Miracle-dz/UniFAR-FTUs huggingface dataset:
A robust semi-automatic approach for ROI segmentation in 3D CT images

In CT-based clinical applications, segmentation of regions of interest (ROIs) is a preliminary but vital step. The task is, however, quite challenging, especially for 3D objects, because suspicious ROIs are usually soft-tissue structures, which include a various organs and anatomical objects while sharing a small intensity dynamic range in CT images. Furthermore, the ROIs usually vary significantly in size, shape, and boundary conditions. Among considerable efforts contributed to addressing the problem, live wire, also known as intelligent scissors, has been recognized as an efficient and robust tool for dealing with a wide range of 2D ROIs. Such an approach provides full user control during the process while minimizing human interaction to optimally counterbalance automatic and manual approaches. In this work, we improve our previous live-wire-based segmentation of 3D objects and the experiment results show its efficiency and robustness.
AN INVESTIGATION INTO THE LINKAGES BETWEEN EURO AND STERLING SWAP SPREADS

This paper examines the causal relationship between euro and sterling swap spreads during the period January, 1999 to March, 2003. The absence of any correlation between changes in the two swap spreads would indicate that credit risk factors are country-specific. But euro swap spreads showed some correlation with the interest rate differentials between the two markets. Both spreads follow a GARCH process but sterling swap spreads reacted more intensely to market movements and were more volatile than their euro counterparts. There was evidence of mild volatility transmission from the sterling swap spreads to the euro swap spreads but the causality was one sided.
Modelling causal reasoning

Although human causal reasoning is widely acknowledged as an object of scientific enquiry, there is little consensus on an appropriate measure of progress. Up-to-date evidence of the standard method of research in the field shows that this method has been rejected at the birth of modern science. We describe an instance of the standard scientific method for modelling causal reasoning (causal calculators). The method allows for uniform proofs of three relevant computational properties: correctness of the model with respect to the intended model, full abstraction of the model (function) with respect to the equivalence of reasoning scenarios (input), and formal relations of equivalence and subsumption between models. The method extends and exploits the systematic paradigm [Handbook of Logic in Artificial Intelligence and Logic Programming, volume IV, p. 439-498, Oxford 1995] to fit with our interpretation of it. Using the described method, we present results for some major models, with an updated summary spanning seventy-two years of research in the field.
Tuberculosis and cigarette smoke exposure: An update of in vitro and in vivo studies

ABSTRACT Tuberculosis (TB) has been declared the first cause of death by an infectious agent. Annually, 10.4 million people suffer active TB. Most infected individuals live in low-income countries, where social and economic conditions enhance the dissemination and progression of the disease. These countries have a high percentage of smokers. Thousands of studies have linked cigarette smoke (CS) with increased risk of many diseases, such as cancer and lung diseases. Numerous in vitro studies have been conducted to evaluate the general and specific toxic effects of CS in lung immune function. Smoke exposure increases the risk of TB development three-fold. However, until now, only few animal studies have been performed to analyze the association between smoke and TB. In the present work, we review in vitro and in vivo studies whose aim was to analyze the molecular basis of TB susceptibility caused by exposure to CS.
Identification Method of Iron-Ore Type in Open Pit Based on Measured Spectra and Random Forest

ABSTRACT:Iron ore is the main mineral resources to support China's national economy, and open-pit mining is the main way. Chemical analysis has its disadvantages in terms of the determination of iron-ore type, such as slow speed and high cost. Therefore this study has put forward a method to determine iron-ore type through field spectrum analysis. First various types of iron-ore samples were collected in Anqian mine of Liaoning Province, China, including 48 magnetite and 84 hematite samples. Then, through the hole drilling and cutting, the circular sheets of 1~2 cm thick are formed. After that the chemical composition, visible/near-infrared spectra of these samples were tested and analyzed. The principal component analysis is used to reduce the data dimension of spectrum, and the random forest algorithm is applied to classify the iron ore type of samples, while the accuracy of classification results is validated. The results show that the random forest method can classify different types of iron ore, and the successful rate is over 95%, which lay the foundation for the determination of the ironore type in open pit based on the portable spectroradiometer or the airborne imaging spectrometer.
Early modifications of host cell gene expression induced by HIV‐1

Objective:Characterization of the effects of infection with HIV-1 on cellular gene expression. Design and methods:Differential RNA display was applied to compare uninfected and HIV-1LAI-infected CEM cells 24 h post-inoculation. Differential bands were selected, cloned and several clones per band were sequenced. RNase protection assay was used to confirm differential display findings in HIV-1LAI-infected CEM cells as well as in another T-cell line (H9) infected with a different strain (HIV-1SF33). Results:Twelve differentially expressed bands, six up- and six downregulated in HIV-infected cells compared with controls, were selected. Four of the six upregulated bands were HIV transcripts. RNase protection assay of the remaining eight bands confirmed differential expression of four genes, including induction of a mariner transposase and moesin as well as suppression of α-nascent polypeptide-associated complex and mitochondrial heat shock protein 75 in HIV-1-infected cell cultures. Furthermore, a significant increase of glioma pathogenesis-related protein was found by RNase protection assay. Conclusions:Based on this initial limited differential display analysis, it was estimated that expression of 3% of the host genes was altered by HIV-1. Amongst the identified gene modifications, the induction of a mariner transposase may alter cellular gene expression itself, whilst the enhanced expression of glioma pathogenesis-related protein suggests a role in the host cell response to viral infection. The increase in moesin may facilitate viral budding and uptake. Furthermore, the suppression of α-nascent polypeptide-associated complex may promote translocation of HIV-1 polypeptides into the endoplasmic reticulum, whereas the downregulation of mitochondrial heat shock protein 75 may contribute to a cytopathic effect on mitochondria and possibly impairs antigen presentation.
How to share secrets simultaneously

Each member of a team consisting of n person has a secret. The k out of n simultaneous threshold secret sharing requires that any group of k members should be able to recover the secret of the other n-k members, while any group of k-1 or less members should have no information on the secret of other team members. We show that when all secrets are independent and have size s then each team member must receive a share of size at least (n-k)s, and we present a scheme which achieves this bound. This result shows a significant saving over n independent applications of the k out of n-1 threshold schemes which assigns shares of size (n-1)s to each team member independently of k.
Zanamivir Susceptibility Monitoring and Characterization of Influenza Virus Clinical Isolates Obtained during Phase II Clinical Efficacy Studies

ABSTRACT Zanamivir is a highly selective neuraminidase (NA) inhibitor with demonstrated clinical efficacy against influenza A and B virus infections. In phase II clinical efficacy trials (NAIB2005 and NAIB2008), virological substudies showed mean reductions in virus shedding after 24 h of treatment of 1.5 to 2.0 log1050% tissue culture infective doses compared to a placebo, with no reemergence of virus after the completion of therapy. Paired isolates (n = 41) obtained before and during therapy with zanamivir demonstrated no shifts in susceptibility to zanamivir when measured by NA assays, although for a few isolates NA activity was too low to evaluate. In plaque reduction assays in MDCK cells, the susceptibility of isolates to zanamivir was extremely variable even at baseline and did not correlate with the speed of resolution of virus shedding. Isolates with apparent limited susceptibility to zanamivir by plaque reduction proved highly susceptible in vivo in the ferret model. Further sequence analysis of paired isolates revealed no changes in the hemagglutinin and NA genes in the majority of isolates. The few changes observed were all natural variants. No amino acid changes that had previously been identified in vitro as being involved with reduced susceptibility to zanamivir were observed. These studies highlighted problems associated with monitoring susceptibility to NA inhibitors in the clinic, in that no reliable cell-based assay is available. At present the NA assay is the best available predictor of susceptibility to NA inhibitors in vivo, as measured in the validated ferret model of infection.
TMPM–ICD9: A Trauma Mortality Prediction Model Based on ICD-9-CM Codes

Objective:To develop and validate a new ICD-9 injury model that uses regression modeling, as opposed to a simple ratio measurement, to estimate empiric injury severities for each of the injuries in the ICD-9-CM lexicon. Background:The American College of Surgeons now requires International Classification of diseases ninth Edition (ICD-9-CM) codes for injury coding in the National Trauma Databank. International Classification of diseases ninth Edition Injury Severity Score (ICISS) is the best-known risk-adjustment model when injuries are recorded using ICD-9-CM coding, and would likely be used to risk-adjust outcome measures for hospital trauma report cards. ICISS, however, has been criticized for its poor calibration. Methods:We developed and validated a new ICD-9 injury model using data on 749,374 patients admitted to 359 hospitals in the National Trauma Databank (version 7.0). Empiric measures of injury severity for each of the trauma ICD-9-CM codes were estimated using a regression-based approach, and then used as the basis for a new Trauma Mortality Prediction Model (TMPM-ICD9). ICISS and the Single-Worst Injury (SWI) model were also re-estimated. The performance of each of these models was compared using the area under the receiver operating characteristic (ROC), the Hosmer-Lemeshow statistic, and the Akaike information criterion statistic. Results:TMPM-ICD9 exhibits significantly better discrimination (ROCTMPM = 0.880 [0.876–0.883]; ROCICISS = 0.850 [0.846–0.855]; ROCSWI = 0.862 [0.858–0.867]) and calibration (HLTMPM = 29.3 [12.1–44.1]; HLICISS = 231 [176–279]; HLSWI = 462 [380–548]) compared with both ICISS and the Single Worst Injury model. All models were improved with the addition of age, gender, and mechanism of injury, but TMPM-ICD9 continued to demonstrate superior model performance. Conclusions:Because TMPM-ICD9 uniformly out-performs ICISS and the SWI model, it should be used in preference to ICISS for risk-adjusting trauma outcomes when injuries are recorded using ICD9-CM codes.
Implant Surfaces and Interface Processes

The past decades and current R&D of biomaterials and medical implants show some general trends. One major trend is an increased degree of functionalization of the material surface, better to meet the demands of the biological host system. While the biomaterials of the past and those in current use are essentially bulk materials (metals, ceramics, polymers) or special compounds (bioglasses), possibly with some additional coating (e.g., hydroxyapatite), the current R&D on surface modifications points toward much more complex and multifunctional surfaces for the future. Such surface modifications can be divided into three classes, one aiming toward an optimized three-dimensional physical micro-architecture of the surface (pore size distributions, "roughness", etc.), the second one focusing on the (bio) chemical properties of surface coatings and impregnations (ion release, multi-layer coatings, coatings with biomolecules, controlled drug release, etc.), and the third one dealing with the viscoelastic properties (or more generally the micromechanical properties) of material surfaces. These properties are expected to affect the interfacial processes cooperatively, i.e., there are likely synergistic effects between and among them: The surface is "recognized" by the biological system through the combined chemical and topographic pattern of the surface, and the viscoelastic properties. In this presentation, the development indicated above is discussed briefly, and current R&D in this area is illustrated with a number of examples from our own research. The latter include micro- and nanofabrication of surface patterns and topographies by the use of laser machining, photolithographic techniques, and electron beam and colloidal lithographies to produce controlled structures on implant surfaces in the size range 10 nm to 100 μm. Examples of biochemical modifications include mono- or lipid membranes and protein coatings on different surfaces. A new method to evaluate, e.g., biomaterial-protein and biomaterial-cell interactions-the Quartz Crystal Microbalance-is described briefly.
Risk factors for moderate‐to‐severe acute graft‐vs.‐host disease after allogeneic stem cell transplantation in children

Abstract: Severe acute graft‐vs.‐host disease (aGVHD) remains a major cause of transplantation‐related mortality. However, because of a graft‐vs.‐leukaemia effect, a mild (grade I) aGVHD is desirable. As risk factors predisposing for aGVHD are not necessarily the same in children and adults, we have performed a retrospective analysis of risk factors (RFs) for grade II–IV aGVHD in 258 paediatric patients undergoing allogeneic stem cell transplantation at our centre. Thirty‐two potential RFs were assessed with univariate analysis in logistic regression. Eleven factors were selected for further evaluation in stepwise elimination multivariate analysis. Three independent RFs were found: (1) donor other than human lekocyte antigen (HLA)‐identical sibling [odds ratio (OR) 6.1, p < 0.001); (2) single drug [cyclosporine A (CsA) or methotrexate (Mtx)] graft‐vs.‐host disease (GVHD) prophylaxis (OR 7.0, p < 0.001); and (3) ABO disparity of any kind (OR 2.4, p = 0.02). The RFs were additive: moderate‐to‐severe aGVHD was seen in none of the patients without any RFs; in 16% with one RF; in 32% with two RFs and in 67% with all three RFs present. Single drug GVHD prophylaxis (CsA or Mtx), any kind of ABO mismatch, and non‐sibling donors are RFs for grade II–IV acute GVHD in paediatric SCT. We encourage the use of combination GVHD prophylaxis in children. ABO mismatch should be considered when choosing between otherwise equally suitable donors.
Multi-channel LED driver with CLL resonant converter

This paper proposes a two-stage multi-channel LED driver, which contains a buck converter as the first stage and a multi-channel constant current (MC3) CLL resonant converter as the second stage. The forward current of one specific LED string is sensed for feedback control to regulate the bus voltage, which is also the input voltage of the MC3 CLL resonant converter. In contrast, the MC3 CLL is unregulated and always working around the resonant frequency point to achieve best efficiency. Therefore, this two-stage LED driver could achieve high efficiency within a wide load range. Furthermore, for the MC3 CLL resonant converter, the magnetizing inductance of the transformer can be as large as possible, so the current sharing among the transformer modules is very good, even under unbalanced load conditions. Meanwhile, the currents of two LED strings driven by the same transformer is balanced via a DC blocking capacitor. As a result, this two-stage LED driver can achieve good current balance even with a large load variation. Finally, the merits of this two-stage LED driver are verified by experiment.
Feasibility and benefits of computerized cognitive exercise to adults with chronic moderate-to-severe cognitive impairments following an acquired brain injury: A pilot study

Abstract Primary objective: The purpose of this pilot study was to explore feasibility and effects of participation in a computerized cognitive fitness exercise program by a group of adults with chronic moderate-to-severe cognitive impairments following an acquired brain injury (ABI). Research design: This study used a mixed methods design with a convenience sample of individuals forming two groups (+/– exercise). Methods and procedures: Following neurocognitive and satisfaction with life pre-testing of 14 participants, seven were enrolled in a 5-month, 5-days a week computerized cognitive exercise program. Post-testing of all participants and semi-structured interviews of exercise group participants were completed. Main outcomes and results: It was feasible for adults with chronic moderate-to-severe cognitive impairments post-ABI to participate in a computerized cognitive exercise program with ongoing external cues to initiate exercise sessions and/or to complete them as needed. Significant exercise group improvements were made on memory and verbal fluency post-tests and life satisfaction. The majority of exercise group participants reported some degree of positive impact on cognitive abilities and some on everyday functioning from program participation. Conclusions: Adults with chronic moderate-to-severe cognitive impairments following an ABI may benefit from participation in computerized cognitive exercise programs. Further study is warranted.
Electrophysiologic Evidence for Increased Endogenous GABAergic but Not Glycinergic Inhibitory Tone in the Rat Spinal Nerve Ligation Model of Neuropathy

BackgroundChanges in the inhibitory activity mediated by &ggr;-aminobutyric acid (GABA) and glycine, acting at spinal GABAA receptors and strychnine-sensitive glycine receptors, are of interest in the development of neuropathic pain. There is anatomic evidence for changes in these transmitter systems after nerve injuries, and blocking either GABAA or glycine receptors has been shown to produce allodynia-like behavior in awake normal animals. MethodsIn this study, the possible changes in GABAergic and glycinergic inhibitory activity in the spinal nerve ligation model of neuropathic pain were studied by comparing the effects of the GABAA-receptor antagonist bicuculline and the glycine-receptor antagonist strychnine in neuropathic rats to their effects in sham-operated and nonoperated control rats. ResultsBicuculline produced a dose-related facilitation of the A&dgr;-fiber–evoked activity in all study groups and increased C-fiber–mediated activity in the spinal nerve ligation group but not in either of the control groups. There were no differences in the effect of bicuculline on low threshold responses between the study groups. The glycine receptor antagonist strychnine did not have a statistically significant effect on any of the parameters studied in any of the control groups. ConclusionsThese results support the idea of an increased GABAergic inhibitory tone in the spinal cord of neuropathic rats, possibly as compensation for increased excitability after nerve injury.
Allosteric control of antibody-prion recognition through oxidation of a disulfide bond between the CH and CL chains

Molecular details of the recognition of disordered antigens by their cognate antibodies have not been studied as extensively as folded protein antigens and much is still unknown. To follow the conformational changes in the antibody and cross-talk between its subunits and with antigens, we performed molecular dynamics (MD) simulations of the complex of Fab and prion-associated peptide in the apo and bound forms. We observed that the inter-chain disulfide bond in constant domains restrains the conformational changes of Fab, especially the loops in the CH1 domain, resulting in inhibition of the cross-talk between Fab subdomains that thereby may prevent prion peptide binding. We further identified several negative and positive correlations of motions between the peptide and Fab constant domains, which suggested structural cross-talks between the constant domains and the antigen. The cross-talk was influenced by the inter-chain disulfide bond, which reduced the number of paths between them. Importantly, network analysis of the complex and its bound water molecules observed that those water molecules form an integral part of the Fab/peptide complex network and potential allosteric pathways. On-going work focuses on developing strategies aimed to incorporate these new network communications—including the associated water molecules—toward the grand challenge of antibody design.
Logistics of Referral, Diagnostic Assessment and Treatment of Patients with Breast Symptoms and Signs

Background and Aims: The logistics of diagnosis and treatment in a hospital with slightly above 400 new cases of breast cancer per year is analysed. Materials and Methods: The patient flow from referral, through the diagnostic procedures and through surgical treatment is described. Results and Conclusions: The basic principle of the diagnostic assessment is the triple diagnostic procedure including mammography supplemented by ultrasonography, fine needle aspiration cytology and clinical examination. The radiologist and pathologist are working together in the breast diagnostic centre and are thus able to give a “single visit diagnosis” in most cases. The surgeon sees the patient either the same day or the next. A “consensus meeting” held each week with representatives for all specialities present has an important function in quality assurance and education. If one or more of the triple diagnostic components reach conclusion level “suspicious lesion”, surgery is indicated. In hospital management is based on day surgery for all biopsies, wide excisions with or without sentinel node and some ablatio simplex mammae. For wide excision and ablation with complete axillary node clearance, the patients are transferred from the day surgery unit to a patient hotel after 3–4 hours of observation and stay till the drain can be removed. Only in rare case of high cardiopulmonary risk, beds in ordinary wards are used. This is a highly cost efficient logistic saving the hospital approximately 400 000 EUR a year compared to ordinary in hospital treatment.
Secondary voltage control based on estimation of reactive power deficit

In this paper an approach to perform secondary voltage control in the transmission network is proposed. The approach is based on the nonlinear programming and has two main features in comparison with the already proposed approaches. The first feature is that the buses where compensation devices are connected are selected as pilot nodes which will be called control buses (CB's). The second feature of the proposed approach is that the control variables in the objective function are the required reactive power variations at CB's. This feature allows formulating the optimization problem which yields the deficit of reactive power independent of the used reactive power sources. The IEEE 39-bus test system is used as case study to illustrate the effectiveness of the proposed approach in centralized and decentralized control.