Miracle-dz/UniFAR-FTUs huggingface dataset:
One-step Compact Skeletonization

Computing a skeleton for a discretized boundary typically produces a noisy output, with a skeletal branch produced for each boundary pixel. A simplification step often follows to reduce these noisy branches. As a result, generating a clean skeleton is usually a 2-step process. In this article, we propose a skeletonization process that produces a clean skeleton in the first step, avoiding the creation of branches due to noise. The resulting skeleton compares favorably with the most common pruning methods on a large database of shapes. Our process also reduces execution time and requires only one parameter, e, that designates the desired boundary precision in the Hausdorff distance.
The cellularity of offspring's adipose tissue is programmed by maternal nutritional manipulations

Epidemiological studies initially demonstrated that maternal undernutrition leads to low birth weight with increased risk of adult-onset obesity. Maternal obesity and diabetes associated with high birth weight, excessive nutrition in neonates, and rapid catch-up growth also predispose offspring to fat accumulation. As stated by the Developmental Origin of Health and Disease concept, nutrient supply perturbations in the fetus or neonate result in long-term programming of individual body weight set-point. Adipose tissue is a key fuel storage unit mainly involved in the maintenance of energy homeostasis. Studies in numerous animal models have demonstrated that the adipose tissue is the focus of developmental programming events in a gender- and depot-specific manner. This review summarizes the impact of maternal nutritional manipulations on cellularity (i.e., cell number, size, and type) of adipose tissue in programmed offspring. In rodents, adipose tissue development is particularly active during the perinatal period, especially during the last week of gestation and during early postnatal life. In contrast to rodents, this process essentially takes place before birth in bigger mammals. Despite these different developmental time windows, altricial and precocial species share several mechanisms of adipose tissue programming. Maternal nutritional manipulations result in increased adipogenesis and modified fat distribution and composition. Inflammation changes such as infiltration of macrophages and increased inflammatory markers are also observed. Overall, it may predispose offspring to fat accumulation and obesity. Inappropriate hormone levels, modified tissue sensitivity, and epigenetic mechanisms are key factors involved in the programming of adipose tissue's cellularity during the perinatal period.
Towards Point-based Facial Movement Simulation

Lifelike animated characters are hard to create and involve extensive manual effort during generation of the geometry, adding a rig to the model, and creating the actual movements of limbs and tissue. Blendshapes is the leading technique regarding facial animations. This very simple mathematical model can be computed efﬁciently, thus it is suited for real time visualization. On the other hand it is hard to control, requires a skilled animator, and is still very error prone. Point-based simulation techniques became increasingly popular in recent years for animation of elastic surfaces, but have barely been used for facial animation. We argue, that this kind of technique is much more suited for simulation and animation of the non-rigid deformations of facial tissue. We build our proposal on a meshless ﬁnite elements technique, which has already been used successfully for the elastic simulation of surface models in real time and describe extensions to the approach so it can be applied for facial animation.
A clinical return-to-work rule for patients with back pain

Background: Tools for early identification of workers with back pain who are at high risk of adverse occupational outcome would help concentrate clinical attention on the patients who need it most, while helping reduce unnecessary interventions (and costs) among the others. This study was conducted to develop and validate clinical rules to predict the 2-year work disability status of people consulting for nonspecific back pain in primary care settings. Methods: This was a 2-year prospective cohort study conducted in 7 primary care settings in the Quebec City area. The study enrolled 1007 workers (participation, 68.4% of potential participants expected to be eligible) aged 18–64 years who consulted for nonspecific back pain associated with at least 1 day's absence from work. The majority (86%) completed 5 telephone interviews documenting a large array of variables. Clinical information was abstracted from the medical files. The outcome measure was “return to work in good health” at 2 years, a variable that combined patients' occupational status, functional limitations and recurrences of work absence. Predictive models of 2-year outcome were developed with a recursive partitioning approach on a 40% random sample of our study subjects, then validated on the rest. Results: The best predictive model included 7 baseline variables (patient's recovery expectations, radiating pain, previous back surgery, pain intensity, frequent change of position because of back pain, irritability and bad temper, and difficulty sleeping) and was particularly efficient at identifying patients with no adverse occupational outcome (negative predictive value 78%– 94%). Interpretation: A clinical prediction rule accurately identified a large proportion of workers with back pain consulting in a primary care setting who were at a low risk of an adverse occupational outcome.
Development of a Population Simulation Model for HIV Monotherapy Virological Outcomes Using Lamivudine

Current highly active antiretroviral therapy (HAART) requires the use of combinations of three drugs to minimize the early emergence of drug-resistant HIV strains. Therefore, long-term monotherapy data with new agents are unavailable. However, the development of computer models for Monte-Carlotype simulations of antiviral monotherapy, which incorporate HIV infection dynamic distributions from previously studied populations, together with pharmacokinetics and pharmacodynamic parameters of the new agent, could serve as an important tool. The nucleoside lamivudine (3TC) was used as a representative drug to standardize an improved pharmacodynamic and infection dynamic monotherapy model. 3TC plasma concentration versus time profiles was used to drive the cellular accumulation of 3TC-triphosphate (TP) in primary human lymphocytes in the model, over a 16 week period. The fraction of HIV reverse transcription inhibited was calculated using the median inhibitory concentration and intracellular 3TC-TP levels. Virus loads and activated CD4+T-cell counts were generated for 2,200 theoretical individuals and compared with the outcomes of an actual 3TC monotherapy trial at the same dose. Pharmacokinetic variance alone did not account for the interindividual HIV-load variability. However, selection of appropriate distributions of the various pharmacokinetic and infection dynamics parameters produced a similar range of virus load reductions to actual observations. Therefore, once parameter and variance distributions are standardized, this modelling approach could be helpful in planning clinical trials and predicting the antiviral contribution of each agent in a HAART modality.
A speed of sound aberration correction algorithm for curvilinear ultrasound transducers in ultrasound-based image-guided radiotherapy

Conventional ultrasound (US) devices use the time of flight (TOF) of reflected US pulses to calculate distances inside the scanned tissues and thus create images. The speed of sound (SOS) is assumed to be constant in all human soft tissues at a generally accepted average value of 1540 m s−1. This assumption is a source of systematic errors up to several millimeters and of image distortion in quantitative US imaging. In this work, an extension of a method recently published by Fontanarosa et al (2011 Med. Phys. 38 2665–73) is presented: the aim is to correct SOS aberrations in three-dimensional (3D) US images in those cases where a spatially co-registered computerized tomography (CT) scan is also available; the algorithm is then applicable to a more general case where the lines of view (LOV) of the US device are not necessarily parallel and coplanar, thus allowing correction also for US transducers other than linear. The algorithm was applied on a multi-modality pelvic US phantom, scanned through three different liquid layers on top of the phantom with different SOS values; the results show that the correction restores a better match between the CT and the US images, reducing the differences to sub-millimeter agreement. Fifteen clinical cases of prostate cancer patients were also investigated: the SOS corrections of prostate centroids were on average +3.1 mm (max + 4.9 mm–min + 1.3 mm). This is in excellent agreement with reports in the literature on differences between measured prostate positions by US and other techniques, where often the discrepancy was attributed to other causes.
Autopsy-Controlled Prospective Evaluation of Serial Screening for Circulating Galactomannan by a Sandwich Enzyme-Linked Immunosorbent Assay for Hematological Patients at Risk for Invasive Aspergillosis

ABSTRACT Efforts to improve the diagnosis of invasive aspergillosis (IA) have been directed towards the detection of fungal antigens, including galactomannan (GM). However, previous evaluations of GM detection have been hampered by a lack of proven cases of IA and by a nonserial study design. This prospective study assessed the diagnostic value of serial screening for circulating GM by using a recently developed sandwich enzyme-linked immunosorbent assay (ELISA) for prolonged-neutropenic and/or steroid-treated patients with hematological disorders. Serum GM levels were monitored twice weekly for 186 consecutive patients at increased risk for IA. The patients were stratified according to the likelihood of IA (proven, probable, possible, and no evidence of IA) by using stringent criteria. Proven IA was defined by characteristic histopathological findings together with a positive culture forAspergillus species. Autopsy and culture from autopsy specimens was used to verify both positive and negative test results. A total of 2,172 serum samples were tested from 243 episodes (mean, 9 samples/episode). Based on the analysis of 71 patients with confirmed disease status (culture and histology), the sensitivity and specificity of serial GM monitoring were 92.6 and 95.4%, respectively. The positive predictive value was almost 93%, the negative predictive value was 95%, and the efficacy was 94%. False-positive reactions occurred at a rate of nearly 8%, although this figure might have been overestimated. Less than 1% of all tested sera were considered inconclusive. In more than half of the cases, antigenemia was detected before clinical suspicion of IA (median, 6 days before). Serial determination of serum GM by the sandwich ELISA technique is a sensitive tool for the diagnosis of IA in hematological patients at risk. This approach may substantially influence clinical management with regard to preemptive and empirical antifungal therapy.
Periplasmic copper–zinc superoxide dismutase protects Haemophilus ducreyi from exogenous superoxide

Haemophilus ducreyi causes chancroid, a sexually transmitted genital ulcer disease implicated in increased heterosexual transmission of HIV. As part of an effort to identify H. ducreyi gene products involved in virulence and pathogenesis, we created random TnphoA insertion mutations in an H. ducreyi 35 000 library cloned in Escherichia coli. Inserts encoding exported or secreted PhoA fusion proteins were characterized by DNA sequencing. One such clone encoded a Cu–Zn superoxide dismutase (SOD) enzyme. The Cu–Zn SOD was periplasmic in H. ducreyi and accounted for most of the detectable SOD activity in whole‐cell lysates of H. ducreyi grown in vitro. To investigate the function of the Cu–Zn SOD, we created a Cu–Zn SOD‐deficient H. ducreyi strain by inserting a cat cassette into the sodC gene. The wild‐type and Cu–Zn SOD null mutant strains were equally resistant to excess cytoplasmic superoxide induced by paraquat, demonstrating that the Cu–Zn SOD did not function in the detoxification of cytoplasmic superoxide. However, the Cu–Zn SOD null strain was significantly more susceptible to killing by extracellular superoxide than the wild type. This result suggests that the H. ducreyi Cu–Zn SOD may play a role in bacterial defence against oxidative killing by host immune cells during infection.
A Preliminary Analysis of Methods for Curvature Estimation on Surfaces With Local Reliefs

Curvature estimation is very popular in geometry processing for the analysis of local surface variations. Despite the large number of methods, no quantitative nor qualitative studies have been conducted for a comparative analysis of the different algorithms on surfaces with small geometric variations, such as chiselled or relief surfaces. In this work we compare eight curvature estimation methods that are commonly adopted by the computer graphics community on a number of triangle meshes derived from scans of surfaces with local reliefs
Middle‐down hybrid chromatography/tandem mass spectrometry workflow for characterization of combinatorial post‐translational modifications in histones

We present an integrated middle‐down proteomics platform for sensitive mapping and quantification of coexisting PTMs in large polypeptides (5–7 kDa). We combined an RP trap column with subsequent weak cation exchange–hydrophilic interaction LC interfaced directly to high mass accuracy ESI MS/MS using electron transfer dissociation. This enabled automated and efficient separation and sequencing of hypermodified histone N‐terminal tails for unambiguous localization of combinatorial PTMs. We present Histone Coder and IsoScale software to extract, filter, and analyze MS/MS data, including quantification of cofragmenting isobaric polypeptide species. We characterized histone tails derived from murine embryonic stem cells knockout in suppressor of zeste12 (Suz12−/−) and quantified 256 combinatorial histone marks in histones H3, H4, and H2A. Furthermore, a total of 713 different combinatorial histone marks were identified in purified histone H3. We measured a seven‐fold reduction of H3K27me2/me3 (where me2 and me3 are dimethylation and trimethylation, respectively) in Suz12−/− cells and detected significant changes of the relative abundance of 16 other single PTMs of histone H3 and other combinatorial marks. We conclude that the inactivation of Suz12 is associated with changes in the abundance of not only H3K27 methylation but also multiple other PTMs in histone H3 tails.
Zearalenone (ZEN) metabolism and residue concentrations in physiological specimens of dairy cows exposed long-term to ZEN-contaminated diets differing in concentrate feed proportions

A long-term feeding experiment with dairy cows was performed to investigate the effects of feeding a Fusarium toxin contaminated (FUS) and a background-contaminated control (CON) ration with a mean concentrate feed proportion of 50% during the first 11 weeks after parturition (Groups FUS-50, CON-50, Period 1), and with concentrate feed proportions of 30% or 60% during the remaining 17 weeks (Groups CON-30, CON-60, FUS-30 and FUS-60, Period 2), on zearalenone (ZEN) residue levels in blood serum, milk, urine and bile. ZEN, α-zearalenol (α-ZEL) and β-zearalenol (β-ZEL), zearalanone (ZAL), α-zearalanol (α-ZAL) and β-zearalanol (β-ZAL) were determined by HPLC with fluorescence detection. The ZEN concentrations of the rations fed to Groups CON-50, FUS-50 (Period 1), CON-30, CON-60, FUS-30 and FUS-60 (Period 2) amounted to 53.1, 112.7, 35.0, 24.4, 73.8 and 72.5 µg/kg dry matter, respectively. The concentrations of ZEN, α-ZEL, β-ZEL, ZAN, α-ZAL and β-ZAL in serum, urine and milk were lower than 1, 1, 4, 100, 50 and 200 ng/g, respectively, while ZEN, α-ZEL and β-ZEL were detected in bile. Their levels changed with oral ZEN exposure in the course of the experiment and in a similar direction with concentrate feed proportion (Period 2 only). Thus the proportions of the individual β-ZEL, α-ZEL and ZEN concentrations of their sum varied only in narrow ranges of 68–76%, 6–13% and 12–20%, respectively. Interestingly, the bile concentrations of β-ZEL, α-ZEL and ZEN of Groups CON-60 and FUS-60 amounted to only approximately 50%, 45% and 62%, respectively, of those of Groups CON-30 and FUS-30 despite a similar or even lower ZEN exposure. The results indicate that conversion of ZEN to its detectable metabolites was not changed by different dietary concentrate feed proportions while their absolute levels were decreased. These findings might suggest concentrate feed proportion-dependent and rumen fermentation-mediated alterations in ZEN/metabolite degradation, and/or liver associated alterations in bile formation and turnover.
Reassessing the role for lamivudine in chronic hepatitis B infection: a four-year cohort analysis.

UNLABELLED BACKGROUND⁄ OBJECTIVES Lamivudine is readily available and inexpensive. Guidelines recommend other antiviral medications because they achieve superior virological suppression with less resistance. These data are based on clinical trial populations and may not be representative of typical hepatitis B virus (HBV) populations. The authors assessed lamivudine in maintaining long-term viral suppression in an adherent, frequently monitored, noninvestigational HBV-infected population. METHODS All HBV patients (n=369) between 2000 and 2010 were evaluated in a retrospective, single-centre study. Virological response was defined by complete suppression of HBV DNA (<400 copies⁄mL) and was assessed at six to 12 month intervals over four years. Enzymatic and serological outcomes, as well as treatment failures were assessed. RESULTS Forty-seven patients (36 men; mean age 44 years, mean alanine aminotransferase level 123 U⁄L; METAVIR stage 3⁄4 [n=21], treatment naive [n=41]) received lamivudine 100 mg to 300 mg daily. The mean pretreatment viremia was 5.19 log10 copies⁄mL, and was above the limit of detection (>6.91 log10 copies⁄mL) in 11 patients (23%). The mean (± SD) dosing duration was 32±22 months. Virological suppression was achieved in 45 (96%) patients. Mean viremia declined to 3.06 log10 copies⁄mL (n=27) and 2.68 log10 copies⁄mL (n=18) at 12 and 48 months, respectively, with 78% and 88% with undetectable viremia at these time points, respectively. The mean alanine aminotransferase level declined to 31 U⁄L and 36 U⁄L at 12 and 48 months, respectively. Seven of 13 (54%) hepatitis B e antigen-positive patients seroconverted. The treatment failure rate was 11%. CONCLUSIONS In a selected group of HBV patients, successful long-term viremia suppression was achieved with low treatment failure rates. With strict dosing adherence and monitoring for virological breakthrough, sustained virological suppression can be reliably achieved with lamivudine in carefully selected patients.
Biphasic spiral computed tomography for detection of hepatocellular carcinoma before resection or orthotopic liver transplantation.

RATIONALE AND OBJECTIVES The authors correlate computed tomography (CT) findings in biphasic spiral technique with histopathology in patients with hepatocellular carcinoma (HCC) who had undergone liver resection (LR) or orthotopic liver transplantation (OLT). METHODS Preoperative biphasic spiral CT findings in 33 consecutive patients (23 men, 10 women, aged 43-74 years; LR group: n = 17; OLT group; n = 16) with liver cirrhosis and HCC were reviewed retrospectively by consensus of two radiologists and correlated with pathology from liver specimens. RESULTS Of the 16 patients in the OLT group with 1 to 5 confirmed HCC lesions (total lesions: 29; mean lesion diameter: 2 cm; range: 0.6-5.0 cm), CT before OLT depicted 22 lesions in 15 patients (sensitivity for lesions with a diameter of 0.5-1.0 cm, 20%; for lesions 1.1-2.0 cm, 82%; and for lesions 2.1-3.0 cm and > 3.0 cm, 86% and 100%, respectively). Among the 17 patients in the LR group (total lesions: 21; mean lesion diameter: 5.4 cm; range: 1.0-11.0 cm), CT detected 18 lesions. Lesion-by-lesion sensitivity, as correlated with pathology, was calculated at 76% and 86% in the OLT and LR groups, respectively (overall sensitivity, 80%). The diameter of CT detected lesions, compared with liver specimens, corresponded in 90% of lesions (maximum deviation, 15%). Characteristic CT findings of HCC included unenhanced hypoattenuating focal liver lesions (32 lesions), with hyperattenuation (38 lesions) in the arterial phase of contrast material administration. CONCLUSIONS Biphasic spiral CT for preoperative HCC detection correlated with pathology in 80%, thus proving this technique to represent a sensitive imaging modality for pretherapeutic evaluation of HCC.
A review of the efficacy of dexamethasone in the prevention of postoperative nausea and vomiting.

AIMS OF THE REVIEW To consider the efficacy of dexamethasone in preventing postoperative nausea and vomiting following general anaesthesia and a range of surgical procedures, compared with a placebo of sodium chloride (normal saline). To inform nurses' pharmacological knowledge of the effects of this medication during peri-operative care. BACKGROUND Dexamethasone was serendipitously discovered to have an effect on reducing postoperative nausea and vomiting for patients receiving various chemotherapeutic regimes. Experience suggests many nurses remain unaware of the anti-emetic effect of this medication. METHODS Multiple databases were searched and selected articles were restricted to experiments published within the past 10 years. Participants of each study had received dexamethasone or sodium chloride (not administered in combination with any other anti-emetics) preoperatively, undergone general anaesthesia and received a common surgical procedure. Thirteen research articles met these criteria and were reviewed. RESULTS The surgical procedures represented have shown high incidences of postoperative nausea and vomiting associated with them. Importantly, 12 of the 13 trials reported significant reductions suggesting dexamethasone has a significant preventative effect in reducing the incidence of postoperative nausea and vomiting when given during induction. However, as a preventative of postoperative nausea alone, dexamethasone does not appear to have a significant effect. CONCLUSIONS The findings clearly support the notion that dexamethasone does have anti-emetic properties. Research examining dexamethasone in combination with other drugs as a cocktail of anti-emetics is welcomed. Future research into the usefulness of dexamethasone given beyond the induction period as an anti-emetic to inform postoperative protocols of care is needed. RELEVANCE TO CLINICAL PRACTICE Nurses in the peri-operative arena can administer this medication, when ordered, with the knowledge based on research evidence as to why it has been included in preoperative protocols. However, dexamethasone has been noted in postanaesthesia recovery care units as a clinical pathway option for the management of postoperative nausea and vomiting and no retrieved articles discuss this option.