LLukas22/scidocs huggingface dataset:
USING STABLE ISOTOPE ANALYSES TO IDENTIFY ALLOCHTHONOUS INPUTS TO LAKE NAIVASHA MEDIATED VIA THE HIPPOPOTAMUS GUT *

The hippopotamus grazes nocturnally on land and resides in water during the day. Much of the ingested material must therefore be defecated directly into the aquatic system and can thus be considered an allochthonous resource available to aquatic consumers. The utility of stable isotope analyses of carbon and nitrogen to distinguish hippo faecal matter from other potential basal resources was tested at Lake Naivasha, Kenya. Hippopotami proved faithful to a short grass diet although supplementary grazing of aquatic macrophytes was observed. The typical isotopic ratios of C4 grasses ingested were not altered substantially by gut processes, and were clearly distinct from algal and aquatic macrophyte isotopic ratios. However, marginal plants such as Cyperus papyrus exhibit C4 ratios, and so the technique is suitable only for use in localities where ‘contamination’ from such sources is negligible.
Femoral hernias: a register analysis of 588 repairs

From 1 January 1992 to 31 December 1997 18,281 inguinal hernias and 588 femoral hernias were recorded in the Swedish Hernia Register. The aim of the present study was to characterise these femoral hernias and to evaluate the reoperation rate following their repair. 64% of all femoral hernias were located in the right groin and 36% in the left groin (p < 0.001). The male to female ratio for femoral hernia was 1:1.6; mean ages of patients with femoral and inguinal hernia were 63.4 ± 17.1 and 59.1 ± 16.4 years, respectively (p < 0.001). Emergency surgery and bowel resection at emergency surgery were more common with femoral than with inguinal hernia. The rate of ambulatory surgery was lower for femoral hernia than for inguinal hernia, mainly due to the higher emergency rate for femoral hernia. At three years the cumulative incidence of reoperation was 4.6% (95% confidence interval 2.4–6.8%) for femoral hernia and 4.0% (95% confidence interval 3.6–4.4%) for inguinal hernia (p > 0.05). Male sex and postoperative complications were associated with a significantly increased risk of reoperation following femoral hernia repair. The relative risk of reoperation was not affected by patient age, elective/emergency surgery, primary/recurrent hernia or hernia side. Repair techniques using mesh were associated with a lower reoperation rate than techniques without mesh, although the difference did not reach statistical significance.
Parents' Use of Physical Interventions in the Management of Their Children's Severe Challenging Behaviour.

Background Although training staff supporting people with challenging behaviour in physical interventions has become accepted practice, parents are often left to fend for themselves while managing equivalent behaviours. The study explores parents’ experience of managing severe challenging behaviours, their use of physical interventions and access to training in reactive strategies. Method A postal survey methodology was employed that utilized a novel 20-item questionnaire. The questionnaire yielded both quantitative and qualitative data concerning the types of challenging behaviour displayed by the children, frequency of use and nature of physical interventions, types of training received and any difficulties experienced in obtaining training. The sample was drawn from the membership of a national charitable organization and comprised of 72 respondents. Results The majority of respondents had experienced major episodes of challenging behaviour. The emotional impact of living with such behaviours was apparent. Although the vast majority of respondents had employed restrictive physical interventions, few had received any formal training in such strategies. There was evidence that a number of high-risk physical interventions were sometimes being employed. Accessing training appeared more problematic for parents when compared with paid care staff. Conclusions In this specific sample, parental use of physical intervention was high while parent training in physical intervention was uncommon. Impediments to parent training in physical intervention are discussed, as are wider issues concerning parental support.
Bone age determination based on the study of the medial extremity of the clavicle

The development of the medial clavicular epiphysis and its fusion with the clavicular shaft have been a subject of medical research since the second decade of this century. Computed tomography provides the imaging modality of choice in analyzing the maturation process of the sternal end of the clavicle. In a retrospective study, we analyzed normal development in 380 individuals under the age of 30 years. The appearance of an epiphyseal ossification center occurred between ages 11 and 22 years. Partial union was found from age 16 until age 26 years. Complete union was first noted at age 22 years and in 100 % of the sample at age 27 years. Based on these data, age-related standardized age distributions and 95 % reference intervals were calculated. Compared to the experience recorded in the relevant literature, there are several landmarks that show no significant change between different ethnic groups and different periods of publication; these are the onset of ossification, the time span of partial union, and the appearance of complete union. Despite the relatively long time spans of the maturation stages, bone age estimation based on the study of the development of the medial clavicular epiphysis may be a useful tool in forensic age identification in living individuals, especially if the age of the subject is about the end of the second or the beginning of the third decade of life (e. g. in determining the applicability of adult or juvenile penal systems). Another possible use is in identifying human remains whose age is estimated at under 30 years.
The mystery of the quantum cakes

In an attempt to make the concept and consequences of quantum mechanical entanglement more accessible to the non-physicist, we present a simple “real-world” explanation of the proof of quantum mechanical nonlocality without the use of inequalities.
Image Analysis and Deep Learning for Applications in Microscopy

Ishaq, O. 2016. Image Analysis and Deep Learning for Applications in Microscopy. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 1371. 76 pp. Uppsala: Acta Universitatis Upsaliensis. ISBN 978-91-554-9567-1. Quantitative microscopy deals with the extraction of quantitative measurements from samples observed under a microscope. Recent developments in microscopy systems, sample preparation and handling techniques have enabled high throughput biological experiments resulting in large amounts of image data, at biological scales ranging from subcellular structures such as fluorescently tagged nucleic acid sequences to whole organisms such as zebrafish embryos. Consequently, methods and algorithms for automated quantitative analysis of these images have become increasingly important. These methods range from traditional image analysis techniques to use of deep learning architectures. Many biomedical microscopy assays result in fluorescent spots. Robust detection and precise localization of these spots are two important, albeit sometimes overlapping, areas for application of quantitative image analysis. We demonstrate the use of popular deep learning architectures for spot detection and compare them against more traditional parametric model-based approaches. Moreover, we quantify the effect of pre-training and change in the size of training sets on detection performance. Thereafter, we determine the potential of training deep networks on synthetic and semi-synthetic datasets and their comparison with networks trained on manually annotated real data. In addition, we present a two-alternative forced-choice based tool for assisting in manual annotation of real image data. On a spot localization track, we parallelize a popular compressed sensing based localization method and evaluate its performance in conjunction with different optimizers, noise conditions and spot densities. We investigate its sensitivity to different point spread function estimates. Zebrafish is an important model organism, attractive for whole-organism image-based assays for drug discovery campaigns. The effect of drug-induced neuronal damage may be expressed in the form of zebrafish shape deformation. First, we present an automated method for accurate quantification of tail deformations in multi-fish micro-plate wells using image analysis techniques such as illumination correction, segmentation, generation of branch-free skeletons of partial tail-segments and their fusion to generate complete tails. Later, we demonstrate the use of a deep learning-based pipeline for classifying micro-plate wells as either drug-affected or negative controls, resulting in competitive performance, and compare the performance from deep learning against that from traditional image analysis approaches.
Spinal cord stimulation is not cost-effective for non-surgical management of critical limb ischaemia.

OBJECTIVE
To quantify the costs of treatment in critical limb ischaemia (CLI) and to compare costs and effectiveness of two treatment strategies: spinal cord stimulation (SCS) and best medical treatment.


METHODS
One hundred and twenty patients with CLI not suitable for vascular reconstruction were randomised to either SCS in addition to best medical treatment or best medical treatment alone. Primary outcomes were mortality, amputation and cost. Cost analysis was based on resources used by patients for 2 years after randomisation. Both medical and non-medical costs were included.


RESULTS
Patient and limb survival were similar in the two treatment groups. Costs of in-hospital-stay and institutional rehabilitation constituted the predominant part (+/-70%) of the total costs of medical care in CLI. Cost of SCS-implantation and complications (7950 euro per patient) exceeded by far cost due to amputation procedures (410 euro per patient). The total costs of treatment were 36,600 euro per patient over 2 years for the SCS-group vs. 28,700 euro for best medical treatment alone (28% higher for SCS-group, p=0.009).


CONCLUSIONS
Total costs of treatment in CLI are high. Major components are hospital and rehabilitation costs. In contrast to recent reviews, there were no long-term benefits of SCS-treatment. Therefore, cost-effectiveness is reduced to cost-minimisation and SCS-treatment is considerably more expensive than best medical treatment.
Early detection of impending physiologic deterioration among patients who are not in intensive care: development of predictive models using data from an automated electronic medical record.

BACKGROUND
Ward patients who experience unplanned transfer to intensive care units have excess morbidity and mortality.


OBJECTIVE
To develop a predictive model for prediction of unplanned transfer from the medical-surgical ward to intensive care (or death on the ward in a patient who was "full code") using data from a comprehensive inpatient electronic medical record (EMR).


DESIGN
Retrospective case-control study; unit of analysis was a 12-hour patient shift. Shifts where a patient experienced an unplanned transfer were event shifts; shifts without a transfer were comparison shifts. Hospitalization records were transformed into 12-hour shift records, with 10 randomly selected comparison shifts identified for each event shift. Analysis employed logistic regression and split validation.


SETTING
Integrated healthcare delivery system in Northern California.


PATIENTS
Hospitalized adults at 14 hospitals with comprehensive inpatient EMRs.


MEASUREMENTS
Predictors included vital signs, laboratory test results, severity of illness scores, longitudinal chronic illness burden scores, transpired hospital length of stay, and care directives. Patients were also given a retrospective, electronically (not manually assigned) Modified Early Warning Score, or MEWS(re). Outcomes were transfer to the intensive care unit (ICU) from the ward or transitional care unit, or death outside the ICU among patients who were "full code".


RESULTS
We identified 4,036 events and 39,782 comparison shifts from a cohort of 102,422 patients' hospitalizations. The MEWS(re) had a c-statistic of 0.709 in the derivation and 0.698 in the validation dataset; corresponding values for the EMR-based model were 0.845 and 0.775.


LIMITATIONS
Using these algorithms requires hospitals with comprehensive inpatient EMRs and longitudinal data.


CONCLUSIONS
EMR-based detection of impending deterioration outside the ICU is feasible in integrated healthcare delivery systems.
The Next Step for Learning Analytics

Learning Analytics Initiatives Learning analytics is the third wave of developments in instructional technology, which began with the advent of the learning management system (LMS) in 1991. The second wave integrated the LMS into the wider educational enterprise by involving learners on social networks (also known as the Web 2.0 wave). During this third wave, learning analytics as a term has been significantly popularized by the Educause International Conferences on Learning Analytics and Knowledge (LAK),2 which started in 2011 (https://tekri.athabascau. ca/analytics). Learning analytics focuses on collecting and analyzing data from a variety of sources to provide information on what works (and what doesn’t) with respect to teaching and learning.3,4 This helps educational institutions improve their quality of learning and overall competitiveness. Consequently, many research communities have developed a variety of promising initiatives, models, and applications to improve learner success. For example, Santa Monica College’s Glass Classroom initiative,5 introduced in December 2012, aims to enhance student and teacher performance by collecting and analyzing large amounts of data. Using realtime feedback of the student’s performance, Glass Class room adjusts the courseware to meet educational objectives. Another example is at the University of Wisconsin-Madison. Since May 2012, the university has been working to develop a data-driven “early-warning” system that faculty and advisors can use to support student academic success.6 The system will help identify academically at-risk students, using nontraditional indicators that can be gathered early in a student’s career, even at the beginning of a semester. The system aims to intervene early, improve students’ academic success, and bolster the campus’s retention and graduation rates. Furthermore, many research groups and societies are providing excellent networks for researchers who are exploring the impact of analytics on teaching, learning, training, and development (see the “Related Learning Analytics Research” sidebar). In particular, these groups and societies are promoting several learning analytics models, which have been Related Learning Analytics Research
MOBILE LEARNING FOR TEACHERS > Exploring the Potential of Mobile Technologies to Support Teachers and Improve Practice IN AFRICA and the MIDDLE EAST

.......................................................................................................................6 BACKGROUND AND METHODOLOGY .........................................................................8 MOBILE LEARNING FOR TEACHERS .............................................................................10 Responses to technology by AME teachers Mobile phones and teacher support Overcoming technophobia Extending education to remote areas Supporting teaching practice in classrooms Improving educational management and administration Enabling peer support Supporting teacher training Enhancing professional development Strengthening teacher competencies Analysis of mobile learning initiatives FACTORS INFLUENCING MOBILE LEARNING FOR TEACHERS ...................................24 Drivers and enablers
A Context-Aware Recurrent Encoder for Neural Machine Translation

Neural machine translation NMT heavily relies on its encoder to capture the underlying meaning of a source sentence so as to generate a faithful translation. However, most NMT encoders are built upon either unidirectional or bidirectional recurrent neural networks, which either do not deal with future context or simply concatenate the history and future context to form context-dependent word representations, implicitly assuming the independence of the two types of contextual information. In this paper, we propose a novel context-aware recurrent encoder CAEncoder, as an alternative to the widely-used bidirectional encoder, such that the future and history contexts can be fully incorporated into the learned source representations. Our CAEncoder involves a two-level hierarchy: The bottom level summarizes the history information, whereas the upper level assembles the summarized history and future context into source representations. Additionally, CAEncoder is as efficient as the bidirectional RNN encoder in terms of both training and decoding. Experiments on both Chinese–English and English–German translation tasks show that CAEncoder achieves significant improvements over the bidirectional RNN encoder on a widely-used NMT system. 1
Severe Endothelial Damage in Chronic Kidney Disease Patients Prior to Haemodialysis Vascular Access Surgery.

BACKGROUND
Hemodialysis as an efficient therapy for advanced CKD is the most used treatment modality all over the world. Even though primary AVF is widely accepted as a best permanent vascular access in hemodialysis patients, up to 60% of all fistulas fail to mature. The pathogenesis of early fistula failure is not very well understood. Many general and local factors are involved: patient's age, sex, primary renal disease, small vessel's diameter, presence of accessory veins, prior venipunctures, surgical skill, genetics, etc. Histological investigations have confirmed the neointimal venous hyperplasia as a major pathological finding in stenotic lesions of AVF failure, due to local inflammation, oxidative stress and migration and proliferation of myofibroblasts, fibroblasts and endothelial cells.


MATERIALS AND METHODS
A total of 89 patients with stadium 4-5 of CKD are involved in the study. A typical radio-cephalic AVF is created in all patients. Part of the fistula vein was taken for histological, immunohistochemical (Vimentin, TGF β and KI67) and morphometric analysis. Appriopriate statistical method was applied.


RESULTS
Up to 80% of the patients showed some degree of endothelial changes at the time of creation of AVF, among them 19 pts with substantial intimal hyperplasia, 51 with medial hypertrophy and 19 pts with normal histology. Almost two thirds of the patients did not have expression of TGFβ. More than 95% had some expression of Vimentin. None of the patients had expression of the marker KI 67.


CONCLUSION
Medial hypertrophy is predominant preexisting pathohistological lesion prior the AVF creation, despite the presence of neointimal hyperplasia. The absence of TGFβ expression in majority of our patients could suggest that inflammation and oxidative stress are developing later, after vascular access surgery. The dominant cells within the stenosis in the veins are myofibroblasts. Their increased presence maybe a reason why some patients are prone to developing venous endothelial changes as a results of exaggerated vascular endothelial response to the effect of uremia, hypertension and other insults.
Modeling the Dynamic Characteristics of Pneumatic Muscle

A pneumatic muscle (PM) system was studied to determine whether a three-element model could describe its dynamics. As far as the authors are aware, this model has not been used to describe the dynamics of PM. A new phenomenological model consists of a contractile (force-generating) element, spring element, and damping element in parallel. The PM system was investigated using an apparatus that allowed precise and accurate actuation pressure (P) control by a linear servovalve. Length change of the PM was measured by a linear potentiometer. Spring and damping element functions of P were determined by a static perturbation method at several constant P values. These results indicate that at constant P, PM behaves as a spring and damper in parallel. The contractile element function of P was determined by the response to a step input in P, using values of spring and damping elements from the perturbation study. The study showed that the resulting coefficient functions of the three-element model describe the dynamic response to the step input of P accurately, indicating that the static perturbation results can be applied to the dynamic case. This model is further validated by accurately predicting the contraction response to a triangular P waveform. All three elements have pressure-dependent coefficients for pressure P in the range 207 ⩽ P⩽ 621 kPa (30⩽ P⩽ 90 psi). Studies with a step decrease in P (relaxation of the PM) indicate that the damping element coefficient is smaller during relaxation than contraction.© 2003 Biomedical Engineering Society. PAC2003: 8719Rr, 8719Ff, 8710+e, 8768+z
Modified Hirt procedure for rapid purification of extrachromosomal DNA from mammalian cells.

Methods for extracting extrachromosomal DNA from eukaryotic cells are important for many studies such as DNA replication and identification of certain viruses (2). The procedure described by Hirt (4), which has been widely used over the last thirty years, is laborious and time-consuming and requires phenol extraction. More rapid methods using anion-exchange chromatography (5) or silicon-based resins (3) use the alkaline lysis procedure that was originally developed for extracting plasmid DNA from bacterial cells (1). Only covalently closed circular DNA renatures correctly and stays in solution on rapid neutralization of the alkaline lysis buffer, whereas linear and open circular DNA precipitate together with the denatured proteins and chromosomal DNA (3). Thus, certain DNA replication intermediates are not recovered. This report describes a modification in which lysis at neutral pH, as in the Hirt procedure, combined with purification on a silica-gel membrane, enables the rapid recovery of linear and relaxed circular DNA along with the supercoiled form. Cells (106–107) are dispersed with trypsin, pelleted and washed in Ca2+/ Mg2+-free phosphate-buffered saline (PBS). They are resuspended in 250 μL 50 mM Tris-HCl, pH 7.5, 10 mM EDTA containing 100 μg/mL RNase A and lysed by the addition of 250 μL 1.2% sodium dodecyl sulfate (SDS). The suspension is gently mixed by inverting the tube several times and then stands for 5 min at ambient temperature. Adherent cells can be lysed directly in the culture plate after washing with PBS by overlaying them with 500 μL of a mixture of equal volumes of the above resuspension and lysis solutions. The plates are gently agitated to completely cover all cells, and the lysate is subsequently transferred to 1.5-mL microcentrifuge tubes. Cellular debris and chromosomal DNA are precipitated by the addition of 350 μL 3 M CsCl, 1 M potassium acetate and 0.67 M acetic acid. The tubes are immediately but gently mixed and placed on ice for 15 min. After centrifugation for 15 min at 14 000× g, the supernatant is loaded onto a silica gel membrane column (QIAprep Spin Column; Qiagen GmbH, Hilden, Germany). The column is washed with 750 μL 80 mM potassium acetate, 10 mM Tris-HCl, pH 7.5, 40 μM EDTA and 60% ethanol. DNA is then eluted with 50 μL water or TE buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA). These columns are loaded, washed and eluted by centrifugation at 14 000× g or vacuum. COS cells were transfected with pSL3-EGFP, an 8.0-kb plasmid that contains the simian virus 40 (SV40) origin of replication. Twenty-four hours posttransfection, cells were suspended
Search result diversification

Result diversification has recently attracted much attention as a means of increasing user satisfaction in recommender systems and web search. Many different approaches have been proposed in the related literature for the diversification problem. In this paper, we survey, classify and comparatively study the various definitions, algorithms and metrics for result diversification.