LLukas22/scidocs huggingface dataset:
A prospective cohort study of surgical treatment for back pain with degenerated discs; study protocol

BACKGROUND
The diagnosis of discogenic back pain often leads to spinal fusion surgery and may partly explain the recent rapid increase in lumbar fusion operations in the United States. Little is known about how patients undergoing lumbar fusion compare in preoperative physical and psychological function to patients who have degenerative discs, but receive only non-surgical care.


METHODS
Our group is implementing a multi-center prospective cohort study to compare patients with presumed discogenic pain who undergo lumbar fusion with those who have non-surgical care. We identify patients with predominant low back pain lasting at least six months, one or two-level disc degeneration confirmed by imaging, and a normal neurological exam. Patients are classified as surgical or non-surgical based on the treatment they receive during the six months following study enrollment.


RESULTS
Three hundred patients discogenic low back pain will be followed in a prospective cohort study for two years. The primary outcome measure is the Modified Roland-Morris Disability Questionnaire at 24-months. We also evaluate several other dimensions of outcome, including pain, functional status, psychological distress, general well-being, and role disability.


CONCLUSION
The primary aim of this prospective cohort study is to better define the outcomes of lumbar fusion for discogenic back pain as it is practiced in the United States. We additionally aim to identify characteristics that result in better patient selection for surgery. Potential predictors include demographics, work and disability compensation status, initial symptom severity and duration, imaging results, functional status, and psychological distress.
Primary chemotherapy with gemcitabine as prolonged infusion, non-pegylated liposomal doxorubicin and docetaxel in patients with early breast cancer: final results of a phase II trial.

BACKGROUND
Combinations of anthracyclines, taxanes and gemcitabine have shown high activity in breast cancer. This trial was designed to evaluate a modified combination regimen as primary chemotherapy. Non-pegylated liposomal doxorubicin (NPLD) was used instead of conventional doxorubicin to improve cardiac safety. Gemcitabine was given 72 h after NPLD and docetaxel as a prolonged infusion over 4 h in order to optimize synergistic effects and accumulation of active metabolites.


PATIENTS AND METHODS
Forty-four patients with histologically confirmed stage II or III breast cancer were treated with NPLD (60 mg/m(2)) and docetaxel (75 mg/m(2)) on day 1 and gemcitabine as 4-h infusion (350 mg/m(2)) on day 4. Treatment was repeated every 3 weeks for a maximum of six cycles. All patients received prophylactically recombinant granulocyte colony-stimulating factor. Patients with axillary lymph node involvement after primary chemotherapy received adjuvant treatment with cyclophosphamide, methotrexate and fluorouracil.


RESULTS
The clinical response rate was 80%, and complete remissions of the primary tumor occurred in 10 patients (25%). Breast conservation surgery was performed in 19 out of 20 patients (95%) with an initial tumor size of less than 3 cm and in 14 patients (70%) with a tumor size <or=3 cm. Seven patients had histologically confirmed complete responses accounting for a pCR rate of 17.5%. Expression of Ki--67 was the most important predictive parameter for response with high 38.9% breast pCR rate in patients with elevated Ki--67 expression. Although the predominant toxicity was myelosuppression with grade 3/4 neutropenia in 61% of patients few neutropenic complications resulted. Non-hematological toxicity was generally moderate with grade 3 or 4 toxicity in 10.0% of cycles. Most common non-hematologic toxicities were nausea, vomiting, alopecia, mucositis, asthenia and elevation of liver enzymes.


CONCLUSION
The evaluated schedule provides a safe and highly effective combination treatment for patients with early breast cancer, which is suitable for phase III studies.
GUIDELINES FOR HANDHELD MOBILE DEVICE INTERFACE DESIGN

While there has been much successful work in developing rules to guide the design and implementation of interfaces for desktop machines and their applications, the design of mobile device interfaces is still relatively unexplored and unproven. This paper discusses the characteristics and limitations of current mobile device interfaces, especially compared to the desktop environment. Using existing interface guidelines as a starting point, a set of practical design guidelines for mobile device interfaces is proposed.
Learning to Program = Learning to Construct Mechanisms and Explanations

Teaching effective problem-solving skills in the context of teaching programming necessitates a revised curriculum for introductory computer programming courses.
Lean Software Development

Lean deveLopment is a product development paradigm with an endto-end focus on creating value for the customer, eliminating waste, optimizing value streams, empowering people, and continuously improving (see Figure 11). Lean thinking has penetrated many industries. It was first used in manufacturing, with clear goals to empower teams, reduce waste, optimize work streams, and above all keep market and customer needs as the primary decision driver.2 This IEEE Software special issue addresses lean software development as opposed to management or manufacturing theories. In that context, we sought to address some key questions: What design principles deliver value, and how are they introduced to best manage change?
Risk prediction models for hospital readmission: a systematic review.

CONTEXT
Predicting hospital readmission risk is of great interest to identify which patients would benefit most from care transition interventions, as well as to risk-adjust readmission rates for the purposes of hospital comparison.


OBJECTIVE
To summarize validated readmission risk prediction models, describe their performance, and assess suitability for clinical or administrative use.


DATA SOURCES AND STUDY SELECTION
The databases of MEDLINE, CINAHL, and the Cochrane Library were searched from inception through March 2011, the EMBASE database was searched through August 2011, and hand searches were performed of the retrieved reference lists. Dual review was conducted to identify studies published in the English language of prediction models tested with medical patients in both derivation and validation cohorts.


DATA EXTRACTION
Data were extracted on the population, setting, sample size, follow-up interval, readmission rate, model discrimination and calibration, type of data used, and timing of data collection.


DATA SYNTHESIS
Of 7843 citations reviewed, 30 studies of 26 unique models met the inclusion criteria. The most common outcome used was 30-day readmission; only 1 model specifically addressed preventable readmissions. Fourteen models that relied on retrospective administrative data could be potentially used to risk-adjust readmission rates for hospital comparison; of these, 9 were tested in large US populations and had poor discriminative ability (c statistic range: 0.55-0.65). Seven models could potentially be used to identify high-risk patients for intervention early during a hospitalization (c statistic range: 0.56-0.72), and 5 could be used at hospital discharge (c statistic range: 0.68-0.83). Six studies compared different models in the same population and 2 of these found that functional and social variables improved model discrimination. Although most models incorporated variables for medical comorbidity and use of prior medical services, few examined variables associated with overall health and function, illness severity, or social determinants of health.


CONCLUSIONS
Most current readmission risk prediction models that were designed for either comparative or clinical purposes perform poorly. Although in certain settings such models may prove useful, efforts to improve their performance are needed as use becomes more widespread.
Transmembrane helix prediction using amino acid property features and latent semantic analysis

Prediction of transmembrane (TM) helices by statistical methods suffers from lack of sufficient training data. Current best methods use hundreds or even thousands of free parameters in their models which are tuned to fit the little data available for training. Further, they are often restricted to the generally accepted topology "cytoplasmic-transmembrane-extracellular" and cannot adapt to membrane proteins that do not conform to this topology. Recent crystal structures of channel proteins have revealed novel architectures showing that the above topology may not be as universal as previously believed. Thus, there is a need for methods that can better predict TM helices even in novel topologies and families. Here, we describe a new method "TMpro" to predict TM helices with high accuracy. To avoid overfitting to existing topologies, we have collapsed cytoplasmic and extracellular labels to a single state, non-TM. TMpro is a binary classifier which predicts TM or non-TM using multiple amino acid properties (charge, polarity, aromaticity, size and electronic properties) as features. The features are extracted from sequence information by applying the framework used for latent semantic analysis of text documents and are input to neural networks that learn the distinction between TM and non-TM segments. The model uses only 25 free parameters. In benchmark analysis TMpro achieves 95% segment F-score corresponding to 50% reduction in error rate compared to the best methods not requiring an evolutionary profile of a protein to be known. Performance is also improved when applied to more recent and larger high resolution datasets PDBTM and MPtopo. TMpro predictions in membrane proteins with unusual or disputed TM structure (K+ channel, aquaporin and HIV envelope glycoprotein) are discussed. TMpro uses very few free parameters in modeling TM segments as opposed to the very large number of free parameters used in state-of-the-art membrane prediction methods, yet achieves very high segment accuracies. This is highly advantageous considering that high resolution transmembrane information is available only for very few proteins. The greatest impact of TMpro is therefore expected in the prediction of TM segments in proteins with novel topologies. Further, the paper introduces a novel method of extracting features from protein sequence, namely that of latent semantic analysis model. The success of this approach in the current context suggests that it can find potential applications in other sequence-based analysis problems. http://linzer.blm.cs.cmu.edu/tmpro/ and http://flan.blm.cs.cmu.edu/tmpro/
Heat Advisory: Protecting Health on a Warming Planet

The 2016 John S. Curran Lecture: Oct 13 Assessing the Quality of Perinatal Care: Advances and Barriers Scott Lorch, MD Associate Professor of Pediatrics at the Perelman School of Medicine at the University of Pennsylvania, and Senior Fellow of the Leonard Davis Institute of Health Economics at the University of Pennsylvania Please join us for a breakfast reception in the MacInnes Auditorium foyer following the Curran Lecture
On line PD measurements and diagnosis on power transformers

On line partial discharge (PD) measurements provide information on the dielectric integrity of the high voltage insulation of oil insulated power transformers during service. These PD measurements are performed using a broadband antenna on an oil valve and UHF detection of PD signals. The sensitivity of this new detection technique is high and immunity for electromagnetic (EM) interference and corona discharges in air outside the transformer is very good. Dielectric faults can be detected in this way in an early stage of development and are classified in four categories. Automatic pattern recognition techniques of phase resolved pulse sequence (PRPS) data are very useful in risk assessment of dielectric faults.
Outcomes in patients with cardiogenic shock following percutaneous coronary intervention in the contemporary era: an analysis from the BCIS database (British Cardiovascular Intervention Society).

OBJECTIVES
This study sought to determine mortality rates among cardiogenic shock (CGS) patients undergoing percutaneous coronary intervention (PCI) for acute coronary syndrome in the contemporary treatment era and to determine predictors of mortality.


BACKGROUND
It is unclear whether recent advances in pharmacological and interventional strategies have resulted in further improvements in short- and long-term mortality and which factors are associated with adverse outcomes in patients presenting with CGS and undergoing PCI in the setting of acute coronary syndrome.


METHODS
This study analyzed prospectively collected data for patients undergoing PCI in the setting of CGS as recorded in the BCIS (British Cardiovascular Intervention Society) PCI database.


RESULTS
In England and Wales, 6,489 patients underwent PCI for acute coronary syndrome in the setting of CGS. The mortality rates at 30 days, 90 days, and 1 year were 37.3%, 40.0%, and 44.3%, respectively. On multiple logistic regression analysis, age (for each 10-year increment of age: odds ratio [OR]: 1.59, 95% confidence interval [CI]: 1.51 to 1.68; p < 0.0001), diabetes mellitus (OR: 1.47, 95% CI: 1.28 to 1.70; p < 0.0001), history of renal disease (OR: 2.03, 95% CI: 1.63 to 2.53; p < 0.0001), need for artificial mechanical ventilation (OR: 2.56, 95% CI: 2.23 to 2.94; p < 0.0001), intra-aortic balloon pump use (OR: 1.57, 95% CI: 1.40 to 1.76; p < 0.0001), and need for left main stem PCI (OR: 1.90, 95% CI: 1.62 to 2.23; p < 0.0001) were associated with higher mortality at 1 year.


CONCLUSIONS
In this large U.K. cohort of patients undergoing PCI in the context of CGS, mortality remains high in spite of the use of contemporary PCI strategies. The highest mortality occurs early, and this time period may be a particular target of therapeutic intervention.
Combination of two urinary biomarkers predicts acute kidney injury after adult cardiac surgery.

BACKGROUND
Urinary L-type fatty acid-binding protein (L-FABP) has not been evaluated for adult post-cardiac surgery acute kidney injury (AKI) to date. This study was undertaken to evaluate a biomarker panel consisting of urinary L-FABP and N-acetyl-β-D-glucosaminidase (NAG), a more established urinary marker of kidney injury, for AKI diagnosis in adult post-cardiac surgery patients.


METHODS
This study prospectively evaluated 77 adult patients who underwent cardiac surgery at 2 general hospitals. Urinary L-FABP and NAG were measured before surgery, at intensive care unit arrival after surgery (0 hours), 4, and 12 hours after arrival. The AKI was diagnosed by the Acute Kidney Injury Network criteria.


RESULTS
Of 77 patients, 28 patients (36.4%) developed AKI after surgery. Urinary L-FABP and NAG were significantly increased. However, receiver operating characteristic (ROC) analysis revealed that the biomarkers' performance was statistically significant but limited for clinical translation (area under the curve of ROC [AUC-ROC] for L-FABP at 4 hours 0.72 and NAG 0.75). Urinary L-FABP showed high sensitivity and NAG detected AKI with high specificity. Therefore, we combined these 2 biomarkers, which revealed that this combination panel can detect AKI with higher accuracy than either biomarker measurement alone (AUC-ROC 0.81). Moreover, this biomarker panel improved AKI risk prediction significantly compared with predictions made using the clinical model alone.


CONCLUSIONS
When urinary L-FABP and NAG are combined, they can detect AKI adequately, even in a heterogeneous population of adult post-cardiac surgery AKI. Combining 2 markers with different sensitivity and specificity presents a reasonable strategy to improve the diagnostic performance of biomarkers.
Comparison of glucosamine sulfate and a polyherbal supplement for the relief of osteoarthritis of the knee: a randomized controlled trial [ISRCTN25438351]

BACKGROUND
The efficacy and safety of a dietary supplement derived from South American botanicals was compared to glucosamine sulfate in osteoarthritis subjects in a Mumbai-based multi-center, randomized, double-blind study.


METHODS
Subjects (n = 95) were screened and randomized to receive glucosamine sulfate (n = 47, 1500 mg/day) or reparagen (n = 48, 1800 mg/day), a polyherbal consisting of 300 mg of vincaria (Uncaria guianensis) and 1500 mg of RNI 249 (Lepidium meyenii) administered orally, twice daily. Primary efficacy variable was response rate based on a 20% improvement in WOMAC pain scores. Additional outcomes were WOMAC scores for pain, stiffness and function, visual analog score (VAS) for pain, with assessments at 1, 2, 4, 6 and 8 weeks. Tolerability, investigator and subject global assessments and rescue medication consumption (paracetamol) were measured together with safety assessments including vital signs and laboratory based assays.


RESULTS
Subject randomization was effective: age, gender and disease status distribution was similar in both groups. The response rates (20% reduction in WOMAC pain) were substantial for both glucosamine (89%) and reparagen (94%) and supported by investigator and subject assessments. Using related criteria response rates to reparagen were favorable when compared to glucosamine. Compared to baseline both treatments showed significant benefits in WOMAC and VAS outcomes within one week (P < 0.05), with a similar, progressive improvement over the course of the 8 week treatment protocol (45-62% reduction in WOMAC or VAS scores). Tolerability was excellent, no serious adverse events were noted and safety parameters were unchanged. Rescue medication use was significantly lower in the reparagen group (p < 0.01) at each assessment period. Serum IGF-1 levels were unaltered by treatments.


CONCLUSION
Both reparagen and glucosamine sulfate produced substantial improvements in pain, stiffness and function in subjects with osteoarthritis. Response rates were high and the safety profile was excellent, with significantly less rescue medication use with reparagen. Reparagen represents a new natural productive alternative in the management of joint health.


TRIAL REGISTRATION
Current Controlled Trials ISRCTN25438351.
Neurologic features of Hutchinson-Gilford progeria syndrome after lonafarnib treatment.

OBJECTIVES
The objective of this study was to retrospectively evaluate neurologic status pre- and posttreatment with the oral farnesyltransferase inhibitor lonafarnib in children with Hutchinson-Gilford progeria syndrome (HGPS), a rare, fatal disorder of segmental premature aging that results in early death by myocardial infarction or stroke.


METHODS
The primary outcome measure for intervention with lonafarnib was to assess increase over pretherapy in estimated annual rate of weight gain. In this study, neurologic signs and symptoms were compared pre- and posttreatment with lonafarnib.


RESULTS
Twenty-six participants were treated for a minimum of 2 years. Frequency of clinical strokes, headaches, and seizures was reduced from pretrial rates. Three patients with a history of frequent TIAs and average clinical stroke frequency of 1.75/year during the year before treatment experienced no new events during treatment. One patient with a history of stroke died due to large-vessel hemispheric stroke after 5 months on treatment. Headache prevalence and frequency were reduced. Four patients exhibited pretherapy seizures and no patients experienced recurrent or new-onset seizures.


CONCLUSIONS
This study provides preliminary evidence that lonafarnib therapy may improve neurologic status of children with HGPS. To address this question, we have incorporated prospective neuroimaging and neurologic assessments as measures in subsequent studies involving children with HGPS.


CLASSIFICATION OF EVIDENCE
This study provides Class IV evidence that lonafarnib 115-150 mg/m(2) for 24 to 29 months reduces the prevalence of stroke and TIA and the prevalence and frequency of headache over the treatment period.
Minimally invasive, non-ablative Er:YAG laser treatment of stress urinary incontinence in women—a pilot study

The study presents an assessment of mechanism of action and a pilot clinical study of efficacy and safety of the Er:YAG laser for the treatment of stress urinary incontinence (SUI). The subject of this study is a treatment of SUI with a 2940 nm Er:YAG laser, operating in a special SMOOTH mode designed to increase temperature of the vaginal mucosa up to maximally 60–65 °C without ablating the epidermis. Numerical modelling of the temperature distribution within mucosa tissue following an irradiation with the SMOOTH mode Er:YAG laser was performed in order to determine the appropriate range of laser parameters. The laser treatment parameters were further confirmed by measuring in vivo temperatures of the vaginal mucosa using a thermal camera. To investigate the clinical efficacy and safety of the SMOOTH mode Er:YAG laser SUI treatment, a pilot clinical study was performed. The study recruited 31 female patients suffering from SUI. Follow-ups were scheduled at 1, 2, and 6 months post treatment. ICIQ-UI questionnaires were collected as a primary trial endpoint. Secondary endpoints included perineometry and residual urine volume measurements at baseline and all follow-ups. Thermal camera measurements have shown the optimal increase in temperature of the vaginal mucosa following treatment of SUI with a SMOOTH mode Er:YAG laser. Primary endpoint, the change in ICIQ-UI score, showed clinically relevant and statistically significant improvement after all follow-ups compared to baseline scores. There was also improvement in the secondary endpoints. Only mild and transient adverse events and no serious adverse events were reported. The results indicate that non-ablative Er:YAG laser therapy is a promising minimally invasive non-surgical option for treating women with SUI symptoms.
Dogs do look at images: eye tracking in canine cognition research

Despite intense research on the visual communication of domestic dogs, their cognitive capacities have not yet been explored by eye tracking. The aim of the current study was to expand knowledge on the visual cognition of dogs using contact-free eye movement tracking under conditions where social cueing and associative learning were ruled out. We examined whether dogs spontaneously look at actual objects within pictures and can differentiate between pictures according to their novelty or categorical information content. Eye movements of six domestic dogs were tracked during presentation of digital color images of human faces, dog faces, toys, and alphabetic characters. We found that dogs focused their attention on the informative regions of the images without any task-specific pre-training and their gazing behavior depended on the image category. Dogs preferred the facial images of conspecifics over other categories and fixated on a familiar image longer than on novel stimuli regardless of the category. Dogs’ attraction to conspecifics over human faces and inanimate objects might reflect their natural interest, but further studies are needed to establish whether dogs possess picture object recognition. Contact-free eye movement tracking is a promising method for the broader exploration of processes underlying special socio-cognitive skills in dogs previously found in behavioral studies.