Miracle-dz/UniFAR-FTUs huggingface dataset:
Bisphosphonate anticancer activity

Bone metastases have a major impact on morbidity and on mortality in cancer patients. Despite its clinical relevance, metastasis remains the most poorly elucidated aspect of carcinogenesis. Different pathways or molecules such as RANK/RANKL/OPG, cathepsin K, endothelin-1, Wnt/DKK1 and Src have recently emerged as potential targets, and preclinical and clinical trials are now underway. The results from clinical trials indicate the importance of treating and preventing bone metastases in many different cancer populations.
The Common HOL Platform

The Common HOL project aims to facilitate porting source code and proofs between members of the HOL family of theorem provers. At the heart of the project is the Common HOL Platform, which defines a standard HOL theory and API that aims to be compatible with all HOL systems. So far, HOL Light and hol90 have been adapted for conformance, and HOL Zero was originally developed to conform. In this paper we provide motivation for a platform, give an overview of the Common HOL Platform's theory and API components, and show how to adapt legacy systems. We also report on the platform's successful application in the hand-translation of a few thousand lines of source code from HOL Light to HOL Zero.
Belief Revision and Update: Complexity of Model Checking

One of the main challenges in the formal modeling of common-sense reasoning is the ability to cope with the dynamic nature of the world. Among the approaches put forward to address this problem are belief revision and update. Given a knowledge base T, representing our knowledge of the “state of affairs” of the world of interest, it is possible that we are led to trust another piece of information P, possibly inconsistent with the old one T. The aim of revision and update operators is to characterize the revised knowledge base T� that incorporates the new formula P into the old one T while preserving consistency and, at the same time, avoiding the loss of too much information. In this paper we study the computational complexity, in the propositional case, of one of the main reasoning problems of belief revision and update: deciding if an interpretation M is a model of the revised knowledge base.
Training hard to learn networks using advanced simulated annealing methods

We describe a method for avoiding local minima by combining Very Fast Simulated Reannealing (VFSR) with BEP. While convergence to the best. training weights can be slower than gradient descent, methods, it is faster than other SA network training methods. More importantly, convergence to the optimal weight set is statistically guaranteed. We demonstrate VFSR network training on learning a set of difficult but. linearly separable logic functions and a set. of nonlinearly separable parity problems, and compare performances of VFSR network training with conjugate gradient trained backpropagation networks. I n t r o d u c t i o n Backpropagation networks [1] are nonlinear methods for mapping a set of multidimensional input patterns x = xl . xo, to a corresponding set of dimensional output patterns y = Yl,. ,YM. While they have a variety of networks architectures, they are typified by a set of input, hidden, and outpul units taking on different values. The units are arranged in feed forward layers in the network• Units between layers have connections to each other with weights w associated with each connection. A typical architecture is the three layer network that has its input units connected to its hidden units, and its hidden units connected to its output. • Additionally, there may are often direct, connections between the input and output units. Bias unit. may be included to reflect constant input values. Networks operate by first, assigning an input pattern x to the input units. Then, the values of the hidden units h and output unit o values are calculated as follows: h~. (~.) = f(w~,0 + ~ u,~,jzj)
Antibacterial activity of oregano tea and a commercial oregano water against Escherichia coli O 157 : H 7 , Listeria monocytogenes 4 b , Staphylococcus aureus and Yersinia enterocolitica 03

The amtimicrobial effect of oregano tea (1/10, w/v, in distilled water), commercial oregano water, and 1⁄2 oregano water (1/1, commercial oregano water/distilled water, v/v) against Escherichia coli O157:H7, Listeria monocytogenes 4b, Staphylococcus aureus and Yersinia enterocolitica 03 after direct contact at 20 ±2 C for 1, 10, 30, and 60 min were comparatively evaluated. The Plate Count Agar was used for colony counts and the content of each treatment tube was enriched in Brain Heart Infusion broth after the 60 min direct contact period. All the four pathogens in oregano water and 1⁄2 oregano water decreased to uncountable level (1 CFU/ml) in one min. No growth has also occured in enrichments. Oregano tea was less effective than the oregano waters after 1 min, but counts of E. coli O157:H7, L. monocytogenes 4b, S. aureus and Y. enterocolitica 03 decrease to uncountable level after 60, 60, 10, and 10 min treatment periods, respectively. All the four test pathogens demonstrated grow ability in enrichment broth after a 60 min treatment period in oregano tea. E. coli O157:H7 appeared to be the most resistant pathogen followed by L. monocytogenes 4b, S. aureus and Y. enterocolitica, respectively. The use of water extracts or hydrosol of oregano for the decontamination or disinfection in food safety strategies should be evaluated in comparison with other natural antimicrobial spices.
Outcomes of Early Endovascular Versus Surgical Treatment of Ruptured Cerebral Aneurysms: A Prospective Randomized Study

Background and Purpose This prospective study was conducted to compare the outcomes of surgical clipping and endovascular treatment in acute (<72 hours) aneurysmal subarachnoid hemorrhage (SAH). Methods One hundred nine consecutive patients were randomly assigned to either surgical (n=57) or endovascular (n=52) treatment. Clinical and neuropsychological outcome was assessed at 3 and 12 months after treatment; MRI of the brain was performed at 12 months. Follow-up angiography was scheduled after clipping and 3 and 12 months after endovascular treatment. Results One year postoperatively, 43/41 (surgical/endovascular) patients had good or moderate recovery, 5/4 had severe disability or were in a vegetative state, and 9/7 had died (NS) according to intention to treat. Patients with good clinical recovery did not differ in their neuropsychological test scores. Symptomatic vasospasm (OR 2.47; 95% CI 1.45 to 4.19;P <0.001), poorer Hunt and Hess grade (OR 2.50; 95% CI 1.31 to 4.75;P =0.005), need for permanent shunt (OR 8.90; 95% CI 1.80 to 44.15;P =0.008), and larger size of the aneurysm (OR 1.22; 95% CI 1.02 to 1.45;P =0.032) independently predicted worsened clinical outcome regardless of the treatment modality. In MRI, superficial brain retraction deficits (P <0.001) and ischemic lesions in the territory of the ruptured aneurysm (P =0.025) were more frequent in the surgical group. Kaplan-Meier analysis (mean±SD follow-up 39±18 months) revealed equal survival in both treatment groups. No late rebleedings have occurred. Conclusions One-year clinical and neuropsychological outcomes seem comparable after early surgical and endovascular treatment of ruptured intracranial aneurysms. The long-term efficacy of endovascular treatment in preventing rebleeding remains open.
Efficacy of the Maze Procedure for Atrial Fibrillation Associated with Atrial Septal Defect

Background Atrial fibrillation (AF) is a common complication in elderly patients with atrial septal defect (ASD). The purpose of this study was to examine the efficacy of the maze procedure in these patients. Materials and Methods Between February 2000 and May 2011, 46 patients underwent the maze procedure as a concomitant operation with ASD closure. Three patients who underwent a right-sided maze were excluded, and one patient was lost to follow-up. The mean follow-up duration was 3.2±2.5 years. Electrocardiography was performed 1 month, 3 months, 6 months, and 1 year after surgery, and checked annually after that. Results AF persisted in 4 patients after surgery. One year after surgery, among 38 patients, 55.3% remained in sinus rhythm without antiarrhythmic drugs. However, when including the patients who took antiarrhythmic drugs, 92.1% were in sinus rhythm. Freedom from AF recurrence at 3 months, 6 months, 1 year, 2 years, 3 years, and 5 years after surgery were 97.4±2.6, 94.4±3.8, 91.2±4.9, 87.8±5.8, 79.5±7.6, and 68.2±12.4, respectively. There was no early mortality after operation. Conclusion Concomitant treatment with the maze procedure and ASD closure is safe and effective for restoring the sinus rhythm.
Marijuana: Current Concepts

Marijuana (cannabis) remains a controversial drug in the twenty-first century. This paper considers current research on use of Cannabis sativa and its constituents such as the cannabinoids. Topics reviewed include prevalence of cannabis (pot) use, other drugs consumed with pot, the endocannabinoid system, use of medicinal marijuana, medical adverse effects of cannabis, and psychiatric adverse effects of cannabis use. Treatment of cannabis withdrawal and dependence is difficult and remains mainly based on psychological therapy; current research on pharmacologic management of problems related to cannabis consumption is also considered. The potential role of specific cannabinoids for medical benefit will be revealed as the twenty-first century matures. However, potential dangerous adverse effects from smoking marijuana are well known and should be clearly taught to a public that is often confused by a media-driven, though false message and promise of benign pot consumption.
UNEQUAL BREAKS IN TWO SISTER CHROMATIDS INDUCED BY X-RAYS IN DROSOPHILA MELANOGASTER.

of chromosomes might be supplied by supernumerary spermatozoa, since the eggs of newts and other salamanders are normally polyspermic. Usually, the accessory sperm nuclei remain well separated from the pronuclei and degenerate before the first cleavage.6 On rare occasions, however, two spermatozoa may possibly penetrate into the egg so near each other that the nuclei fuse, as is frequently seen in highly polyspermic eggs which do not cleave. In eggs of the salamander, Hynobius retardatus, which seem to be monospermic as a rule, Makino7 has actually observed the fusion of three nuclei. However, whether such a situation would lead to a bipolar triploid mitosis or to a tetrapolar mitosis with irregular distribution of the chromosomes, as it does in dispermic sea urchin eggs, is not known, since the behavior of the division centers associated with the sperm nuclei has not been observed. Fankhauser, G. , Proc. Am. Phil. Soc. , 79, 715-739 (1938). ' Fankhauser, G. , Jour. Hered. , 30, 379-388 (1939). 8 Fankhauser, G. , Jour. Morph. (in press) (1940). 4 Kaylor, C. T. , Jour. Exp. Zool. , 76, 375-394 (1937). 6 Fankhauser, G. , and R. B. Griffiths, Proc. Nat. Accad. Sci., 25, 233-238 (1939). s Fankhauser, G. , Jour. Exp. Zool. , 62, 185-225 (1932). 7 Makino S. , Jour. Fac. Sci., Hokkaido Imp. Univ., Ser. VI, Zool. , 3, 117-167 (1934).
Omni-directional vehicle control based on body configuration

– The purpose of this paper is to develop a new wheel control scheme for wheeled vehicle with passive linkage mechanism which realizes high step‐overcoming performance. , – Developing wheeled vehicle realizes omni‐directional motion on flat floor using special wheels and passes over non‐flat ground using the passive suspension mechanism. The vehicle changes its body shape and wheel control references according to ground condition when it runs over the rough terrain. , – Utilizing the proposed wheel control scheme, the slip ratio and the disturbance ratio of the wheel reduce when the vehicle passes over the step and its step‐overcoming performance is improved. , – The paper's key idea is modification of its kinematic model referring to the body configuration dynamically and using this model for wheel control of the vehicle. The controller adjusts the wheel control references when the vehicle passes over the rough terrain changing the body shape and reduces the slippage and the rotation error of wheels.
Long-Term Prognostic Value of Coronary Calcification Detected by Electron-Beam Computed Tomography in Patients Undergoing Coronary Angiography

Background— Electron-beam CT (EBCT) quantification of coronary artery calcification (CAC) allows noninvasive assessment of coronary atherosclerosis. We undertook a follow-up study to determine whether CAC extent, measured at the time of angiography by EBCT, predicted future hard cardiac events, comprising cardiac death and nonfatal myocardial infarction (MI). We also assessed the potential of selected coronary artery disease (CAD) risk factors, prior CAD event history (MI or revascularization), and angiographic findings (number of diseased vessels and overall disease burden) to predict subsequent hard events. Methods and Results— Two hundred eighty-eight patients who underwent contemporaneous coronary angiography and EBCT scanning were contacted after a mean of 6.9 years. Vital status and history of MI during follow-up were determined. Cox proportional hazards models were used to compare the predictive ability of CAC extent with selected CAD risk factors, CAD event history, and angiographic findings. Median CAC score was 160 (range 0 to 7633). The 22 patients who experienced hard events during follow-up were older and had more extensive CAC and angiographic disease (P <0.05). Only 1 of 87 patients with CAC score <20 experienced a subsequent hard event during follow-up. Event-free survival was significantly higher for patients with CAC scores <100 than for those with scores ≥100 (relative risk 3.20; 95% CI 1.17 to 8.71). When a stepwise multivariable model was used, only age and CAC extent predicted hard events (risk ratios 1.72 and 1.88, respectively;P <0.05). Conclusions— In patients undergoing angiography, CAC extent on EBCT is highly predictive of future hard cardiac events and adds valuable prognostic information.
Gradient Recovery and A Posteriori Estimate for Bilinear Element on Irregular Quadrilateral Meshes

A polynomial preserving gradient recovery method is proposed and analyzed for bilinear element under general quadrilateral meshes. It has been proven that the recovered gradient converges at a rate O(hl+P) for p = min( a, 1) when the mesh is distorted O(hl+a) (a > 0) from a regular one. Consequently, the a posteriori error estimator based on the recovered gradient is asymptotically exact. 2000 Mathematics Subject Classification. Primary 65N30, Secondary 65N15, 41A10, 41A25, 41A27, 41A63.
Staphylococcal and Streptococcal Superantigen Exotoxins

SUMMARY This review begins with a discussion of the large family of Staphylococcus aureus and beta-hemolytic streptococcal pyrogenic toxin T lymphocyte superantigens from structural and immunobiological perspectives. With this as background, the review then discusses the major known and possible human disease associations with superantigens, including associations with toxic shock syndromes, atopic dermatitis, pneumonia, infective endocarditis, and autoimmune sequelae to streptococcal illnesses. Finally, the review addresses current and possible novel strategies to prevent superantigen production and passive and active immunization strategies.
Changing the Paradigms of Treatment in Peripheral T-cell Lymphoma: From Biology to Clinical Practice

Despite enormous advances in our understanding of aggressive lymphomas, it is clear that progress in the peripheral T-cell lymphomas (PTCL) has lagged well behind other B-cell malignancies. Although there are many reasons for this, the one commonly cited notes that the paradigms for diffuse large B-cell lymphoma (DLBCL) were merely applied to all patients with PTCL, the classic “one-size-fits-all” approach. Despite these challenges, progress is being made. Recently, the FDA has approved four drugs for patients with relapsed/refractory PTCL over the past 5 years, and if one counts the recent Japanese approval of the anti-CCR4 monoclonal antibody for patients with adult T-cell leukemia/lymphoma, five drugs have been approved worldwide. These efforts have led to the initiation of no fewer than four randomized clinical studies exploring the integration of these new agents into standard CHOP (cyclophosphamide–Adriamycin–vincristine–prednisone)–based chemotherapy regimens for patients with newly diagnosed PTCL. In addition, a new wave of studies are exploring the merits of novel drug combinations in the disease, an effort to build on the obvious single-agent successes. What has emerged most recently is the recognition that the PTCL may be a disease-characterized by epigenetic dysregulation, which may help explain its sensitivity to histone deacetylase (HDAC) inhibitors, and open the door for even more creative combination approaches. Nonetheless, advances made over a relatively short period of time are changing how we now view these diseases and, hopefully, have poised us to finally improve its prognosis. See all articles in this CCR Focus section, “Paradigm Shifts in Lymphoma. ” Clin Cancer Res; 20(20); 5240–54. ©2014 AACR.
A New Method for Discovering Disease-Specific MiRNA-Target Regulatory Networks

Genes and their expression regulation are among the key factors in the comprehension of the genesis and development of complex diseases. In this context, microRNAs (miRNAs) are post-transcriptional regulators that play an important role in gene expression since they are frequently deregulated in pathologies like cardiovascular disease and cancer. In vitro validation of miRNA - targets regulation is often too expensive and time consuming to be carried out for every possible alternative. As a result, a tool able to provide some criteria to prioritize trials is becoming a pressing need. Moreover, before planning in vitro experiments, the scientist needs to evaluate the miRNA-target genes interaction network. In this paper we describe the miRable method whose purpose is to identify new potentially relevant genes and their interaction networks associate to a specific pathology. To achieve this goal miRable follows a system biology approach integrating together general-purpose medical knowledge (literature, Protein-Protein Interaction networks, prediction tools) and pathology specific data (gene expression data). A case study on Prostate Cancer has shown that miRable is able to: 1) find new potential miRNA-targets pairs, 2) highlight novel genes potentially involved in a disease but never or little studied before, 3) reconstruct all possible regulatory subnetworks starting from the literature to expand the knowledge on the regulation of miRNA regulatory mechanisms.
Bypass Surgery Versus Stenting for the Treatment of Multivessel Disease in Patients With Unstable Angina Compared With Stable Angina

Background—Earlier reports have shown that the outcome of balloon angioplasty or bypass surgery in unstable angina is less favorable than in stable angina. Recent improvements in percutaneous treatment (stent implantation) and bypass surgery (arterial grafts) warrant reevaluation of the relative merits of either technique in treatment of unstable angina. Methods and Results—Seven hundred fifty-five patients with stable angina were randomly assigned to coronary stenting (374) or bypass surgery (381), and 450 patients with unstable angina were randomly assigned to coronary stenting (226) or bypass surgery (224). All patients had multivessel disease considered to be equally treatable by either technique. Freedom from major adverse events, including death, myocardial infarction, and cerebrovascular events, at 1 year was not different in unstable patients (91.2% versus 88.9%) and stable patients (90.4% versus 92.6%) treated, respectively, with coronary stenting or bypass surgery. Freedom from repeat revascularization at 1 year was similar in unstable and stable angina treated with stenting (79.2% versus 78.9%) or bypass surgery (96.3% versus 96%) but was significantly higher in both unstable and stable patients treated with stenting (16.8% versus 16.9%) compared with bypass surgery (3.6% versus 3.5%). Neither the difference in costs between stented or bypassed stable or unstable angina ($2594 versus $3627) nor the cost-effectiveness was significantly different at 1 year. Conclusions—There was no difference in rates of death, myocardial infarction, and cerebrovascular event at 1 year in patients with unstable angina and multivessel disease treated with either stented angioplasty or bypass surgery compared with patients with stable angina. The rate of repeat revascularization of both unstable and stable angina was significantly higher in patients with stents.
Using transparent compression to improve SSD-based I/O caches

Flash-based solid state drives (SSDs) offer superior performance over hard disks for many workloads. A prominent use of SSDs in modern storage systems is to use these devices as a cache in the I/O path. In this work, we examine how transparent, online I/O compression can be used to increase the capacity of SSD-based caches, thus increasing the costeffectiveness of the system. We present FlaZ, an I/O system that operates at the block-level and is transparent to existing file-systems. To achieve transparent, online compression in the I/O path and maintain high performance, FlaZ, provides support for variable-size blocks, mapping of logical to physical blocks, block allocation, and cleanup. FlaZ, mitigates compression and decompression overheads that can have a significant impact on performance by leveraging modern multicore CPUs. We implement FlaZ, in the Linux kernel and evaluate it on a commodity server with multicore CPUs, using TPC-H, PostMark, and SPECsfs. Our results show that compressed caching trades off CPU cycles for I/O performance and enhances SSD efficiency as a cache by up to 99%, 25%, and 11% for each workload, respectively.
MRMaid, the Web-based Tool for Designing Multiple Reaction Monitoring (MRM) Transitions*

Multiple reaction monitoring (MRM) of peptides uses tandem mass spectrometry to quantify selected proteins of interest, such as those previously identified in differential studies. Using this technique, the specificity of precursor to product transitions is harnessed for quantitative analysis of multiple proteins in a single sample. The design of transitions is critical for the success of MRM experiments, but predicting signal intensity of peptides and fragmentation patterns ab initio is challenging given existing methods. The tool presented here, MRMaid (pronounced “mermaid”) offers a novel alternative for rapid design of MRM transitions for the proteomics researcher. The program uses a combination of knowledge of the properties of optimal MRM transitions taken from expert practitioners and literature with MS/MS evidence derived from interrogation of a database of peptide identifications and their associated mass spectra. The tool also predicts retention time using a published model, allowing ordering of transition candidates. By exploiting available knowledge and resources to generate the most reliable transitions, this approach negates the need for theoretical prediction of fragmentation and the need to undertake prior “discovery” MS studies. MRMaid is a modular tool built around the Genome Annotating Proteomic Pipeline framework, providing a web-based solution with both descriptive and graphical visualizations of transitions. Predicted transition candidates are ranked based on a novel transition scoring system, and users may filter the results by selecting optional stringency criteria, such as omitting frequently modified residues, constraining the length of peptides, or omitting missed cleavages. Comparison with published transitions showed that MRMaid successfully predicted the peptide and product ion pairs in the majority of cases with appropriate retention time estimates. As the data content of the Genome Annotating Proteomic Pipeline repository increases, the coverage and reliability of MRMaid are set to increase further. MRMaid is freely available over the internet as an executable web-based service at www.mrmaid. info.