LLukas22/scidocs huggingface dataset:
The Association of Coloproctology of Great Britain and Ireland study of large bowel obstruction caused by colorectal cancer.

BACKGROUND
This study was designed to investigate the early outcomes after surgical treatment of malignant large bowel obstruction (MBO) and to identify risk factors affecting operative mortality.


METHODS
Data were prospectively collected from 1046 patients with MBO by 294 surgeons in 148 UK hospitals during a 12-month period from April 1998. A predictive model of in-hospital mortality was developed using a 3-level Bayesian logistic regression analysis.


RESULTS
The median age of patients was 73 years (interquartile range 64-80). Of the 989 patients having surgery, 91.7% underwent bowel resection with an overall mortality of 15.7%. The multilevel model used the following independent risk factors to predict mortality: age (odds ratio [OR] 1.85 per 10 year increase), American Society of Anesthesiologists grade (OR for American Society of Anesthesiologists grade I versus II,III,IV-V = 3.3,11.7,22.2), Dukes' staging (OR for Dukes' A versus B,C,D = 2.0, 2.1, 6.0), and mode of surgery (OR for scheduled versus urgent, emergency = 1.6, 2.3). A significant interhospital variability in operative mortality was evident with increasing age (variance = 0.004, SE = 0.001, P < 0.001). No detectable caseload effect was demonstrated between specialist colorectal and other general surgeons.


CONCLUSIONS
Using prognostic models, it was possible to develop a risk-stratification index that accurately predicted survival in patients presenting with malignant large bowel obstruction. The methodology and model for risk adjusted survival can set the reference point for more accurate and reliable comparative analysis and be used as an adjunct to the process of informed consent.
Introduction to automata theory, languages, and computation, 2nd edition

G' A. Linz, Peter. An introduction to formal languages and automata / Peter Linz'--3'd cd charrgcs ftrr the second edition wercl t)volutionary rather than rcvolrrtionary and addressed Initially, I felt that giving solutions to exercises was undesirable hecause it lirrritcd the Chapter 1 fntroduction to the Theory of Computation. Issuu solution manual to introduction to languages. Introduction theory computation 2nd edition solution manual sipser. Structural Theory of automata: solution manual of theory of computation. Kellison theory of interest pdf. Transformation, Sylvester's theorem(without proof), Solution of Second Order. Linear Differential Higher Engineering Mathematics by B.S. Grewal, 40th Edition, Khanna. Publication. 2. Introduction Of Automata Theory, Languages and computationHopcroft. Motwani&Ulman UNIX system Utilities manual. 4.
BioC: a minimalist approach to interoperability for biomedical text processing

A vast amount of scientific information is encoded in natural language text, and the quantity of such text has become so great that it is no longer economically feasible to have a human as the first step in the search process. Natural language processing and text mining tools have become essential to facilitate the search for and extraction of information from text. This has led to vigorous research efforts to create useful tools and to create humanly labeled text corpora, which can be used to improve such tools. To encourage combining these efforts into larger, more powerful and more capable systems, a common interchange format to represent, store and exchange the data in a simple manner between different language processing systems and text mining tools is highly desirable. Here we propose a simple extensible mark-up language format to share text documents and annotations. The proposed annotation approach allows a large number of different annotations to be represented including sentences, tokens, parts of speech, named entities such as genes or diseases and relationships between named entities. In addition, we provide simple code to hold this data, read it from and write it back to extensible mark-up language files and perform some sample processing. We also describe completed as well as ongoing work to apply the approach in several directions. Code and data are available at http://bioc.sourceforge.net/. Database URL: http://bioc.sourceforge.net/
MuseGAN: Multi-track Sequential Generative Adversarial Networks for Symbolic Music Generation and Accompaniment

Generating music has a few notable differences from generating images and videos. First, music is an art of time, necessitating a temporal model. Second, music is usually composed of multiple instruments/tracks with their own temporal dynamics, but collectively they unfold over time interdependently. Lastly, musical notes are often grouped into chords, arpeggios or melodies in polyphonic music, and thereby introducing a chronological ordering of notes is not naturally suitable. In this paper, we propose three models for symbolic multi-track music generation under the framework of generative adversarial networks (GANs). The three models, which differ in the underlying assumptions and accordingly the network architectures, are referred to as the jamming model, the composer model and the hybrid model. We trained the proposed models on a dataset of over one hundred thousand bars of rock music and applied them to generate piano-rolls of five tracks: bass, drums, guitar, piano and strings. A few intratrack and inter-track objective metrics are also proposed to evaluate the generative results, in addition to a subjective user study. We show that our models can generate coherent music of four bars right from scratch (i.e. without human inputs). We also extend our models to human-AI cooperative music generation: given a specific track composed by human, we can generate four additional tracks to accompany it. All code, the dataset and the rendered audio samples are available at https://salu133445.github.io/musegan/.
Anti-infliximab antibodies are already detectable in most patients with rheumatoid arthritis halfway through an infusioncycle: an open-label pharmacokinetic cohort study

BACKGROUND
This study in patients with rheumatoid arthritis (RA) treated with infliximab describes prospectively the course of (anti)infliximab levels within an infusion cycle to assess at what moment patients develop low/no infliximab trough levels and/or detectable anti-infliximab levels.


METHODS
Infliximab treated RA patients were included in this descriptive open-label cohort study. During one infusion cycle (anti-)infliximab levels were assessed just before and one hour after infusion, and subsequently at 50%, 75% and at the end of the infusion cycle (pre-infusion).


RESULTS
27 patients were included. The median infliximab levels decreased from 77.0 mg/l (p25-p75: 65-89) one hour after the infusion to pre-infusion levels of 0.0 mg/l (p25-p75: 0.0-3.1). In 7 (26%) patients pre-infusion anti-infliximab antibodies were detected; these antibodies were already present halfway through the infusion cycle in 5 of the 7 individuals. Patients with detectable pre-infusion anti-infliximab antibodies have significantly more often low/no infliximab levels (< 1 mg/l) halfway trough the infusion cycle (in 5/7 patients) compared to patients without detectable pre-infusion anti-infliximab antibodies (0/20 patients, p < 0.001).


CONCLUSIONS
Most anti-infliximab forming patients have detectable anti-infliximab antibodies halfway through an infusion cycle, which implies that these patients are exposed to nontherapeutical infliximab levels during more than half of their infusion cycle. As none of the patients without anti-infliximab antibodies had no/low-infliximab levels halfway through the infusion cycle, the presence of pre-infusion anti-infliximab antibodies seems a sensitive and specific predictor for no/low infliximab-levels.
From optimal transport to generative modeling: the VEGAN cookbook

We study unsupervised generative modeling in terms of the optimal transport (OT) problem between true (but unknown) data distribution PX and the latent variable model distribution PG. We show that the OT problem can be equivalently written in terms of probabilistic encoders, which are constrained to match the posterior and prior distributions over the latent space. When relaxed, this constrained optimization problem leads to a penalized optimal transport (POT) objective, which can be efficiently minimized using stochastic gradient descent by sampling from PX and PG. We show that POT for the 2-Wasserstein distance coincides with the objective heuristically employed in adversarial auto-encoders (AAE) [1], which provides the first theoretical justification for AAEs known to the authors. We also compare POT to other popular techniques like variational auto-encoders (VAE) [2]. Our theoretical results include (a) a better understanding of the commonly observed blurriness of images generated by VAEs, and (b) establishing duality between Wasserstein GAN [3] and POT for the 1-Wasserstein distance.
Quinolone-related Achilles tendinopathy in heart transplant patients: incidence and risk factors.

BACKGROUND
A high incidence of Achilles tendinopathy--tendinitis or rupture--has been observed after quinolone treatment in lung and kidney transplant patients. In the absence of relevant published data, we aimed to determine its incidence, clinical features, risk factors and outcome among heart graft recipients.


METHODS
We studied the clinical records of all adult heart transplant patients who were prescribed quinolones at our center between August 1995 and September 2006. Achilles tendinopathy had been diagnosed clinically, with ultrasound assessment when necessary. In all cases, quinolone treatment had been terminated upon diagnosis of tendinopathy.


RESULTS
During this period, quinolones had been given on 242 occasions to 149 heart transplant patients (33 women, 116 men). Achilles tendinopathy developed on 14 occasions (5.8%; 95% confidence interval: 2.8% to 8.7%), affecting 13 men and 1 woman (mean age: 62 years). Three cases involved tendon rupture, and bilateral tendinopathy was present in 8 cases. The median time between the start of treatment and onset of symptoms was 2.5 days, with 12 patients being asymptomatic 2 months after drug withdrawal. Independent risk factors for tendinopathy were renal dysfunction (p = 0.03) and increased time between transplantation and treatment (p = 0.005). Incidence was not influenced by the type, dose or previous administration of quinolones, or by the immunosuppressive regimen.


CONCLUSIONS
Quinolone-related Achilles tendinopathy is frequent among heart transplant patients, especially in the presence of renal dysfunction or lengthy post-transplantation survival. If no alternative anti-bacterial therapy is available for high-risk patients, close clinical surveillance should be warranted.
Ryanodine receptor channelopathies

Ryanodine receptors (RyR) are intracellular Ca2+-permeable channels that provide the sarcoplasmic reticulum Ca2+ release required for skeletal and cardiac muscle contractions. RyR1 underlies skeletal muscle contraction, and RyR2 fulfills this role in cardiac muscle. Over the past 20 years, numerous mutations in both RyR isoforms have been identified and linked to skeletal and cardiac diseases. Malignant hyperthermia, central core disease, and catecholaminergic polymorphic ventricular tachycardia have been genetically linked to mutations in either RyR1 or RyR2. Thus, RyR channelopathies are both of interest because they cause significant human diseases and provide model systems that can be studied to elucidate important structure–function relationships of these ion channels.
Modified HPLC-ESI-MS Method for Glycated Hemoglobin Quantification Based on the IFCC Reference Measurement Procedure and Its Application for Quantitative Analyses in Clinical Laboratories of China.

BACKGROUND
The level of glycated hemoglobin (HbA1c ) has been recognized as an important indicator of long-term glycemic control. However, the HbA1c measurement is not currently included as a diagnostic determinant in China. Current study aims to assess a candidate modified International Federation of Clinical Chemistry reference method for the forthcoming standardization of HbA1c measurements in China.


METHODS
The HbA1c concentration was measured using a modified high-performance liquid chromatography-electrospray ionization-mass spectrometry (HPLC-ESI-MS) method. The modified method replaces the propylcyanide column with a C18 reversed-phase column, which has a lower cost and is more commonly used in China, and uses 0.1% (26.5 mmol/l) formic acid instead of trifluoroacetic acid. Moreover, in order to minimize matrix interference and reduce the running time, a solid-phase extraction was employed. The discrepancies between HbA1c measurements using conventional methods and the HPLC-ESI-MS method were clarified in clinical samples from healthy people and diabetic patients. Corresponding samples were distributed to 89 hospitals in Beijing for external quality assessment.


RESULTS
The linearity, reliability, and accuracy of the modified HPLC-ESI-MS method with a shortened running time of 6 min were successfully validated. Out of 89 hospitals evaluated, the relative biases of HbA1c concentrations were < 8% for 74 hospitals and < 5% for 60 hospitals. Compared with other conventional methods, HbA1c concentrations determined by HPLC methods were similar to the values obtained from the current HPLC-ESI-MS method.


CONCLUSION
The HPLC-ESI-MS method represents an improvement over existing methods and provides a simple, stable, and rapid HbA1c measurement with strong signal intensities and reduced ion suppression.
Cardioprotective Role of Syzygium cumini Against Glucose-Induced Oxidative Stress in H9C2 Cardiac Myocytes

Diabetic patients are known to have an independent risk of cardiomyopathy. Hyperglycemia leads to upregulation of reactive oxygen species (ROS) that may contribute to diabetic cardiomyopathy. Thus, agents that suppress glucose-induced intracellular ROS levels can have therapeutic potential against diabetic cardiomyopathy. Syzygium cumini is well known for its anti-diabetic potential, but its cardioprotective properties have not been evaluated yet. The aim of the present study is to analyze cardioprotective properties of methanolic seed extract (MSE) of S. cumini in diabetic in vitro conditions. ROS scavenging activity of MSE was studied in glucose-stressed H9C2 cardiac myoblasts after optimizing the safe dose of glucose and MSE by 3-(4,5-dimethyl-thiazol-2-yl)-2,5-diphenyl tetrazolium bromide. 2′,7′-dichlorfluorescein diacetate staining and Fluorescence-activated cell sorting analysis confirmed the suppression of ROS production by MSE in glucose-induced cells. The intracellular NO and H2O2 radical–scavenging activity of MSE was found to be significantly high in glucose-induced cells. Exposure of glucose-stressed H9C2 cells to MSE showed decline in the activity of catalase and superoxide dismutase enzymes and collagen content. 4′,6-diamidino-2-phenylindole, propidium iodide and 10-N-nonyl-3,6-bis (dimethylamino) acridine staining revealed that MSE protects myocardial cells from glucose-induced stress. Taken together, our findings revealed that the well-known anti-diabetic S. cumini can also protect the cardiac cells from glucose-induced stress.
Routine use of intravenous low-dose recombinant tissue plasminogen activator in Japanese patients: general outcomes and prognostic factors from the SAMURAI register.

BACKGROUND AND PURPOSE
A retrospective, multicenter, observational study was conducted to document clinical outcomes and to identify outcome predictors in patients treated with low-dose intravenous recombinant tissue plasminogen activator (0.6 mg/kg alteplase), which was approved in Japan in 2005, within 3 hours of stroke onset.


METHODS
Consecutive patients with stroke treated with recombinant tissue plasminogen activator in 10 Japanese stroke centers were included.


RESULTS
A total of 600 patients (377 men, 72+/-12 years old) were studied. Median National Institutes of Health Stroke Scale scores decreased from 13 before recombinant tissue plasminogen activator to 8 at 24 hours later. Symptomatic intracerebral hemorrhage within 36 hours with a >or=1-point increase from the baseline National Institutes of Health Stroke Scale score developed in 23 patients (3.8%; 95% CI, 2.6% to 5.7%). At 3 months, 43 patients had died (7.2%; 5.4% to 9.5%), and 199 patients (33.2%; 29.5% to 37.0%) had a modified Rankin Scale score <or=1. Analysis of 399 patients with a premorbid modified Rankin Scale score <or=1 who met the criteria of the European license (<or=80 years old, an initial National Institutes of Health Stroke Scale score <or=24, etc) showed that 40.6% (35.9% to 45.5%) had a 3-month modified Rankin Scale score <or=1. After multivariate adjustment, younger age, lower initial National Institutes of Health Stroke Scale score, absence of internal carotid artery occlusion, higher Alberta Stroke Program Early CT Score on CT, and absence of intravenous antihypertensives just before recombinant tissue plasminogen activator were independently related to a 3-month modified Rankin Scale score <or=1. Congestive heart failure and hyperglycemia were independently related to mortality.


CONCLUSIONS
Three-month outcomes of patients receiving low-dose intravenous recombinant tissue plasminogen activator therapy in the present study were similar to those from postmarketing surveys using 0.9 mg/kg alteplase.
Feature extraction from higher-lag autocorrelation coefficients for robust speech recognition

In this paper, a feature extraction method that is robust to additive background noise is proposed for automatic speech recognition. Since the background noise corrupts the autocorrelation coefficients of the speech signal mostly at the lowertime lags, while the higher-lag autocorrelation coefficients are least affected, this method discards the lower-lag autocorrelation coefficients and uses only the higher-lag autocorrelation coefficients for spectral estimation. The magnitude spectrum of the windowed higher-lag autocorrelation sequence is used here as an estimate of the power spectrum of the speech signal. This power spectral estimate is processed further (like the well-known Mel frequency cepstral coefficient (MFCC) procedure) by the Mel filter bank, log operation and the discrete cosine transform to get the cepstral coefficients. These cepstral coefficients are referred to as the autocorrelation Mel frequency cepstral coefficients (AMFCCs). We evaluate the speech recognition performance of the AMFCC features on the Aurora and the resource management databases and show that they perform as well as the MFCC features for clean speech and their recognition performance is better than the MFCC features for noisy speech. Finally, we show that the AMFCC features perform better than the features derived from the robust linear prediction-based methods for noisy speech. 2006 Elsevier B.V. All rights reserved.
Demonstration of an electronic photonic integrated circuit in a commercial scaled bulk CMOS process

We demonstrate the first photonic chip designed in a commercial bulk CMOS process (65 nm node) using standard process layers combined with scalable post-processing, enabling dense photonic integration with high-performance microprocessor electronics.
Effect of Glucocorticoid Treatment on Computed Tomography Angiography Detected Large-Vessel Inflammation in Giant-Cell Arteritis. A Prospective, Longitudinal Study

Computed tomography angiography (CTA) detects signs of large-vessel vasculitis (LVV) in about 67.5% of patients with giant-cell arteritis (GCA) at the time of diagnosis and early aortic dilatation in 15%. The outcome of CTA-findings of LVV upon glucocorticoid treatment has not been prospectively evaluated. The aim of our study was to prospectively assess glucocorticoid-induced changes in CTA findings of LVV in patients with GCA. Forty biopsy-proven GCA patients evaluated by CTA at diagnosis were prospectively followed and scheduled a new CTA approximately after 1 year of treatment. Vessel wall thickening, diameter, and contrast enhancement of the aorta and its tributaries were evaluated. Results were compared to those obtained at the time of diagnosis. CTA was repeated to 35 patients after a median follow-up of 13.5 months (IQ25-75% 12.4-15.8). Arterial wall thickening was still present in 17 patients (68% of the patients who initially had LVV). The number of affected segments and wall thickness at various aortic segments significantly decreased and no patients developed new lesions, new aortic dilation or increase in previous dilation. Contrast enhancement disappeared in 15 (93.75%) of 16 patients in whom this finding could be assessed. Signs of LVV improve with treatment. While contrast enhancement resolves in the majority of patients, vessel wall thickening persists in two thirds. However, the number of affected aortic segments as well as aortic wall thickness significantly decreases. Longer follow-up is necessary to determine the clinical significance of persisting wall thickening and its relationship with relapses or subsequent development of aortic dilatation or large-vessel stenoses.
Implicit Function Theorem. Part I

In this article, we formalize in Mizar [1], [3] the existence and uniqueness part of the implicit function theorem. In the first section, some composition properties of Lipschitz continuous linear function are discussed. In the second section, a definition of closed ball and theorems of several properties of open and closed sets in Banach space are described. In the last section, we formalized the existence and uniqueness of continuous implicit function in Banach space using Banach fixed point theorem. We referred to [7], [8], and [2] in this formalization.
Wide Variation and Excessive Dosage of Opioid Prescriptions for Common General Surgical Procedures.

OBJECTIVE
To examine opioid prescribing patterns after general surgery procedures and to estimate an ideal number of pills to prescribe.


BACKGROUND
Diversion of prescription opioids is a major contributor to the rising mortality from opioid overdoses. Data to inform surgeons on the optimal dose of opioids to prescribe after common general surgical procedures is lacking.


METHODS
We evaluated 642 patients undergoing 5 outpatient procedures: partial mastectomy (PM), partial mastectomy with sentinel lymph node biopsy (PM SLNB), laparoscopic cholecystectomy (LC), laparoscopic inguinal hernia repair (LIH), and open inguinal hernia repair (IH). Postoperative opioid prescriptions and refill data were tabulated. A phone survey was conducted to determine the number of opioid pills taken.


RESULTS
There was a wide variation in the number of opioid pills prescribed to patients undergoing the same operation. The median number (and range) prescribed were: PM 20 (0-50), PM SLNB 20 (0-60), LC 30 (0-100), LIH 30 (15-70), and IH 30 (15-120). Only 28% of the prescribed pills were taken. This percentage varied by operation: PM 15%, PM SLNB 25%, LC 33%, LIH 15%, and IH 31%. Less than 2% of patients obtained refills.We identified the number of pills that would fully supply the opioid needs of 80% of patients undergoing each operation: PM 5, PM SLNB 10, LC 15, LIH 15, and IH 15. If this number were prescribed, the number of opioid initially prescribed would be 43% of the actual number prescribed.


CONCLUSIONS
There is wide variability in opioid prescriptions for common general surgery procedures. In many cases excess pills are prescribed. Using our ideal number, surgeons can adequately treat postoperative pain and markedly decrease the number of opioids prescribed.