Miracle-dz/UniFAR-FTUs huggingface dataset:
Empirical free energy calculations: a blind test and further improvements to the method.

Empirical Gibbs functions estimate free energies of non-covalent reactions (deltaG) from atomic coordinates of reaction products (e.g. antibody-antigen complexes). The function previously developed by us has four terms that quantify the effects of hydrophobic, electrostatic and entropy changes (conformational, association) upon complexation. The function was used to calculate delta deltaG of ten lysozyme mutants affecting the stability of the HyHEL-10 antibody-lysozyme complex. The mutants were computer-modeled from the X-ray structure of the wild-type, and free energy calculations produced a correlation coefficient of 0.5 with the experimental delta deltaG data (average absolute error +/-3 kcal). The following changes were then introduced into the Gibbs function: (1) the hydrophobic force was made proportional to the molecular surface, as calculated by the GEPOL93 algorithm, with the scaling constant of 70 cal/mol/A2; (2) calculation of the electrostatics of binding was carried out by the finite difference Poisson-Boltzmann algorithm, which employed uniform grid charging, dielectric boundary smoothing and charge anti-aliasing; and (3) side-chain conformational entropy was estimated from the CONGEN sampling of torsional degrees of freedom. In the new calculations, correlation with experimental data improved to 0.6 or 0.8 if a single outlying mutant, K96M, was neglected. Analysis of the errors remaining in our calculations indicated that molecular mechanics-based modeling of the mutants, rather than the form of our amended Gibbs function, was the main factor limiting the accuracy of the free energy estimates.
3p microsatellite signature in exhaled breath condensate and tumor tissue of patients with lung cancer.

RATIONALE Our group has recently demonstrated the possibility of studying microsatellite alterations (MAs) of 3p in the DNA of exhaled breath condensate (EBC) of patients with non-small cell lung cancer (NSCLC). OBJECTIVES To verify whether MAs analyzed in DNA from EBC reflect a profile of alterations present in tumor tissue of NSCLC. METHODS Fifty-nine subjects undergoing histologic diagnosis for clinical suspicion of lung cancer entered the study: 41 were found to have NSCLC and 18 to have nonneoplastic diseases. All subjects underwent allelotyping on DNA from whole blood, EBC, and lung tissue removed for histologic diagnosis by analyzing a panel of five microsatellites located in chromosomal region 3p. Results obtained from DNA of the three biological sites and nonneoplastic tissues from controls were compared. MEASUREMENTS AND MAIN RESULTS MAs in DNA from tumor tissues and EBC of each patient with cancer presented an overlapping profile of loss of heterozygosity and microsatellite instability. An MA profile of DNA of lung tissue reflecting the DNA of EBC profile from controls was also confirmed. Smoking status was associated with the presence of MAs in patients with NSCLC and in control subjects. CONCLUSIONS We demonstrated that MAs in DNA from EBC of patients with NSCLC are significantly more frequent than in control subjects. More interesting, the MA profile of DNA from EBC corresponds to that from lung cancer tissue of each patient with NSCLC.
Adaptive Digital Equalization in Optical Coherent Receivers With Stokes-Space Update Algorithm

In this paper, we describe a novel update algorithm for the filter coefficients of the adaptive digital equalizer in coherent receivers, which is based on error signals evaluated in Stokes space and is insensitive to both phase-noise and frequency-offset. We also introduce an optimized decision rule in the Stokes space, which takes into account the exact statistics of noise and yields a performance improvement with respect to the minimum distance decision criterion. We compare the performance of the new algorithm to the standard constant-modulus algorithm (CMA) for polarization-multiplexed 16QAM modulation, achieving similar performance in the absence of phase noise, with comparable complexity. Differently from CMA, the proposed Stokes-space algorithm allows us to remove the phase offset between polarizations, thus enabling the use of a joint carrier-phase estimation algorithm on both polarizations, which in turns yields a nearly doubled phase noise tolerance.
Social Utilities and Personality Traits for Group Recommendation: A Pilot User Study

Recommendations to a group of users can be provided by the aggregation of individual usersâ recommendations using social choice functions. Standard aggregation techniques do not consider the possibility of evaluating social interactions, roles, and influences among groupâs members, as well as their personalities, which are, indeed, crucial factors in the groupâs decision-making process. Instead of defining a specific social choice function to take into account such features, the proposed solution relies on the definition of a utility function, for each agent, that takes into account other group membersâ preferences. Such function models the level of a userâs altruistic behavior starting from his/her agreeableness personality trait. Once such utility values are evaluated, the goal is to recommend items that maximize the social welfare. Performance is evaluated with a pilot user study and compared with respect to Least Misery. Results showed that while for small groups LM performs slightly better, in the other cases the two methods are comparable.
Development of ductal adenocarcinoma during follow-up of branch-duct IPMNs.

We greatly appreciated reading the comprehensive review of recent advances in Budd–Chiari syndrome (BCS) and veno-occlusive disease/sinusoidal obstruction syndrome by D-C Valla ( Gut 2008; 57 :1469–78). Regarding the epidemiology of BCS, we would like to bring to your attention that estimates …
Loss of Y chromosome with retention of Y heterochromatin in a marker chromosome from a human melanoma

A single copy of a der 15 chromosome (m3) characterized by a C‐ and distamycin A‐Dapi‐positive region was observed in the ‐Y hyperploid karyotype of a primary human melanoma (Me 1402). The heterochromatic region was located pericentromerically, adjacent at one end to the NOR region of chromosome 15, and at the other to an unclassifiable chromosomal piece. We established that the C‐positive block in the marker chromosome originated from Y heterochromatin by high‐stringency in situ hybridization with a DNA probe for the 2.1 Hae III Y‐specific repeat. Loss of the Y chromosome in tumors has been considered to be a secondary event associated with malignant evolution. It is significant that Me 1402 cells, which are highly malignant, lack the Y chromosome, but retain its heterochromatic portion in the rearranged m3 chromosome.
Nonlinear H∞ Control of a Bilateral Nonlinear Teleoperation System

Abstract In this paper, we present a nonlinear H ∞ control technique for the bilateral teleoperation of a nonlinear master-slave system. The proposed controller guarantees robust stability in the presence of uncertainty in operator and environment impedances. The guidelines to include nonlinear intervening tool between master and slave robot are suggested. The proposed technique enables adjusting weighting of position and force tracking error functions for both amplitude and frequency domain. To solve the corresponding partial differential equation, called HJI, an approximation method based on Taylor series expansion of the solution is used. A numerical simulation demonstrates that the linear controller tends to instability in contact tasks while the third order approximated nonlinear controller yields desired performance.
Etravirine limits the emergence of darunavir and other protease inhibitor resistance-associated mutations in the DUET trials

Etravirine is a recently approved nonnucleoside reverse transcriptase inhibitor. The ability of etravirine to limit the emergence of resistance to protease inhibitors, and specifically to darunavir, was investigated in the subset of treatment-experienced patients with virologic rebound in the phase III DUET trials. Of those experiencing rebound, fewer etravirine-treated than placebo-treated patients developed mutations associated with resistance to protease inhibitors in general and to darunavir in particular, and more patients in the etravirine than the placebo-group maintained baseline darunavir susceptibility at endpoint.
Utility of COPD Assessment Test (CAT) in primary care consultations: a randomised controlled trial

Background: One of the aims of the COPD Assessment Test (CAT) is to aid communication between the physician and patient about the burden of chronic obstructive pulmonary disease (COPD) on the patient's life. Aims: To investigate the impact of the CAT on the quality of primary care consultations in COPD patients. Methods: Primary care physicians across Europe conducted six consultations with standardised COPD patients (played by trained actors). Physicians were randomised to see the patient with the completed CAT (CAT+ arm) or without (no CAT arm) during the consultation. These were videoed and independent assessors scored the physicians on their ability to identify and address patient-specific issues such as depression (sub-score A); review standard COPD issues such as breathlessness (sub-score B); their understanding of the case (understanding score); and their overall performance. The primary endpoint was the global score (sub-scores A+B; scale range 0–40). Results: A total of 165 physicians enrolled in the study and carried out six consultations each; 882 consultations were deemed suitable for analysis. No difference was seen between the arms in the global score (no CAT arm 20.3; CAT+ arm 20.7; 95% CI −1.0 to 1.8; p=0.606) or on sub-score A (p=0.255). A statistically significant difference, though of limited clinical relevance, was observed in mean sub-score B (no CAT arm 8.8; CAT+ arm 9.6; 95% CI 0.0 to 1.6; p=0.045). There was no difference in understanding score (p=0.824) or overall performance (p=0.655). Conclusions: The CAT is a disease-specific instrument that aids physician assessment of COPD. It does not appear to improve detection of non-COPD symptoms and co-morbidities.
Everolimus inAdvancedPancreaticNeuroendocrineTumors : The Clinical Experience

The incidence of neuroendocrine tumors (NET) has increased dramatically in the past 30 years. This information has revitalized basic and clinical research into the molecular biology of NET and has resulted in the recent approval of new therapies for pancreatic NET (pNET), including the oral inhibitor of the mTOR everolimus. Everolimus significantly improved progression-free survival among patients with pNET in the phase III RADIANT-3 study. Here, we review the clinical studies showing the efficacy of everolimus in pNET and summarize the translational science from these studies. To understand the mechanisms of resistance and cause of treatment failure, we compared the type of progression events observed in the everolimus and placebo arms of the RADIANT-3 study. Comparison of the everolimus arm to the placebo arm indicated the fractions of progression events due to new metastasis only (21% vs. 22%), growth of preexisting lesions only (54% vs. 49%), and new metastasis along with growth of preexisting lesions (24% vs. 27%) were similar. These results suggest that although everolimus delays disease progression in patients with pNET, patients who experience disease progression while on everolimus do not appear to have a more aggressive metastatic phenotype than those whose disease progresses while on placebo. Cancer Res; 73(5); 1–5. 2013
Trazodone for antidepressant-associated insomnia.

OBJECTIVE The authors investigated trazodone as a hypnotic for depressed patients who had persistent, exacerbated, or new insomnia while taking either fluoxetine or bupropion. METHOD Seventeen depressed patients who had insomnia while taking fluoxetine or bupropion were given either trazodone or placebo in a double-blind crossover trial. Sleep was assessed by self-report with the Pittsburgh Sleep Quality Index and the sleep items of the Yale-New Haven Hospital Depressive Symptom Inventory. RESULTS Improvement with trazodone, but not with placebo, was shown by the total Pittsburgh index scores and Yale-New Haven inventory total sleep scores and by the Pittsburgh index measures of sleep duration and Yale-New Haven inventory measures of early morning awakening, and there was a trend toward improvement in the Yale-New Haven inventory item regarding middle of the night awakenings. Subjective sleep quality and sleep latency also showed a trend toward improvement, but the Pittsburgh index measures of sleep efficiency and disturbances and the Yale-New Haven inventory item regarding difficulty falling asleep were unaffected by trazodone. One patient dropped out because of excessive daytime sedation with trazodone, and another dropped out because of nonresponse to placebo. Of the completers, 67% experienced overall improvement in sleep with trazodone according to a priori criteria, whereas only 13% experienced improvement with placebo. CONCLUSIONS Trazodone is an effective hypnotic for patients with antidepressant-associated insomnia.
A wireless sensor network environment monitoring system based on TinyOS

A wireless sensor network in a greenhouse area environment monitoring system based on TinyOS is designed in this paper. A design approach of the wireless sensor network environment monitoring system of greenhouse, which is based on TinyOS, is presented in this thesis. The design of the hardware and software of the monitoring system is based on the using of the MSP430 microcontroller and NesC language. And the control application program on PC is designed with Visual Basic, which realizes the remote control between the PC and the monitoring system. It also enhances the efficiency, accuracy, reliability and has higher value of applications.
Finite Time Distance-based Rigid Formation Stabilization and Flocking

Abstract Most of the existing results on distributed distance-based rigid formation control establish asymptotic and often exponentially asymptotic convergence. To further improve the convergence rate, we explain in this paper how to modify existing controllers to obtain finite time stability. For point agents modeled by single integrators, the controllers proposed in this paper drive the whole formation to converge to a desired shape with finite settling time. For agents modeled by double integrators, the proposed controllers allow all agents to both achieve the same velocity and reach a desired shape in finite time. All controllers are totally distributed. Simulations are also provided to validate the proposed control.
Comparative Aspects of Gastrointestinal Phosphorus Metabolism

C O N T E N T S I N T R O D U C T I O N . 125 E N D O G E N O U S S E C R E T I O N I N T O T H E G A S T R O I N T E S T I N A L T R A C T . 126 SITES A N D M E C H A N I S M S O F G A S T R O I N T E S T I N A L P i A B S O R P T I O N . 126 N O N R U M I N A N T S . 126 Small intestines . 126 Large intestines . 128 RUMINANTS . 129 Forestomach and abomasum . 129 Small intestines . 129 Large intestines . 130 H O R M O N A L R E G U L A T I O N OF P H O M E O S T A S I S . 130 CONTROL OF EPITHELIAL P , TRANSPORT . 131 I N T E R A C T I O N S B E T W E E N P A N D ca HOMEOSTASIS . 131 D I E T A R Y P D E F I C I E N C Y I N R U M I N A N T S : E F F E C T S O N M I C R O B I A L M E T A B O L I S M I N T H E G A S T R O I N T E S T I N A L T R A C T . 133 C O N C L U S I O N S . 134 R E F E R E N C E S . 135
Factor 8 Gene Mutations and Risk of Inhibitor Development in Hemophilia A Algerian Patients

Background: Neutralizing inhibitors development toward factor VIII is one of the most challenging complications in the treatment of hemophilia A. Several studies have suggested that genetic factors influence the development of factor VIII inhibitors such as ethnicity, family history, mutations in the factor 8 gene and in genes of the immune system. The aim of the present study was to analyze the relationship between inhibitor development and F8 gene mutation types in a sample of hemophiliac patients from West Algeria. Methods: To study the molecular predisposition for inhibitor development, we genotyped 24 hemophiliac patients with and without inhibitors. A conventional Fisher’s exact test was used for statistical analysis. A p-value<0.05 was considered to indicate statistical significance. Results: A total of seven patients had developed inhibitors, while seventeen had not. Six patients with inhibitors (86%) were classified as low responder; whereas, one patient (14%) was categorized as high responder with the Bethesda inhibitor level above five unit. Among the inhibitor-positive patients, we identified 4 with intron 22 inversion, 1 with a nonsense mutation (c.322A > T, p.Lys108*) and 2 without an identified F8 mutation. We showed that there was any association of the F8 gene mutations and the inhibitor development in our studygroup. However, these findings should be confirmed in a larger group of patients. In conclusion, genetic factors are not the only determinant of inhibitor development in HA; environmental factors play an important role.
Cardiovascular risk reduction in patients with severe mental illness.

Health care reform, as outlined in the Patient Protection and Affordable Care Act, will provide many opportunities for cardiovascular nurses to focus on the management of chronic disease, much of which consists of optimizing cardiovascular risk reduction strategies in the management of hypertension, dyslipidemia, and diabetes. There will be ample opportunity to address the 6 quality improvement dimensions in our healthcare system as referenced in the Institute of Medicine’s landmark report Crossing the Quality Chasm: safety, effectiveness, patient centeredness, timeliness, efficiency, and equity. A model of primary care that champions the use of systematic, patient-centered, coordinated care management processes, the PatientCentered Medical Home, is growing, with 2189 practices having achieved designation by the National Center for Quality Assurance, one of several certifying organizations, as of May 2011. The year 2012 will see the launch of the Centers for Medicare and Medicaid Services Accountable Care Organization pilot project. As a consequence of the Patient Protection and Affordable Care Act and these associated initiatives, many persons who have previously experienced obstacles to accessing high-quality healthcare will now have better access to systems that are poised to deliver coordinated, evidence-based, patient-centered care. One of these underserved populations is persons with severe mental illness (SMI), in particular patients with schizophrenia and bipolar disorder. It has long been recognized that those with schizophrenia and bipolar disorder die prematurely, on average 10 to 20 years earlier than the general population. Although, intuitively, suicide and trauma constitute a portion of premature death for many of these patients, physical illnesses account for 75% of mortality. Cardiovascular disease (CVD) is the most common cause of death. The prevalence of diabetes is high; the components of the metabolic syndrome are common in this population and are noted at an earlier age than in the general population. The reasons for this are complex. In 2009, the European Psychiatric Association, supported by the European Association for the Study of Diabetes and the European Society of Cardiology, published a position statement on CVD and diabetes in those with SMI. The report demonstrates that a great deal of the excess risk among those with SMI can be attributed to lifestyle factors. It is known that there is a high prevalence of cigarette smoking (nearly 80% of those with SMI are tobacco dependent; those with SMI and addictions tend to be heavier smokers, consuming 44% of all cigarettes smoked in the United States), a tendency toward unhealthy convenience food, and sedentary lifestyles. A genetic predisposition may contribute, as may high levels of inflammatory markers and stress hormones in some patients with SMI. Added to the genetic and lifestyle risk factors are the well-described adverse effects of certain antipsychotic medications, which are associated with potentially significant weight gain and worsening of associated metabolic
Using incentive schemes to alleviate supply chain risks

This paper describes a methodology and toolkit for the analysis of risks due to insiders' dysfunctional behavior in supply chains. It shows how risk analysis techniques based on value models [15] can incorporate the design and distribution of incentives as a risk-alleviation technique. Some important new functionalities of our SCRS (Supply Chain Risk Simulator v1 [14]) tool are presented. Such functionalities allow for (i) import/export of value models and (ii) execution of incentive-aware risk analysis. Functionality (i) fully integrates the SCRS tool with the e3-value tool suite, increasing synergy with existing value model toolkits. Functionality (ii) substantially extends the original palette of techniques for risk analysis and alleviation. Finally, the paper presents the results of an extensive experimentation of our methodology and simulation tool taking into account different combinations of incentive schemes and simulation options.
An 11‐year‐old boy with an incidental mass in the left lateral cerebellum

An 11 year-old male presented after falling from a tree. Prior to this accident the patient was in a good state of health. On physical examination the patient was afebrile with stable vital signs. A neurological examination revealed no focal deficits. Laboratory studies were all within normal limits. MRI revealed a single incidental well-circumscribed 2.0 × 1.8 × 1.3 cm left cerebellar mass (Fig. 1A). The mass was hypo-intense on T1 and hyper-intense on T2-weighted images, respectively. No enhancement was seen with intravenous contrast material. There was no evidence of intraparenchymal hemorrhage, calcification, or midline shift. A left paramedian suboccipital craniotomy for the excision of the mass was performed. The tumor was soft, gray and well delineated from surrounding tissue with involvement of the overlying leptomeninges. Post-operative MRI showed gross total resection.
Discovery and Characterization of a Ca2+-independent Phosphatidylethanolamine N-Acyltransferase Generating the Anandamide Precursor and Its Congeners*

N-Acylphosphatidylethanolamines (NAPEs) are precursors of bioactive N-acylethanolamines, including the endocannabinoid anandamide. In animal tissues, NAPE is formed by transfer of a fatty acyl chain at the sn-1 position of glycerophospholipids to the amino group of phosphatidylethanolamine (PE), and this reaction is believed to be the principal rate-limiting step in N-acylethanolamine synthesis. However, the Ca2+-dependent, membrane-associated N-acyltransferase (NAT) responsible for this reaction has not yet been cloned. In this study, on the basis of the functional similarity of NAT to lecithin-retinol acyltransferase (LRAT), we examined a possible PE N-acylation activity in two rat LRAT homologous proteins. Upon overexpression in COS-7 cells, one protein, named rat LRAT-like protein (RLP)-1, catalyzed transfer of a radioactive acyl group from phosphatidylcholine (PC) to PE, resulting in the formation of radioactive NAPE. However, the RLP-1 activity was detected mainly in the cytosolic rather than membrane fraction and was little stimulated by Ca2+. Moreover, RLP-1 did not show selectivity with respect to the sn-1 and sn-2 positions of PC as an acyl donor and therefore could generate N-arachidonoyl-PE (anandamide precursor) from 2-arachidonoyl-PC and PE. In contrast, under the same assay conditions, partially purified NAT from rat brain was highly Ca2+-dependent, membrane-associated, and specific for the sn-1-acyl group of PC. RLP-1 mRNA was expressed predominantly in testis among various rat tissues, and the testis cytosol exhibited an RLP-1-like activity. These results reveal that RLP-1 can function as a PE N-acyltransferase, catalytically distinguishable from the known Ca2+-dependent NAT.