LLukas22/scidocs huggingface dataset:
TBCRC 008: early change in 18F-FDG uptake on PET predicts response to preoperative systemic therapy in human epidermal growth factor receptor 2-negative primary operable breast cancer.

UNLABELLED
Epigenetic modifiers, including the histone deacetylase inhibitor vorinostat, may sensitize tumors to chemotherapy and enhance outcomes. We conducted a multicenter randomized phase II neoadjuvant trial of carboplatin and nanoparticle albumin-bound paclitaxel (CP) with vorinostat or placebo in women with stage II/III, human epidermal growth factor receptor 2 (HER2)-negative breast cancer, in which we also examined whether change in maximum standardized uptake values corrected for lean body mass (SUL(max)) on (18)F-FDG PET predicted pathologic complete response (pCR) in breast and axillary lymph nodes.


METHODS
Participants were randomly assigned to 12 wk of preoperative carboplatin (area under the curve of 2, weekly) and nab-paclitaxel (100 mg/m(2) weekly) with vorinostat (400 mg orally daily, days 1-3 of every 7-d period) or placebo. All patients underwent (18)F-FDG PET and research biopsy at baseline and on cycle 1 day 15. The primary endpoint was the pCR rate. Secondary objectives included correlation of change in tumor SUL(max) on (18)F-FDG PET by cycle 1 day 15 with pCR and correlation of baseline and change in Ki-67 with pCR.


RESULTS
In an intent-to-treat analysis (n = 62), overall pCR was 27.4% (vorinostat, 25.8%; placebo, 29.0%). In a pooled analysis (n = 59), we observed a significant difference in median change in SUL(max) 15 d after initiating preoperative therapy between those achieving pCR versus not (percentage reduction, 63.0% vs. 32.9%; P = 0.003). Patients with 50% or greater reduction in SUL(max) were more likely to achieve pCR, which remained statistically significant in multivariable analysis including estrogen receptor status (odds ratio, 5.1; 95% confidence interval, 1.3-22.7; P = 0.023). Differences in baseline and change in Ki-67 were not significantly different between those achieving pCR versus not.


CONCLUSION
Preoperative CP with vorinostat or placebo is associated with similar pCR rates. Early change in SUL(max) on (18)F-FDG PET 15 d after the initiation of preoperative therapy has potential in predicting pCR in patients with HER2-negative breast cancer. Future studies will further test (18)F-FDG PET as a potential treatment-selection biomarker.
Epidemiology of knee injuries among boys and girls in US high school athletics.

BACKGROUND
The knee joint is the second most commonly injured body site and the leading cause of high school sports-related surgeries. Knee injuries are among the most economically costly sports injuries and may require subsequent surgery or extensive and expensive rehabilitation.


PURPOSE
To report the incidence, risk, and severity of high school knee injuries across sports, genders, and type of exposure.


STUDY DESIGN
Descriptive epidemiology study.


METHODS
During the 2005-2006 and 2006-2007 school years, 100 US high schools were randomly selected for a nationally representative sample. Certified athletic trainers tracked injuries using an online injury surveillance system, High School RIO, in 9 high school sports.


RESULTS
There were 1383 knee injuries reported during 3,551131 athlete exposures for a rate of 3.89 knee injuries per 10,000 athlete exposures. Although boys had a higher overall rate of knee injury (rate ratio, 1.38; confidence interval, 1.22-1.55), girls were twice as likely to sustain knee injuries requiring surgery (major knee injuries) than were boys (injury proportion ratio, 1.98; confidence interval, 1.45-2.70) and twice as likely to incur noncontact major knee injuries (injury proportion ratio, 1.98; confidence interval, 1.23-3.19) as were boys. Although illegal play was identified as a contributing factor in only 5.7% of all knee injuries, 20% of knee injuries resulting from illegal play required surgery.


CONCLUSION
Knee injury rates and patterns varied by sport, gender, and type of exposure. Identified gender differences included differences in injury rates, injury severity, and basic injury mechanism. Further surveillance is crucial for the development of targeted, evidence-based injury prevention strategies to reduce the morbidity and economic impact of knee surgeries.
Suspended Alexandrium Spp . Hypnozygote Cysts in the Gulf of Maine

The life cycle of dinoflagellates of the genus Alexandrium includes sexual reproduction followed by the formation of a dormant hypnozygote cyst, which serves as a resting stage. Negatively buoyant cysts purportedly fall to the benthos where they undergo a mandatory period of quiescence. Previous reports of cysts in the surficial sediments of the Gulf of Maine, where Alexandrium blooms are well documented, show a broad distribution of cysts, with highest concentrations generally in sediments below 100m depth. We report here an exploration of cysts suspended in the water column, where they would be better positioned to inoculate springtime Alexandrium populations. During cruises in February, April, and June of 2000, water samples were collected at depths just off the bottom (within 5m), at the top of the bottom nepheloid layer, and near the surface (1m) and examined for cyst concentrations. Suspended cysts were found throughout the Gulf of Maine and westernmost Bay of Fundy. Planktonic cyst densities were generally greater in near-bottom and top of the bottom nepheloid layer samples than in near-surface water samples; densities were of the order of 10 cystsm 3 in surface waters, and 10–10 cystsm 3 at near-bottom depths. Temporally, they were most abundant in February and least abundant in April. Reports by earlier workers of cysts in the underlying sediments were on the order of 10 cysts cm . We present calculations that demonstrate the likelihood of cyst resuspension from bottom sediments forced by swell and tidal currents, and propose that such resuspended cysts are important in inoculating the seasonal bloom. We estimate that suspended cysts may contribute significantly to the annual vegetative cell population in the Gulf of Maine. r 2005 Elsevier Ltd. All rights reserved.
Sentiment analysis of twitter data

Social networks are the main resources to gather information about people’s opinion and sentiments towards different topics as they spend hours daily on social medias and share their opinion. In this technical paper, we show the application of sentimental analysis and how to connect to Twitter and run sentimental analysis queries. We run experiments on different queries from politics to humanity and show the interesting results. We realized that the neutral sentiment for tweets are significantly high which clearly shows the limitations of the current works. Keywords—Twitter sentiment analysis, Social Network analysis.
Wavelets in Economics and Finance : Past and Future

In this paper I review what insights we have gained about economic and financial relationships from the use of wavelets and speculate on what further insights we may gain in the future. Wavelets are treated as a “lens” that enables the researcher to explore relationships that previously were
Gambling cognition and subjective well-being as mediators between perceived stress and problem gambling: a cross-cultural study on White and Chinese problem gamblers.

This study aimed to delineate various pathways whereby cognitive and emotional vulnerabilities triggered by stress would lead to disruptive gambling. A multiple mediation framework was proposed to specify that gambling cognition and subjective well-being would mediate the influence of perceived stress on problem gambling. The cross-cultural validity of the proposed framework was examined with 132 White gamblers in Australia and 154 Chinese gamblers in China. They completed psychological scales on perceived stress, gambling expectancy bias, gambling refusal efficacy, negative affect, life satisfaction, and problem gambling. Compared to Chinese gamblers, White gamblers reported higher levels of perceived stress, gambling expectancy bias, and problem gambling as well as more pervasive negative affect and lower levels of life satisfaction. Results showed that the proposed multiple mediation framework fit the data better than two alternative plausible models. Life satisfaction and gambling refusal efficacy were two consistent mediators across White and Chinese gamblers.
Recurrent basal cell carcinoma after incomplete resection.

BACKGROUND
Because the probability of basal cell carcinoma (BCC) recurrence was thought to be 30% to 50%, surgical tradition became not to perform additional resection when the margin was positive.


OBJECTIVE
To determine whether there is an association among age or sex of the patient, anatomic location, histologic type, or reconstructive procedures and the signs and symptoms of the recurrence, interval between incomplete resection and Mohs micrographic surgery (MMS), or extent of MMS resection.


DESIGN
During 20 years, all patients with incompletely excised BCC of the head referred for MMS were sequentially prospectively accrued into the cohort.


SETTING
An outpatient MMS practice.


PATIENTS
Nine hundred ninety-four patients.


MAIN OUTCOME MEASURES
Interval to tumor recurrence, interval to MMS, and extent of MMS as determined by mean surface area resected, depth of resection, and number of tumor nests.


RESULTS
The interval to signs or symptoms of recurrence and to MMS from incomplete resection was greater for men, patients older than 65 years, those having a tumor on the nose or cheek, those with aggressive or fibrosing BCC, and those who underwent flap reconstruction (P =.001). The extent of MMS resection was greater for those with flap and split-thickness skin graft repairs. The number of tumor nests identified by MMS was significantly greater in those treated with split-thickness skin graft and flap (P =.001).


CONCLUSION
Because it is more difficult to control recurrent BCC, treating tumor remaining at the margin of resection in the immediate postoperative period could result in less extensive surgery.
Energy and mass spectroscopy studies during triode ion plating of TiN films in two different layouts

Abstract Plasma properties are compared in two triode ion-plating systems using a low-voltage arc discharge. The systems differ in the configuration of the chamber and magnetic field. Mass and energy distributions of positive ions during deposition of TiN films were measured by an energy-resolved mass spectrometer. Plasma parameters were determined also by Langmuir probe diagnostics. In both systems, single and multiple charged ions of Ar and N 2 gas and the evaporated Ti were detected. The system with a strong magnetic field confinement exhibits a higher plasma potential ( U p =55 V) under standard deposition conditions, the peak ion energy is higher and the energy distribution is narrower than in the system without magnetic confinement ( U p =12 to 35 V). The probability for the multiple charged ions in this system is much higher than in the system without the magnetic confinement, so the population of Ti ++ in this system is even higher than that of Ti + . The presence of high-energy neutral Ti is also observed.
What oncologists tell patients about survival benefits of palliative chemotherapy and implications for informed consent: qualitative study

OBJECTIVE
To examine how much oncologists tell patients about the survival benefit of palliative chemotherapy during consultations at which decisions about treatment are made.


DESIGN
Qualitative study in which consultations were observed and digitally recorded.


SETTING
Teaching hospital and district general hospital in south west England.


PARTICIPANTS
37 patients with advanced non-small cell lung cancer (n=12), pancreatic cancer (n=13), and colorectal cancer (n=12); and nine oncologists, including four consultants and five registrars.


MAIN OUTCOME MEASURES
All recordings were transcribed completely, anonymised, and electronically coded with ATLAS.ti. Constant comparison was used to identify themes and patterns. The framework method of data management, in which data were charted, was used to aid transparency of interpretation.


RESULTS
During the consultations, information given to patients about survival benefit included numerical data ("about four weeks"), an idea of timescales ("a few months extra"), vague references ("buy you some time"), or no mention at all. In most consultations (26/37) discussion of survival benefit was vague or non-existent.


CONCLUSIONS
Most patients were not given clear information about the survival gain of palliative chemotherapy. To aid decision making and informed consent, we recommend that oncologists sensitively describe the benefits and limitations of this treatment, including survival gain.
Laboratory environments and rodents' behavioural needs: a review.

Laboratory housing conditions have significant physiological and psychological effects on rodents, raising both scientific and humane concerns. Published studies of rats, mice and other rodents were reviewed to document behavioural and psychological problems attributable to predominant laboratory housing conditions. Studies indicate that rats and mice value opportunities to take cover, build nests, explore, gain social contact, and exercise some control over their social milieu, and that the inability to satisfy these needs is physically and psychologically detrimental, leading to impaired brain development and behavioural anomalies (e.g. stereotypies). To the extent that space is a means to gain access to such resources, spatial confinement likely exacerbates these deficits. Adding environmental 'enrichments' to small cages reduces but does not eliminate these problems, and I argue that substantial changes in housing and husbandry conditions would be needed to further reduce them.
Neurogenic orthostatic hypotension: a pathophysiological approach.

Orthostatic hypotension (OH) is defined as a persistent, consistent, orthostatic fall in systolic blood pressure of 20 mm Hg or diastolic pressure of 10 mm Hg by 3 minutes of standing up.1 Acute, unexpected, episodic falls in blood pressure while standing, as in neurocardiogenic syncope, do not satisfy criteria for OH. Medical records for 0.4% of all hospitalizations in the United States include OH as a diagnosis, and of these 17% have OH as the primary diagnosis.2 OH is associated with increased mortality in middle-aged adults3 and occurs especially commonly in the elderly, with a prevalence in the United States of 12%.4 The rate of hospitalization for nonacute OH increases exponentially with age.2 Therefore, as the US population ages, the prevalence of OH and the incidence of OH-related morbidity are likely to increase. OH can be an asymptomatic sign or manifest as symptoms that range from lightheadedness to loss of consciousness. In our experience, patients with OH do not typically present with recurrent syncope because they come to recognize and respond to premonitory symptoms such as generalized weakness, dizziness, fading vision, or lightheadedness that are relieved by lying down. Instead, OH patients often present with orthostatic intolerance and recurrent falls, an important risk factor for hip fracture and head trauma. Moreover, OH often occurs concurrently with supine hypertension, which can be severe.5 The combination of OH and supine hypertension poses a challenging clinical dilemma because the clinician must balance the risk of chronic high blood pressure versus the immediate risk of falls and consequent morbid events.
Factored Neural Language Models

We present a new type of neural probabilistic language model that learns a mapping from both words and explicit word features into a continuous space that is then used for word prediction. Additionally, we investigate several ways of deriving continuous word representations for unknown words from those of known words. The resulting model significantly reduces perplexity on sparse-data tasks when compared to standard backoff models, standard neural language models, and factored language models.
Reliability of the metaphyseal-diaphyseal angle in tibia vara as measured on digital images by pediatric orthopaedic surgeons.

BACKGROUND
Levine and Drennan described the tibial metaphyseal-diaphyseal angle (MDA) in an attempt to identify patients with infantile Blount's disease. Pediatric orthopaedic surgeons have debated not only the use, but also the reliability of this measure. Two techniques have been described to measure the MDA. These techniques involved using both the lateral border of the tibial cortex and the center of the tibial shaft as the longitudinal axis for radiographic measurements. The use of digital images poses another variable in the reliability of the MDA as digital images are used more commonly.


METHODS
The radiographs of 21 children (42 limbs) were retrospectively reviewed by 27 staff pediatric orthopaedic surgeons. Interobserver reliability was determined using the intraclass correlation coefficients (ICCs). Nine duplicate radiographs (18 duplicate limbs) that appeared in the data set were used to calculate ICCs representing the intraobserver reliability. A scatter plot was created comparing the mean MDA determined by the 2 methods. The strength of a linear relationship between the 2 methods was measured with the Pearson correlation coefficient. Finally, we tested for a difference in variability between the 2 measures at angles of 11 degrees or less and greater than 11 degrees by comparing the variance ratios using the F test.


RESULTS
The interobserver reliability was calculated using the ICC as 0.821 for the single-measure method and 0.992 for the average-measure method. The intraobserver reliability was similarly calculated using the ICC as 0.886 for the single-measure method and 0.940 for the average-measure method. Pearson correlation coefficient (0.9848) revealed a highly linear relationship between the 2 methods (P = 0.00001). We also found that there was no statistically significant variability between the 2 methods of calculating the MDA at angles of 11 degrees or less compared with angles greater than 11 degrees (P = 0.596688).


CONCLUSIONS
There was excellent interobserver reliability and intraobserver reliability among reviewers. Using either the lateral diaphyseal line or center diaphyseal line produces reasonable reliability with no significant variability at angles of 11 degrees or less or greater than 11 degrees.


LEVEL OF EVIDENCE
Level IV.
RobotReviewer: evaluation of a system for automatically assessing bias in clinical trials

OBJECTIVE
To develop and evaluate RobotReviewer, a machine learning (ML) system that automatically assesses bias in clinical trials. From a (PDF-formatted) trial report, the system should determine risks of bias for the domains defined by the Cochrane Risk of Bias (RoB) tool, and extract supporting text for these judgments.


METHODS
We algorithmically annotated 12,808 trial PDFs using data from the Cochrane Database of Systematic Reviews (CDSR). Trials were labeled as being at low or high/unclear risk of bias for each domain, and sentences were labeled as being informative or not. This dataset was used to train a multi-task ML model. We estimated the accuracy of ML judgments versus humans by comparing trials with two or more independent RoB assessments in the CDSR. Twenty blinded experienced reviewers rated the relevance of supporting text, comparing ML output with equivalent (human-extracted) text from the CDSR.


RESULTS
By retrieving the top 3 candidate sentences per document (top3 recall), the best ML text was rated more relevant than text from the CDSR, but not significantly (60.4% ML text rated 'highly relevant' v 56.5% of text from reviews; difference +3.9%, [-3.2% to +10.9%]). Model RoB judgments were less accurate than those from published reviews, though the difference was <10% (overall accuracy 71.0% with ML v 78.3% with CDSR).


CONCLUSION
Risk of bias assessment may be automated with reasonable accuracy. Automatically identified text supporting bias assessment is of equal quality to the manually identified text in the CDSR. This technology could substantially reduce reviewer workload and expedite evidence syntheses.
Wavelet Transforms | A Quick Study

The wavelet transform has become a useful computational tool for a variety of signal and image processing applications. For example, the wavelet transform is useful for the compression of digital image files; smaller files are important for storing images using less memory and for transmitting images faster and more reliably. The FBI uses wavelet transforms for compressing digitally scanned fingerprint images. NASA’s Mars Rovers used wavelet transforms for compressing images acquired by their 18 cameras. The wavelet-based algorithm implemented in software onboard the Mars Rovers is designed to meet the special requirements of deep-space communication. In addition, JPEG2K (the newer JPEG image file format) is based on wavelet transforms. Wavelet transforms are also useful for ‘cleaning’ signals and images (reducing unwanted noise and blurring). Some algorithms for processing astronomical images, for example, are based on wavelet and wavelet-like transforms. This Quick Study describes the wavelet transform, illustrates why it is effective for noise reduction, and briefly describes several improvements of the basic wavelet transform and basic noise reduction method used in the illustration. We describe what the wavelet transform is, and we describe algorithms for processing a signal after its wavelet transform has been computed. First we should point out that there are two basic types of wavelet transform. One type of wavelet transform is designed to be easily reversible (invertible); that means the original signal can be easily recovered after it has been transformed. This kind of wavelet transform is used for image compression and cleaning (noise and blur reduction). Typically, the wavelet transform of the image is first computed, the wavelet representation is then modified appropriately, and then the wavelet transform is reversed (inverted) to obtain a new image. The second type of wavelet transform is designed for signal analysis; for example, to detect faults in machinery from sensor measurements, to study EEG or other biomedical signals, to determine how the frequency content of a signal evolves over time. In these cases, a modified form of the original signal is not needed and the wavelet transform need not be inverted (it can be done in principle, but requires a lot of computation time in comparison with the first type of wavelet transform). In this Quick Study we will focus on those wavelet transforms that are easily invertible. The most basic wavelet transform is the Haar transform described by Alfred Haar in 1910. It serves as the prototypical wavelet transform. We will describe the (discrete) Haar transform, as it