Miracle-dz/UniFAR-FTUs huggingface dataset:
Matrix-Induced Liver Cell Aggregates (MILCA) for Bioartificial Liver Use

Ex vivo reproduction of liver microstructure using isolated hepatocytes is critical for bioartificial liver use. We have developed a method of producing matrix-induced liver cell aggregates (MILCA) using a small number of collagen-coated beads as a nidus for formation of hepatocyte aggregates. Porcine hepatocytes were obtained by EDTA/collagenase digestion. Cell viability was assessed by trypan blue exclusion and LDH release. Cytochrome P-450 activity was determined at 4 and 24 hours by measuring the formation of 7-hydroxycoumarine (7-HC) from 7-ethoxycoumarine (7-EC). At 4 hours, the viability of MILCA was 92±2%, LDH release was 100+22 U/L and 7-HC formation was 140±34 nM/g cells. At 24 hours, MILCA viability remained greater than 90%, but 7-HC formation was lower than that of parallel control monolayer hepatocyte cultures (194±43 vs 481±78 nM/g cells; p<0.002). On transmission electron microscopy, MILCA ultrastructure resembled that of a normal liver (maintenance of cell polarity, gap junctions, bile canaliculi, intact organellae, glycogen granules). MILCA were subsequently inoculated into hollow-fiber bioreactors which were perfused for 6 hours with plasma recovered from patients with fulminant hepatic failure (n=6; 5x109 cells/cartridge, recirculation of 350 ml of plasma at 400 ml/min). In these studies, lidocaine (20 μg/ml) was cleared in less than 3 hours and 7-HC production at 6 hours was 71+8 nM/g cells. Other MILCA effects noted in this system included lowering of plasma lactate, bilirubin and ammonia and increase in the level of several non-essential amino acids.
Obesity: Beyond Cardiovascular Disease and Diabetes — Learn About Obesity’s Far Reach and Ill Effects in Lesser-Described Conditions

Despite more attention and focus on obesity as a national and global pandemic from the scientific, health care, and political communities, high rates continue to prevail. Nearly 35% of the US adult population is obese, and, according to the World Health Organization (WHO), deaths linked to obesity have surpassed deaths caused by being underweight. According to the systematic Global Burden of Disease Study 2010, deaths attributable to malnutrition, infectious disease, and maternal-child diseases are on the decline compared to 20 years ago and are surpassed by noncommunicable diseases of obesity such as heart disease and cancer. Beyond mortality alone, obesity is irrefutably responsible for increasing the risk of developing some of the leading causes of preventable chronic conditions. For example, obesity has been widely discussed for its role in diseases of the cardiovascular system such as heart disease and stroke; the endocrine system, such as diabetes; and the digestive system, such as fatty liver or gallbladder disease. But while those diseases get the lion’s share of media and research attention, other diseases have been associated with obesity.
Romosozumab and Blosozumab: Alternative Drugs of Mechanical Strain-Related Stimulus Toward a Cure for Osteoporosis

In addition to other chronic diseases such as hypertension, hypercholesterolemia, and diabetes, a treat-to-target strategy was recently applied in rheumatoid arthritis and has now been discussed in osteoporosis. An important goal of osteoporosis therapy is normal risk of hip fracture associated with significant morbidity and mortality, but the anti-fracture efficacies of currently approved drugs are limited (1, 2). Although fundamental methods to effectively prevent osteoporotic fracture include pharmacological treatment of sarcopenia that results in improving bone fragility as well as reducing fall risk, the present article focuses on anti-sclerostin antibodies such as romosozumab and blosozumab, the investigational agents for osteoporosis, and provides new insights into their effects from natural homeostatic system in the skeleton.
Cognitively adequate modelling of spatial reference in human-robot interaction

The question addressed in this paper is which types of spatial reference human users employ in their interaction with a robot and how a cognitively adequate model of these strategies can be implemented. Experiments in human-robot interaction were carried out which show how human users approach an artificial communication partner which was designed on the basis of empirical findings regarding spatial references among humans. The results are considerable differences in the strategies which speakers employ to achieve spatial reference in human-robot interaction and in natural communication.
Evidence for on‐going inflation of the Socorro Magma Body, New Mexico, from interferometric synthetic aperture radar imaging

Interferometric synthetic aperture radar (InSAR) imaging of the central Rio Grande rift (New Mexico, USA) during 1992–1999 reveals a crustal uplift of several centimeters that spatially coincides with the seismologically determined outline of the Socorro magma body, one of the largest currently active magma intrusions in the Earth's continental crust. Modeling of interferograms shows that the observed deformation may be due to elastic opening of a sill‐like intrusion at a rate of a few millimeters per year. Despite an apparent constancy of the geodetically determined uplift rate, thermodynamic arguments suggest that it is unlikely that the Socorro magma body has formed via steady state elastic inflation.
Suppression of fungal and nematode plant pathogens through arbuscular mycorrhizal fungi

Arbuscular mycorrhizal (AM) fungi represent ubiquitous mutualists of terrestrial plants. Through the symbiosis, plant hosts, among other benefits, receive protection from pathogens. A meta-analysis was conducted on 106 articles to determine whether, following pathogen infection of AM-colonized plants, the identity of the organisms involved (pathogens, AM fungi and host plants) had implications for the extent of the AM-induced pathogen suppression. Data on fungal and nematode pathogens were analysed separately. Although we found no differences in AM effectiveness with respect to the identity of the plant pathogen, the identity of the AM isolate had a dramatic effect on the level of pathogen protection. AM efficiency differences with respect to nematode pathogens were mainly limited to the number of AM isolates present; by contrast, modification of the ability to suppress fungal pathogens could occur even through changing the identity of the Glomeraceae isolate applied. N-fixing plants received more protection from fungal pathogens than non-N-fixing dicotyledons; this was attributed to the more intense AM colonization in N-fixing plants. Results have implications for understanding mycorrhizal ecology and agronomic applications.
Biological Effects of a De Novo Designed Myxoma Virus Peptide Analogue: Evaluation of Cytotoxicity on Tumor Cells

Background The Resonant Recognition Model (RRM) is a physico-mathematical model that interprets protein sequence linear information using digital signal processing methods. In this study the RRM concept was employed for structure-function analysis of myxoma virus (MV) proteins and the design of a short bioactive therapeutic peptide with MV-like antitumor/cytotoxic activity. Methodology/Principal Findings The analogue RRM-MV was designed by RRM as a linear 18 aa 2.3 kDa peptide. The biological activity of this computationally designed peptide analogue against cancer and normal cell lines was investigated. The cellular cytotoxicity effects were confirmed by confocal immunofluorescence microscopy, by measuring the levels of cytoplasmic lactate dehydrogenase (LDH) and by Prestoblue cell viability assay for up to 72 hours in peptide treated and non-treated cell cultures. Our results revealed that RRM-MV induced a significant dose and time-dependent cytotoxic effect on murine and human cancer cell lines. Yet, when normal murine cell lines were similarly treated with RRM-MV, no cytotoxic effects were observed. Furthermore, the non-bioactive RRM designed peptide RRM-C produced negligible cytotoxic effects on these cancer and normal cell lines when used at similar concentrations. The presence/absence of phosphorylated Akt activity in B16F0 mouse melanoma cells was assessed to indicate the possible apoptosis signalling pathway that could be affected by the peptide treatment. So far, Akt activity did not seem to be significantly affected by RRM-MV as is the case for the original viral protein. Conclusions/Significance Our findings indicate the successful application of the RRM concept to design a bioactive peptide analogue (RRM-MV) with cytotoxic effects on tumor cells only. This 2.345 kDa peptide analogue to a 49 kDa viral protein may be suitable to be developed as a potential cancer therapeutic. These results also open a new direction to the rational design of therapeutic agents for future cancer treatment.
Calculating terrain indices along streams: A new method for separating stream sides

There is increasing interest in assessing riparian zones and their hydrological and biogeochemical buffering capacity with indices derived from hydrologic landscape analysis of digital elevation data. Upslope contributing area is a common surrogate for lateral water flows and can be used to assess the variability of local water inflows to riparian zones and streams. However, current geographic information system algorithms do not provide a method for easily separating riparian zone and adjacent upland lateral contributions on each side of the stream. Here we propose a new algorithm to compute side‐separated contributions along stream networks. We describe the new algorithm and illustrate the importance of distinguishing between lateral inflows on each side of streams with hillslope–riparian zone–stream hydrologic connectivity results from high‐frequency water table data collected in the 22 km2 Tenderfoot Creek catchment, Montana.
Comparative analysis between osteosarcoma and Ewing's sarcoma: evaluation of the time from onset of signs and symptoms until diagnosis.

OBJECTIVE The purposes of this study were to describe the early signs and symptoms of osteosarcoma and Ewing's sarcoma, identify symptoms that could be used to help differentiate the two types of tumors, and determine the time elapsed between the onset of signs and symptoms and the definitive diagnosis in our service, providing information and imputus for earlier diagnosis of these tumors. METHODS A retrospective analysis of the medical dossiers of 365 patients under 30 years of age diagnosed with osteosarcoma or Ewing's sarcoma was performed, and the aspects of the clinical diagnosis were statistically analyzed and compared. RESULTS The time between the onset of signs and the symptoms was 5.25 months for osteosarcoma and 8.1 months for Ewing's sarcoma, and the most frequent (89.5%) early symptom of osteosarcoma and Ewing's sarcoma was local pain. Symptoms that might aid diagnosis included early local volume increase and the presence of fever. CONCLUSION The time until diagnosis of both neoplasias was higher than that reported for North America and Europe. Education of the lay public and medical professionals regarding suspicious early signs and symptoms might shorten the delay of diagnosis.
Contextualising Tags in Collaborative Tagging Systems

Collaborative tagging systems are now popular tools for organising and sharing information on the Web. While collaborative tagging offers many advantages over the use of controlled vocabularies, they also suffer from problems such as the existence of polysemous tags. We investigate how the different contexts in which individual tags are used can be revealed automatically without consulting any external resources. We consider several different network representations of tags and documents, and apply a graph clustering algorithm on these networks to obtain groups of tags or documents corresponding to the different meanings of an ambiguous tag. Our experiments show that networks which explicitly take the social context into account are more likely to give a better picture of the semantics of a tag.
H-Formulation FEM Modeling of the Current Distribution in 2G HTS Tapes and Its Experimental Validation Using Hall Probe Mapping

One of the most widespread mathematical formulations applied to simulate the electromagnetic phenomena of coated conductor in the recent literature is the H-formulation. However, the only validation of the model has been indirect by using measurements taken from the applications, as measurements of the energy losses in ac fields, forces developed in levitation systems, or any other parameter related to a specific application. Direct validation of the calculation requires the observation of the local out-of-plane magnetic field over the surface of the sample, and it is only accessible under magneto-optical observations and, in a larger scale and better dynamic range, by the Hall scanning microscopy. We propose here the experimental validation of the H-formulation by comparing the simulated results with measurements made by a Hall probe mapping in a second-generation (2G) tape sample for several dc transported currents at 77 K. This paper presents a methodology to simulate the 2G tape by using only measured data obtained from a sample and its normalized J(B) experimental curves. Some boundary conditions that allow a faster convergence of the problem are investigated. Simulated results of the 2G tape modeled considering only the 1-μm high-temperature superconductor (HTS) layer were compared with others that represent the most important layers of the coated conductor structure in the calculations. The simulated and measured results present a good agreement, proving that this model can calculate precisely the magnetic field and, hence, the current distribution in HTS samples.
The Microbial Role in Hot Spring Silicification

Abstract Recent experimental studies indicate that microorganisms play a passive role in silicification. The organic functional groups that comprise the outer cell surfaces simply serve as heterogeneous nucleation sites for the adsorption of polymeric and/or colloidal silica, and because different microorganisms have different cell ultrastructural chemistry, species-specific patterns of silicification arise. Despite their templating role, they do not appear to increase the kinetics of silicification, and at the very most, they contribute only marginally to the magnitude of silicification. Instead, silicification is due to the polymerization of silicasupersaturated hydrothermal fluids upon discharge at the surface of the hot spring. Microorganisms do, however, impart an influence on the fabric of the siliceous sinters that form around hot spring vents. Different microorganisms have different growth patterns, that in turn, affect the style of laminations, the primary porosity of the sinter and the distribution of later-stage diagenetic cementation.
Prophylactic Negative Pressure Dressing Use in Closed Laparotomy Wounds Following Abdominal Operations: A Randomized, Controlled, Open-label Trial The P.I.C.O. Trial

Objective: A randomized controlled trial was undertaken to investigate the effect of prophylactic negative pressure dressings on postoperative surgical site infection (SSI) rates in closed laparotomy wounds. Summary of Background Data: Laparotomy wounds are associated with high rates of SSI. The effect of prophylactic negative pressure dressing of closed incisional wounds on SSI rate is unknown. Methods: A randomized, controlled, open-label trial was conducted (clinicaltrials.gov registration number NCT02780453). Fifty patients undergoing open abdominal surgery were included, with 25 patients randomized to the negative pressure dressing group and 25 to the standard dressing group. The primary endpoint was SSI incidence at 30 days postoperatively. Secondary endpoints included SSI incidence at 4 days, length of stay, cosmetic outcome, and patient satisfaction. Statistical analysis was performed on a per-protocol basis using SPSS version 23.0. Results: The incidence of SSI at 30 days postoperatively was significantly reduced in the treatment group compared with the control group [8.3% vs 32.0%, P = 0.043 (1-sided), P = 0.074 (2-sided)]. There was no difference in SSIs at 4 days postoperatively [4.1% vs 8.0%, P = 0.516 (1-sided), P = 1.0 (2-sided)]. Analysis of predictors of wound infection identified standard wound dressings as the only significant predictor of SSI development. Length of stay was significantly reduced in the negative pressure dressing group [6.1 vs 14.7 days, P = 0.019 (2-sided)]. Cosmetic outcome and patient satisfaction did not show any difference between the 2 groups. Conclusions: Prophylactic use of negative pressure dressings for closed laparotomy wounds significantly reduces the incidence of SSI at 30 days postoperatively.
Association Between State Medical Malpractice Environment and Surgical Quality and Cost in the United States

Context:The US medical malpractice system is designed to deter negligence and encourage quality of care through threat of liability. Objective:To examine whether state-level malpractice environment is associated with outcomes and costs of colorectal surgery. Design, Setting, and Patients:Observational study of 116,977 Medicare fee-for-service beneficiaries who underwent colorectal surgery using administrative claims data. State-level malpractice risk was measured using mean general surgery malpractice insurance premiums; paid claims per surgeon; state tort reforms; and a composite measure. Associations between malpractice environment and postoperative outcomes and price-standardized Medicare payments were estimated using hierarchical logistic regression and generalized linear models. Main Outcome Measures:thirty-day postoperative mortality; complications (pneumonia, myocardial infarction, venous thromboembolism, acute renal failure, surgical site infection, postoperative sepsis, any complication); readmission; total price-standardized Medicare payments for index hospitalization and 30-day postdischarge episode-of-care. Results:Few associations between measures of state malpractice risk environment and outcomes were identified. However, analyses using the composite measure showed that patients treated in states with greatest malpractice risk were more likely than those in lowest risk states to experience any complication (OR: 1.31; 95% CI: 1.22–1.41), pneumonia (OR: 1.36; 95%: CI, 1.16–1.60), myocardial infarction (OR: 1.44; 95% CI: 1.22–1.70), venous thromboembolism (OR:2.11; 95% CI: 1.70–2.61), acute renal failure (OR: 1.34; 95% CI; 1.22–1.47), and sepsis (OR: 1.38; 95% CI: 1.24–1.53; all P < 0.001). There were no consistent associations between malpractice environment and Medicare payments. Conclusions:There were no consistent associations between state-level malpractice risk and higher quality of care or Medicare payments for colorectal surgery.
Hemodynamic Responses to Resistance Exercise in Patients with Coronary Artery Disease.

PURPOSE Investigate hemodynamic responses of resistance exercise (RE) with moderate load (i.e., international guidelines for RE of patients) versus RE with high load in patients with coronary artery disease (CAD). METHODS Medically stable male (n = 11) and female patients (n = 4) treated with PCI or percutaneous coronary intervention, or coronary artery bypass surgery a minimum of 6 months before this study, performed three sets of 15RM and 4RM RE in a randomized order on separate days. Beat-to-beat systolic (SBP), diastolic (DBP) blood pressure, heart rate (HR), stroke volume (SV), cardiac output (CO), and systemic vascular resistance (SVR) were monitored at preexercise, and continuously during RE. RESULTS Compared with preexercise, SBP and DBP (mean of three sets) increased by 12% to 13% (both; P < 0.001) and 35% to 40% after 15RM RE (both; P < 0.001). 15RM SBP and DBP were higher than 4RM SBP and DBP (both; P < 0.001). The SBP of the fourth repetition of 15 RM RE was similar to the SBP of the fourth repetition of 4RM RE. Compared with preexercise, SV increased moderately after 4RM and 15 RM RE, respectively (both, P < 0.001). HR increased more after 15RM compared with 4RM RE (P < 0.05); thus, higher CO after 15RM (compared with 4RM RE; P < 0.05) was mainly caused by higher HR. SVR decreased by 15% (P < 0.001) and 50% (P < 0.01) after 4RM and 15RM RE. CONCLUSIONS SBP and DBP increased significantly more during moderate load RE; thus, the magnitude of the external load is not the prime determinant of the pressure response during RE. If management of blood pressure is of concern, high load/low rep RE is preferable to medium load/high rep RE.
Shared information and program plagiarism detection

A fundamental question in information theory and in computer science is how to measure similarity or the amount of shared information between two sequences. We have proposed a metric, based on Kolmogorov complexity, to answer this question and have proven it to be universal. We apply this metric in measuring the amount of shared information between two computer programs, to enable plagiarism detection. We have designed and implemented a practical system SID (Software Integrity Diagnosis system) that approximates this metric by a heuristic compression algorithm. Experimental results demonstrate that SID has clear advantages over other plagiarism detection systems. SID system server is online at http://software.bioinformatics. uwaterloo.ca/SID/.
Penetration of Cultured Mouse Fibroblasts (L Cells) by Rickettsia prowazeki

The association of Rickettsia prowazeki with L cells was examined by using a novel radioactive assay in which [α-32P]ATP-labeled rickettsiae were incubated with L-cell monolayers. Rickettsial association with the monolayer involved adherence and internalization steps that could be experimentally distinguished. Since R. prowazeki but not L cells possess an ATP-ADP obligate exchange transport system, addition of excess unlabeled ATP resulted in exchange of the labeled ATP from external, adherent rickettsiae but not from internalized rickettsiae. Rickettsial association was temperature dependent and was a linear function of both time and concentration. More than 90% of the biologically active rickettsiae associated with L cells was internalized. Rickettsial internalization required active participation of both rickettsiae and L cells; inactivation of either greatly reduced internalization. Rickettsial adherence to poisoned L cells was a saturable function of time and concentration. Adherence showed less temperature dependence than did internalization, but like rickettsial internalization, the extent of adherence was extremely low at 0°C. The rate and extent of adherence by inactivated and native rickettsiae to inactivated L cells were similar. Although inactive rickettsiae adhered to active and inactive L cells to a similar extent, inactive rickettsiae were internalized poorly by active L cells. These data form the basis for the hypothesis that R. prowazeki are internalized by the host cell through a process of “induced phagocytosis” and that inactivated rickettsiae adhere to the host cell differently from native rickettsiae, failing to trigger the endocytosis mechanism.
Searching worst cases of a one-variable function using lattice reduction

We propose a new algorithm to find worst cases for the correct rounding of a mathematical function of one variable. We first reduce this problem to the real small value problem - i.e., for polynomials with real coefficients. Then, we show that this second problem can be solved efficiently by extending Coppersmith's work on the integer small value problem - for polynomials with integer coefficients - using lattice reduction. For floating-point numbers with a mantissa less than N and a polynomial approximation of degree d, our algorithm finds all worst cases at distance less than N/sup -d2//2d+1 from a machine number in time O(N/sup (d+1/2d+1)+/spl epsiv//). For d=2, a detailed study improves on the O(N/sup 2/(3+/spl epsiv/)/) complexity from Lefevre's algorithm to O(N/sup 4/(7+/spl epsiv/)/). For larger d, our algorithm can be used to check that there exist no worst cases at distance less than N/sup -k/ in time O(N/sup 1/(2+/spl epsiv/)/).