Miracle-dz/UniFAR-FTUs huggingface dataset:
A hepatic stellate cell gene expression signature associated with outcomes in hepatitis C cirrhosis and hepatocellular carcinoma after curative resection

Objective We used an informatics approach to identify and validate genes whose expression is unique to hepatic stellate cells and assessed the prognostic capability of their expression in cirrhosis. Design We defined a hepatic stellate cell gene signature by comparing stellate, immune and hepatic transcriptome profiles. We then created a prognostic index using a combination of hepatic stellate cell signature expression and clinical variables. This signature was derived in a retrospective–prospective cohort of hepatitis C-related early-stage cirrhosis (prognostic index derivation set) and validated in an independent retrospective cohort of patients with postresection hepatocellular carcinoma (HCC). We then examined the association between hepatic stellate cell signature expression and decompensation, HCC development, progression of Child–Pugh class and survival. Results The 122-gene hepatic stellate cell signature consists of genes encoding extracellular matrix proteins and developmental factors and correlates with the extent of fibrosis in human, mouse and rat datasets. Importantly, association of clinical prognostic variables with overall survival was improved by adding the signature; we used these results to define a prognostic index in the derivation set. In the validation set, the same prognostic index was associated with overall survival. The prognostic index was associated with decompensation, HCC and progression of Child–Pugh class in the derivation set, and HCC recurrence in the validation set. Conclusions This work highlights the unique transcriptional niche of stellate cells, and identifies potential stellate cell targets for tracking, targeting and isolation. Hepatic stellate cell signature expression may identify patients with HCV cirrhosis or postresection HCC with poor prognosis.
CARDIAC REHABILITATION

This chapter looks at the role of cardiac rehabilitation for those at risk of cardiac disease or who have sustained a cardiac event. Cardiac rehabilitation has been a priority area for a long time in the National Service Framework for Coronary Heart Disease, NHS Improvement Plan, and now features in the NHS Long Term Plan. The introduction of certification for cardiovascular prevention and rehabilitation programmes (CPRP) has meant that their quality can be measured. The introduction of more technology-based interventions has opened up the opportunity for more people to participate, particularly for individuals who could not, or did not want to attend a traditional CPRP.
Temperature-constrained fixed-outline floorplanning for die-stacking system-in-package design

In this paper, we study a floorplanning problem for die-stacking System-in-Package (SiP) design in which the wire bonding method is used to connect signals between different dies. We present an approach which sequentially determines a floorplan for each die such that the generated floorplan has minimal on-chip wirelength and satisfies given fixed-outline and temperature constraints. The experimental results indicate that our approach has 100% successful rate in producing a feasible floorplan for each test case.
FunSAV: Predicting the Functional Effect of Single Amino Acid Variants Using a Two-Stage Random Forest Model

Single amino acid variants (SAVs) are the most abundant form of known genetic variations associated with human disease. Successful prediction of the functional impact of SAVs from sequences can thus lead to an improved understanding of the underlying mechanisms of why a SAV may be associated with certain disease. In this work, we constructed a high-quality structural dataset that contained 679 high-quality protein structures with 2,048 SAVs by collecting the human genetic variant data from multiple resources and dividing them into two categories, i.e., disease-associated and neutral variants. We built a two-stage random forest (RF) model, termed as FunSAV, to predict the functional effect of SAVs by combining sequence, structure and residue-contact network features with other additional features that were not explored in previous studies. Importantly, a two-step feature selection procedure was proposed to select the most important and informative features that contribute to the prediction of disease association of SAVs. In cross-validation experiments on the benchmark dataset, FunSAV achieved a good prediction performance with the area under the curve (AUC) of 0.882, which is competitive with and in some cases better than other existing tools including SIFT, SNAP, Polyphen2, PANTHER, nsSNPAnalyzer and PhD-SNP. The sourcecodes of FunSAV and the datasets can be downloaded at http://sunflower.kuicr. kyoto-u.ac. jp/sjn/FunSAV.
Helminths of guineafowls in Limpopo Province, South Africa.

Between July 2005 and November 2006 the gastro-intestinal helminths of 15 Helmeted guineafowls and a single Crested guineafowl from Musina, Limpopo Province were examined, and in July and August 2005 helminths were collected from five Helmeted guineafowls from Mokopane in the same province. The acanthocephalan Mediorhynchus gallinarum, the cestodes Abuladzugnia gutterae, Davainea nana, Hymenolepis cantaniana, Numidella numida, Octopetalum numida, Ortleppolepis multiuncinata, Porogynia paronai, Raillietina angusta, Raillietina pintneri, Raillietina steinhardti and Raillietina sp. and the nematodes Ascaridia numidae, Cyrnea parroti, Gongylonema congolense, Hadjelia truncata, Sicarius caudatus, Subulura dentigera, Subulura suctoria, Subulura sp. , Tetrameres numida and an unidentified subulurid were recovered. A single trematode species, Dicrocoelium macrostomum, was present in the liver. Mediorhynchus gallinarum, A. gutterae, O. multiuncinata, H. truncata and S. caudatus are recorded for the first time from Helmeted guineafowls, as well as from South Africa. South Africa is a new geographic record for D. macrostomum, G. congolense and D. nana. Subulura suctoria, G. congolense and H. truncata from the Crested guineafowl constitute new host-parasite associations.
Automated MRI segmentation for individualized modeling of current flow in the human head

Objective. High-definition transcranial direct current stimulation (HD-tDCS) and high-density electroencephalography require accurate models of current flow for precise targeting and current source reconstruction. At a minimum, such modeling must capture the idiosyncratic anatomy of the brain, cerebrospinal fluid (CSF) and skull for each individual subject. Currently, the process to build such high-resolution individualized models from structural magnetic resonance images requires labor-intensive manual segmentation, even when utilizing available automated segmentation tools. Also, accurate placement of many high-density electrodes on an individual scalp is a tedious procedure. The goal was to develop fully automated techniques to reduce the manual effort in such a modeling process. Approach. A fully automated segmentation technique based on Statical Parametric Mapping 8, including an improved tissue probability map and an automated correction routine for segmentation errors, was developed, along with an automated electrode placement tool for high-density arrays. The performance of these automated routines was evaluated against results from manual segmentation on four healthy subjects and seven stroke patients. The criteria include segmentation accuracy, the difference of current flow distributions in resulting HD-tDCS models and the optimized current flow intensities on cortical targets.Main results. The segmentation tool can segment out not just the brain but also provide accurate results for CSF, skull and other soft tissues with a field of view extending to the neck. Compared to manual results, automated segmentation deviates by only 7% and 18% for normal and stroke subjects, respectively. The predicted electric fields in the brain deviate by 12% and 29% respectively, which is well within the variability observed for various modeling choices. Finally, optimized current flow intensities on cortical targets do not differ significantly.Significance. Fully automated individualized modeling may now be feasible for large-sample EEG research studies and tDCS clinical trials.
Study on aero-acoustic structural interactions in fan-ducted system

Mitigation of sound radiation from subsonic axial fan in the fan-ducted system at low frequencies remains a technical challenge. Traditional dissipative approach such as absorption material often requires sufficiently long attenuation path for desirable noise reduction performance. More advanced passive control technology such as membrane housing which relies on vibro-acoustic coupling mechanism works effectively on the attenuation of the first and second blade passage frequency in case of steady flow. However, the performance of such device which is composed of thin membrane may be affected by unsteady flow field. This study examined the interaction between vortex unsteady motion, a tensioned membrane housing of finite length and axial fan with dipole nature using the matched asymptotic expansion technique and potential theory. A two-dimensional numerical model is established to explore the sound radiation of each components and the performance of the membrane housing for controlling sound radiation from axial fan in the present of vortex inside uniform mean flow. The results show that there is higher chance of sound amplification when a vortex stream is closer to the light membrane under weak mean flow speed. Under the condition of weak mean flow speed, the sound radiation from the membrane is also amplified when the cavity height is shallower. The result is beneficial for the design of the device of membrane housing.
Sevoflurane Reduces Synaptic Glutamate Release in Human Synaptosomes

Volatile anesthetics reduce excitatory synaptic transmission in the mammalian brain. In the present study, the effect of sevoflurane on synaptic glutamate release, free cytosolic Ca2+ ([Ca2+]i), and glutamate uptake was investigated using isolated presynaptic terminals prepared from human cerebral cortex. The tissue was obtained from standard temporal lobe specimens removed because of epilepsy. The glutamate release and [Ca2+]i was measured as the fluorescence of nicotinamide adenine dinucleotide phosphate (NADPH) and fura-2, respectively. The uptake of radiolabeled glutamate was measured in a &bgr;-scintillation counter. Membrane depolarization with 4-aminopyridine for three minutes evoked a Ca2+-dependent glutamate release of 3.4 ± 0.5 nmol/mg. Sevoflurane 2.5 and 4.0% attenuated the evoked release by 45 and 55%, respectively. The evoked increase in [Ca2+]i was not significantly altered by the anesthetic agent. The uptake studies were performed in the high-affinity area, and Km was calculated to 19.3 ± 5.7 × 10−6 M and Vmax to 5.7 ± 1.0 &mgr;mol g−1 min−1. The Km and Vmax values were not significantly altered by sevoflurane 2.5%. These results demonstrate that sevoflurane in the human brain reduces Ca2+-dependent glutamate release. The exact mode of action is still to be resolved.
Improving the Understanding of the Coupled Thermal-Mechanical-Hydrologic Behavior of Consolidating Granular Salt.

This project will improve the understanding of key aspects of the coupled thermal-mechanical-hydrologic response of granular (or crushed) salt used as a seal material for shafts, drifts, and boreholes in mined repositories in salt. Consolidation of granular salt in response to creep closure of excavations in salt is a fundamental element of the long-term waste isolation strategy, and it is critical that the process is sufficiently understood to confidently predict consolidation under all likely conditions (stress, temperature, and moisture regimes). Granular salt consolidation will be investigated through an integrated program of laboratory measurements and observations, and constitutive model development and evaluation. This project focuses on the deformation and corresponding permeability reduction of granular salt as it consolidates to fractional densities greater than 0.90 since this is when the permeability of granular salt is expected to dramatically decrease to a condition comparable to intact salt, that is, it becomes nearly impermeable. Measurements of salt consolidation along with thermal properties and permeability measurements will be conducted under a range of conditions expected for potential mined repositories in salt, including temperatures up to 250 oC. Consolidated samples will be characterized using microscopy to gain insight into the consolidation mechanisms. Data from the consolidation testing and microstructural characterization tasks will be used to evaluate, calibrate, and verify a mathematical model of granular salt behavior that describes the effect of consolidation on mechanical, thermal and hydrologic properties. Specific objectives of the project are: 1. Measure the consolidation (pore volume reduction) and corresponding changes in hydrologic and thermal properties of granular rock at the critical range of conditions expected for nuclear waste repositories. 2. Interpret deformation mechanisms as a function of moisture, temperature and stress conditions from microstructural observations on consolidated samples. 3. Extend an existing constitutive model to include coupled thermal-mechanical-hydrologic behavior of consolidating granular salt for application in simulations of repository performance. The outcome of this study will be an improved understanding of and ability to predict granular salt consolidation as it compacts to high fractional densities and very small permeabilities, and will result in greater confidence in granular salt consolidation as a principal strategy for permanent isolation.
Hibernation does not affect memory retention in bats

Long-term memory can be critically important for animals in a variety of contexts, and yet the extreme reduction in body temperature in hibernating animals alters neurochemistry and may therefore impair brain function. Behavioural studies on memory impairment associated with hibernation have been almost exclusively conducted on ground squirrels (Rodentia) and provide conflicting results, including clear evidence for memory loss. Here, we for the first time tested memory retention after hibernation for a vertebrate outside rodents—bats (Chiroptera). In the light of the high mobility, ecology and long life of bats, we hypothesized that maintenance of consolidated memory through hibernation is under strong natural selection. We trained bats to find food in one out of three maze arms. After training, the pre-hibernation performance of all individuals was at 100 per cent correct decisions. After this pre-test, one group of bats was kept, with two interruptions, at 7°C for two months, while the other group was kept under conditions that prevented them from going into hibernation. The hibernated bats performed at the same high level as before hibernation and as the non-hibernated controls. Our data suggest that bats benefit from an as yet unknown neuroprotective mechanism to prevent memory loss in the cold brain.
Projected Dietary Intake of Zinc, Copper, and Cerium from Consumption of Carrot (Daucus carota) Exposed to Metal Oxide Nanoparticles or Metal Ions

The expanding production and use of engineered nanomaterials (ENMs) have raised concerns about the potential risk of those materials to food safety and human health. In a prior study, the accumulation of Zn, Cu, and Ce from ZnO, CuO, or CeO2, respectively, was examined in carrot (Daucus carota L.) grown in sand culture in comparison to accumulation from exposure to equivalent concentrations of ionic Zn2+, Cu2+, or Ce4+. The fresh weight concentration data for peeled and unpeeled carrots were used to project dietary intake of each metal by seven age-mass classes from child to adult based on consumption of a single serving of carrot. Dietary intake was compared to the oral reference dose (oral RfD) for chronic toxicity for Zn or Cu and estimated mean and median oral RfD values for Ce based on nine other rare earth elements. Reverse dietary intake calculations were also conducted to estimate the number of servings of carrot, the mass of carrot consumed, or the tissue concentration of Zn, Cu, or Ce that would cause the oral RfD to be exceeded upon consumption. The projections indicated for Zn and Cu, the oral RfD would be exceeded in only a few highly unrealistic scenarios of exceedingly high Zn or Cu concentrations in the substrate from ZnO or CuO or consumption of excessive amounts of unpeeled carrot. The implications associated with the presence of Ce in the carrot tissues depended upon whether the mean or median oral RfD value from the rare earth elements was used as a basis for comparison. The calculations further indicated that peeling carrots reduced the projected dietary intake by one to two orders of magnitude for both ENM- and ionic-treated carrots. Overall in terms of total metal concentration, the results suggested no specific impact of the ENM form on dietary intake. The effort here provided a conservative view of the potential dietary intake of these three metals that might result from consumption of carrots exposed to nanomaterials (NMs) and how peeling mitigated that dietary intake. The results also demonstrate the potential utility of dietary intake projections for examining potential risks of NM exposure from agricultural foods.
Classifying Health Information Technology patient safety related incidents – an approach used in Wales

Summary Interest in the field of patient safety incident reporting and analysis with respect to Health Information Technology (HIT) has been growing over recent years as the development, implementation and reliance on HIT systems becomes ever more prevalent. One of the rationales for capturing patient safety incidents is to learn from failures in the delivery of care and must form part of a feedback loop which also includes analysis; investigation and monitoring. With the advent of new technologies and organizational programs of delivery the emphasis is increasingly upon analyzing HIT incidents. This thematic review had two objectives, to test the applicability of a framework specifically designed to categorize HIT incidents and to review the Welsh incidents as communicated via the national incident reporting system in order to understand their implications for healthcare. The incidents were those reported as IT/ telecommunications failure/ overload. Incidents were searched for within a national reporting system using a standardized search strategy for incidents occurring between 1st January 2009 and 31st May 2011. 149 incident reports were identified and classified. The majority (77%) of which were machine related (technical problems) such as access problems; computer system down/too slow; display issues; and software malfunctions. A further 10% (n = 15) of incidents were down to human-computer interaction issues and 13% (n = 19) incidents, mainly telephone related, could not be classified using the framework being tested. On the basis of this review of incidents, it is recommended that the framework be expanded to include hardware malfunctions and the wrong record retrieved/missing data associated with a machine output error (as opposed to human error). In terms of the implications for clinical practice, the incidents reviewed highlighted critical issues including the access problems particularly relating to the use of mobile technologies.
Interannual variability in atmospheric CO2 uptake on the northeast U.S. continental shelf

occurring in the MAB. In the MAB the difference in annual air-sea flux of CO2 is due mainly to changes in near-surface wind speed, while the flux difference in the GOM is controlled primarily by surface water pCO2 (CO2 partial pressure) changes resulting from changes in sea surface temperature and new production. The large magnitude of interannual variability in the air-sea flux of CO2 simulated here suggests the potential for even more significant flux changes in the future as climate change accelerates.
Guilty by Suspicion? Criminal Behavior in Frontotemporal Lobar Degeneration

Objective:Our aim was to compare the frequency of criminal conduct in patients with behavioral variant frontotemporal dementia (bvFTD), semantic dementia (SD), and Alzheimer disease. Background:A few small-scale studies of antisocial and criminal behavior in patients with frontotemporal lobar degeneration have focused on the clinical subtype bvFTD. It is not yet known whether antisocial behavior affects patients with other clinical subtypes of frontotemporal lobar degeneration, like SD, and patients with other dementing disorders, like Alzheimer disease. Methods:We used a standardized caregiver interview to assess criminal behavior in 83 outpatients: 32 with bvFTD, 18 with SD, and 33 with Alzheimer disease. Results:We found criminal behavior (theft, willful damage to property, housebreaking, assault, or indecent behavior) in 54% of the patients with bvFTD and 56% of those with SD, but only 12% of those with Alzheimer disease. Conclusions:Just over half of our patients with bvFTD or SD had committed crimes. When middle-aged or older patients commit minor crimes, frontotemporal lobar degeneration should be considered as a possible cause. If an affected person faces criminal charges, the court might take incapability or diminished responsibility into account in reaching a verdict.
Socialization to the Model: The Active Component in the Therapeutic Alliance? A Preliminary Study

Background: Therapeutic alliance has been found to be a significant predictor of outcome in psychotherapy yet what constitutes therapeutic alliance remains unclear. Examining the common constructs of therapeutic alliance, it is possible that there may be a conceptual overlap between active components of therapeutic alliance and socialization to the treatment model. Aim: To investigate the relationship between socialization to the model and therapeutic alliance. Method: Participants (N = 43) were taken from the active treatment arm in a RCT for the treatment of chronic fatigue syndrome (CFS/ME). Therapeutic alliance was measured using a 5-item questionnaire (brief CALPAS) and socialization to the model was extracted from therapy tapes using a novel coding system. Results: Key findings were that when patients and therapists agreed about goals of treatment, there were higher levels of concordance, less evidence of applying principles incongruent to the model, and less resistance during the treatment sessions. Conclusions: The outcome of this preliminary study contributes to the potential understanding of active components in the therapeutic alliance, and supports further research to achieve a more detailed picture of “non-specific” factors in therapy, including the active process of socialization in therapeutic alliance.