LLukas22/scidocs huggingface dataset:
Relationship between cervical disease and infection with human papillomavirus types 16 and 18, and herpes simplex virus 1 and 2.

Persistent infection with high-risk HPV, particularly Type HPV 16 and 18, is necessary in the development of cervical cancer, but apart from HPV infection, other causative factors of most cervical cancers remain unknown. The aim of this study was to determine the prevalence of HPV 16 and HPV 18 and HSV 1 and HSV 2 in cervical samples, and to assess the role of HSVs in cervical carcinogenesis. Two hundred thirty-three healthy controls and 567 cases (333 of cervicitis, 210 of cervical intraepithelial neoplasia, and 24 of squamous cell carcinoma) in cervical exfoliative cells were tested for HPV 16, HPV 18, HSV 1, and HSV 2 DNA using the triplex real-time polymerase chain reaction method. In contrast to healthy women, positive rate of HPV is related significantly to cervical lesions (odds ratios (ORs) = 4.1, P < 0.01 for cervical intraepithelial neoplasia; ORs = 24.9, P < 0.01 for squamous cell carcinoma), but not cervicitis (ORs = 2.3, P > 0.05). HSV 2 prevalence in cervical intraepithelial neoplasia and squamous cell carcinoma was higher than in healthy women (ORs = 4.9, P < 0.05 for cervical intraepithelial neoplasia; ORs = 4.7, P < 0.05 for squamous cell carcinoma). HSV 2 coinfection with HPV in cervical intraepithelial neoplasia and squamous cell carcinoma was strongly higher than in healthy women (ORs = 34.2, P < 0.01 for cervical intraepithelial neoplasia; ORs = 61.1, P < 0.01 for squamous cell carcinoma). The obtained results indicated that the presence of HPV is associated closely with cervical cancer, and that HSV 2 infection or co-infection with HPV might be involved in cervical cancer development, while HSV 1 might not be involved.
An organ-preserving selective arterial chemotherapy strategy for head and neck cancer.

PURPOSE
Squamous cancer of the upper aerodigestive tract is a disheartening disease. Despite our best efforts, the long-term survival rate remains only 15% to 40%, and surgical cures often decrease the quality of life owing to the loss of swallowing and speech organs. A better understanding of tumor dynamics and the discovery that thiosulfate can neutralize cisplatin led us to develop a treatment plan that combines a rapid superselective high-dose intraarterial delivery of cisplatin (CDDP), simultaneous intravenous infusion of its antagonist, thiosulfate, and radiation therapy.


METHODS
Patients with advanced head and neck squamous cancer were entered into the protocol after a multidisciplinary evaluation that included CT or MR imaging. Forty-two patients constituted the first cohort. After baseline angiography, an arterial acceptance test determined the maximum infusion rate that the tumor's nutrient artery would accept. CDDP was then infused at that rate, usually within 3 to 5 minutes, while the antagonist thiosulfate was given intravenously. In the second cohort of 85 patients with stage 3 or 4 previously untreated and unresectable disease, local radiation was added to the treatment plan. The radiation dose (180-200 cGy/d x 35) was delivered regionally on the basis of the known radiosensitizing effect of CDDP.


RESULTS
Cohort 1 allowed us to develop the infusion technique and to establish a dose quantity and delivery frequency. When 150 mg/m2 was administered weekly for 4 weeks, no severe toxicity was found. In cohort 2, 72 (92%) of the remaining 78 patients had complete disappearance of their tumor. Seventeen severe toxic events were associated with 323 femoral catheterizations. One patient died of pulmonary embolus, precluding follow-up evaluation. Six patients had neurologic sequelae, three with transient and three with permanent strokes.


CONCLUSION
Rapid superselective chemotherapy with CDDP combined with a circulatory systemic antagonist allowed delivery of an antitumoral drug directly into the lesion while protecting the kidneys and bone marrow from the agent's systemic effects. Use of a dose regimen of 150 mg CDDP/m2 per week for 4 weeks resulted in the disappearance of a large percentage of advanced squamous cancers.
Towards a scalable resource-driven approach for detecting repackaged Android applications

Repackaged Android applications (or simply apps) are one of the major sources of mobile malware and also an important cause of severe revenue loss to app developers. Although a number of solutions have been proposed to detect repackaged apps, the majority of them heavily rely on code analysis, thus suffering from two limitations: (1) poor scalability due to the billion opcode problem; (2) unreliability to code obfuscation/app hardening techniques. In this paper, we explore an alternative approach that exploits core resources, which have close relationships with codes, to detect repackaged apps. More precisely, we define new features for characterizing apps, investigate two kinds of algorithms for searching similar apps, and propose a two-stage methodology to speed up the detection. We realize our approach in a system named ResDroid and conduct large scale evaluation on it. The results show that ResDroid can identify repackaged apps efficiently and effectively even if they are protected by obfuscation or hardening systems.
Vitamin D metabolism-related genetic variants, dietary protein intake and improvement of insulin resistance in a 2 year weight-loss trial: POUNDS Lost

Vitamin D and related genetic variants are associated with obesity and insulin resistance. We aimed to examine whether vitamin D metabolism-related variants affect changes in body weight and insulin resistance in response to weight-loss diets varying in macronutrient content. Three vitamin D metabolism-related variants, DHCR7 rs12785878, CYP2R1 rs10741657 and GC rs2282679, were genotyped in 732 overweight/obese participants from a 2 year weight-loss trial (POUNDS Lost). We assessed genotype effects on changes in body weight, fasting levels of glucose and insulin, and HOMA-IR at 6 months (up to 656 participants) and 2 years (up to 596 participants) in response to low-protein vs high-protein diets, and low-fat vs high-fat diets. We found significant interactions between DHCR7 rs12785878 and diets varying in protein, but not in fat, on changes in insulin and HOMA-IR at both 6 months (p for interaction <0.001) and 2 years (p for interaction ≤0.03). The T allele (vitamin-D-increasing allele) of DHCR7 rs12785878 was associated with greater decreases in insulin and HOMA-IR (p < 0.002) in response to high-protein diets, while there was no significant genotype effect on changes in these traits in the low-protein diet group. Generalised estimating equation analyses indicated significant genotype effects on trajectory of changes in insulin resistance over the 2 year intervention in response to high-protein diets (p < 0.001). We did not observe significant interaction between the other two variants and dietary protein or fat on changes in these traits. Our data suggest that individuals carrying the T allele of DHCR7 rs12785878 might benefit more in improvement of insulin resistance than noncarriers by consuming high-protein weight-loss diets. Trial registration: ClinicalTrials.gov NCT00072995
REVEAL-1, a phase 2 dose regimen optimization study of vosaroxin in older poor-risk patients with previously untreated acute myeloid leukaemia

This phase 2 study (N = 116) evaluated single-agent vosaroxin, a first-in-class anticancer quinolone derivative, in patients ≥60 years of age with previously untreated unfavourable prognosis acute myeloid leukaemia. Dose regimen optimization was explored in sequential cohorts (A: 72 mg/m(2)  d 1, 8, 15; B: 72 mg/m(2)  d 1, 8; C: 72 mg/m(2) or 90 mg/m(2)  d 1, 4). The primary endpoint was combined complete remission rate (complete remission [CR] plus CR with incomplete platelet recovery [CRp]). Common (>20%) grade ≥3 adverse events were thrombocytopenia, febrile neutropenia, anaemia, neutropenia, sepsis, pneumonia, stomatitis and hypokalaemia. Overall CR and CR/CRp rates were 29% and 32%; median overall survival (OS) was 7·0 months; 1-year OS was 34%. Schedule C (72 mg/m(2) ) had the most favourable safety and efficacy profile, with faster haematological recovery (median 27 d) and lowest incidence of aggregate sepsis (24%) and 30-d (7%) and 60-d (17%) all-cause mortality; at this dose and schedule, CR and CR/CRp rates were 31% and 35%, median OS was 7·7 months and 1-year OS was 38%. Overall, vosaroxin resulted in low early mortality and an encouraging response rate; vosaroxin 72 mg/m(2)  d 1, 4 is recommended for further study in this population. Registered at www.clinicaltrials.gov: #NCT00607997.
Sketch of the public surveys in Michigan.

Map shows mid-nineteenth century Michigan township grid and government reserve. Inset: [Isle Royale]. Includes explanation key to symbols. Scale [1:1,140,480].
Hospital-based, acute care use among patients within 30 days of discharge after coronary artery bypass surgery.

BACKGROUND
There is growing interest in how frequently patients undergoing coronary artery bypass graft (CABG) surgery require hospital readmission within 30 days of discharge. Readmissions, however, may not capture all hospital-based, acute care needs after discharge. The purpose of this study is to describe the frequency of and diagnoses associated with emergency department (ED) visits and hospital readmissions within 30 days of discharge after CABG surgery and to compare outcomes across hospitals.


METHODS
Using the California State Inpatient and Emergency Department Databases, we identified all adults who underwent isolated CABG surgery between January 2005 and June 2009. We then calculated hospitals' 30-day, risk-standardized readmission and ED visit rates using hierarchic generalized linear models. The correlation between hospital readmission and ED visit rates was estimated, weighting for hospital volume.


RESULTS
We identified 63,911 adults who underwent isolated CABG surgery at 114 hospitals. Hospital 30-day, risk-standardized ED visit without readmission rates (median ED visit rate = 11.9%, 25th to 75th percentile, 10.5% to 13.7%) nearly equaled the hospital 30-day risk-standardized readmission rates (median readmission rate = 15.0%, 25th to 75th percentile, 13.5% to 16.5%). Both outcomes varied widely among hospitals. A composite of these outcomes, the median 30-day risk-standardized hospital-based, acute care rate was 23.9% (25th to 75th percentile, 22.2% to 25.5%). Postoperative infections, congestive heart failure, and chest discomfort were among the most common reasons for both readmissions and ED visits. Hospitals' 30-day risk-standardized ED visit and readmission rates were not significantly correlated (weighted correlation coefficient = -0.07, p = 0.44).


CONCLUSIONS
Patients discharged after CABG surgery frequently experienced ED visits and hospital readmissions within 30 days, often for similar diagnoses. Monitoring both hospital readmissions and ED visits after CABG surgery is important to our understanding of hospital-based, acute care needs after discharge.
Substrate utilization during submaximal exercise in obese and normal-weight women

In this study we compared substrate use at submaximal intensities of a maximal graded exercise test (GXT) with that derived from equivalent intensities during continuous submaximal steady-state exercise in obese and normal-weight women. Sedentary obese (n = 20, body fat >30%) and normal-weight (n = 15, body fat ≤30%) women performed three treadmill tests with concurrent metabolic measurements. Maximal oxygen consumption (V˙O2max) was determined using the Bruce protocol, followed by two, randomly assigned, continuous 15-min, steady-state exercise bouts, on different days; one bout at 50% and one bout at 75% V˙O2max. Analysis of variance revealed no significant differences between groups for blood lactate or respiratory exchange ratio (R) values at any point during exercise. Therefore, obese and normal-weight group data were combined for subsequent analyses. The R at 50% V˙O2max from the GXT [0.83 (0.01)] was significantly (P < 0.05) lower than at 8 min [0.90 (0.01)] and 15 min [0.89 (0.01)] of steady-state exercise, whereas at 75% V˙O2max, the GXT R [0.96 (0.01)] was similar to that seen at 8 min [0.96 (0.01)] and at 15 min of steady-state exercise [0.93 (0.01)]. Blood lactate values at 50% V˙O2max were similar between the GXT [1.66 (0.10) mM] and steady-state exercise [1.65 (0.09) mM], but at 75% V˙O2max the GXT blood lactate values [2.58 (0.21) mM] were lower than after 15 min of steady-state exercise [4.65 (0.46) mM]. Total exercise fat oxidation was greater at 50% compared to 75% V˙O2max. There was no difference in substrate use between sedentary obese and normal-weight women either at rest or during steady-state exercise at the same relative intensity. Total fat oxidation was greater during low- (50% V˙O2max) compared to high-intensity (75% V˙O2max) exercise. Data from a GXT cannot be used to predict R or substrate utilization values for the purpose of exercise prescription.
Global stability of a class of continuous-time recurrent neural networks

This paper investigates global asymptotic stability (GAS) and global exponential stability (GES) of a class of continuous-time recurrent neural networks. First, we introduce a necessary and sufficient condition for existence and uniqueness of equilibrium of the neural networks with Lipschitz continuous activation functions. Next, we present two sufficient conditions to ascertain the GAS of the neural networks with globally Lipschitz continuous and monotone nondecreasing activation functions. We then give two GES conditions for the neural networks whose activation functions may not be monotone nondecreasing. We also provide a Lyapunov diagonal stability condition, without the nonsingularity requirement for the connection weight matrices, to ascertain the GES of the neural networks with globally Lipschitz continuous and monotone nondecreasing activation functions. This Lyapunov diagonal stability condition generalizes and unifies many the existing GAS and GES results. Moreover, two higher exponential convergence rates are estimated.
Generative Design Patterns

A design pattern encapsulates the knowledge of object-oriented designers into re-usable artifacts. A design pattern is a descriptive device that fosters software design re-use. There are several reasons why design patterns are not used as generative constructs that support code re-use. The first reason is that design patterns describe a set of solutions to a family of related design problems and it is difficult to generate a single body of code that adequately solves each problem in the family. A second reason is that it is difficult to construct and edit generative design patterns. A third major impediment is the lack of a tool-independent representation. A common representation could lead to a shared repository to make more patterns available. In this paper we describe a new approach to generative design patterns that solves these three difficult problems. We illustrate this approach using tools called CO2P2S and Meta-CO2P2S, but our approach is tool-independent.
Self-reported socio-economic status, social, physical and leisure activities and risk for malnutrition in late life: a cross-sectional population-based study.

OBJECTIVES
Our goal was to evaluate the proportion of community-dwelling elderly people at risk for malnutrition and the effect of different socioeconomic status (SES) indicators as well as social, physical and leisure activities in late life on the risk for malnutrition.


DESIGN
A cross-sectional population-based study.


SETTING
A sub-urban area in Northern Italy.


PARTICIPANTS
698 community-dwelling older persons.


MEASUREMENTS
The nutritional status of participants was assessed through the Mini Nutritional Assessment-Short Form (MNA-SF). SES was defined by means of early-life education, longest occupation, and late-life financial conditions. The following indicators were also evaluated: social contacts, and performing mental, physical and leisure activities during late-life. Chronic diseases, functional, cognitive and affective status were considered as potential confounders when examining the risk for malnutrition by logistic regression models.


RESULTS
8% of the participants (average age 75.6 years, 408 women) were at risk for malnutrition (MNA-SF ≤ 11). Low education, poor financial condition, and lack of physical and leisure activities showed a crude association with risk for malnutrition. Multi-adjusted logistic regression models showed that only low education (OR=2.9; 95% CI=1.2-6.8) and lack of physical activity (OR=4.4;95%CI=2.0-9.7) were independently associated with the risk for malnutrition.


CONCLUSIONS
Low education and lack of physical activity in late-life may affect the risk for malnutrition in the elderly. Further studies are needed to clarify the cause-effect relationship between lack of physical activity and malnutrition.
Two-scale composite finite element method for Dirichlet problems on complicated domains

In this paper, we will define a new class of finite elements for the discretization of problems with Dirichlet boundary conditions. In contrast to standard finite elements, the minimal dimension of the approximation space is independent of the domain geometry and this is especially advantageous for problems on domains with complicated micro-structures. For the proposed finite element method we prove the optimal-order approximation (up to logarithmic terms) and convergence estimates valid also in the cases when the exact solution has a reduced regularity due to re-entering corners of the domain boundary. 2000 Mathematics Subject Classification: 35J20, 65N15, 65N30
A Graph-based Lattice Dependency Parser for Joint Morphological Segmentation and Syntactic Analysis

Space-delimited words in Turkish and Hebrew text can be further segmented into meaningful units, but syntactic and semantic context is necessary to predict segmentation. At the same time, predicting correct syntactic structures relies on correct segmentation. We present a graph-based lattice dependency parser that operates on morphological lattices to represent different segmentations and morphological analyses for a given input sentence. The lattice parser predicts a dependency tree over a path in the lattice and thus solves the joint task of segmentation, morphological analysis, and syntactic parsing. We conduct experiments on the Turkish and the Hebrew treebank and show that the joint model outperforms three state-of-the-art pipeline systems on both data sets. Our work corroborates findings from constituency lattice parsing for Hebrew and presents the first results for full lattice parsing on Turkish.
Generating synthetic CTs from magnetic resonance images using generative adversarial networks.

PURPOSE
While MR-only treatment planning using synthetic CTs (synCTs) offers potential for streamlining clinical workflow, a need exists for an efficient and automated synCT generation in the brain to facilitate near real-time MR-only planning. This work describes a novel method for generating brain synCTs based on generative adversarial networks (GANs), a deep learning model that trains two competing networks simultaneously, and compares it to a deep convolutional neural network (CNN).


METHODS
Post-Gadolinium T1-Weighted and CT-SIM images from fifteen brain cancer patients were retrospectively analyzed. The GAN model was developed to generate synCTs using T1-weighted MRI images as the input using a residual network (ResNet) as the generator. The discriminator is a CNN with five convolutional layers that classified the input image as real or synthetic. Fivefold cross-validation was performed to validate our model. GAN performance was compared to CNN based on mean absolute error (MAE), structural similarity index (SSIM), and peak signal-to-noise ratio (PSNR) metrics between the synCT and CT images.


RESULTS
GAN training took ~11 h with a new case testing time of 5.7 ± 0.6 s. For GAN, MAEs between synCT and CT-SIM were 89.3 ± 10.3 Hounsfield units (HU) and 41.9 ± 8.6 HU across the entire FOV and tissues, respectively. However, MAE in the bone and air was, on average, ~240-255 HU. By comparison, the CNN model had an average full FOV MAE of 102.4 ± 11.1 HU. For GAN, the mean PSNR was 26.6 ± 1.2 and SSIM was 0.83 ± 0.03. GAN synCTs preserved details better than CNN, and regions of abnormal anatomy were well represented on GAN synCTs.


CONCLUSIONS
We developed and validated a GAN model using a single T1-weighted MR image as the input that generates robust, high quality synCTs in seconds. Our method offers strong potential for supporting near real-time MR-only treatment planning in the brain.
GO-Elite: a flexible solution for pathway and ontology over-representation

UNLABELLED
We introduce GO-Elite, a flexible and powerful pathway analysis tool for a wide array of species, identifiers (IDs), pathways, ontologies and gene sets. In addition to the Gene Ontology (GO), GO-Elite allows the user to perform over-representation analysis on any structured ontology annotations, pathway database or biological IDs (e.g. gene, protein or metabolite). GO-Elite exploits the structured nature of biological ontologies to report a minimal set of non-overlapping terms. The results can be visualized on WikiPathways or as networks. Built-in support is provided for over 60 species and 50 ID systems, covering gene, disease and phenotype ontologies, multiple pathway databases, biomarkers, and transcription factor and microRNA targets. GO-Elite is available as a web interface, GenMAPP-CS plugin and as a cross-platform application.


AVAILABILITY
http://www.genmapp.org/go_elite