]
Measuring the Impact of Diabetes Through Patient Report of Treatment Satisfaction, Productivity and Symptom Experience

Objective: Diabetes is a common, debilitating chronic illness with multiple impacts. The impact on treatment satisfaction, productivity impairment and the symptom experience may be among the most important for patient-reported outcomes. This study developed and validated disease-specific, patient-reported measures for these outcomes that address limitations in currently available measures. Methods: Data was collected from the literature, experts and patients and a conceptual model of the patient-reported impact of diabetes was created. Item pools, based on the conceptual model, were then generated. The items were administered to 991 diabetes patients via a web-based survey to perform item reduction, identify relevant factor structures and assess reliability and validity following an a-priori analysis plan. Results: All validation criteria and hypotheses were met resulting in three new, valid measures: a 21-item Satisfaction Measure (three sub-scales: burden, efficacy and symptoms), a 30-item Symptom Measure and a 14-item Productivity Measure assessing both life and work productivity impairments.Conclusion: This triad of measures captures important components of the multifaceted diabetes patient experience and can be considered as valid, viable options when choosing measures to assess patient-reported outcomes. Addressing these outcomes may assist researchers and clinicians to develop more patient-centered diabetes interventions and care.