Miracle-dz/UniFAR-FTUs huggingface dataset:
Computerized planning of prostate cryosurgery with pullback operation

This study is a part of an ongoing project to develop computerized tools for cryosurgery planning. Prostate cryosurgery is frequently performed as a two-stage process in which the first-stage targets are frozen with the cryoprobes at a greater insertion depth, while the second stage of freezing is performed after some cryoprobes are pulled back to new locations, this process being known as the pullback procedure. This paper proposes a method to generate computationally a preferred cryoprobe layout for the pullback operation, using a previously proposed bubble-packing method for cryosurgery planning. For this purpose, additional constraints are imposed to align packed bubbles along the same insertion path between the different stages, and to vary the number of bubbles at each stage. The method is demonstrated on 3D patient models from four individuals, using cryoprobes with a diameter of 1.5 mm and an active length of 15 mm. Results are verified with bioheat transfer simulations, and compared with the non-pullback operations using cryoprobes with longer (25 mm) active lengths. When compared with results of the non-pullback procedure, results with pullback suggest some improvement in freezing in the apex region of the prostate, with a slight increase in overall freezing damage to surrounding healthy tissues.
Analysis of the Role of  Variation of Major Histocompatibility Complex Class II Expression on Nonobese Diabetic (NOD) Peripheral T Cell Response

The current paradigm of major histocompatibility complex (MHC) and disease association suggests that efficient binding of autoantigens by disease-associated MHC molecules leads to a T cell–mediated immune response and resultant autoimmune sequelae. The data presented below offer a different model for this association of MHC with autoimmune diabetes. We used several mouse lines expressing different levels of I-Ag7 and I-Ak on the nonobese diabetic (NOD) background to evaluate the role of MHC class II in the previously described NOD T cell autoproliferation. The ratio of I-Ag7 to I-Ak expression correlated with the peripheral T cell autoproliferative phenotype in the mice studied. T cells from the NOD, [NOD × NOD.I-Anull]F1, and NOD I-Ak transgenic mice demonstrated autoproliferative responses (after priming with self-peptides), whereas the NOD.H2h4 (containing I-Ak) congenic and [NOD × NOD.H2h4 congenic]F1 mice did not. Analysis of CD4+ NOD I-Ak transgenic primed lymph node cells showed that autoreactive CD4+ T cells in the NOD I-Ak transgenic mice were restricted exclusively by I-Ag7. Considered in the context of the avidity theory of T cell activation and selection, the reported poor peptide binding capacity of NOD I-Ag7 suggested a new hypothesis to explain the effects of MHC class II expression on the peripheral autoimmune repertoire in NOD mice. This new explanation suggests that the association of MHC with diabetes results from “altered” thymic selection in which high affinity self-reactive (potentially autoreactive) T cells escape negative selection. This model offers an explanation for the requirement of homozygous MHC class II expression in NOD mice (and in humans) in susceptibility to insulin-dependent diabetes mellitus.
Robot-aided therapy on the upper limb of subacute and chronic stroke patients: A biomechanical approach

The goal of this study is to propose a methodology for evaluating recovery mechanisms in subacute and chronic post-stroke patients after a robot-aided upper-limb therapy, using a set of biomechanical parameters. Fifty-six post-stroke subjects, thirteen subacute and forty-three chronic patients participated in the study. A 2 dof robotic system, implementing an “assist-as-needed” control strategy, was used. Biomechanical parameters related (i) to the speed measured at the robot's end-effector and (ii) to the movement's smoothness were computed. Outcome clinical measures show a decrease in motor impairment after the treatment both in chronic and subacute patients. All the biomechanical parameters show an improvement between admission and discharge. Our results show that the robot-aided training can contribute to reduce the motor impairment in both subacute and chronic patients and identify neurophysiological mechanisms underlying the different stages of motor recovery.
Sialic acid and oxidizability of lipid and proteins and antioxidant status in patients with coronary artery disease

The aim of this study was to investigate the possible relationship between serum total sialic acid (TSA) concentration, recently shown to be a cardiovascular risk factor, and lipid and protein oxidation and antioxidant status and the severity of coronary artery disease (CAD) according to the obstructive vessel number in patients. The study was carried out on a total of 200 patients (142 men and 58 women) who were hospitalized for elective coronary angiographic evaluation with complaint of typical angina pectoris. According to the results of angiography, 150 patients had angiographically proven CAD (CAD group) and 50 patients had a history suggestive of angina pectoris but normal coronary angiograms (control group). The CAD group was further divided into single‐, double‐ and triple‐vessel disease groups according to the number of vessels involved. Lipid parameters were determined by routine laboratory methods. Plasma malondialdehyde (MDA) and vitamin E concentrations were determined by high‐performance liquid chromatography. TSA and other oxidant and antioxidant parameters were studied spectrophotometrically. Our results demonstrated significant increases both in TSA levels and in indicators of oxidative stress in the patients with CAD compared with the controls. However, antioxidant parameters were decreased in the patients with CAD. We found strong positive correlations between TSA and plasma MDA, Δ‐MDA which represents the degree of oxidative modification of apolipoprotein B‐containing lipoproteins, serum protein carbonyls and apolipoprotein B and weak correlations between TSA and low density lipoprotein cholesterol, triacylglycerol, paraoxonase, glutathione peroxidase (GPx), vitamin C and vitamin E. In conclusion, TSA is related to markers of lipid and protein oxidation, paraoxonase and GPx activities, vitamin C and E levels and the severity of CAD. Copyright © 2006 John Wiley & Sons, Ltd.
FPGA platform based digital design education

This paper gives an overview of how the FPGA (field-programmable gate array) technology is integrated into digital design educational process at Tallinn University of Technology (TUT). Paper focuses on the set of laboratory exercises introduced for "Advanced Digital Design" (IAY0080) course taught to postgraduate students, covering equipment, software and methodology, as well as plans for future improvements.
Global existence and regularity for the 3D stochastic primitive equations of the ocean and atmosphere with multiplicative white noise

The primitive equations (PEs) are a basic model in the study of large scale oceanic and atmospheric dynamics. These systems form the analytical core of the most advanced general circulation models. For this reason and due to their challenging nonlinear and anisotropic structure, the PEs have recently received considerable attention from the mathematical community. On the other hand, in view of the complex multi-scale nature of the earth's climate system, many uncertainties appear that should be accounted for in the basic dynamical models of atmospheric and oceanic processes. In the climate community stochastic methods have come into extensive use in this connection. For this reason there has appeared a need to further develop the foundations of nonlinear stochastic partial differential equations in connection with the PEs and more generally. In this work we study a stochastic version of the PEs. We establish the global existence and uniqueness of strong, pathwise solutions for these equations in dimension 3 for the case of a nonlinear multiplicative noise. The proof makes use of anisotropic estimates, estimates on the pressure and stopping time arguments.
Multi-periodic climate dynamics: spectral analysis of long-term instrumental and proxy temperature records

Abstract. The longest six instrumental temperature records of monthly means reach back maximally to 1757 AD and were recorded in Europe. All six show a V-shape, with temperature drop in the 19th and rise in the 20th century. Proxy temperature time series of Antarctic ice cores show this same characteristic shape, indicating this pattern as a global phenomenon. We used the mean of the six instrumental records for analysis by discrete Fourier transform (DFT), wavelets, and the detrended fluctuation analysis (DFA). For comparison, a stalagmite record was also analyzed by DFT. The harmonic decomposition of the abovementioned mean shows only six significant frequencies above periods over 30 yr. The Pearson correlation between the mean, smoothed by a 15-yr running average (boxcar) and the reconstruction using the six significant frequencies, yields r = 0.961. This good agreement has a > 99.9% confidence level confirmed by Monte Carlo simulations. It shows that the climate dynamics is governed at present by periodic oscillations. We find indications that observed periodicities result from intrinsic dynamics.
Intravenous Medication Administration in Intensive Care: Opportunities for Technological Solutions

Medication administration errors have been shown to be frequent and serious. Error is particularly prevalent in highly technical specialties such as critical care. The purpose of this study was to describe the characteristics of intravenous medication administration in five intensive care units. These data were used within the context of a larger study to design information system decision support in these settings. Nurses were observed during the course of their work and their intravenous medication administration process, order source, references used, calculation method, number of medications prepared simultaneously, and any interruptions occurring during the preparation and delivery phases of the administration event were recorded. In addition, chart reviews of medication administration records were completed and nurses were asked to complete an anonymous drop-box questionnaire regarding their experiences with medication administration error. The results of this study are discussed in terms of potential informatics solutions for reducing medication administration error.
Modelling the spatial effects of the anaesthetic-induced phase-transition in the cerebral cortex

In this thesis I investigate the theoretical stochastic behaviour of a one-dimensional model of the cerebral cortex, exposed to varying concentrations of a general anaesthetic agent. The model is that of Steyn-Ross et al. (2003). Theirs is a continuum theory based on the electrical response of a neural mass known as the macrocolum. The model predicts that as anaethetic concentration is increased the cortex will undergo a sudden electrical phase transition corresponding to loss of consciousness (LOC). Similarly, at return of consciousness (ROC) a second distinct phase transition is predicted. Spatial variability is incorporated into the original homogeneous cortical model of Steyn-Ross et al. (1999). This is done by including the possibility of spatial variation in distant excitatory and inhibitory inputs. By modelling the cortex in this way, we hope to gain an understanding of how the cortex functions, and how anaethestic agents “shut-down” the brain. I simulate the one-dimensional system numerically in order to verify analytical predictions. Both analytical and numerical results show an increase in the coherence (spatial-correlation) of the electrical activity along the one-dimensional rod on approach to both LOC and ROC. Theory and simulations also show that the electrical fluctuations in the unconscious cortex should have a larger correlation length than for the cortex in the conscious state, suggesting that the unconscious state is the more ordered. I derive the theoretical power spectrum and discuss some of its properties. By expanding the model to include spatial variability, we discover the possibility of selforganized structures forming spontaneously in the one-dimensional cortex. These “Turing” or dissipative structures are stationary in time, showing giant DC voltage variations along the cortical rod. Although the dissipative structures can from a rich variety of pseudo-periodic patterns, the physiological significance of such stationary neural structures is not yet clear.
Significant Association of Glutathione S-Transferase T1 Null Genotype with Prostate Cancer Risk: A Meta-Analysis of 26,393 Subjects

Background Recent studies on the association between Glutathione S-transferase T1 (GSTT1) polymorphism and risk of prostate cancer showed inconclusive results. To clarify this possible association, we conducted a meta-analysis of published studies. Methods Data were collected from the following electronic databases: Pubmed, Embase, and Chinese Biomedical Database (CBM). The odds ratio (OR) and its 95% confidence interval (95%CI) was used to assess the strength of the association. We summarized the data on the association between GSTT1 null genotype and risk of prostate cancer in the overall population, and performed subgroup analyses by ethnicity, adjusted ORs, and types of controls. Results Ultimately, a total of 43 studies with a total of 26,393 subjects (9,934 cases and 16,459 controls) were eligible for meta-analysis. Overall, there was a significant association between GSTT1 null genotype and increased risk of prostate cancer (OR = 1.14, 95%CI 1.01–1.29, P = 0.034). Meta-analysis of adjusted ORs also showed a significant association between GSTT1 null genotype and increased risk of prostate cancer (OR = 1.34, 95%CI 1.09–1.64, P = 0.006). Similar results were found in the subgroup analyses by ethnicity and types of controls. Conclusion This meta-analysis demonstrates that GSTT1 null genotype is associated with prostate cancer susceptibility, and GSTT1 null genotype contributes to increased risk of prostate cancer.
The Left Hemisphere's Role in Hypothesis Formation

In a probability guessing experiment, subjects try to guess which of two events will occur next. Humans tend to match the frequency of previous occurrences in their guesses. Animals other than humans tend to maximize or always choose the option that has occurred the most frequently in the past. Investigators have argued that frequency matching results from the attempt of humans to find patterns in sequences of events even when told the sequences are random. There is independent evidence that the left hemisphere of humans houses a cognitive mechanism that tries to make sense of past occurrences. We performed a probability guessing experiment with two split-brain patients and found that they approximated frequency matching in their left hemispheres and approached maximizing in their right hemispheres. We obtained a conceptual replication of that finding on patients with unilateral damage to either the left or right hemisphere. We conclude that the neural processes responsible for searching for patterns in events are housed in the left hemisphere.
Gay Male Pornography's “Actors”

ABSTRACT Gay male pornography harms men. It harms some of the men who are used to perform in it and more broadly, men in general once used and distributed. It is, at its core, harmful to the movement for social, sexual, gender, and racial justice. In this article, we examine gay male pornography under the lens developed by over twenty years of feminist scholarship and activism relative to heterosexual pornography. We find that, like heterosexual pornography, gay male pornography uses real people, many vulnerable and easily exploited, to sexualize racism and promote both homophobia and sexism. Rather than being a tool for liberation, as some gay and bisexual men have argued, we conclude that gay male pornography promotes degradation, violence and harm-and as such, is degradation, violence, and harm. No job No money No self-esteem No confidence All I have is my looks and body And that's not working anymore. I feel washed up. Drug problem. Hate life. HIV-positive -Joey Iacona Stefano, gay pornography actor who died of a drug overdose (Isherwood, 1990, p. 162)
Core Binding Factor Beta Plays a Critical Role by Facilitating the Assembly of the Vif-Cullin 5 E3 Ubiquitin Ligase

ABSTRACT The HIV-1 virion infectivity factor (Vif) targets the cellular cytidine deaminases APOBEC3G (A3G) and APOBEC3F (A3F) for degradation via the host ubiquitin-proteasome pathway. Vif recruits a cellular E3 ubiquitin ligase to polyubiquitinate A3G/F. The activity of Vif critically depends on the cellular core binding factor beta (CBFβ). In this study, we investigated the Vif-CBFβ interaction and the role of CBFβ in the E3 ligase assembly. Vif-CBFβ interaction requires an extensive region of Vif spanning most of its amino terminus and zinc finger region, and cullin 5 (Cul5) binding enhances the stability of the Vif-CBFβ interaction. Our results further demonstrate that CBFβ plays a critical role in facilitating Cul5 binding to the Vif/elongin B/elongin C complex. Vif, with or without bound substrate, is unable to bind Cul5 in the absence of CBFβ. These studies support the notion that CBFβ serves as a molecular chaperone to facilitate Vif-E3 ligase assembly. IMPORTANCE The host antiviral restriction factors A3G/F inhibit viral replication. The HIV-1 protein Vif targets A3G/F for degradation. This immune evasion activity of Vif is dependent on the cellular factor CBFβ. Multiple regions of Vif are known to be important for Vif function, but the mechanisms are unclear. The studies described here provide important information about the Vif-CBFβ interaction interface and the function of CBFβ in E3 ligase assembly. In particular, our comprehensive Vif-CBFβ interface mapping results help to delineate the role of various Vif regions, determining if they are important for binding CBFβ or A3G/F. Furthermore, our studies reveal an important potential mechanism of CBFβ that has not been shown before. Our results suggest that CBFβ may serve as a molecular chaperone to enable Vif to adopt an appropriate conformation for interaction with the Cul5-based E3 ligase. This study advances our understanding of how CBFβ facilitates the Vif-mediated degradation of APOBEC3 proteins.
Replicating and extending a model of effects of universal preventive intervention during early adolescence on young adult substance misuse.

OBJECTIVE This brief report summarizes a replication and extension of a developmental outcome modeling study, by examining whether delayed substance initiation during adolescence, resulting from universal middle school preventive interventions, reduces problematic use in young adults Ages 25 and 27, up to 14.5 years after baseline. METHOD Participants were middle school students from 36 Iowa schools randomly assigned to the Strengthening Families Program plus Life Skills Training (SFP 10-14 + LST), LST-only, or a control condition. Self-report questionnaires originally were collected at 11 time points, through Age 22. A subsequent grant allowed for assessments at Ages 25 and 27, including measures of drunkenness, alcohol-related problems, cigarette use, illicit drug use (lifetime and frequency), marijuana use and prescription drug misuse. These outcomes were modeled as variables influenced by growth factors describing substance initiation during adolescence. Models included the effects of baseline risk, intervention condition assignment, and their interaction; risk-related moderation effects were examined and relative reduction rates were calculated for dichotomous variables. RESULTS Model fits were good. Analyses showed significant or marginally significant indirect intervention effects on all outcomes, through effects on adolescent substance initiation growth factors. Intervention × Risk interaction effects favored the higher risk subsample, replicating earlier findings. Additional direct effects on young adult use were observed only for cigarette frequency. Relative reduction rates were larger for the higher risk subsamples, ranging from 3.9% to 36.2%. CONCLUSIONS Universal preventive interventions implemented during early adolescence have the potential to decrease the rates of substance misuse and associated problems into young adulthood. (PsycINFO Database Record
A Self-Tuning Filter-Based Adaptive Linear Neuron Approach for Operation of Three-Level Inverter-Based Shunt Active Power Filters under Non-Ideal Source Voltage Conditions

This paper presents a self-tuning filter (STF)-based adaptive linear neuron (ADALINE) reference current generation algorithm to enhance the operation of a three-phase three-level neutral-point diode clamped (NPC) inverter-based shunt active power filter (SAPF) under non-ideal (unbalanced and/or distorted) source voltage conditions. SAPF is an effective and versatile mitigation tool for current harmonics. As for its controller, ADALINE-based reference current generation algorithmd have widely been applied and proven to work effectively under balanced and purely sinusoidal source voltage conditions. However, no work has been conducted to study its performance under non-ideal source voltage conditions. In this work, a STF-based fundamental voltage extraction algorithm is integrated with an ADALINE algorithm, serving as synchronizer algorithm to ensure in-phase operation of the generated reference current with the non-ideal source voltage. Hence, it completely eliminates any dependency on conventional synchronizer algorithms such as phase-locked loop (PLL) and zero-crossing detector (ZCD). Additionally, the proposed STF-based ADALINE algorithm implements the modified Widrow-Hoff (W-H) weight updating algorithm for fast generation of reference current. Both simulation and experimental works are performed to verify design concept and effectiveness of the proposed algorithm. Comparative study with another recently reported algorithm is performed to investigate the performance improvement achieved by SAPF while using the proposed algorithm.
Are "Non-functional" Requirements really Non-functional? An Investigation of Non-functional Requirements in Practice

Non-functional requirements (NFRs) are commonly distinguished from functional requirements by differentiating how the system shall do something in contrast to what the system shall do. This distinction is not only prevalent in research, but also influences how requirements are handled in practice. NFRs are usually documented separately from functional requirements, without quantitative measures, and with relatively vague descriptions.As a result, they remain difficult to analyze and test.Several authors argue, however, that many so-called NFRs actually describe behavioral properties and may be treated the same way as functional requirements. In this paper, we empirically investigate this point of view and aim to increase our understanding on the nature of NFRs addressing system properties. We report on the classification of 530 NFRs extracted from 11 industrial requirements specifications and analyze to which extent these NFRs describe system behavior.Our results suggest that most "non-functional" requirements are not non-functional as they describe behavior of a system. Consequently, we argue that many so-called NFRs can be handled similarly to functional requirements.
Behavioral model of charge pumps with VHDL

A behavioral model of an N-stages charge pump is here presented. The description language used to develop the model is the VHDL thus permitting simulations of both digital and analog systems, such as nonvolatile memories. Moreover, the presented model allows a huge reduction in the simulation time also maintaining a good agreement with transistor level simulations. For a useful comparison, a three stages charge pump was simulated with Symphony EDA Sonata (event-driven VHDL simulator) and Spectre (transistor level simulator). The obtained result confirmed the validity of the developed description in terms of accuracy and low required simulation's time.