Miracle-dz/UniFAR-FTUs huggingface dataset:
Consensus statement on peritoneal mesothelioma

Diffuse malignant peritoneal mesothelioma (DMPM) has been traditionally regarded as a rapidly lethal disease. Recently, several independent prospective trials have reported improved survival with an intensive loco‐regional treatment strategy including cytoreductive surgery (CRS) along with peri‐operative intra‐peritoneal chemotherapy (PIC). However, most of the surgical data comes from mono‐institutional phase I or II studies and there is a broad range of variability regarding inclusion criteria, cytoreductive surgical procedures, drugs, temperatures and methods of delivering the heated chemotherapy (open vs. closed abdomen). This manuscript critically analyze and discuss the results of a group of health care providers trying to achieve a consensus statement in the management of this group of patients. The main conflicting points regarding preoperative evaluation, patient eligibility, combined treatment methodology, postoperative follow‐up and future investigational perspectives were summarized as a list of multiple‐choice questions. A questionnaire was placed on the website of the “5th International Workshop on Peritoneal Surface Malignancies” and the group members voted via internet. The results were presented for further debate during a dedicated session of the Workshop. The general treatment guidelines and future investigational perspectives were defined. J. Surg. Oncol. 2008;98:268–272. © 2008 Wiley‐Liss, Inc.
Estimating the Severity and Subclinical Burden of Middle East Respiratory Syndrome Coronavirus Infection in the Kingdom of Saudi Arabia

Abstract Not all persons infected with Middle East respiratory syndrome coronavirus (MERS-CoV) develop severe symptoms, which likely leads to an underestimation of the number of people infected and an overestimation of the severity. To estimate the number of MERS-CoV infections that have occurred in the Kingdom of Saudi Arabia, we applied a statistical model to a line list describing 721 MERS-CoV infections detected between June 7, 2012, and July 25, 2014. We estimated that 1,528 (95% confidence interval (CI): 1,327, 1,883) MERS-CoV infections occurred in this interval, which is 2.1 (95% CI: 1.8, 2.6) times the number reported. The probability of developing symptoms ranged from 11% (95% CI: 4, 25) in persons under 10 years of age to 88% (95% CI: 72, 97) in those 70 years of age or older. An estimated 22% (95% CI: 18, 25) of those infected with MERS-CoV died. MERS-CoV is deadly, but this work shows that its clinical severity differs markedly between groups and that many cases likely go undiagnosed.
Unruptured intracranial aneurysms conservatively followed with serial CT angiography: could morphology and growth predict rupture?

Background and purpose Despite several landmark studies, the natural history of unruptured intracranial aneurysms (UIA) remains uncertain. Our aim was to identify or confirm factors predictive of rupture of UIA being observed conservatively with serial CT angiography (CTA) in a North American patient population. Methods We performed a retrospective review of patients with UIA being followed with serial CTA studies from 1999 to 2010. The following features for each aneurysm were cataloged from the official radiologic reports and CTA images: maximum diameter, growth between follow-up studies, location, multiplicity, wall calcification, intraluminal thrombus and morphology. Univariate logistic regression analysis of the potential independent risk factors for aneurysm rupture was performed. Statistically significant risk factors from the univariate analysis were then entered into a multivariate logistic regression analysis. Results 152 patients with a total of 180 UIA had at least two CTA studies. Six aneurysms in six different patients ruptured during the CTA follow-up period for an overall rupture rate of 3.3% and an annual rupture rate of 0.97%. All ruptured aneurysms were ≥9 mm. In the univariate analysis, the statistically significant predictors of aneurysm rupture were aneurysm size (p=0.003), aneurysm growth (p<0.0001) and aneurysm multilobulation (p=0.001). The risk factors that remained significant following the multivariate analysis were growth (OR 55.9; 95% CI 4.47 to 700.08; p=0.002) and multilobulation (OR 17.4; 95% CI 1.52 to 198.4; p=0.022). Conclusions Aneurysm morphology and interval growth are characteristics predictive of a higher risk of subsequent rupture during conservative CTA follow-up.
Particle-filter approach and motion strategy for cooperative localization

This paper proposes a Particle-Filter approach and a set of motion strategies to cooperatively localize a team of three robots. The allocated mission consists on the path following of a closed trajectory and obstacle avoidance in isolated and unstructured scenarios. The localization methodology required for the correct path following relies on distance and orientation measurements among the robots and the robots and a fixed active beacon. Simulation results are presented.
On-axis spectroscopy of the z = 0.144 radio-loud quasar HE 1434-1600: an elliptical host with a highly ionized ISM

VLT on-axis optical spectroscopy of the $z=0.144$ radio-loud quasar HE 1434-1600 is presented. The spatially resolved spectra of the host galaxy are deconvolved and separated from those of the central quasar in order to study the dynamics of the stars and gas as well as the physical conditions of the ISM. We find that the host of HE 1434-1600 is an elliptical galaxy that resides in a group of at least 5 member galaxies, and that most likely experienced a recent collision with its nearest companion. Compared with other quasar host galaxies, HE 1434-1600 has a highly ionized ISM. The ionization state corresponds to that of typical Seyferts, but the ionized regions are not distributed in a homogeneous way around the QSO, and are located preferentially several kiloparsecs away from it. While the stellar absorption lines do not show any significant velocity field, the gas emission lines do. The observed gas velocity field is hard to reconcile with dynamical models involving rotating disk, modified Hubble laws or power laws, that all require extreme central masses ($M>10^{9}~M_{\odot}$) to provide only poor fit to the data. Power law models, which best fit the data, provide a total mass of M (<10 kpc) = 9.2 $\times$ $10^{10}~M_{\odot}$. We conclude that the recent interaction between HE 1434-1600 and its closest companion has strongly affected the gas velocity and ionization state, from the center of the galaxy to its most external parts.
Friction and wear characterization of a new ecological composite: glass waste beads reinforced epoxy

Sandblasting is a process that allows smoothing and cleaning rough surfaces, by means of a hard abrasive material streamed at high pressure against the interested surface. The abrasive material could be glass beads, which are wasted after the process. This paper investigated the opportunity to recycle the glass beads as reinforcement inside a polymeric matrix. This new composite material could be an economic and green alternative to the more common polymer matrix composite (PMC). Therefore, the tribological properties of this composite were studied through reciprocating sliding tribotest. The influence on friction and wear of different glass dimensions and concentrations within epoxy resin were analyzed.
Contemporary approaches to saphenous vein graft interventions: A survey of 275 interventional cardiologists

Background: We sought to examine contemporary practice patterns of saphenous vein graft (SVG) interventions. Methods: A link to a 10‐item online questionnaire was completed in June 2009 by 275 (7%) of 3,771 US interventional cardiologists surveyed. Results: Sixty‐five percent of the respondents use an embolic protection device (EPD) in >75% of SVG interventions. The main reason for not using an EPD was “anatomic difficulties” (55%), followed by device complexity (20%). Filter‐based EPDs were the most widely available, well known, and commonly used EPDs, whereas the Guardwire (Medtronic Vascular) was the least commonly used EPD. The main factors underlying EPD selection were lesion location (83%), familiarity with devices (72%), and SVG diameter (64%). Factors that could increase EPD use included availability of simpler to use devices (63%), and more studies demonstrating benefit from EPD use (37%). Compared with interventionalists who used EPDs in most cases (>75%), those who utilized EPDs less frequently were less likely to be familiar with each EPD and had less EPDs available for use. Many interventionalists (84%) administer intragraft vasodilators during SVG interventions, prefer drug‐eluting stents (63%) and administer >12 months antiplatelet therapy poststent implantation.Conclusions: During SVG interventions (1) “anatomic difficulties” are the most common reason for not utilizing an EPD; (2) filter‐based EPDs are most commonly used; (3) lesion location is the most important factor for EPD selection; (4) availability of simpler to use devices could increase EPD use; and (5) intragraft vasodilators, drug‐eluting stents and prolonged antiplatelet therapy are commonly utilized. © 2011 Wiley‐Liss, Inc.
Module Anchored Network Inference: A Sequential Module-Based Approach to Novel Gene Network Construction from Genomic Expression Data on Human Disease Mechanism

Different computational approaches have been examined and compared for inferring network relationships from time-series genomic data on human disease mechanisms under the recent Dialogue on Reverse Engineering Assessment and Methods (DREAM) challenge. Many of these approaches infer all possible relationships among all candidate genes, often resulting in extremely crowded candidate network relationships with many more False Positives than True Positives. To overcome this limitation, we introduce a novel approach, Module Anchored Network Inference (MANI), that constructs networks by analyzing sequentially small adjacent building blocks (modules). Using MANI, we inferred a 7-gene adipogenesis network based on time-series gene expression data during adipocyte differentiation. MANI was also applied to infer two 10-gene networks based on time-course perturbation datasets from DREAM3 and DREAM4 challenges. MANI well inferred and distinguished serial, parallel, and time-dependent gene interactions and network cascades in these applications showing a superior performance to other in silico network inference techniques for discovering and reconstructing gene network relationships.
P53 and its molecular basis to chemoresistance in breast cancer

Introduction: TP53 mutations have been associated with resistance to anthracyclines and mitomycin in breast cancer. This review examines the potential roles of different components in the p53 cascade with respect to drug resistance. Areas covered: Literature was searched using the ISI Web and Pubmed. Considering p53 activation in response to genotoxic stress and phsphorylations by ataxia telangiectasia mutated/ataxia telangiectasia and radiation resistance gene 3 related (ATM/ATR). Downstream checkpoint proteins chk1 and chk2 are also considered to be of major importance. Recently, nonsense mutations in CHEK2, encoding the chk2 protein, were found to predict resistance to anthracycline therapy in some tumours harbouring wild-type TP53. While mouse double minute (MDM)2 or MDMX protein overexpression (often due to gene amplifications) may inactivate p53 in different tumour forms, so far, there is no evidence for MDM2 amplifications in breast cancers resistant to anthracyclines. The roles of p53 isoforms and p53-induced transcription of non-coding RNA remain to be defined. Expert opinion: Disturbances affecting the ‘p53 pathway(s)’ may play a key role in chemoresistance in cancer. Although TP53 is not a clinical marker for drug resistance, like other genes (such as breast cancer associated 1/2 (BRCA1/2)) it may be considered a ‘beacon’ identifying critical gene cascades.
Effect of foamed pattern density on the lost foam process

The study examines the effect of the foamed polystyrene pattern density on the process of making castings by the lost foam technique with emphasis put on the analysis of simulation tests. The simulation regarded the effect that pattern density is said to have on the mould cavity filling rate, pressure in the gas gap, and size of this gap. For simulation tests of the full mould process, a mathematical model presented in this study was used. For calculations, the author's own algorithm was applied. The investigations have proved that with decreasing pattern density the pouring rate increases, while pressure in the gas gap and the size of the gap are decreasing. The increasing pouring rate ensures correct making of castings, even if their shapes are very intricate and the wall cross-sections are very small. Smaller size of the gas gap and lower pressure of gases in this gap reduce the risk of mould damage. The author’s own investigations have proved a very significant effect of the density of foamed polystyrene pattern on the casting process, and specially on the mould pouring rate. The best pouring rate is ensured by patterns of the density comprised in a range of ρ2 =18÷25 kg/m.
Urinary corticoid/creatinine ratios in the differentiation between pituitary-dependent hyperadrenocorticism and hyperadrenocorticism due to adrenocortical tumour in the dog.

In a study on the differentiation between pituitary-dependent hyperadrenocorticism (PDH) and hyperadrenocorticism due to adrenocortical tumour (AT), two questions were addressed: 1. Do basal urinary corticoid/creatinine (c/c) ratios have any value in this respect, and 2. what is the reference percentage suppression of the urinary c/c ratios in the high-dose dexamethasone suppression test? Data obtained from 160 dogs with hyperadrenocorticism were analysed. In 49 dogs the diagnosis AT was confirmed by the finding of plasma ACTH concentrations < 40 ng/l, by visualisation of the tumour by ultrasonography and/or computed tomography, and by histological examination of the adrenal tissue obtained at surgery or autopsy. Among the 111 dogs with PDH, there were 31 animals with resistance to dexamethasone suppression, i.e., suppression < 50%. The basal urinary c/c ratios of dogs with PDH and AT did not differ significantly, although urinary c/c ratios > 100 x 10(-6) almost exclusively occurred in association with PDH. Among the dogs with hyperadrenocorticism, the positive predictive value of a basal urinary c/c ratio > 100 x 10(-6) for the diagnosis of PDH was 0.90 (95% CI: 0.74-0.98). Of the 49 dogs with AT, 34 had a urinary c/c ratio after dexamethasone administration higher than the basal urinary c/c ratio. The maximum suppression of the basal urinary c/c ratio in dogs with AT was 43.7%. It is concluded that in dogs with hyperadrenocorticism basal urinary c/c ratios only have predictive value in the differentiation between AT and PDH when the ratio exceeds 100 x 10(-6). The generally accepted criterion of 50% suppression by dexamethasone in the differentiation between PDH and AT is also applicable to the urinary c/c ratio.
Preoperative antibiotic prophylaxis.

POSTOPERATIVE wound infections affect at least 920,000 of the 23 million patients who undergo surgery each year in the United States.1 The rates of infection vary according to the procedure: less than 3 infections per 100 for clean procedures (i.e., those in which there is no violation of aseptic technique and the alimentary, respiratory, and genitourinary systems are not entered), up to 4 per 100 for clean—contaminated procedures (i.e., those in which these systems are entered but without spillage), and up to 9 per 100 for grossly contaminated procedures. For specific operations, such as cholecystectomy, the rate may be five .
Cryopreservation of platelets using trehalose: The role of membrane phase behavior during freezing

In blood banks, platelets are stored at 20–24°C, which limits the maximum time they can be stored. Platelets are chilling sensitive, and they activate when stored at temperatures below 20°C. Cryopreservation could serve as an alternative method for long term storage of platelet concentrates. Recovery rates using dimethyl sulfoxide (DMSO) as cryoprotective agent, however, are low, and removal of DMSO is required before transfusion. In this study, we have explored the use of trehalose for cryopreservation of human platelets while using different cooling rates. Recovery of membrane intact cells and the percentage of nonactivated platelets were used as a measure for survival. In all cases, survival was optimal at intermediate cooling rates of 20°C min−1. Cryopreservation using DMSO resulted in high percentages of activated platelets; namely 54% of the recovered 94%. When using trehalose, 98% of the platelets had intact membranes after freezing and thawing, whereas 76% were not activated. Using Fourier transform infrared spectroscopy, subzero membrane phase behavior of platelets has been studied in the presence of trehalose and DMSO. Furthermore, membrane hydraulic permeability parameters were derived from these data to predict the cell volume response during cooling. Both trehalose and DMSO decrease the activation energy for subzero water transport across cellular membranes. Platelets display a distinct lyotropic membrane phase transition during freezing, irrespective of the presence of cryoprotective agents. We suggest that concomitant uptake of trehalose during freezing could explain the increased survival of platelets cryopreserved with trehalose. © 2012 American Institute of Chemical Engineers Biotechnol. Prog. , 2012
Ieee Transactions on Affective Computing Dynamic Cascades with Bidirectional Bootstrapping for Action Unit Detection in Spontaneous Facial Behavior

—Automatic facial action unit detection from video is a long standing problem in facial expression analysis. Research has focused on registration, choice of features, and classifiers. A relatively neglected problem is the choice of training images. Nearly all previous work uses one or the other of two standard approaches. One approach assigns peak frames to the positive class and frames associated with other actions to the negative class. This approach maximizes differences between positive and negative classes, but results in a large imbalance between them, especially for infrequent AUs. The other approach reduces imbalance in class membership by including all target frames from onsets to offsets in the positive class. However, because frames near onsets and offsets often differ little from those that precede them, this approach can dramatically increase false positives. We propose a novel alternative, dynamic cascades with bidirectional bootstrapping (DCBB) to select training samples. Using an iterative approach, DCBB optimally selects positive and negative samples in the training data. Using Cascade Adaboost as basic classifier, DCBB exploits the advantages of feature selection, efficiency, and robustness of Cascade Adaboost. To provide a real-world test, we used the RU-FACS (a.k.a. M3) database of non-posed behavior recorded during interviews. For most tested action units, DCBB improved AU detection relative to alternative approaches.
Sequence-similar, structure-dissimilar protein pairs in the PDB

It is often assumed that in the Protein Data Bank (PDB), two proteins with similar sequences will also have similar structures. Accordingly, it has proved useful to develop subsets of the PDB from which “redundant” structures have been removed, based on a sequence‐based criterion for similarity. Similarly, when predicting protein structure using homology modeling, if a template structure for modeling a target sequence is selected by sequence alone, this implicitly assumes that all sequence‐similar templates are equivalent. Here, we show that this assumption is often not correct and that standard approaches to create subsets of the PDB can lead to the loss of structurally and functionally important information. We have carried out sequence‐based structural superpositions and geometry‐based structural alignments of a large number of protein pairs to determine the extent to which sequence similarity ensures structural similarity. We find many examples where two proteins that are similar in sequence have structures that differ significantly from one another. The source of the structural differences usually has a functional basis. The number of such proteins pairs that are identified and the magnitude of the dissimilarity depend on the approach that is used to calculate the differences; in particular sequence‐based structure superpositioning will identify a larger number of structurally dissimilar pairs than geometry‐based structural alignments. When two sequences can be aligned in a statistically meaningful way, sequence‐based structural superpositioning provides a meaningful measure of structural differences. This approach and geometry‐based structure alignments reveal somewhat different information and one or the other might be preferable in a given application. Our results suggest that in some cases, notably homology modeling, the common use of nonredundant datasets, culled from the PDB based on sequence, may mask important structural and functional information. We have established a data base of sequence‐similar, structurally dissimilar protein pairs that will help address this problem (http://luna.bioc.columbia.edu/rachel/seqsimstrdiff.htm). Proteins 2008. © 2007 Wiley‐Liss, Inc.
On the Death Rate of Abortively Infected Cells: Estimation from Simian-Human Immunodeficiency Virus Infection

ABSTRACT Progressive T cell depletion during chronic human immunodeficiency virus type 1 (HIV) infection is a key mechanism that leads to the development of AIDS. Recent studies have suggested that most T cells in the tissue die through pyroptosis triggered by abortive infection, i.e., infection of resting T cells in which HIV failed to complete reverse transcription. However, the contribution of abortive infection to T cell loss and how quickly abortively infected cells die in vivo, key parameters for a quantitative understanding of T cell population dynamics, are not clear. Here, we infected rhesus macaques with simian-human immunodeficiency viruses (SHIV) and followed the dynamics of both plasma SHIV RNA and total cell-associated SHIV DNA. Fitting mathematical models to the data, we estimate that upon infection a majority of CD4+ T cells (approximately 65%, on average) become abortively infected and die at a relatively high rate of 0.27 day−1 (half-life, 2.6 days). This confirms the importance of abortive infection in driving T cell depletion. Further, we find evidence suggesting that an immune response may be restricting viral infection 1 to 3 weeks after infection. Our study serves as a step forward toward a quantitative understanding of the mechanisms driving T cell depletion during HIV infection. IMPORTANCE In HIV-infected patients, progressive CD4+ T cell loss ultimately leads to the development of AIDS. The mechanisms underlying this T cell loss are not clear. Recent experimental data suggest that the majority of CD4+ T cells in tissue die through abortive infection, where the accumulation of incomplete HIV transcripts triggers cell death. To investigate the role of abortive infection in driving CD4+ T cell loss in vivo, we infected macaques with simian-human immunodeficiency viruses (SHIV) and followed the viral kinetics of both plasma RNA and cell-associated DNA during infection. Fitting mathematical models, we estimated that a large fraction of infected cells dies through abortive infection and has a half-life of approximately 2.6 days. Our results provide the first in vivo quantitative estimates of parameters characterizing abortive infection and support the notion that abortive infection represents an important mechanism underlying progressive CD4+ T cell depletion in vivo.