Miracle-dz/UniFAR-FTUs huggingface dataset:
An algebra of bayesian belief universes for knowledge-based systems

Causal probabilistic networks (CPNs) have proved to be a useful knowledge representation tool for modeling domains where causal relations-in a broad sense-are a natural way of relating domain concepts and where uncertainty is inherited in these relations. The domain is modeled in a CPN by use of a directed graph where the nodes represent concepts in the domain and the arcs represent causal relations. Furthermore, the quantitative relation between a node and its immediate causes is expressed as conditional probabilities. During the last few years, several schemes based on probability theory for incorporating and propagating new information throughout a CPN has emerged. As long as the domain can be modeled by use of a singly connected CPN (i. e., no more than one path between any pair of nodes), the schemes operate directly in the CPN and perform conceptually simple operations in this structure. When it comes to more complicated structures such as multiply connected CPNs (i. e., more than one path is allowed between pairs of nodes), the schemes operate in derived structures where the embedded domain knowledge no longer is as explicit and transparent as in the CPN. Furthermore, the simplicity in the operations is lost also. This report outlines a scheme-the algebra of Bayesian belief universes-for absorbing and propagating evidence in multiply connected CPNs. The scheme provides a secondary structure, a junction tree, and a simple set of algebraic operations between objects in this structure, Collect Evidence and Distribute Evidence. These are the basic tools for making inference in a CPN domain model and yield a calculus as simple as in the case of singly connected CPNs.
Data-driven deep-syntactic dependency parsing†

Abstract ‘Deep-syntactic’ dependency structures that capture the argumentative, attributive and coordinative relations between full words of a sentence have a great potential for a number of NLP-applications. The abstraction degree of these structures is in between the output of a syntactic dependency parser (connected trees defined over all words of a sentence and language-specific grammatical functions) and the output of a semantic parser (forests of trees defined over individual lexemes or phrasal chunks and abstract semantic role labels which capture the frame structures of predicative elements and drop all attributive and coordinative dependencies). We propose a parser that provides deep-syntactic structures. The parser has been tested on Spanish, English and Chinese.
Fiber intake and pancreatic cancer risk: a case-control study.

BACKGROUND Scanty and inconsistent studies are available on the relation between dietary fiber intake and pancreatic cancer. A case-control study was carried out in northern Italy to further investigate the role of various types of dietary fibers in the etiology of pancreatic cancer. PATIENTS AND METHODS Cases were 326 patients with incident pancreatic cancer, excluding neuroendocrine tumors, admitted to major teaching and general hospitals during 1991-2008. Controls were 652 patients admitted for acute, nonneoplastic conditions to the same hospital network of cases. Information was elicited using a validated food frequency questionnaire. Odds ratios (ORs) and the corresponding 95% confidence intervals (CIs) were estimated for intake quintiles of different types of fiber after allowance for total energy intake and other potential confounding factors. RESULTS Total fiber intake was inversely related to risk of pancreatic cancer (OR=0.4 for highest versus lowest quintile of intake; 95% CI 0.2-0.7). An inverse association emerged between pancreatic cancer and both soluble (OR=0.4; 95% CI 0.2-0.7) and total insoluble fiber (OR=0.5; 95% CI 0.3-0.8), particularly cellulose (OR=0.4; 95% CI 0.3-0.7) and lignin (OR=0.5; 95% CI 0.3-0.9). Fruit fiber intake was inversely associated with pancreatic cancer (OR=0.5; 95% CI 0.3-0.8), whereas grain fiber was not (OR=1.2; 95% CI 0.7-2.0). CONCLUSIONS This study suggests that selected types of fiber and total fiber are inversely related to pancreatic cancer.
Abstract 2034: Development of 3D bioprinted human breast cancer forin vitrodrug screening

As breast cancer is a disease of multiple cell types in which the growth, invasion, and metastasis of epithelial carcinomas is heavily influenced by the surrounding cell types, screening of anti-cancer compounds using cancer cell lines grown in 2D often overestimates drug potency. Regulatory agencies are currently seeking improved preclinical oncology models to overcome hurdles to efficient drug development, including bridging the gap between the use of 2D cell lines and 3D animal models. One way to more accurately determine the effects of anti-cancer compounds is through the use of cancer tissue models that incorporate stromal cells of the tumor microenvironment. Breast stroma, composed of fibroblasts, endothelial cells, and adipocytes, plays a key role in the process of carcinogenesis and metastasis. These cell types secrete extracellular matrix, growth factors, and hormones that affect how therapeutic agents access and target cancer cells. We have used Organovo9s NovoGen Bioprinting TM Platform to develop a model of human breast cancer in which a core of breast cancer cells is surrounded by a physiologically-relevant stromal milieu consisting of adipocytes, mammary fibroblasts, and endothelial cells. This system has several advantages over current screening tools, including the ability to simultaneously measure the effects of small molecules on cancer cells as well as different cell types in the breast microenvironment. Histological analyses of bioprinted neotissues demonstrated that they were stable and viable for at least 14 days in culture and characterized by interaction between stroma and carcinoma compartments. Incorporation of endothelial cells into the 3D neotissue led to the formation of robust microvascular networks. Breast cancer neotissues were fabricated directly into multi-well plates and used to establish biological response profiles to the standard chemotherapeutic agents cisplatin, paclitaxel, methotrexate, and tamoxifen. The cytotoxic effects of chemotherapeutic drugs on specific cell types within the neotissues were assessed biochemically and histologically. he response of the 3D breast cancer neotissues to chemotherapeutic gents was compared to the response of 2D breast cancer cell lines to determine he relative efficacy of compounds in 2D versus 3D. This model can be used to screen new anti-cancer therapeutics in the context of the in vivo-like microenvironment, leading to enhanced efficiency and accuracy of the drug development process. Citation Format: Shelby M. King, Sharon C. Presnell, Deborah G. Nguyen. Development of 3D bioprinted human breast cancer for in vitro drug screening. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2034. doi:10.1158/1538-7445.AM2014-2034
Setting Up a Standardized Peripheral Blood Mononuclear Cells Processing Laboratory to Support Multi-center HIV/AIDS Vaccine and Intervention Trials

Despite infrastructure and capacity challenges in Africa, significant development has been made in the number of laboratories supporting immunological and safety studies required for large-scale HIV/AIDS vaccine or intervention trials. In Uganda, cohorts participating in HIV intervention trials are often recruited from rural areas. To avoid transporting samples from intervention trial areas over long distances (120 km) to central laboratories in Entebbe, we set up a standardized peripheral blood mononuclear cells (PBMCs) processing laboratory at a field station in Masaka, southwest Uganda. The laboratory was well equipped and enrolled into the International AIDS Vaccine Initiative (IAVI) Quality Assurance (QA) program. Staff was trained in laboratory techniques and Good Clinical Laboratory Practice (GCLP). The laboratory received IAVI and GCLP accreditation in 2008. In this paper we describe the process and achievements of measures taken to overcome challenges, to build staff capacity, and to optimize the quality of the cells yielded. * PBMCs : peripheral blood mononuclear cells IAVI : International AIDS Vaccine Initiative QA : quality assurance GCLP : Good Clinical Laboratory Practice CTL : cytotoxic T lymphocytes Th : T helper UVRI : Uganda Virus Research Institute SOPs : standard operating procedures SPARTAC : short pulse anti-retroviral treatment at seroconversion S101 : sample 1, operator 1 S1O2 : sample 1, operator 2 S2O1 : sample 2, operator 1 S2O2 : sample 2, operator 2 ELISPOT : enzyme-linked immunosorbent spot CLS : Clinical Support laboratory DAIDS : division of AIDS
Multicenter phase II study of trabectedin in patients with metastatic castration-resistant prostate cancer.

BACKGROUND This multicenter phase II trial evaluated the efficacy and safety of trabectedin in metastatic castration-resistant prostate cancer (CRPC). PATIENTS AND METHODS Two schedules were evaluated in three cohorts: weekly as 3-h i.v. infusion at 0.58 mg/m(2) for 3 out of 4 weeks (Cohort A, n = 33), and every 3 weeks (q3wk) as 24-h infusion at 1.5 mg/m(2) (Cohort B1, n = 5) and 1.2 mg/m(2) (Cohort B2, n = 20). The primary end point was prostate-specific antigen (PSA) response; secondary end points included safety, tolerability and time to progression (TTP). RESULTS Trabectedin resulted in PSA declines ≥ 50% in 12.5% (Cohort A) and 10.5% (Cohort B2) of patients. Among men pretreated with taxane-based chemotherapy, PSA response was 13.6% (Cohort A) and 15.4% (Cohort B2). PSA responses lasted 4.1-8.6 months, and median TTP was 1.5 months (Cohort A) and 1.9 months (Cohort B2). The dose of 1.5 mg/m(2) (approved for soft tissue sarcoma) given as 24-h infusion q3wk was not tolerable in these patients. At 1.2 mg/m(2) q3wk and 0.58 mg/m(2) weekly, the most common adverse events were nausea, fatigue and transient neutropenia and transaminase increase. CONCLUSIONS Two different trabectedin schedules showed modest activity in metastatic CRPC. Further studies may require identification of predictive factors of response in prostate cancer.
Overlapping for preconditioners based on incomplete factorizations and nested arrow form

In this paper, we discuss the usage of overlapping techniques for improving the convergence of preconditioners based on incomplete factorizations. To enable parallelism, these preconditioners are usually applied after the input matrix is permuted into a nested arrow form using k‐way nested dissection. This graph partitioning technique uses k‐way partitionning by vertex separator to recursively partition the graph of the input matrix into k subgraphs using a subset of its vertices called a separator. The overlapping technique is then based on algebraically extending the associated subdomains of these subgraphs and their corresponding separators obtained from k‐way nested dissection by their direct neighbours. A similar approach is known to accelerate the convergence of domain decomposition methods, where the input matrix is partitioned into a number of independent subdomains using k‐way vertex partitioning of a graph by edge separators, a different graph decomposition technique. We discuss the effect of the overlapping technique on the convergence of two classes of preconditioners, on the basis of nested factorization and block incomplete LDU factorization. Copyright © 2014 John Wiley & Sons, Ltd.
When the Problem is Beneath the Surface in OCD: The Cognitive Treatment of a Case of Pure Mental Contamination

Background: Mental contamination is a phenomenon whereby people experience feelings of contamination from a non-physical contaminant. Rachman (2006) proposes that standard cognitive behavioural treatments (CBT) need to be adapted here and there is a developing empirical grounding supporting the concept, although suggestions on adapting treatment have yet to be tested. Method: A single case study is presented of a man with a 20-year history of severe treatment resistant Obsessive Compulsive Disorder (OCD) characterized by mental contamination following the experience of “betrayal”. He was offered two consecutive treatments: standard CBT and then (following disengagement with this) a cognitive therapy variant adapted for mental contamination. Clinician and patient rated OCD severity was measured at baseline and the start and end of both interventions. Results: Six sessions of high quality CBT were initially attended before refusal to engage with further sessions. There were no changes in OCD severity ratings across these sessions. A second course of cognitive therapy adapted for mental contamination was then offered and all 14 sessions and follow-ups were attended. OCD severity fell from the severe to non-clinical range across these sessions. Conclusions: The need to consider adapting standard treatments for mental contamination is suggested. Limitations and implications are discussed.
Fast tensor method for summation of long‐range potentials on 3D lattices with defects

In this paper, we present a method for fast summation of long‐range potentials on 3D lattices with multiple defects and having non‐rectangular geometries, based on rank‐structured tensor representations. This is a significant generalization of our recent technique for the grid‐based summation of electrostatic potentials on the rectangular L × L × L lattices by using the canonical tensor decompositions and yielding the O(L) computational complexity instead of O(L3) by traditional approaches. The resulting lattice sum is calculated as a Tucker or canonical representation whose directional vectors are assembled by the 1D summation of the generating vectors for the shifted reference tensor, once precomputed on large N × N × N representation grid in a 3D bounding box. The tensor numerical treatment of defects is performed in an algebraic way by simple summation of tensors in the canonical or Tucker formats. To diminish the considerable increase in the tensor rank of the resulting potential sum, the ϵ‐rank reduction procedure is applied based on the generalized reduced higher‐order SVD scheme. For the reduced higher‐order SVD approximation to a sum of canonical/Tucker tensors, we prove the stable error bounds in the relative norm in terms of discarded singular values of the side matrices. The required storage scales linearly in the 1D grid‐size, O(N), while the numerical cost is estimated by O(NL). The approach applies to a general class of kernel functions including those for the Newton, Slater, Yukawa, Lennard‐Jones, and dipole‐dipole interactions. Numerical tests confirm the efficiency of the presented tensor summation method; we demonstrate that a sum of millions of Newton kernels on a 3D lattice with defects/impurities can be computed in seconds in Matlab implementation. The tensor approach is advantageous in further functional calculus with the lattice potential sums represented on a 3D grid, like integration or differentiation, using tensor arithmetics of 1D complexity. Copyright © 2015 John Wiley & Sons, Ltd.
HER2-negative (1+) breast cancer with unfavorable prognostic features: to FISH or not to FISH?

stated in the conclusions of our article, the EZH2 626-394C>T SNP needs to be rigorously challenged in larger prospective independent series in order to definitively establish its value as a prognostic and/or predictive biomarker in mCRC [4]. L. Fornaro*, F. Crea, G. Masi, E. Paolicchi, F. Loupakis, F. Graziano, L. Salvatore, M. Ronzoni, V. Ricci, C. Cremolini, M. Schirripa, R. Danesi & A. Falcone Department of Oncology, Transplants and New Technologies in Medicine, Division of Medical Oncology, University of Pisa, Pisa, Department of Internal Medicine, Division of Pharmacology, University of Pisa, Pisa, Medical Oncology Unit, Department of Onco-Hematology, Azienda Ospedaliera S. Salvatore, Pesaro, Division of Medical Oncology, S. Raffaele Scientific Institute, Milano, Italy (*E-mail: lorenzo.fornaro@gmail.com)
Internalizing early memories of shame and lack of safeness and warmth: the mediating role of shame on depression.

BACKGROUND Growing evidence supports the association between early memories of shame and lack of safeness and current shame and depression. Nevertheless, it is unclear whether shame serves as a mediator between such early memories and depressive symptoms. AIMS This study aimed at testing whether the impact of shame traumatic memory, centrality of shame memory, early memories of warmth and safeness (predictors), on depressive symptoms (outcome) would be mediated by current external and internal shame. METHOD Student participants (N = 178) recalled an early shame experience and completed self-report instruments measuring centrality and traumatic characteristics of the shame memory, early memories of warmth and safeness, external and internal shame and depressive symptoms. RESULTS Path analysis' results revealed that internal shame fully mediated the relationship between shame traumatic memory, centrality of shame memory, and early memories of warmth and safeness, and depression. However, current feelings of external shame, highly linked to internal shame, did not significantly predict depression. CONCLUSION These findings shed light on the role of internalizing early shame and lack of safeness memories into a sense of self as globally self-condemning in the vulnerability to experience depressive symptoms.
Lack of Insight in Psychosis: Theoretical Concepts and Clinical Aspects

Background: Different theories concerning pathways to insight have been proposed which underpin the numerous assessment measures. Cognitive behavioural therapy (CBT) is one treatment approach that has been used to improve insight. Aims: The aim of this review was to promote a greater focus on developing effective CBT strategies to ameliorate insight in psychosis through the exploration of the concept of insight in psychosis and evaluation of research in the area. Method: A comprehensive search and review of published studies examining the impact of CBT on insight in psychosis was conducted. We searched the databases PubMed, Medline, PsychInfo, the Psychology and Behavioral Sciences Database, and CINAHL with limits set to 10 years, humans, and English language. We hand-searched reference lists of major studies on insight, and theoretical review papers. We filtered our results according to relevance and chose 50 papers for final consideration. Results: The multidimensionality of insight is reflected in the variety of different insight measures in clinical use. Research findings on the impact of CBT on insight are conflicting. Cognitive insight and clinical insight appear to be different concepts that are not fully captured by existing measurement scales. Conclusions: The conflicting results found in research examining the impact of CBT on insight may be partially explained by the different theories underpinning insight in psychosis communicated through psychoeducation in CBT. Furthermore, the use of more than one insight assessment measure may capture the complexity of insight more effectively. Qualitative research with service users would enrich the knowledge in this area.
Interpersonal Processes and Attachment in Voice-Hearers

Background: Studies of both clinical and non-clinical voice hearers suggest that distress is rather inconsistently associated with the perceived relationship between voice and hearer. It is also not clear if their beliefs about voices are relevant. Aims: This study investigated the links between attachment anxiety/avoidance, interpersonal aspects of the voice relationship, and distress whilst considering the impact of beliefs about voices and paranoia. Method: Forty-four voice-hearing participants completed a number of self-report measures tapping attachment, interpersonal processes in the voice relationship, beliefs about voices, paranoia, distress and depression. Results: Attachment avoidance was related to voice intrusiveness, hearer distance and distress. Attachment anxiety was related to voice intrusiveness, hearer dependence and distress. A series of simple mediation analyses were conducted that suggest that the relationship between attachment and voice related distress may be mediated by interpersonal dynamics in the voice-hearer relationship, beliefs about voices and paranoia. Conclusions: Beliefs about voices, the hearer's relationship with their voices, and the distress voices sometimes engender appear to be meaningfully related to their attachment style. This may be important to consider in therapeutic work.
Numerical validation of solutions of saddle point matrix equations

A numerical validation method for verifying the accuracy of approximate solutions of saddle point matrix equations is presented and analysed. The method only requires iterative solutions of two symmetric positive definite linear systems. Moreover, it is shown that preconditioning can be used to improve the error bounds. The method is illustrated by several examples derived from mixed finite element discretization of the Stokes equations. Preliminary numerical results indicate that the method is efficient. Copyright © 2003 John Wiley & Sons, Ltd.
Circulation of Porcine Parvovirus Types 1 through 6 in Serum Samples Obtained from Six Commercial Polish Pig Farms

Porcine parvoviruses are small non-enveloped DNA viruses, very resistant to inactivation, and ubiquitous in the global pig population. Porcine parvovirus type 1 (PPV1) has been known since the 1960s and is a major causative agent of reproductive failure in breeding herds. During the last decade, several new parvoviruses have been identified in pigs by molecular methods and have been consecutively designated as PPV2 through PPV6. Epidemiology data for these viruses are limited, and the impact of these newly recognized parvoviruses on pigs is largely unknown. To further generate knowledge on the distribution of PPVs in pigs, a total of 247 serum samples were collected from six commercial Polish pig farms during 2013-2015 and tested by PCR assays and ELISAs. The pigs ranged from two to 18 weeks of age at sample collection. Breeding herds supplying the investigated farms were routinely vaccinated against PPV1. While all growing pig samples were negative for PPV1 DNA, young pigs were frequently negative for PPV1 antibodies and seroconversion to PPV1 was commonly seen at 9-10 weeks of age. The PPV2 antibody detection was highest in young pigs (2-6-week-old) and decreased in older pigs indicating passively acquired antibodies. The DNA prevalence rates in the serum samples analysed were 19% for PPV2, 7.7% for PPV3, 2.4% for PPV4, 4.0% for PPV5 and 6.1% for PPV6. Most PPV DNA-positive samples were identified in 9- to 18-week-old pigs with no obvious association with disease on the farm. All recently emerging PPV genotypes were detected in Polish farms. Similar to previous reports in other pig populations, PPV2 was the most frequent PPV genotype circulating in Poland.
A multigrid method for anisotropic PDEs in elastic image registration

This paper deals with the solution of a non‐linear ill‐conditioned inverse problem arising in digital image registration. In the first part of the paper, we define the problem as the minimization of a regularized non‐linear least‐squares functional, which measures the image difference and smoothness of the transformation. We study inexact Newton methods for solving this problem, i.e. we linearize the functional around a current approximation and replace the Hessian by a suitable operator in order to obtain well‐posed subproblems in each step of the iteration.