Miracle-dz/UniFAR-FTUs huggingface dataset:
Experience in therapeutic plasma exchange by membrane filtration at an academic center in Colombia: Registry of the first 500 sessions

Introduction: Therapeutic plasma exchange (TPE) is an extracorporeal blood purification therapy that is part of the treatment of various diseases. Plasma and blood cells can be separated by centrifugation or using membrane separators. Materials and methods: A descriptive analysis, in which the first 500 TPE sessions using membrane filtration without anticoagulation of the extracorporeal circuit are described. Results: Five hundred (500) TPE sessions were performed on 68 patients over a period of 5 years. Therapeutic indications were 17 different diseases. 5% albumin was the most frequent replacement solution used in 62% of sessions. The mean number of plasma volume replacements was 1.33. Complications occurred in 7.6% of the sessions. Arterial hypotension was the most common event and clotting of the extracorporeal circuit was documented in just one TPE session. Electrolyte tests performed in patients during the procedure showed: 11% hypocalcemia, with a similar distribution of hypokalemia. Twenty‐two percent (22%) and 37% of phosphorus and magnesium records, respectively, were higher than normal. No symptoms associated with electrolyte abnormalities were documented. Conclusions: TPE by membrane filtration is one of the techniques by which it is possible to perform such therapy. In this registry, a low rate of complications was documented. While the need for anticoagulation may be related not only to clotting of the circuit but also to the efficiency of the therapy, clinical response in this series of patients was as expected for each disease. Continuous monitoring and an individualized analysis of electrolytes should be performed in TPE patients. J. Clin. Apheresis 30:347–352, 2015. © 2015 Wiley Periodicals, Inc.
Large Scale Mass Spectrometry-based Identifications of Enzyme-mediated Protein Methylation Are Subject to High False Discovery Rates*

All large scale LC-MS/MS post-translational methylation site discovery experiments require methylpeptide spectrum matches (methyl-PSMs) to be identified at acceptably low false discovery rates (FDRs). To meet estimated methyl-PSM FDRs, methyl-PSM filtering criteria are often determined using the target-decoy approach. The efficacy of this methyl-PSM filtering approach has, however, yet to be thoroughly evaluated. Here, we conduct a systematic analysis of methyl-PSM FDRs across a range of sample preparation workflows (each differing in their exposure to the alcohols methanol and isopropyl alcohol) and mass spectrometric instrument platforms (each employing a different mode of MS/MS dissociation). Through 13CD3-methionine labeling (heavy-methyl SILAC) of Saccharomyces cerevisiae cells and in-depth manual data inspection, accurate lists of true positive methyl-PSMs were determined, allowing methyl-PSM FDRs to be compared with target-decoy approach-derived methyl-PSM FDR estimates. These results show that global FDR estimates produce extremely unreliable methyl-PSM filtering criteria; we demonstrate that this is an unavoidable consequence of the high number of amino acid combinations capable of producing peptide sequences that are isobaric to methylated peptides of a different sequence. Separate methyl-PSM FDR estimates were also found to be unreliable due to prevalent sources of false positive methyl-PSMs that produce high peptide identity score distributions. Incorrect methylation site localizations, peptides containing cysteinyl-S-β-propionamide, and methylated glutamic or aspartic acid residues can partially, but not wholly, account for these false positive methyl-PSMs. Together, these results indicate that the target-decoy approach is an unreliable means of estimating methyl-PSM FDRs and methyl-PSM filtering criteria. We suggest that orthogonal methylpeptide validation (e.g. heavy-methyl SILAC or its offshoots) should be considered a prerequisite for obtaining high confidence methyl-PSMs in large scale LC-MS/MS methylation site discovery experiments and make recommendations on how to reduce methyl-PSM FDRs in samples not amenable to heavy isotope labeling. Data are available via ProteomeXchange with the data identifier PXD002857.
Mapping of Prion Structures in the Yeast Rnq1

The Rnq1 protein is one of the best-studied yeast prions. It has a large potentially prionogenic C-terminal region of about 250 residues. However, a previous study indicated that only 40 C-terminal residues form a prion structure. Here, we mapped the actual and potential prion structures formed by Rnq1 and its variants truncated from the C-terminus in two [RNQ+] strains using partial proteinase K digestion. The location of these structures differed in most cases from previous predictions by several computer algorithms. Some aggregation patterns observed microscopically for the Rnq1 hybrid proteins differed significantly from those previously observed for Sup35 prion aggregates. The transfer of a prion from the full-sized Rnq1 to its truncated versions caused substantial alteration of prion structures. In contrast to the Sup35 and Swi1, the terminal prionogenic region of 72 residues was not able to efficiently co-aggregate with the full-sized Rnq1 prion. GFP fusion to the Rnq1 C-terminus blocked formation of the prion structure at the Rnq1 C-terminus. Thus, the Rnq1-GFP fusion mostly used in previous studies cannot be considered a faithful tool for studying Rnq1 prion properties.
Modelling and Simulation of Plate Heat Exchanger

This paper presents simulation investigation of a plate heat exchanger. Basically, it includes the development of a mathematical model to describe its operation and analysis. The model, after testing against the existing experimental data, has been solved to obtain the effect of various parameters like mass flow rate, number of flow channels, plate configuration and f low patterns. Model of a plate heat exchanger has been described by a set of continuity, momentum and energy equations with a number of simplifying assumptions. Heat transfer rate equation has also been included in the energy balance equation to take care of phenomena occurring therein. Mathematical model has been solved by the use of finite difference technique with interval of Δt =0.005s and Δz = 0.005m to obtain the transient and steady state behavior.
Hemidouble Stapling Technique versus Ghosting Double Stapling Technique for Esophagojejunostomy after Laparoscopic Total Gastrectomy

The hemidouble stapler technique (HDST) in laparoscopic intracorporeal esophagojejunostomy has aspects that pose risks to the safety of the anastomosis. We developed a new esophagojejunostomy technique that converts a double-stapled anastomosis to a single-stapled anastomosis in laparoscopic total gastrectomy (LTG). The aim of this study is to compare the results of two techniques. Patients who underwent LTG for gastric cancer in our hospital between October 2016 and May 2022 were included in the study. Patients were retrospectively reviewed in two groups: those who underwent HDST and the ghosting double stapling technique (GDST). Both groups were analysed in terms of demographics, perioperative findings, and postoperative outcomes. The GDST was used in 14 patients. The HDST was used on 16 patients. Two patients in the HDST group whose esophagojejunal anastomosis was not assessed on endoscopic imaging were excluded. The mean total operative times were 292.6 ± 43.7 and 224.3 ± 36.1 min (p < 0.001). The mean times for esophagojejunostomy were 38.6 ± 4.3 and 26.8 ± 6.4 min (p < 0.001). One case of anastomotic stenosis was observed in the HDST group. Anastomotic leakage was not observed in both groups. However, there was no significant difference in overall morbidity between the groups (p > 0.05). Both HDST and GDST can be safely performed in the esophagojejunostomy for LTG.
GraphTracker: a topology projection invariant optical tracker

In this paper, we describe a new optical tracking algorithm for pose estimation of interaction devices in virtual and augmented reality. Given a 3D model of the interaction device and a number of camera images, the primary difficulty in pose reconstruction is to find the correspondence between 2D image points and 3D model points. Most previous methods solved this problem by the use of stereo correspondence. Once the correspondence problem has been solved, the pose can be estimated by determining the transformation between the 3D point cloud and the model. Our approach is based on the projective invariant topology of graph structures. The topology of a graph structure does not change under projection: in this way we solve the point correspondence problem by a subgraph matching algorithm between the detected 2D image graph and the model graph. There are four advantages to our method. First, the correspondence problem is solved entirely in 2D and therefore no stereo correspondence is needed. Consequently, we can use any number of cameras, including a single camera. Secondly, as opposed to stereo methods, we do not need to detect the same model point in two different cameras, and therefore our method is much more robust against occlusion. Thirdly, the subgraph matching algorithm can still detect a match even when parts of the graph are occluded, for example by the users hands. This also provides more robustness against occlusion. Finally, the error made in the pose estimation is significantly reduced as the amount of cameras is increased.
Gradient-like observer design on the Special Euclidean group SE(3) with system outputs on the real projective space

A nonlinear observer on the Special Euclidean group SE(3) for full pose estimation, that takes the system outputs on the real projective space directly as inputs, is proposed. The observer derivation is based on a recent advanced theory on nonlinear observer design. A key advantage with respect to existing pose observers on SE(3) is that we can now incorporate in a unique observer different types of measurements such as vectorial measurements of known inertial vectors and position measurements of known feature points. The proposed observer is extended allowing for the compensation of unknown constant bias present in the velocity measurements. Rigorous stability analyses are equally provided. Excellent performance of the proposed observers are shown by means of simulations.
A Study of Reinjection and Connectivity between Wells in the Los Azufres (Mexico) Geothermal Field

Historical records of production and reservoir-monitoring data gathered in the Los Azufres geothermal field were studied to assess the effect of geothermal reinjection and the connectivity among geothermal wells. The former data correspond to wells producing vapor or a liquid-vapor mixture. To estimate the connectivity between pairs of injection-production wells, the known nonparametric regression ACE (Alternating Conditional Expectation) method was used to correlate injection rate histories to either chloride concentration histories for liquid/mixture production wells or to bottom-hole pressure histories for vapor production wells. The statistical results were analyzed in light of earlier field studies based on tracer tests as well as on histories of both chemical species and isotope concentrations. Our study assessed the relative effect of reinjection through monitoring chloride concentration and, for the first time, bottom-hole pressure histories measured at production wells of both southern and northern Los Azufres geothermal field. Our analysis suggests that the connectivity indices yielded by the ACE method for some well pairs are in agreement with earlier reservoir data. Further comparison with other types of reservoir data is required to evaluate or calibrate our estimations.
Using credibility intervals instead of hypothesis tests in SAGE analysis

MOTIVATION Statistical methods usually used to perform Serial Analysis of Gene Expression (SAGE) analysis are based on hypothesis testing. They answer the biologist's question: 'what are the genes with differential expression greater than r with P-value smaller than P? '. Another useful and not yet explored question is: 'what is the uncertainty in differential expression ratio of a gene? '. RESULTS We have used Bayesian model for SAGE differential gene expression ratios as a more informative alternative to hypothesis tests since it provides credibility intervals. AVAILABILITY The model is implemented in R statistical language script and is available under GNU/GLP copyleft at supplemental web site. SUPPLEMENTARY INFORMATION http://www.ime. usp.br/~rvencio/SAGEci/
Male Weaponry in a Fighting Cricket

Sexually selected male weaponry is widespread in nature. Despite being model systems for the study of male aggression in Western science and for cricket fights in Chinese culture, field crickets (Orthoptera, Gryllidae, Gryllinae) are not known to possess sexually dimorphic weaponry. In a wild population of the fall field cricket, Gryllus pennsylvanicus, we report sexual dimorphism in head size as well as the size of mouthparts, both of which are used when aggressive contests between males escalate to physical combat. Male G. pennsylvanicus have larger heads, maxillae and mandibles than females when controlling for pronotum length. We conducted two experiments to test the hypothesis that relatively larger weaponry conveys an advantage to males in aggressive contests. Pairs of males were selected for differences in head size and consequently were different in the size of maxillae and mandibles. In the first experiment, males were closely matched for body size (pronotum length), and in the second, they were matched for body mass. Males with proportionately larger weaponry won more fights and increasing differences in weaponry size between males increased the fighting success of the male with the larger weaponry. This was particularly true when contests escalated to grappling, the most intense level of aggression. However, neither contest duration nor intensity was related to weaponry size as predicted by models of contest settlement. These results are the first evidence that the size of the head capsule and mouthparts are under positive selection via male-male competition in field crickets, and validate 800-year-old Chinese traditional knowledge.
Lighting-Up Geometry: Accurate 3D Modelling of Museum Artifacts with a Torch and a Camera

This paper addresses the problem of obtaining complete, very detailed re constructions of shiny objects such as glazed ceramics. We present an algorithm which uses silhouettes of the ob ject, as well as images obtained under changing illumination conditions. In contrast with previous photometric stere o techniques, ours is not limited to a single viewpoint but produces accurate reconstructions in full 3D. A n umber of images of the object are obtained from multiple viewpoints, under varying lighting conditions. Starting fro m the silhouettes, the algorithm recovers camera motion and constructs the object’s visual hull. This is the n used to recover the illumination and initialise a multi-view photometric stereo scheme to obtain a closed surface reco nstruction. The algorithm has been implemented as a practical model acquisition system. Here, we present a number of complete reconstructions of challenging real objects.
FolC2‐mediated folate metabolism contributes to suppression of inflammation by probiotic Lactobacillus reuteri

Bacterial‐derived compounds from the intestinal microbiome modulate host mucosal immunity. Identification and mechanistic studies of these compounds provide insights into host–microbial mutualism. Specific Lactobacillus reuteri strains suppress production of the proinflammatory cytokine, tumor necrosis factor (TNF), and are protective in a mouse model of colitis. Human‐derived L. reuteri strain ATCC PTA 6475 suppresses intestinal inflammation and produces 5,10‐methenyltetrahydrofolic acid polyglutamates. Insertional mutagenesis identified the bifunctional dihydrofolate synthase/folylpolyglutamate synthase type 2 (folC2) gene as essential for 5,10‐methenyltetrahydrofolic acid polyglutamate biosynthesis, as well as for suppression of TNF production by activated human monocytes, and for the anti‐inflammatory effect of L. reuteri 6475 in a trinitrobenzene sulfonic acid‐induced mouse model of acute colitis. In contrast, folC encodes the enzyme responsible for folate polyglutamylation but does not impact TNF suppression by L. reuteri. Comparative transcriptomics between wild‐type and mutant L. reuteri strains revealed additional genes involved in immunomodulation, including previously identified hdc genes involved in histidine to histamine conversion. The folC2 mutant yielded diminished hdc gene cluster expression and diminished histamine production, suggesting a link between folate and histadine/histamine metabolism. The identification of genes and gene networks regulating production of bacterial‐derived immunoregulatory molecules may lead to improved anti‐inflammatory strategies for digestive diseases.
Mathematical Models Applied to On-Chip Network on FPGA for Resource Estimation

One main challenge of prototyping a SoC (System on Chip) on FPGA (Field Programmable Gate Array) is to tune at best the communication architecture according to the task graph of an application and the available resources of the chosen FPGA. The exploration of the potential design candidates is time consuming, tedious and does not scale. The sheer number of parameters leads to a wide design space that cannot be explored in a limited time. The aim of this paper is to identify mathematical models applied to NoC to estimate FPGA resources. Mathematical models are obtained from a database containing a set of observed results. Using the database, the Pearson's correlation coefficient and the variable clustering are used to set the most appropriate variables and constants. The mathematical models are obtained and then validated with a set of experimental results. The validation shows that the error rate between observed results and the analytically estimated results is less than 5%. The designer can therefore tune the NoC in shorter exploration time.
New Solutions for Aircraft Wing and Helicopter Blade Airfoils

In this paper are presented some analytical and numerical results regarding airfoil characteristics, lift coefficient improvement solutions and possible applications for airplane wing and helicopter blade. Starting from the general theory of aerodynamics and based on the CFD methods, the paper deals with the mathematical model of flow around an airfoil with a filed cavity, where a free rotational cylinder is placed in order to delay the flow separation. The numerical solutions were made in Maplesoft environment.
Liquid detection with InGaAsP semiconductor lasers having multiple short external cavities.

A liquid detection system consisting of a diode laser with multiple short external cavities (MSXC's) is reported. The MSXC diode laser operates single mode on one of 18 distinct modes that span a range of 72 nm. We selected the modes by setting the length of one of the external cavities using a piezoelectric positioner. One can measure the transmission through cells by modulating the injection current at audio frequencies and using phase-sensitive detection to reject the ambient light and reduce 1/f noise. A method to determine regions of single-mode operation by the rms of the output of the laser is described. The transmission data were processed by multivariate calibration techniques, i.e., partial least squares and principal component regression. Water concentration in acetone was used to demonstrate the performance of the system. A correlation coefficient of R(2) = 0.997 and 0.29% root-mean-square error of prediction are found for water concentration over the range of 2-19%.
Ideal Predictors for the Severity of Acute Pancreatitis: A single center Egyptian study

Background & Aims: The ideal predictor of acute pancreatitis should be inexpensive, readily available in most emergency departments, easily applicable, consistent, non-invasive and has the statistical power. Although such predictor has not been detected, the research continues to pursue such one. This survey was created to research and evaluate different simple laboratory tests as possible predictors of severe acute pancreatitis. Materials and Methods: The study population consists of 40 patients admitted to the gastroenterology and Hepatology unit, Tanta University emergency hospital after being diagnosed to have acute pancreatitis. The following data were collected from all patients within 24 hours of admission: Age, sex, complete blood count, body mass index, blood glucose level, serum creatinine, blood urea nitrogen, total bilirubin, aspartate aminotransferase, C-reactive protein, total serum calcium, serum lipase and amylase, arterial blood gases, abdominal ultrasonography and chest X-ray. Results: The study population consisted of 17 males and 23 females. The patients were being divided into two groups: group 1 that included 28 patients diagnosed as mild acute pancreatitis and group 2 that included 12 patients diagnosed as moderate to severe acute pancreatitis. Blood glucose, BUN, AST, CRP, serum lipase, BMI, hematocrit value, leukocytes and platelets count showed significant P value on comparing the two groups. Area under the curve (AUC) had been calculated for the above mentioned possible predictors and it represents the overall accuracy of all points. Blood glucose, AST and platelets count showed the highest AUC, sensitivity, specificity, PPV, NPV and accuracy among other proposed predictors, However, other proposed predictors showed high NPV. Conclusion: Blood glucose level, AST and platelets count showed the highest AUC, sensitivity, specificity, PPV, NPV and accuracy among other proposed predictors. Although other proposed predictors showed lower results than the above mentioned predictors, they still have a very significant NPV and can be used to rule out severe acute pancreatitis.
Buffering Impostor Feelings with Kindness: The Mediating Role of Self-compassion between Gender-Role Orientation and the Impostor Phenomenon

The impostor phenomenon (IP) refers to high-achievers who underestimate their abilities and thus fear being unmasked as impostors. IP sufferers attribute their success to factors other than their abilities, entailing negative emotions, unfavorable motivations, and reduced well-being. The IP was originally conceptualized as a predominantly female experience, and is thus seen as an important psychological barrier for female academic careers. Empirical findings of gender differences in the IP are equivocal, but sparse research on associations between gender-role orientation and the IP indicates that feminine students suffer more intensely from the IP than masculine students. Femininity and masculinity are also related to self-compassion, a rather young construct that enhances emotional resilience, well-being, and academic achievement. Self-compassion involves being kind to oneself when failing, perceiving one’s inadequacies as part of the human condition, and being mindful about negative aspects of oneself. It reduces fear of failure, denial of competences, and self-doubts which are central components of the IP. However, relations between self-compassion and the IP have not been investigated to date. In this study, we examine self-compassion as a potential resilience factor against the IP, taking gender and gender-role orientation into account. In a cross-sectional online survey, we investigated 459 (315 female) high-achieving first-year undergraduate students. Results include: Female, feminine, and undifferentiated students score higher on measures of the IP and lower on measures of self-compassion than male, masculine, or androgynous students. Higher levels of the IP are associated with lower levels of self-compassion across all students tested. Self-compassion further mediates the relationship between gender-role orientation and the IP. Interventions to enhance self-compassion might thus be an effective way to overcome impostor feelings. Female, feminine, and undifferentiated students might benefit most from facilitation of self-compassion in education.